XCyting DNA FISH Probes

Transcription

1 XCyting DNA FISH Catalog 2017/18 MetaSystems 1. Industriestr. 7 D Altlussheim Germany Phone: Fax: info: info@metasystems-probes.com orders: orders@metasystems-probes.com 1

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3 XCyting DNA FISH Catalog 2017/18 Dear Customer, XCyting times indeed! This edition of MetaSystems DNA Probe Catalog is the first one that is brought to you by our new company MetaSystems GmbH, a sister company to MetaSystems Hard & Software GmbH. Due to its dynamic growth our DNA Probe business outgrew MetaSystems existing premises which led us to constructing a new building right next (and directly connected) to our existing one some time ago. Since July 2015 the new building houses our probe activities on a total surface of 2,000 square meters providing plenty of lab and office space for the years to come and a pleasant working environment for our probe colleagues. And since early 2016 we have been preparing the transformation of the probe business into a new legal entity, MetaSystems GmbH. Recently the new company received ISO13485 certification and has become the official manufacturer of the XCyting MetaSystems range of probes. What will change for you? Actually not much, except for a few details like a new phone number, street address, and bank account number. Please note the following changes in our nomenclature: in our previous catalogs probe products validated for tissue applications were named XT.... As these products are equally well suited for other cytogenetic preparations they are now within the... group of products. This change affects only the name, the product number remains unchanged. To indicate the suitability of a probe for tissue FISH a new column has been added to the product index pages at the end. Finally, where appropriate, the product map documentation has been updated to the latest genome browser version HG19. This has led to some minor changes like new gene names or slightly different probe sizes. We invite you to visit our new website regularly to check for new products and other XCyting news. If you need a DNA probe that you find neither in the catalog nor on the website, please do not hesitate to contact us; it may well be that the particular probe you are seeking is already in development or production, and if not, we are always open to suggestions. Altlussheim, Germany, November

4 Contents...for Hematology / Oncology 5 XA for Aneuploidy Detection 77 XCE XCyting Centromere Enumeration 87 XCP XCyting Chromosome Paints 91 XCyte mfish XCyting Multicolor FISH 95 XCyte mband XCyting Multicolor Banding 97 Non-Human DNA Chromosome Paints and mfish Kits for Mouse, Rat and Chinese Hamster 99 Addendum DAPI / Antifade MetaSystems Imaging Systems Filters and Fluorochromes Index All MetaSystems human FISH probe products are classified as IVD products according to the directive 98/79 EC and marked with the CE label. Please note some products may not be available in all markets. 4

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6 CDKN2C / CKS1B Amplification/Deletion Probe CDKN2C/CKS1B hybridized to lymphocytes. One normal metaphase is shown. The CDKN2C/CKS1B locus-specific probe detects deletions or amplifications in the long and short arm of chromosome 1. The orange labeled probe hybridizes to a specific region at 1q21 including the CKS1B gene. The green labeled probe hybridizes specifically to 1p32 and includes the CDKN2C (p18) gene. Please note that this probe is the replacement for 1p32/1q21 (D OG). Two green (2G) and two orange (2O) signals. Two green (2G) and three orange (3O) signals, indicating a duplication of the CKS1B locus. Multiple myeloma (MM) is a plasma cell malignancy characterized by very complex cytogenetic and molecular genetic aberrations. Hyperdiploid karyotypes are characterized mainly by trisomies of chromosomes 3, 5, 7, 9, 11, 15, 19, and 21, non-hyperdiploid karytoypes typically have translocations involving the IGH locus at 14q32. The most frequent deletions are 13q, 17p and 1p32. One green (1G) and two orange (2O) signals, indicating a deletion of the CDKN2C locus. Deletions of chromosome 1p have been described in 7 % to 15 % of cases of myeloma with inconsistent clinical consequences. CDKN2C at 1p32.3 has been identified in myeloma cell lines as the potential target of the deletion. Gain of 1q is one of the most recurrent chromosomal aberrations in MM. Amplification and overexpression of the CKS1B gene in chromosome band 1q21 has been associated with an aggressive clinical course in multiple myeloma. MM Shaughnessy, J (2005) Hematology 10: Leone et al (2008) Clin Cancer Res 14: Broyl et al (2010) Blood 116: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 6 Chr1

7 ALK BA Break Apart Probe ALK BA is a break apart probe with an orange labeled probe hybridizing to the proximal region within ALK in 2p23 and a green labeled probe hybridizing distal to ALK. ALK BA hybridized on lung cancer tissue. Separated green and orange signals indicate an ALK rearrangement. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green-orange (2GO) fusion signals representing the two normal ALK loci. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the ALK locus. The EML4/ALK fusion gene is responsible for approximately 3-5 % of non-smallcell lung cancer (NSCLC). The vast majority of cases are adenocarcinomas. Two other fusion partners of ALK have been reported in lung cancer - TFG and KIF5B. Up to 12 other translocation partners have been described in anaplastic large-cell lymphomas (ACLC), renal cancer, esophageal squamous cell, colon, and breast carcinoma. Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase that was discovered in anaplastic large-cell lymphoma (ALC). The formation of a fusion protein with a partner through chromosomal translocations is the most common mechanism of ALK overexpression and ALK kinase domain activation. The ALK inhibitor crizotinib has increased the significance of detecting ALK rearrangements in lung cancer and ALCL. Solid Tumors Kutok et al (2002) J Clin Oncol 20: Perner et al (2008) Neoplasia 10: Shaw et al (2009) J Clin Oncol 27: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 7 Chr2

8 IGK Break Apart Probe IGK hybridized to lymphocytes. One normal partial metaphase is shown. The IGK probe is designed as a break apart probe with two probes juxtaposed and differently labeled. The orange labeled probe hybridizes to the IGK distal Variable Region at 2p11.2, while a green labeled probe hybridizes distal to the breakpoint in the proximal IGK Variable, C and J regions. Two green-orange (2GO) fusion signals. One green-orange fusion signal (1GO) and one green (1G), one orange (1O) indicating a chromosome break in the IGK locus. Primary karyotypic changes in lymphoid neoplasms commonly juxtapose oncogenes to the potent transcriptional enhancers associated with IG and TCR loci in B and T cells, respectively, often resulting in elevated levels of protein expression and loss of normal mechanisms of control. Less commonly, fusion genes are created that encode novel hybrid proteins. Variant translocations involving the IG kappa (IGK) locus in 2p11.2 or the IG lambda (IGL) locus in 22q11 occur recurrently in B-cell neoplasias. The different translocations involving immunoglobulin genes have a diagnostic value and can be used to monitor the clinical course of the disease. NHL Martin-Subero et al (2002) Int J Cancer 98: Wlodarska et al (2004) Leukemia 10: Einerson et al (2006) Leukemia 10: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 8 Chr2

9 BCL6 BA Break Apart Probe The BCL6 BA probe is designed as a break apart probe. Its green labeled part hybridizes proximal to the BCL6 gene at 3q27, the orange labeled probe hybridizes to the region distal of BCL6. BCL6 BA hybridized to a positive case. The cell to the left shows one normal orange green fusion signal and one separated orange and green signal, indicating a break in BCL6. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green-orange (2GO) fusion signals. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the BCL6 locus. Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBL) represent the two most common entities of non-hodgkin's lymphoma (NHL) worldwide with up to 22% and 31% of tumors, respectively. FLs have been classically associated with the translocation t(14;18)(q32;q21) in 70% to 95% of reported tumors, whereas translocations involving the BCL6 proto-oncogene locus in chromosomal band 3q27 are encountered in 6% to 14%. In DLBLs a BCL6 translocation can be found in up to 40% of cases, while BCL2 translocations occur in 20% to 30%. The relative wide separation of the probe binding sites allows for the detection of translocations in the MBR (major breakpoint cluster region) as well as in the ABR (alternative breakpoint cluster region). Solid Tumors Lymphomas Butler et al (2002) Cancer Res 62: Katzenberger et al (2004) Am J Pathol 165: Iqbal et al (2007) Leukemia 21: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 9 Chr3

10 EVI1 Break Apart Probe - Triple Color EVI1 hybridized to lymphocytes. A normal interphase is displayed with two blue-greenorange fusion signals. The EVI1 probe is designed as a three color break apart probe. A blue labeled probe hybridizes proximal to EVI1 in 3q26, a green probe hybridizes to the entire EVI1 gene with its flanking regions, and an orange probe hybridizes distal to the MDS1 and MYNN genes. Two blue-greenorange (2BGO) fusion signals representing the two normal EVI1 loci. One green-blue (1GB) signal and one separate orange (1O) signal from the translocated chromosome and one blue-green-orange (1BGO) fusion signal from the normal chromosome. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3). Chromosomal translocations involving the EVI1 locus are a recurrent finding in myeloid leukemia and are associated with poor prognosis. Two common recurrent rearrangements affect the 3q26 locus. One is the inv(3)(q21q26) and the translocation t(3;3)(q21;q26), in which EVI1 overexpression is caused by juxtaposition of the EVI1 gene to enhancer elements of the Ribophorin gene at 3q21. EVI1 activation is also observed in the translocations t(3;12)(q26;p13) and t(3;21)(q26;q22) and is due to generation of the fusion genes ETV6/EVI1 and RUNX1/EVI1, respectively. One green-orange (1GO) signal and one separate blue (1B) signal from the translocated chromosome and one blue-green-orange (1BGO) fusion signal from the normal chromosome. MDS AML De Melo et al (2007) Leukemia 22: De Wer et al (2008) Haematologica 93: De Braekeleer et al (2015) Future Oncology 11: Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 10 Chr3

11 MECOM 3q26 Break Apart Probe The MECOM 3q26 probe is designed as a break apart probe. Its orange labeled part hybridizes proximal to the MECOM gene locus at 3q26; the green labeled probe hybridizes to the distal gene region. MECOM stands for 'MDS1 and EVI1 complex locus'. MECOM 3q26 hybridized to lymphocytes. One normal metaphase and two normal interphases are shown. Two green-orange (2GO) fusion signals representing the two normal MECOM loci. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the MECOM locus. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3). Chromosomal translocations involving the MECOM locus are a recurrent finding in myeloid leukemia and are associated with poor prognosis. Two common recurrent rearrangements affect the 3q26 locus. One is the inv(3)(q21q26) and the translocation t(3;3)(q21;q26), in which EVI1 overexpression is caused by juxtaposition of the EVI1 gene to enhancer elements of the Ribophorin gene at 3q21. EVI1 activation is also observed in the translocations t(3;12)(q26;p13) and t(3;21)(q26;q22) and is due to generation of the fusion genes ETV6/EVI1 and RUNX1/EVI1, respectively. One green (1G) and two green-orange (2GO) fusion signals, indicating a variant chromosome break at a more distal region of the MECOM locus. MDS AML Lugthart et al (2008) Blood 111: De Melo et al (2008) Leukemia 22: De Braekeleer et al (2015) Future Oncology 11: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 11 Chr3

12 4q12 Deletion/Fusion Probe 4q12 hybridized to lymphocytes. Two normal interphases are shown with two bluegreen-orange fusion signals each. The 4q12 probe is a triple-color probe which detects rearrangements and deletions at 4q12. The probe contains an orange probe hybridizing to the CHIC2 gene region. A green probe hybridizes proximal to FIP1L1, and a blue probe hybridizes to PDGFRA and the region distal to the gene. Two blue-greenorange fusion signals (2BGO). One blue-greenorange (1BGO) and one blue-green (1BG) fusion signal, indicating a deletion of CHIC2. In 2008 the World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues introduced a new category for myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB or FGFR1. Many of these cases present as a myeloproliferative neoplasm, usually with eosinophilia. The hypereosinophilic syndrome may result from a novel fusion tyrosine kinase - FIP1L1/PDGFRA - that is a consequence of an interstitial chromosomal deletion which includes the CHIC2 gene region. The FIP1L1/PDGFRA fusion protein has been proven to be a therapeutic target of Imatinib. By triple-color FISH not only deletions involving CHIC2 but also translocations involving the 4q12 region can be detected. CML/MPN Cools et al (2003) N Engl J Med 348: Griffin et al (2003) PNAS 100: Pardanani et al (2003) Blood 102: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 12 Chr4

13 TET2 Deletion Probe The TET2 locus-specific probe detects deletions in 4q24. This probe is labeled in orange and extends from marker RH43141 proximal to RH69608 distal of the TET2 gene. A green labeled probe hybridizes to 4q12, functioning as a reference probe. TET2 hybridized to lymphocytes. One partial normal metaphase and two normal interphases are shown. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating a deletion of TET2 (4q24). The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3). A minimally deleted region on chromosome 4q24 is described in subgroups of patients with myelodysplastic syndromes and acute myeloid leukemia (AML). The region encompasses the TET2 gene. The frequency of TET2 mutations in unselected patients was 19 % (15 of 81 patients) with myelodysplastic syndromes, 12 % (24 of 198 patients) with myeloproliferative disorders, 24 % (5 of 21 patients) with secondary AML, and 22 % (2 of 9 patients) with chronic myelomonocytic leukemia. MDS Jankowska et al (2009) Blood 113: Delhommeau et al (2009) N Engl J Med 360: Flach et al (2010) Haematologica 95: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 13 Chr4

14 t(4;14) Translocation/Dual Fusion Probe The t(4;14) is designed as a dual fusion probe. An orange labeled probe flanks the breakpoint at the FGFR3 gene at 4p16. A green labeled probe flanks the 14q32 IGH breakpoint region. Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(4;14) hybridized to lymphocytes. One normal metaphase and two normal interphases are shown. Genetic aberrations present in multiple myeloma cells play a significant role in the risk stratification and therapeutic approach in multiple myeloma patients. Chromosomal translocations affecting the IGH locus are recurrent in many types of leukemias and lymphomas.the malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus. The t(4;14)(p16;q32) is a primary event in multiple myeloma (MM) and deregulates the expression of the fibroblast growth factor receptor 3 (FGFR3) and MMSET. Multivariate analysis has identified t(4;14) as the only adverse prognostic factor for both progression-free survival and overall survival. MM Chesi et al (1998) Blood 92: Chang et al (2004) Br J Haematol 125:64-68 Saez et al (2007) Onco Reports 18: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 14 Chr4

15 5q31 / 5q33 Deletion Probe The 5q31/5q33 locus-specific probe detects deletions in the long arm of chromosome 5. The orange labeled probe hybridizes to a specific region at 5q31 including the EGR1 gene. The green labeled probe hybridizes specifically to 5q33 and includes the RPS14 gene. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating a deletion in 5q q31/5q33 hybridized to bone marrow cells. Both metaphase and interphase show a signal pattern of one orange and two green signals indicating a deletion in 5q31. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3). The 5q- syndrome is defined as a primary myelodysplastic syndrome (MDS) with del(5q) as the sole karyotypic abnormality. Two different critical regions are described; one is located at 5q31 and contains the EGR1 and CDC25C genes; a more distal region at 5q32-q33 contains RPS14 which has been identified as a causal gene for the 5q- syndrome. One green (1G) and two orange (2O) signals, indicating a deletion in 5q33. One green (1G) and one orange (1O) signal, indicating deletions of both loci in 5q31.2 and 5q33. MDS AML Horrigan et al (2000) Blood 95: Wei et al (2009) Proc Natl Acad Sci USA 106: Boultwood et al (2010) Blood 16: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 15 Chr5

16 5q31 / 5q33 / 5p15 Deletion Probe 5q31/5q33/5p15 hybridized to lymphocytes. One normal metaphase is shown. The 5q31/5q33/5p15 locus-specific probe detects deletions in the long arm of chromosome 5. The orange labeled probe hybridizes to a specific region at 5q31 including the EGR1 gene. The green labeled probe hybridizes to 5q33 and includes the RPS14 gene. A blue (aqua) labeled probe hybridizes to 5p15 as a control. Two green (2G), two orange (2O) and two blue (2B) signals. One green (1G), one orange (1O), and two blue (2B) signals, indicating a large 5q deletion including 5q31 and 5q33. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3,3). The 5q- syndrome is defined as a primary myelodysplastic syndrome (MDS) with del(5q) as the sole karyotypic abnormality. Two different critical regions are described, one is located at 5q31 and contains the EGR1 and CDC25C genes. A more distal region at 5q32-q33 containing RPS14 has been identified as a causal region for the 5q- syndrome. Two green (2G), one orange (1O), and two blue (2B) signals, indicating a deletion in 5q31. One green (1G), two orange (2O), and two blue (2B) signals, indicating a deletion in 5q33 only. One green (1G), one orange (1O), and one blue (1B) signal indicating a monosomy 5. MDS AML Horrigan et al (2009) Blood 95: Wei et al (2009) PNAS 106: Boultwood et al (2010) Blood 16: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 16 Chr5

17 Del(5)(q31) Deletion Probe The Del(5)(q31) detects deletions in the long arm of chromosome 5. The orange labeled probe is designed to hybridize to the EGR1 locus at 5q31. A green labeled probe hybridizes to a specific locus at 5p15 and functions as a control probe. Del(5)(q31) hybridized to lymphocytes. One partial normal metaphase is shown. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating the deletion of EGR1 at 5q31. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3,3). The 5q- syndrome is defined as primary myelodysplastic syndrome (MDS) with del(5q) as the sole karyotypic abnormality. Two different critical regions are described, one is located at 5q31 and contains the EGR1 and CDC25C genes. A more distal region at 5q32-q33 containing RPS14 which has been identified as a causal gene for the 5q- syndrome. MDS AML Horrigan et al (2000) Blood 95: Wei et al (2009) Proc Natl Acad Sci USA 106(31): Boultwood et al (2010) Blood 16: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 17 Chr5

18 Del(5)(q33) Deletion Probe The Del(5)(q33) detects deletions in the long arm of chromosome 5. The orange labeled probe is designed to hybridize to the RPS14 locus at 5q33. A green labeled probe is designed to hybridize to a specific locus at 5p15 and functions as a control probe. Del(5)(q33) was hybridized to lymphocytes. One normal interphase and metaphase are shown. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating the deletion of RPS14 at 5q33. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3,3). The 5q- syndrome is defined as primary myelodysplastic syndrome (MDS) with del(5q) as the sole karyotypic abnormality. Two different critical regions are described, one is located at 5q31 and contains the EGR1 and CDC25C genes. A more distal region at 5q32-q33 containing RPS14 which has been identified as a causal gene for the 5q- syndrome. MDS AML Boultwood et al (1994) Blood 894: Ebert et al (2008) Nature 451: Boultwood et al (2010) Blood 16: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 18 Chr5

19 PDGFRB Break Apart Probe The PDGFRB probe is designed as a break apart probe with two probes juxtaposed and differently labeled. The probe hybridizing proximal to the PDGFRB locus at 5q33 is labeled in orange while a green labeled probe hybridizes distal to the breakpoint. PDGFRB hybridized to normal lymphocytes. Three interphases are displayed showing two fusion signals each. Two green-orange fusion signals (2GO) representing the two normal PDGFRB loci. One green-orange fusion signal (1GO) and one green (1G), one orange (1O) indicating a chromosome break in the PDGFRB locus. In 2008 the World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues introduced a new category for myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB, or FGFR1. Many of these cases present as a myeloproliferative neoplasm, usually with eosinophilia. Myeloid neoplasms (MPNs) with rearrangement of PDGFRB are phenotypically and genotypically diverse. The fusion genes involving PDGFRB described to date have been associated with cytogenetically detectable translocations. MPNs associated with rearrangement of PDGFRB are responsive to Imatinib. CML/MPN Wlodarska et al (1997) Blood 89: Apperley et al (2002) N Engl J Med 347: Wilkinson et al (2003) Blood 102: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 19 Chr5

20 5p15 / 9q22 / 15q22 Hyperdiploidy Amplification Probe The 5p15/9q22/15q22 Hyperdiploidy probe is designed as a triple color assay and allows enumeration of chromosomes 5, 9 and 15. A green labeled probe hybridizes to a region at 5p15, a blue one to the 9q22 region, and an orange one to the 15q22 region. 5p15/9q22/15q22 hybridized to lymphocytes. Two normal interphases are shown. Two green (2G), two blue (2B), and two orange (2O) signals. Three green (3G), two blue (2B) and three orange (3O) signals, indicating hyperdiploidy. In multiple myeloma (MM) pathogenesis hyperdiploidy and non-hyperdiploidy are recognized as two major cytogenetic pathways. The hyperdiploid group is characterized by gains of the odd chromosomes 3, 5, 7, 9, 11, 15, 19, and 21. Hyperdiploidy has been internationally defined and requires trisomy for at least 2 of the 3 chromosomes 5, 9, and 15. Two green (2G), three blue (3B) and three orange (3O) signals, indicating hyperdiploidy. Three green (3G), three blue (3B) and two orange (2O) signals, indicating hyperdiploidy. Patients with hyperdiploid multiple myeloma, which can be observed in 50% to 60% of patients, tend to have a better prognosis than those with a non-hyperdiploid subtype. MM Wuilleme et al (2005) Leukemia 19: Kumar et al (2009) Mayo Clin Proc. 84: Bochtler et al (2011) Blood 117: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 20 Chr5

21 6q21 / 6q23 Deletion Probe 6q21/6q23 hybridized to lymphocytes. One normal interphase and metaphase are shown. The 6q21/6q23 locus-specific probe detects deletions in the long arm of chromosome 6. The green labeled probe hybridizes to a specific region at 6q21 including the distal half for the SEC63 gene. The orange labeled probe hybridizes specifically to the MYB gene region at 6q23 and an area proximal to the gene. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating a deletion in 6q23 (MYB). The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13, and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. One green (1G) and two orange (2O) signals, indicating a deletion in 6q21. One green (1G) and one orange (1O) signal, indicating deletions of both loci in 6q21 and 6q23. Deletions involving the long arm of chromosome 6 (6q) are among the most common structural aberrations leading to a loss of chromosomal material in lymphoproliferative disorders and non-hodgkin's lymphoma (NHL). Two distinct regions, one at 6q , the other at 6q , have been found as minimal deleted regions in 6q- patients. A 6q deletion has also been found in a variety of other human malignancies as well, including breast carcinoma, malignant melanoma, renal cell carcinoma, salivary gland adenocarcinoma, ovarian carcinoma, acute lymphoblastic leukemia, and nodal non-hodgkin's lymphomas. ALL CLL NHL Stilgenbauer et al (1999) Leukemia 13: Zhang et al (2000) Genes Chrom Canc 27:52-58 Starostik et al (2000) Blood 95: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 21 Chr6

22 6q21 / 6q23 / 6cen Deletion Probe 6q21/6q23/6cen hybridized to lymphocytes. Two normal interphases are shown. The 6q21/6q23/6cen locus-specific probe detects deletions in the long arm of chromosome 6. The green labeled probe hybridizes to a specific region at 6q21 including the SEC63 gene. The orange labeled probe hybridizes specifically to the MYB gene region at 6q23. A blue (aqua) labeled probe which hybridizes to the centromere of chromosome 6 functions as a reference probe. Two green (2G) and two orange (2O) and two blue (2B) signals. One green (1G), one orange (1O), and two blue (2B) signals, indicating a large 6q deletion including 6q21 and 6q23. The prognosis and clinical course of CLL is heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13, and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. Two green (2G), one orange (1O), and two blue (2B) signals, indicating a deletion in 6q23. One green (1G), two orange (2O), and two blue (2B) signals, indicating a deletion in 6q21 only. Deletions involving the long arm of chromosome 6 (6q) are among the most common structural aberrations leading to a loss of chromosomal material in lymphoproliferative disorders and non-hodgkin's lymphoma (NHL). Two distinct regions, one at 6q , the other at 6q , have been found as minimal deleted regions in 6q- patients. A 6q deletion has also been found in a variety of other human malignancies as well, including breast carcinoma, malignant melanoma, renal cell carcinoma, salivary gland adenocarcinoma, ovarian carcinoma, acute lymphoblastic leukemia, and nodal non-hodgkin's lymphomas. ALL CLL NHL Stilgenbauer et al (1999) Leukemia 13: Zhang et al (2000) Genes Chrom Canc 27:52-58 Starostik et al (2000) Blood 95: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 22 Chr6

23 ROS1-GOPC BA Break Apart Probe ROS1-GOPC BA hybridized to the U-138 cell line. Several interphase nuclei show the expected fusion pattern, while one cell to the left is showing a homozygous deletion of the orange signals. The ROS1-GOPC BA probe is designed as a break apart probe. Its green labeled part hybridizes proximal to the ROS1 gene at 6q22 and the orange labeled probe hybridizes to the distal region of ROS1. This probe is also suited to analyze the ROS1-GOPC (formerly called FIG-ROS) fusion, caused by an interstitial deletion of 240 kb in size. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green-orange (2GO) fusion signals representing the two normal ROS1-GOPC loci. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the ROS1-GOPC locus. Translocations involving the ROS1 receptor tyrosine kinase gene have recently been described in a subset of non-small-cell lung cancers (NSCLCs). Chromosomal rearrangements involving the ROS1 gene were originally described in glioblastomas, where ROS1 is fused to the GOPC gene by an interstitial deletion. Fusions of ROS1 with other genes lead to constitutive kinase activity and are associated with sensitivity in vitro to tyrosine kinase inhibitors such as Crizotinib. One green (1G) and one greenorange (1GO) fusion signal, indicating a rearrangement of ROS1 by a deletion beetween ROS1 and GOPC. Solid Tumors Charest et al (2003) Genes Chrom Cancer 37:58-71 Takeuchi et al (2011) Nat Med 18: Bergethon et al (2012) J Clin Oncol 30: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 23 Chr6

24 t(6;9) DEK / NUP214 Translocation/Dual Fusion Probe The t(6;9) DEK/NUP214 is designed as a dual fusion probe. The green labeled probe spans the breakpoint at 6p22 (DEK), and the orange labeled probe spans the breakpoint at 9q34 (NUP214). Two green (2G) and two orange (2O) signals. One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(6;9) DEK/NUP214 hybridized to lymphocytes. One normal metaphase is shown. Several recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category AML with recurrent genetic abnormalities. Three new cytogenetically defined entities were recently incorporated: AML with t(6;9) (p23;q34) DEK/NUP214; AML with inv(3)(q21q26.2) or t(3;3)(q21;q26.2) RPN1/EVI1 and AML (megakaryoblastic) with t(1;22)(p13;q13) RBM15/MKL1, a rare leukemia most commonly occurring in infants. The t(6;9)(p23;q34) DEK/NUP214 fusion occurs with an incidence of 1 5% in adult patients with AML. This translocation tends to occur in younger adults and is associated with an unfavorable prognosis at diagnosis. Although the t(6;9) is usually the sole cytogenetic aberration at diagnosis, additional karyotypic abnormalities are frequently identified during disease progression. AML Shearer et al (2005) Leukemia 19: Doehner et al (2010) Blood 115: Sandahl et al (2014) Haematologica 99: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 24 Chr6

25 t(6;14) Translocation/Dual Fusion Probe The t(6;14) is designed as a dual fusion probe. An orange labeled probe flanks the breakpoint at 6p21. A green labeled probe flanks the 14q32 IGH breakpoint region. Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(6;14) hybridized to lymphocytes. One normal metaphase is shown. Genetic aberrations present in multiple myeloma cells play a significant role in the risk stratification and therapeutic approach in multiple myeloma patients. Chromosomal translocations affecting the IGH locus are recurrent in many types of leukemias and lymphomas.the malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus. The chromosomal translocation t(6;14)(p21;q32.3) has been reported as a rare but recurrent event not only in myeloma and plasma cell leukemia but also in diffuse large B-cell non-hodgkin's lymphomas. MM Shaugnessy et al (2001) Blood 98: Sonoki et al (2001) Blood 98: Wlodarska et al (2008) Blood 111: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 25 Chr6

26 7q22 / 7q36 Deletion Probe The 7q22/7q36 locus-specific probe detects deletions in the long arm of chromosome 7. The orange labeled probe hybridizes to a specific region at 7q22 including the KMT2E (formerly MLL5) gene. The green labeled probe hybridizes specifically to 7q36 and includes the EZH2 gene. A blue (aqua) labeled probe which hybridizes to the centromere of chromosome 7 functions as a reference probe. 7q22/7q36 hybridized to lymphocytes. Two normal interphases are shown. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3). Two green (2G) and two orange (2O) and two blue (2B) signals. Two green (2G), one orange (1O), and two blue (2B) signals indicating the deletion of a 7q22 locus or one green (1G), two orange (2O), and two blue (2B) signals, indicating the deletion of a 7q36 locus. Loss of chromosome 7 (-7) or deletion of the long arm (7q-) are recurring chromosome abnormalities in myeloid leukemias. The association of -7/7q- with myeloid leukemia suggests that certain regions contain tumor suppressor gene(s), whose loss of function contribute to leukemic transformation or tumor progression. Two critical regions have been identified, one in band 7q22 including the KMT2E gene and another in bands 7q35-q36 comprising the EZH2 gene. One green (1G), one orange (1O), and two blue (2B) signals indicating the deletion of a 7q22 locus and of a 7q36 locus. One green (1G), one orange (1O), and one blue (1B) signal indicating a monosomy 7. MDS AML Le Beau et al (1996) Blood 88: Emerling et al (2002) Oncogene 21: De Weer et al (2010) PLoS One 13:e8676 Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 26 Chr7

27 del(7)(q22q31) Deletion Probe The del(7)(q22q31) locus-specific probe detects deletions in the long arm of chromosome 7. The orange labeled probe hybridizes to a specific region at 7q22 including the KMT2E (formerly MLL5) gene. The green labeled probe hybridizes specifically to 7q31 and includes the MET proto-oncogene. A blue (aqua) labeled probe which hybridizes to the centromere of chromosome 7 functions as a reference probe. del(7)(q22q31) hybridized to lymphocytes. Two normal interphases are shown. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3). Two green (2G) and two orange (2O) and two blue (2B) signals. Two green (2G), one orange (1O), and 2 blue (2B) signals indicating the deletion of a 7q22 locus or one green (1G), two orange (2O), and 2 blue (2B) signals, indicating the deletion of a 7q31 locus. Partial or complete deletion of chromosome 7 is a common finding in MDS and AML. At least three distinct regions of common deletions have been identified: the band 7q22 and the more telomeric regions 7q31-32 and 7q36. In most studies monosomy 7/del 7q indicates as an isolated abnormality a significantly worse prognosis. One green (1G) and one orange (1O) and two blue (2B) signals indicating the deletion of a 7q22 locus and of a 7q31 locus. One green (1G) and one orange (1O) and one blue (1B) signal indicating a monosomy 7. MDS AML LeBeau et al (1996) Blood 88: Liang et al (1998) Proc Natl Acad Sci USA 95: Haase D (2008) Ann Hematol 87: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 27 Chr7

28 EGFR amp Amplification Probe The EGFR amp probe detects amplifications in the short arm of chromosome 7. The orange labeled probe hybridizes to the EGFR locus at 7p11. A green labeled probe hybridizes to the 7cen region. EGFR amp hybridized to normal cells. Two green and two orange signals in each are shown. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green (2G) and two orange (2O) signals. Two green (2G), one orange (1O), and orange signal clusters, indicating amplification of EGFR (homogenous staining region = HSR). EGFR (epidermal growth factor receptor) gene amplification generally results in increased protein expression in breast carcinomas. About 6 % of breast carcinomas show moderate- to low-level EGFR amplification associated with genuine EGFR protein overexpression. Studies in non-small cell lung cancer (NSCLC) have shown that EGFR expression is associated with reduced survival, frequent lymph node metastasis, and poor chemosensitivity. EGFR is a member of the ErbB family of receptors, a subfamily of four closely related receptor tyrosine kinases which all play an important role in controlling normal cell growth, apoptosis, and other cellular functions. Mutations of EGFRs can lead to nonsmall-cell lung cancer, pancreatic cancer, breast cancer, colon cancer, and some other cancers. New drugs such as gefitinib and erlotinib directly target the EGFR. EGFR-positive patients have shown a 60 % response rate, which exceeds the response rate for conventional chemotherapy. Two green (2G) and multiple copies of orange signals indicating amplification of EGFR (double minutes = dm). Solid Tumors Okada et al (2003) Cancer Res 63: Bhargava et al (2006) Mod Patho 18: Sholl et al (2009) Cancer Res 69: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 28 Chr7

29 t(7;12) Translocation/Dual Fusion Probe The t(7;12) MNX1/ETV6 is designed as a dual fusion probe. The green labeled probes flank the breakpoint at 12p13 (ETV6), and the orange labeled probes flank the breakpoint at 7q36 (MNX1 formerly HLXB9). Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(7;12) hybridized to lymphocytes. One normal metaphase is shown. Several recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category acute myeloid leukemia (AML) with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasiarelated features when 20% or more blood or marrow blasts are present. The t(7;12)(q36;p13) translocation is a recurrent chromosome abnormality that involves the ETV6 gene on chromosome 12 and has been identified in 20 30% of infant patients with AML. The detection of t(7;12) rearrangements relies on the use of fluorescence in situ hybridization (FISH) because this translocation is hardly visible by chromosome banding methods. The clinical outcome of t(7;12) patients is believed to be poor, therefore an early and accurate diagnosis is important in the clinical management and treatment. AML Ballabio et al (2009) Leukemia 23: Naiel et al (2013) Cancers 5: Owokaet al (2015) Hematol Leuk. 3: 1-4 Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 29 Chr7

30 FGFR1 Break Apart Probe The FGFR1 located at 8p11 is designed as a break apart probe with two probes juxtaposed and differently labeled. A green labeled probe hybridizes proximal of FGFR1 and an orange labeled probe hybridizes distal of FGFR1. FGFR1 hybridized to bone marrow cells where a subpopulation with trisomy 8 was observed. One normal interphases is shown and one interphase with three fusion signals. Two green-orange fusion signals (2GO). One green-orange fusion signal (1GO) and one green (1G), one orange (1O) indicating a chromosome break in the FGFR1 locus. In 2008 the World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues introduced a new category for myeloid and lymphoid neoplasms with eosinophilia and abnormalities of PDGFRA, PDGFRB or FGFR1. Many of these cases present as a myeloproliferative neoplasm, usually with eosinophilia. The 8p11 myeloproliferative syndrome (MPD) also known as stem cell leukemialymphoma syndrome (SCLL) is associated with translocations disrupting FGFR1. Imatinib, which induces durable responses in MPDs with PDGFRA and PDGFRB fusion genes, is inactive in patients with FGFR1 translocations. CML/MPN Cross et al (2002) Leukemia 16: Walz et al (2005) Leukemia 19: Chase et al (2007) Blood 110: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 30 Chr8

31 MYC amp Amplification Probe The MYC amp probe detects amplifications in the long arm of chromosome 8. The orange labeled probe is designed to hybridize to the MYC locus at 8q24. A green labeled probe hybridizes to the 8cen region and functions as a control probe. MYC amp hybridized to breast cancer tissue. Multiple orange signals indicate amplification of MYC. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green (2G) and two orange (2O) signals. Two green (2G), one orange (1O), and orange signal clusters, indicating amplification of MYC (homogenous staining region = HSR). Amplification of MYC has been described in many types of tumor, including breast, cervical and colon cancers, as well as in squamous cell carcinomas of the head and neck, myeloma, non-hodgkin's lymphoma, gastric adenocarcinomas and ovarian cancer. MYC is the most frequently amplified oncogene and the elevated expression of its gene product correlates with tumor aggression and poor clinical outcome. The proto-oncogene MYC, located at 8q24.1, encodes a nuclear phosphoprotein transcription factor that has an integral role in a variety of cellular processes, such as cell cycle progression, proliferation, metabolism, adhesion, differentiation, and apoptosis. Two green (2G) and multiple copies of orange signals, indicating amplification of MYC (double minutes = dm). Solid Tumors Rummukainen et al (2001) Mod Pathol 14: Blancato et al (2004) Br J Cancer 90: Singhi et al (2012) Mod Pathol 25: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 31 Chr8

32 MYC BA Break Apart Probe The MYC BA probe is designed as a break apart probe. Its orange labeled part hybridizes proximal to the MYC gene at 8q24 and the green labeled probe hybridizes to the region distal to MYC. MYC BA hybridized to lymphocytes. Separate orange and green signals indicate a split in the MYC gene region. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green-orange (2GO) fusion signals. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the MYC locus. Translocations involving MYC are observed in diffuse large-b-cell lymphoma, follicular lymphoma, mantle cell lymphoma, and other lymphomas. In Burkitt Lymphoma the MYC gene, located at 8q24, is activated by a translocation next to an immunoglobulin constant gene. Most frequently MYC is positioned near the immunoglobulin heavychain (IGH) constant region on chromosome 14q32. However in some tumors, MYC can also be positioned near the light-chain region on chromosome 2p11 (IGK) or 22q11 (IGL). In addtion other translocation partners have been identified (e.g. BCL11A, PAX5, ZCCHC7). The MYC probe is designed as a break apart probe with two probes juxtaposed and differently labeled. The proximal and distal region is sufficiently large to achieve intense signals also on paraffin-embedded tissue sections. The wide gap between the orange and green part of this probe allows for the detection of the t(2;8) translocation as well as t(8;14) and t(8;22). Solid Tumors Lymphomas Hummel et al (2006) N Engl J Med 354: Einerson et al (2006) Leukemia 20: Bertrand et al (2007) Leukemia 21: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 32 Chr8

33 MYC BA Triple-color Break Apart Probe - Triple Color MYC BA triple-color hybridized to lymphocytes. One nucleus shows the normal two green-orange-blue signals, the other nucleus shows a separated green signal indicating a break distal to the MYC gene region. The MYC BA Triple-color probe is designed as a triple-color break apart probe. Its orange labeled part hybridizes proximal to the MYC gene at 8q24, the green labeled probe hybridizes to the distal region of MYC, and a blue (aqua) labeled probe covers MYC and adjacent regions. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two blue-greenorange (2BGO) fusion signals. One green-blue (1GB) signal and one separate orange (1O) signal from the translocated chromosome and one blue-green-orange (1BGO) fusion signal from the normal chromosome. Translocations involving MYC are observed in diffuse large-b-cell lymphoma, follicular lymphoma, mantle cell lymphoma, and other lymphomas. In Burkitt Lymphoma the MYC gene, located at 8q24, is activated by a translocation next to an immunoglobulin constant gene. Most frequently MYC is positioned near the immunoglobulin heavychain (IGH) constant region on chromosome 14q32. However in some tumors, MYC can also be positioned near the light-chain region on chromosome 2p11 (IGK) or 22q11 (IGL). In addtion other translocation partners have been identified (e.g. BCL11A, PAX5, ZCCHC7). The MYC BA Triple-color probe is designed as a break apart probe with three probes juxtaposed and differently labeled. In cases with 8q24 rearrangment the colocalization patterns of orange-blue versus green-blue allows to distinguish different breakpoints in MYC translocations which can be an aid in diagnosis. One orange-blue (1OB) signal and one separate green (1G) signal from the translocated chromosomes and one blue-greenorange (1BGO) fusion signal from the normal chromosome. Solid Tumors Lymphomas Hummel et al (2006) N Engl J Med 354: Einerson et al (2006) Leukemia 20: Bertrand et al (2007) Leukemia 21: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 33 Chr8

34 IGH / MYC / 8cen Translocation/Dual Fusion and Amplification Probe IGH/MYC/8cen hybridized to a lymphocyte cell. Two fusion signals indicate a t(8;14). One green and orange signal represent the normal chromosomes 8 and 14. Two blue signals show the presence of two copies of chromosome 8. The IGH/MYC/8cen is designed as a dual fusion probe with the additional ability to detect chromosome 8 copy number variations. The green labeled probe flanks the 14q32 IGH breakpoint region and the orange labeled probe spans the breakpoint at 8q24 (MYC). A chromosome 8 centromeric probe labeled in blue (aqua) is added as reference probe. Two blue (2B), two green (2G), and two orange (2O) signals. Two blue (2B), one green (1G), one orange (1O), and two green-orange (2GO) fusion signals. Chromosomal translocations affecting the IGH locus are recurrent in many types of lymphomas. The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus. The t(8;14)(q24;q32) MYC/IGH is the hallmark translocation of human Burkitt lymphoma where it accounts for about 85% of cases. The same translocation can be present in almost 5% of ALL patients and in diffuse large B-cell lymphomas. Although this aberration is often described to indicate a good prognosis, it can be an indicator of bad prognosis if associated with other factors, such as second aberrations like t(14;18) or BCL6 rearrangements. Three blue (3B), two green (2G), and three orange (3O) signals indicating a trisomy 8. NHL ALL Siebert et al (1998) Blood 91: Hummel et al (2006) N Engl J Med 354: Boerma et al (2009) Leukemia 23: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 34 Chr8

35 t(8;14) Translocation/Dual Fusion Probe The t(8;14) is designed as a dual color dual fusion probe. The orange labeled probe spans the breakpoint of the MYC gene at 8q24 and a pair of green labeled probes flank the 14q32 IGH breakpoint region. t(8;14) hybridized to a prometaphase cell. Two fusion signals and separated orange and green signals are displayed indicating a translocation between IGH and MYC. Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO) resulting from a reciprocal translocation between the relevant loci. Chromosomal translocations affecting the IGH locus are recurrent in many types of lymphomas. The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus. The t(8;14)(q24;q32) MYC/IGH is the hallmark translocation of human Burkitt lymphoma where it accounts for about 85% of cases. The same translocation can be present in almost 5% of ALL patients and in diffuse large B-cell lymphomas. Although this aberration is often described to indicate a good prognosis, it can be an indicator of bad prognosis if associated with other factors, such as second aberrations like t(14;18) or BCL6 rearrangements. NHL ALL Siebert et al (1998) Blood 91: Hummel et al (2006) N Engl J Med 354: Boerma et al (2009) Leukemia 23: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 35 Chr8

36 t(8;21) plus Translocation/Dual Fusion Probe The t(8;21) plus is designed as a dual fusion probe. The orange labeled probe spans the breakpoint at 21q22.1 RUNX1 (formerly AML1), and the green labeled probe spans the breakpoint at 8q21 RUNX1T1 (formerly ETO). Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(8;21) plus hybridized to lymphocytes. One normal metaphase and two normal interphases are shown. Several recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category acute myeloid leukemia (AML) with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasiarelated features when 20% or more blood or marrow blasts are present. The t(8;21)(q21;q22) is the most common translocation in de novo AML occurring in up to 20% of adult and 40% of pediatric cases of AML. The translocation fuses RUNX1 with RUNX1T1 to produce a RUNX1/RUNX1T1 fusion gene located on the derivative chromosome 8. The prognosis after intensive chemotherapy is better for these patients than for the majoritiy of AML patients. Small hidden interstitial insertions resulting in an RUNX1/RUNX1T1 rearrangement have been found, necessitating the use of a breakpoint spanning rather than a breakpoint flanking FISH probe. AML Levanon et al (2001) Gene 262: Zhang et al (2002) Proc Natl Acad Sci USA 99: Gamerdinger et al (2003) Genes, Chromosomes and Cancer 36: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 36 Chr8

37 CDKN2A Deletion Probe CDKN2A hybridized to bone marrow cells. Two normal cells and several cells with two green signals are shown indicating a homozygous deletion of the CDKN2A. The CDKN2A locus-specific probe detects deletions in band 9p21. This probe is labeled in orange and hybridizes to CDKN2A (p16) as well as CDKN2B (p15). The green labeled probe hybridizes to the centromere of chromosome 9 and functions as a reference probe. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating the deletion of the CDKN2A (p16) at 9p21. Acute lymphoblastic leukaemia (ALL) is the most common type of leukemia in children, representing almost 25 % of pediatric cancer. The majority of patients with ALL demonstrate an abnormal karyotype, either in chromosome number or as structural changes such as translocations, inversions, or deletions. Deletion of chromosome 9p21 is a crucial event for the development of ALL and other types of cancer. Homozygous deletions removing CDKN2A (p16) or heterozygous deletions with inactivation of the normal allele occur in a variety of cancers. Two green (2G) and no orange (no O) signal, indicating a homozygous deletion of the CDKN2A (p16) at 9p21. ALL Takeuchi et al (1997) Leukemia 11: Sulong et al (2009) Blood 113: Novara et al (2009) Hum Genet 126: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 37 Chr9

38 JAK2 Break Apart Probe The JAK2 is designed as a break apart probe with two probes juxtaposed and differently labeled. An orange labeled probe hybridizes proximal, and a green labeled probe hybridizes distal to the breakpoint in 9p24. JAK2 hybridized to lymphocytes. Two normal interphases are shown. Two green-orange fusion signals (2GO). One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the JAK2 locus. Patients with clinical characteristics of CML lacking a BCR/ABL fusion gene are usually referred to as having atypical CML. Most commonly diverse tyrosine kinase genes as the receptors FGFR1, PDGFRA, or PDGFRB are involved. In addition the Janus (tyrosine) kinases (JAK) can be deregulated in leukemia/lymphoma by copy number alterations, mutations and chromosomal translocations. Chromosomal translocations targeting JAK2 are rare but recurrent abnormalities in myeloproliferative neoplasms, acute myeloid leukemia, acute lymphoblastic leukemia and lymphoma. In cell line models and primary patient material it could be shown that treatment with ruxolitinib has significant activity against JAK2 activated by gene rearrangement and presents evidence for potential activity against cells with JAK2 amplification. CML/MPN AML ALL Bousquet et al (2005) Oncogene 24: Chase et al (2012) Haematologica 93: Ehrentraut et al (2013) PLOSone 8: e53767 Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 38 Chr9

39 BCR / ABL1 / ASS Deletion/Dual Fusion Probe BCR/ABL1/ASS hybridized to lymphocytes. One normal metaphase is shown. The BCR/ABL1/ASS probe is specific for the t(9;22). The orange labeled probe hybridizes to an extended region at the ABL1 locus on 9q34 and a green labeled probe hybridizes specifically to extended regions at the BCR gene on 22q11. A blue (aqua) labeled probe hybridizing to the ASS1 (formerly ASS) region is added to analyse deletions at 9q34 which can be associated with t(9;22). Two blue-orange (2BO) fusion signals and two separate green signals (2G). One blue-orange (1BO), one green (1G), one blue-greenorange (1BGO) and one green-orange (1GO) fusion signal. Chronic myelogenous leukemia (CML) is genetically characterized by the presence of the reciprocal translocation t(9;22)(q34;q11), resulting in a BCR/ABL1 gene fusion on the derivative chromosome 22, called the Philadelphia (Ph) chromosome. The same translocation can also be found in acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) with some variation in the breakpoint region. Glivec (Imatinib Mesylate) treatment targeting the BCR/ABL1 active tyrosine kinase has become a major drug in treating CML, gastrointestinal stromal tumors, and other cancers. One blue-orange (1BO), two green (2G), and one green-orange (1GO) fusion signal, indicating a deletion at 9q34 in addition to a t(9;22). Deletions at the t(9;22) breakpoint regions, found in 5% of CML patients with a Ph translocation, have been associated with resistance to treatments in patients receiving tyrosine kinase inhibitors. CML/MPN ALL AML Dewald et al (1998) Blood 91: DeMelo et al (2008) Canc Genet Cytogenet 182: Luatti et al (2012) Blood 120: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 39 Chr9

40 BCR / ABL1 plus Translocation/Dual Fusion Probe The BCR/ABL1 plus probe is specific for the t(9;22). The orange labeled probe hybridizes to an extended region spanning the ABL1 locus on 9q34, and a green labeled probe hybridizes specifically to extended regions spanning the BCR gene on 22q11. The probe is designed as a dual-color, dual-fusion assay. Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). BCR/ABL1 plus hybridized to bone marrow cells. Two interphase cells with two fusion signals and separated orange and green signals each are shown, indicating a BCR/ ABL1 translocation. Chronic myelogenous leukemia (CML) is genetically characterized by the presence of the reciprocal translocation t(9;22)(q34;q11), resulting in a BCR/ABL gene fusion on the derivative chromosome 22, called the Philadelphia (Ph) chromosome. The same translocation can also be found in acute myeloid leukemia (AML) and acute lymphocytic leukemia (ALL) with some variation in the breakpoint region. Glivec (Imatinib Mesylate) treatment targeting the BCR/ABL active tyrosine kinase has become a major drug in treating CML, gastrointestinal stromal tumors, and other cancers. CML/MPN ALL AML Dewald et al (1998) Blood 91: Huntly et al (2003) Blood 102: Primo et al (2003) Leukemia 17: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 40 Chr9

41 ATM/11cen Deletion Probe The ATM/11cen locus-specific probe detects deletions in 11q22.3. This probe is labeled in orange and spans from marker D11S2179 within the ATM gene to the more proximal located NPAT region. A green labeled probe, specific for the centromere of chromosome 11, functions as a reference probe. Please note that this probe is the replacement for ATM (D OG). Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal indicating the deletion of ATM at 11q22. ATM/11cen hybridized to lymphocytes. One normal interphase and metaphase are shown. The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80% of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13, and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. Chromosome 11q deletions involving the ataxia-telangiectasia mutated (ATM) locus are detected at diagnosis in % of cases of B-cell chronic lymphocytic leukemia (CLL) and are associated with a more aggressive disease. CLL Doehner et al (1997) Blood 89: Cuneo et al (2002) Haematologica 87:44-51 Tsimberidou et al (2009) Cancer 115: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 41 Chr11

42 CCND1 Break Apart Probe The CCND1 probe is designed as a break apart probe. Its orange labeled part hybridizes proximal to CCND1 (BCL1) and the MYEOV gene at 11q13; the green labeled probe hybridizes to the distal region of CCND1. CCND1 hybridized to lymphocytes. One normal metaphase and two normal interphases are shown. Two green-orange (2GO) fusion signals representing the two normal CCND1 loci. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the CCND1 locus. The t(11;14)(q13;q32) chromosomal translocation is the hallmark of mantle cell lymphoma (MCL) and is found in approximately 30 % of multiple myeloma (MM) tumors with a 14q32 translocation. Variant translocations can fuse CCND1 also with other genes, such as IGK or IGL. MM NHL Vandraager et al (1997) Blood 89: Fonseca et al (2002) Blood 99: Wlodarska et al (2004) Leukemia 18: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 42 Chr11

43 MLL plus Break Apart Probe MLL plus hybridized to bone marrow cells. Two aberrant interphase nuclei with one fusion signal and one separate orange and green signal each are shown, representing a translocation with KTM2A involvement. The MLL plus probe is designed as a break apart probe. Its orange labeled part hybridizes proximal to the KMT2A (formerly MLL1) gene locus at 11q23, the green labeled probe hybridizes to the distal region. The probe does not cover coding regions within the KMT2A gene. Two green-orange (2GO) fusion signals representing the two normal KMT2A loci. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the KMT2A locus. A number of recurrent chromosomal abnormalities have been shown to have prognostic significance in acute lymphoblastic leukemia, especially in B-precursor ALL. Some chromosomal abnormalities, such as high hyperdiploidy and the TEL- AML1 fusion, are associated with more favorable outcomes, while others, including the t(9;22), rearrangements of the KMT2A gene (chromosome 11q23), and intrachromosomal amplification of the AML1 gene (iamp21), are associated with a poorer prognosis. Chromosomal rearrangements involving the human KMT2A gene are recurrently associated with the disease phenotype of acute leukemias. The identification of KMT2A gene rearrangements is necessary for rapid clinical decisions resulting in specific therapy regimens. Amplification of KMT2A in MDS and AML has also been observed, and transcriptional similarities between KMT2A amplified and KMT2A rearranged leukemias were identified. ALL AML Poppe et al (2004) Blood 103: Meyer et al (2006) Leukemia 20: Cavazzini et al (2006) Haematologica 91: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 43 Chr11

44 NUP98 Break Apart Probe The NUP98 probe is designed as a break apart probe. Its orange labeled part hybridizes proximal to the NUP98 gene at 11p15, the green labeled probe hybridizes to the distal region of NUP98. NUP98 was hybridized to lymphocytes. One normal interphase is shown. Two green-orange fusion signals (2GO). One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the NUP98 locus. Several recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category AML with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasia-related features when 20% or more blood or marrow blasts are present. Translocations involving nucleoporin 98kD (NUP98) on chromosome 11p15 occur at relatively low frequency in acute myeloid leukemia (AML), but can be missed with routine karyotyping. NUP98 is known to be fused to at least 28 different partner genes in patients with hematopoietic malignancies, including acute myeloid leukemia, chronic myeloid leukemia in blast crisis, myelodysplastic syndrome, acute lymphoblastic leukemia, and bilineage/biphenotypic leukemia. AML Nebral et al (2005) Haematologica 90: Romana et al (2006) Leukemia 20: Gough et al (2011) Blood 118: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 44 Chr11

45 t(11;14) Translocation/Dual Fusion Probe The t(11;14) is designed as a dual fusion probe. An orange labeled probe flanks the breakpoint at 11q13 proximal to the MYEOV gene and covering the CCND1 gene region. A green labeled probe flanks the 14q32 IGH breakpoint region. Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(11;14) hybridized to lymphocytes. One normal metaphase and two normal interphases are shown. Genetic aberrations present in multiple myeloma cells play a significant role in the risk stratification and therapeutic approach in multiple myeloma patients. Chromosomal translocations affecting the IGH locus are recurrent in many types of leukemias and lymphomas.the malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus. The t(11;14)(q13;q32) results in up-regulation of cyclin D1 and is the most common translocation detected in multiple myeloma. This translocation represents a unique subset of patients with a relatively favorable outcome. The t(11;14) is also the genetic hallmark of mantle cell lymphoma. MM NHL CLL Jansen et al (2000) Blood 95: Fonseca et al (2002) Blood 99: Sander et al (2008) Haematologica 93: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 45 Chr11

46 ATM / TP53 Deletion Probe ATM/TP53 hybridized to bone marrow cells. Four interphases are shown of which two show a normal signal pattern. The two other interphases show aberrant signal patterns with a deletion of ATM in one cell and a deletion of TP53 in the other one. The ATM/TP53 locus-specific probe detects deletions in the long arm of chromosome 11 and in the short arm of chromosome 17. The green labeled probe hybridizes to a specific region at 11q22 covering the ATM gene. The orange labeled probe hybridizes specifically to the TP53 gene and flanking regions at 17p13. Two green (2G) and two orange (2O) signals. One green (1G) and two orange (2O) signals indicating a deletion of an ATM locus. The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13, and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. TP53 is a tumor suppressor gene that stops cell division when DNA damage is present. Loss of TP53 at 17p13 is a powerful predictor of resistance to therapy with purine analogues and alkylating agents, and of poor prognosis in CLL. Chromosome 11q deletions involving the ataxia telangiectasia mutated (ATM) locus are detected at diagnosis in % of cases of B-cell chronic lymphocytic leukemia (CLL) and are associated with a more aggressive disease. Two green (2G) and one orange (1O) signal indicating a deletion of a TP53 locus. CLL Doehner et al (2000) N Engl J Med 343: Stilgenbauer et al (2002) Leukemia 16: Gunn at al (2008) J Mol Diagn 10: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 46 Chr11

47 CLL Probe Kit ( DLEU / LAMP/ 12cen + ATM / TP53) Deletion/Enumeration Probe The CLL Probe Kit contains two vials of locus-specific probes for the most common aberrations in CLL. One vial contains the DLEU/LAMP/12cen (D TC) and a second vial the ATM/TP53 (D OG). Please refer to DLEU/ LAMP/12cen (D TC) and ATM/ TP53 (D OG) for signal pattern. The CLL probe Kit hybridized to normal lymphocytes. The DLEU/LAMP/12cen probe (top) shows orange signals at 13q14, blue reference signals at 13q34, and green signals at the centromeric region of chromosome 12. The ATM/TP53 probe (bottom) shows orange signals at 17p13 and green signals at 11q22. The CLL Probe Kit is a combination of probes covering the most frequent chromosomal aberrations in CLL. For a more detailed description please refer to product DLEU/LAMP/12cen (D TC) and ATM/TP53 (D OG). CLL Doehner et al (2000) N Engl J Med 343: DeWald et al (2003) Brit J Haem 121: Nelson et al (2007) Am J Clin Pathol 128: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (2x 100 µl / 2x 10 Tests) 47 Chr11

48 ETV6 Break Apart Probe The ETV6 is designed as a break apart probe. Its orange labeled part hybridizes proximal to the ETV6 (TEL) gene at 12p13; the green labeled probe hybridizes to the distal ETV6 region. ETV6 hybridized to lymphocytes. One normal interphase and metaphase are shown. Two green-orange (2GO) fusion signals representing the two normal ETV6 loci. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the ETV6 locus. The leukemia associated gene ETV6 located on 12p13 is involved in different chromosomal translocations found in myeloid and lymphoid malignancies. This results in the formation of fusion proteins with oncogenic potential. While the most common rearrangement t(12;21) ETV6/RUNX1 is associated with a favorable prognosis, other rearrangements, such as ETV6/HLXB9 or ETV6/ABL1, predict a worse prognosis. Identification of translocations linking the ETV6 gene with tyrosine kinases is a marker that indicates response to imatinib therapy. Translocations involving the ETV6 gene can be found in a wide range of leukemias, including AML, ALL, chronic myelomonocytic (CMML), and myelodysplastic syndrome (MDS). It can also be present in sarcoma. ALL AML CML Sato et al(1997) Blood 90: Lierman and Cools (2007) Haematologica 92: Naiel et al(2013) Cancer 5: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 48 Chr12

49 MDM2 Amplification Probe The MDM2 hybridizes with an orange labeled probe to MDM2 and its flanking regions. A green labeled probe hybridizes to the centromere of chromosome 12. MDM2 hybridized to lymphocytes. Two normal interphases and one normal metaphase are shown. Two green (2G) and two orange (2O) signals. Two green (2G) and three orange (3O) signals, indicating a duplication of the MDM2 locus. The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13, and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. Trisomy 12 is a frequent abnormality in chronic lymphocytic leukemia (CLL). Partial trisomy 12 consistently includes the long arm of chromosome 12 and a critical region could be defined to 12q13-22 for CLL including the MDM2 gene. Amplification and overexpression of MDM2 can block TP53 activity preventing apoptosis. The MDM2 inhibitor Nutlin has been shown to reactivate TP53 activity and to restore apoptosis in cancer cells. CLL Dewald et al (2003) Brit J Haem 121: Elnenaei et la (2003) Haematologica 88: Nelson et al (2007) Am J Clin Pathol 128: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 49 Chr12

50 t(12;21) Translocation/Dual Fusion Probe The t(12;21) ETV6/RUNX1 is designed as a dual fusion probe. The green labeled probe flanks the breakpoint at 12p13 (TEL=ETV6), and the orange labeled probe flanks the breakpoint at 21q22 (AML1=RUNX1). Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(12;21) hybridized to lymphocytes. Two normal interphases are shown. A number of recurrent chromosomal abnormalities have been shown to have prognostic significance in acute lymphoblastic leukemia, especially in B-precursor ALL. Some chromosomal abnormalities, such as high hyperdiploidy and the ETV6-RUNX1 fusion, are associated with more favorable outcomes, while others, including the t(9;22), rearrangements of the KMT2A gene (chromosome 11q23), and intrachromosomal amplification of the AML1 gene (iamp21), are associated with a worse prognosis. One orange (1O), and two green-orange fusion (2GO) (adjacent green and orange) signals. In t(12;21) cases the normal ETV6 at 12p13 is often deleted. The most common translocation is the t(12;21)(p13;q22), which is recognized in up to 25 % of B-precursor ALL. This translocation fuses ETV6 with the RUNX1 gene. The resulting fusion transcript is a transcription factor and functions as a corepressor at RUNX1 target genes. The ETV6/RUNX1 translocation generally implies a good prognosis. ALL Romana et al (1995) Blood 85: Sato et al (1997) Blood 90: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 50 Chr12

51 DLEU / LAMP Deletion Probe The DLEU/LAMP probe detects deletions on chromosome 13q. The orange labeled probe hybridizes to the DLEU locus region at 13q14.2, including D13S319 and the green probe hybridizes to the LAMP locus at 13q34. DLEU/LAMP hybridized to lymphocytes. One normal interphase and metaphase are shown. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating the deletion of a 13q14.3 locus. The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13 and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. The most frequently deleted region in B-CLL is located in 13q14.3 distal to RB1. The minimal deleted region (MDR) is 350 kb in size and includes the gene loci for the mi- RNAs 15 and 16. CLL with 13q deletion as the sole cytogenetic abnormality usually have a good prognosis. One green (1G) and two orange (2O) signals, indicating a deletion of the terminal region of the long arm of chromosome 13. One green (1G) and one orange (1O) signal, indicating deletions of both loci in 13q14 and 13qter. Deletions of chromosomal region 13q14 have also been reported in a variety of human tumors, including other types of lymphoid tumors and myeloid leukemias, as well as prostate, head and neck, and non-small-cell lung cancers. MM AML CLL Doehner et al (2000) N Engl J Med 343: Calin et al (2002) Proc Natl Acad Sci USA 99: Gunn at al (2008) J Mol Diagn 10: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 51 Chr13

52 RB1 / DLEU / LAMP Deletion Probe The RB1/DLEU/LAMP locus-specific probe can detect variants of deletions in the long arm of chromosome 13. The orange labeled probe hybridizes to the DLEU locus region at 13q14.2, including D13S319. A green labeled probe hybridizes specifically to the more proximal RB1 gene region at 13q14.2. A blue labeled probe is added as control which hybridizes to the LAMP gene locus at 13q34. Two green (2G), two orange (2O), and two blue (2B) signals. Aberrant Cell: Two green (2G), one orange (1O), and two blue (2B) signals. RB1/DLEU/LAMP hybridized to lymphocytes. Two normal interphases are shown. In chronic lymphocytic leukemia (CLL), deletion at 13q14 with at least one allele occurs in more than 50 % of cases. A minimal deleted region (MDR) of 350 kb in size has been identified and is usually seen as an indicator for good prognosis. However, recent studies using high resolution arrays have shown, that the 13q14 deletion can vary in size and if including the RB1 gene may lead to a change in the prognosis of CLL patients. RB1 is a critical regulator of cell cycle progression and genomic stability, and its loss could explain this change of interpretation in CLL. Deletions of chromosome 13q14 have been reported in a variety of human tumors, including other types of lymphoid tumors and myeloid leukemias, as well as prostate, head and neck, and non-small-cell lung cancers. Aberrant Cell: One green (1G), one orange (1O), and two blue (2B) signals. Aberrant Cell: One green (1G), one orange (1O), and one blue (1B) signal. CLL MM Doehner et al (2000) N Engl J Med 34: Ouillette et al (2008) Cancer Res 68: Dal Bo et al (2011) Genes Chromosomes Cancer 50: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 52 Chr13

53 DLEU / LAMP / 12cen Deletion/Enumeration Probe The DLEU/LAMP/12cen is a 3-color probe that hybridizes to the DLEU gene region at 13q14 (including the D13S319 marker) in orange, the LAMP gene region at 13q34 in blue (aqua), and a chromosome 12 centromeric probe labeled in green. Two green (2G), two orange (2O), and two blue (2B) signals. Aberrant Cell: Three green (3G), two orange (2O), and two blue (2B) signals. DLEU/LAMP/12cen hybridized to bone marrow cells. Three interphases are shown of which one shows a normal signal pattern of 2 orange, 2 green, and 2 blue signals, one nucleus shows a hemizygous, and a third one a homozygous deletion of DLEU (orange). The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15, and deletions 13q14, 17p13, and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. The most frequently deleted region in B-CLL is located in 13q14.3 distal to RB1. The minimal deleted region (MDR) is 350 kb in size and includes the gene loci for the mi- RNAs 15 and 16. CLL with 13q deletion as the sole cytogenetic abnormality usually have a good prognosis. Aberrant Cell: Two green (2G), one orange (1O), and two blue (2B) signals. Aberrant Cell: Two green (2G), one orange (1O), and one blue (1B) signal. Deletions of chromosomal region 13q14 have also been reported in a variety of human tumors, including other types of lymphoid tumors and myeloid leukemias, as well as prostate, head and neck, and non-small-cell lung cancers. MM AML CLL Doehner et al (2000) N Engl J Med 34: DeWald et al (2003) Brit J Haem 121: Nelson at al (2007) Am J Clin Pathol 128: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 53 Chr13

54 DLEU / TP53 Deletion Probe The DLEU/TP53 locus-specific probe detects deletions in the long arm of chromosome 13 and in the short arm of chromosome 17. The orange labeled probe hybridizes to the DLEU locus region at 13q14.2, including D13S319. The green labeled probe hybridizes specifically to the TP53 gene region at 17p13. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating a deletion in 13q14. DLEU/TP53 hybridized to bone marrow cells. A cell with normal signal pattern together with cells with a deletion of TP53 (2 orange, 1 green) and cells with deletions of TP53 and DLEU (1 orange, 1 green) are shown. The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13, and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. TP53 is a tumor suppressor gene that stops cell division when DNA damage is present. Loss of TP53 at 17p13 is a powerful predictor of resistance to therapy with purine analogues and alkylating agents and poor prognosis in CLL. The most frequently deleted region in B-CLL is located in 13q14.3 distal to RB1. The minimal deleted region (MDR) is 350 kb in size and includes the gene loci for the mi-rnas 15 and 16. CLL with 13q deletion as the sole cytogenetic abnormality (del13q-only) usually have a good prognosis. One green (1G) and two orange (2O) signals, indicating a deletion in17p13. MM CLL Doehner et al (2000) N Engl J Med 34: Stilgenbauer et al (2002) Leukemia 16: Gunn at al (2008) J Mol Diagn 10: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 54 Chr13

55 IGH plus Break Apart Probe The IGH plus probe is designed as a break apart probe. Its orange labeled part hybridizes to the constant region of the IGH locus and extends almost to the JAG2 gene at 14q32. The green labeled probe hybridizes to the variable distal region of the IGH locus. IGH plus hybridized to lymphocytes. One normal interphase and metaphase are shown. Two green-orange (2GO) fusion signals representing the two normal IGH loci. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the IGH locus. Chromosomal translocations affecting the IGH locus are recurrent in many types of lymphomas. The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus. Due to the telomeric position of the IgH locus, 14q32.3 translocations may be easily missed by conventional cytogenetics. A break apart IGH probe covering the central IGHV region and located proximally from IGHJ close to the JAG2 gene, allows to identify most IGH rearrangements independent of breakpoint variations. MM NHL ALL Martin-Subero et al (2006) Cancer Res 66: Wlodarska et al (2007) J Mol Diagn 9:47-54 Dyer et al (2010) Blood 115: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 55 Chr14

56 TCRA/D Break Apart Probe The TCRA/D is designed as break apart probe. An orange labeled probe covers the region proximal to TCRA/D at 14q11, and a green labeled probe covers the region distal to the TCRA/D gene. TCRA/D hybridized to lymphocytes. One normal metaphase is shown. Two green-orange fusion signals (2GO). One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the TCRA/D locus. Chromosomal aberrations with breakpoints in T-cell receptor (TCR) gene loci are recurrent in several T-cell malignancies. The chromosomal alterations juxtapose oncogenes next to TCR regulatory sequences leading to deregulated expression of those oncogenes. T-cell prolymphocytic leukemia (T-PLL) harbors frequent alterations of the TCRA/D locus, usually caused by an inv(14)(q11q32). By molecular cytogenetics studies, the incidence of TCRA/D rearrangements is about 24% of all T-ALL cases. ALL NHL Gesk et al (2003) Leukemia 17: Leich et al (2007) J Pathol 213: Feldman et al (2009) Am J Clin Pathol 130: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 56 Chr14

57 t(14;16) Translocation/Dual Fusion Probe The t(14;16) is designed as a dual fusion probe. An orange labeled probe flanks the breakpoint at the MAF/WWOX genes at 16q23. A green labeled probe flanks the 14q32 IGH breakpoint region. Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(14;16) hybridized to lymphocytes. One normal metaphase and one normal interphase are shown. Genetic aberrations present in multiple myeloma cells play a significant role in the risk stratification and therapeutic approach in multiple myeloma patients. Chromosomal translocations affecting the IGH locus are recurrent in many types of leukemias and lymphomas. The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus. The t(14;16) is found in 5-7 % of all MM cases. The presence of t(14;16) has been associated with more aggressive disease and shorter survival among patients treated with either conventional or high-dose chemotherapy. MM Chesi et al (2000) Ann Onco 11: Fonseca et al (2003) Blood 101: Kumar et al (2009) Mayo Clin Proc 84: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 57 Chr14

58 t(14;18) IGH / BCL2 Translocation/Dual Fusion Probe The t(14;18) is designed as a dual fusion probe. An orange labeled probe spans the breakpoint at the BCL2 gene at 18q21. A green labeled probe flanks the 14q32 IGH breakpoint region. Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). t(14;18) IGH/BCL2 hybridized to lymphocytes. One normal interphase and metaphase are shown. Follicular lymphomas (FL) and diffuse large cell lymphoma (DLBCL) represent the most common entities of non-hodgkin's lymphoma (NHL) worldwide with up to 29 % and 37 % of B-cell lymphomas. The translocation t(14;18) juxtaposes the IGH enhancer region with the BCL-2 oncogen at 18q21 and is present in 70 % to 95 % of follicular lymphomas. By this rearrangement BCL-2 gene expression is deregulated, leading to overproduction of the antiapoptotic protein BCL-2. The same aberration is present in % of diffuse large cell lymphomas. NHL Einerson et al (2005) Am J Clin Pathol 124: Weinberg et al (2007) J Mol Diagn 9: Gu et al (2008) Arch Pathol Lab Med 132: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 58 Chr14

59 IGH / MAFB Translocation/Dual Fusion Probe The IGH/MAFB is designed as dual fusion probe. An orange labeled probe flanks the large breakpoint region at 20q12 which is located proximal to the MAFB gene, while a green labeled probe flanks the IGH breakpoint at 14q32. Two green (2G) and two orange signals (2O). One green (1G), one orange (1O), and two green-orange fusion signals (2GO). IGH/MAFB hybridized to lymphocytes. One normal interphase and metaphase are shown. Chromosomal translocations affecting the IGH locus are recurrent in many types of lymphomas. The malignant transformation works via the juxtaposition of oncogenes next to regulatory sequences of the immunoglobulin locus. Aberrant expression of MAFB is reported to be involved in the oncogenic transformation of myeloma cells that harbor the t(14;20). It can be found in about 2 % of multiple myeloma and less frequent in monoclonal gammopathy of undetermined significance (MGUS) patients. Cases characterized by this translocation can be stable for years before progression occurs. MM Boersma-Vreugdenhil et al (2004) Brit J Haem 126: Zhan et al (2006) Blood 108: Ross et al (2010) Haematologica 95: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 59 Chr14

60 PML / RARA Translocation/Dual Fusion Probe The PML/RARA probe is designed as a dual fusion probe. An orange labeled probe spans the breakpoint at 15q24 (PML) and a green labeled probe the breakpoint at 17q21 (RARA). Two green (2G) and two orange (2O) signals. One green (1G), one orange (1O), and two green-orange signals (2GO). PML/RARA was hybridized to lymphocytes. Two normal interphase cells are shown. Several recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category acute myeloid leukemia (AML) with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasiarelated features when 20% or more blood or marrow blasts are present. AML M3 and AML M3v are characterized by a reciprocal translocation between the long arm of chromosome 15 and the long arm of chromosome 17. This translocation leads to a rearrangement of the PML-gene situated on chromosomal band 15q24 and the RARA-gene situated on band 17q21. The PML-RARA-rearrangement has gained major clinical importance as combining all transretinoic acid and conventional anthracy-cline-cytarabin based chemotherapy has improved the prognosis in this subgroup of AML dramatically. AML Lafage-Pochitaloff et al (1995) Blood 85: Grimwade et al (2000) Blood 96: Schoch et al (2002) Hematol-J 3: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 60 Chr15

61 CBFB Break Apart Probe The CBFB probe is designed as a break apart probe with two probes juxtaposed and differently labeled. An orange labeled probe hybridizes proximal to CBFB, and a green labeled probe hybridizes distal to CBFB in 16q22. CBFB hybridized to bone marrow cells. One metaphase with split signals in one chromosome is shown, indicating a chromosome break in the CBFB locus. Two green-orange fusion signals (2GO). One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the CBFB locus. Several recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category AML with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasia-related features when 20% or more blood or marrow blasts are present. The inv(16) and related t(16;16) are found in 10 % of all cases with de novo AML. In these rearrangements the core binding factor b (CBFB) gene on 16q22 is fused to the smooth muscle myosin heavy chain gene (MYH11) on 16p13. This cytogenetic group is usually associated with high complete remission rates and a relatively favorable outcome, especially when treated with repetitive cycles of highdose cytarabine as consolidation therapy. AML Mancini et al (2000) Leukemia 14: Doehner et al (2010) Blood 115: Schwind et al (2013) Blood 121: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 61 Chr16

62 CBFB / MYH11 Translocation/Dual Fusion Probe The CBFB/MYH11 probe is designed as a dual fusion probe. An orange labeled probe spans the breakpoint at 16q22 and includes the CBFB locus. A green labeled probe spans the breakpoint at 16p13 and includes the MYH11 locus. Two green (2G) and two orange (2O) signals. One green (1G), one orange (1O), and two green-orange signals (2GO). CBFB/MYH11 was hybridized to normal lymphocytes. One interphases and one partial metaphase are shown. Several recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category acute myeloid leukemia (AML) with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasiarelated features when 20% or more blood or marrow blasts are present. The inv(16) and related t(16;16) are found in 10 % of all cases with de novo AML. In these rearrangements the core binding factor b (CBFB) gene on 16q22 is fused to the smooth muscle myosin heavy chain gene (MYH11) on 16p13. AML Reijden et al (1999) Oncogene 8: Froehling et al (2002) J Clin Oncol 20: Doehner et al (2010) Blood 115: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 62 Chr16

63 ERBB2 (HER2 / NEU) amp Amplification Probe ERBB2 (HER2/NEU) amp hybridized on breast cancer tissue. Multiple orange signals indicate amplification of ERBB2 (HER2/NEU). The ERBB2 (HER2/NEU) amp probe detects amplifications in the long arm of chromosome 17. The orange labeled probe is designed to hybridize to the ERBB2 (HER2/NEU) locus at 17q12. A green labeled probe hybridizes to the 17cen region and functions as a control probe. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green (2G) and two orange (2O) signals. Two green (2G), one orange (1O), and orange signal clusters, indicating amplification of ERBB2 (homogenous staining region = HSR). Amplification or over-expression of the ERBB2 (HER2/NEU) gene occurs in approximately % of breast cancers. It is strongly associated with increased disease recurrence and a poor prognosis. Over-expression is also known to occur in ovarian, stomach, and aggressive forms of uterine cancer, such as uterine serous endometrial carcinoma. ERBB2 located on the long arm of human chromosome 17 (17q12), is a member of the epidermal growth factor receptor (EGFR/ErbB) family which is composed of four plasma membrane-bound receptor tyrosine kinases. Signaling through the ErbB family of receptors promotes cell proliferation and opposes apoptosis. ERBB2 is the target of the monoclonal antibody trastuzumab (marketed as Herceptin ). Two green (2G) and multiple copies of orange signals, indicating amplification of ERBB2 (double minutes = dm). Solid Tumors Isola et al (1999) Clin Cancer Res 5: Blancato et al (2004) Br J Cancer 90: Singhi et al (2012) Mod Pathol 25: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 63 Chr17

64 Iso(17q) Amplification/Deletion Probe The Iso(17q) is a combination of locusspecific DNA probes for the TP53 region at 17p13 in green and the MPO region located at 17q22 in orange. Two green (2G) and two orange (2O) signals. result): One green (1G), three orange (3O) signals, indicating the presence of i(17q). Iso(17q) hybridized to lymphocytes. One normal metaphase is shown. An isochromosome of the long arm of chromosome 17, i(17q), is the most frequent genetic abnormality observed during the disease progression of Philadelphia chromosome positive chronic myeloid leukemia (CML). The breakpoints are located in the short arm of chromosome 17 within the Smith-Magenis critical region at 17p11. In neuroblastoma and other hematologic malignancies, amplification of 17q is a significant predictive factor for adverse outcome. Isochromosome 17q, or i(17q), is ocurring in primitive neuroectodermal tumor/ medulloblastoma (50 %), chronic myeloid leukemia (CML), acute myeloid leukemia (AML), and myelodysplastic syndrome (MDS). Two green (2G), three orange (3O) signals, indicating a gain of 17q. Aberrant Cells (typical One green (1G) and two orange (2O) signals, indicating a deletion of the TP53 locus. CML MDS ALL Fioretos et al (1999) Blood 94: Barbouti et al (2004) Am J Hum Genet 74:1-10 Carvalho et al (2008) Genome Res 18: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 64 Chr17

65 P53 Deletion Probe The P53 probe detects deletions in 17p13 which involve the TP53 locus. The specific probe is labeled in orange, while a green labeled probe which hybridizes to the centromere of chromosome 17 functions as a reference probe. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal resulting from loss of one orange locus. P53 hybridized to lymphocytes. One normal interphase and metaphase are shown. The prognosis and clinical course of CLL are heterogeneous. Conventional banding techniques in CLL are hampered by the low mitotic index of the neoplastic cells. The introduction of interphase cytogenetics using fluorescent in situ hybridization (FISH) has greatly increased the sensitivity of cytogenetic analyses. With FISH abnormalities can be detected in more than 80 % of patients by using a 4-probe panel for the detection of trisomy 12q13-15 and deletions 13q14, 17p13, and 11q An additional 10 % of patients can be shown to carry a 6q21 deletion, 14q32 translocation, and partial trisomy 3q or 8q. TP53 is a tumor suppressor gene that stops cell division when DNA damage is present. Loss of TP53 at 17p13 is a powerful predictor of resistance to therapy with purine analogues and alkylating agents, and of poor prognosis in CLL. The TP53 tumor suppressor gene is one of the most frequently mutated genes in human cancer with mutations and deletions identified in a wide range of solid tumors and hematological disorders. MM CLL Doehner et al (1995) Blood 85: Drach et al (1998) Blood 92: Doehner et al (2000) N Engl J Med 343: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 65 Chr17

66 TP53 / NF1 Deletion Probe The TP53/NF1 probe detects deletions which occur in 17p13 and involve the TP53 gene locus. The orange labeled probe hybridizes to a larger TP53 specific region while a green labeled probe which hybridizes to the NF1 gene region at 17q11.2 functions as a reference probe. Two green (2G) and two orange (2O) signals. Two green (2G), one orange (1O) signals, indicating a deletion of thetp53 locus. TP53/NF1 hybridized to lymphocytes. One normal metaphase is shown. TP53 is described as 'the guardian of the genome' because of its role in conserving stability by preventing genome mutation. Therefore TP53 is classified as a tumor suppressor gene. It has many mechanisms of anticancer function, and plays a role in apoptosis, genomic stability, and inhibition of angiogenesis. If the TP53 gene is damaged tumor suppression is severely reduced. One green (1G) and one orange (1O) signal indicating the deletion of the TP53 and NF1 locus. Three green (3G), one orange (1O) signals, indicating the presence of isochromosome 17q. The TP53 gene is located on the short arm of chromosome 17 (17p13.1). More than 50 % of human tumors contain either a mutation or deletion of the TP53 gene. CLL MM CML Fioretos et al (1999) Blood 94: Barbouti et al (2004) Am J Hum Genet 74:1-10 Carvalho et al (2008) Genome Res 18: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 66 Chr17

67 BCL2 BA Break Apart Probe The BCL2 BA probe is designed as a break apart probe. Its orange labeled part hybridizes proximal to the BCL2 gene at 18q21, the green labeled probe hybridizes to the distal region of BCL2. BCL2 BA hybridized to a prostate tissue section. The normal green-orange fusion signal pattern is observed. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green-orange (2GO) fusion signals representing the two normal BCL2 loci. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the BCL2 locus. The BCL2 gene rearrangement can be found in 50 % of follicular lymphoma, 23.3 % of B-cell lymphoma, and about 15 % of diffuse large B-cell lymphoma. A consequence of this translocation is an overexpression of anti-apoptotic protein BCL2, which most likely represents the initial step of malignant transformation. The majority of rearrangements in BCL2 occur at two distinct chromosomal regions, the major breakpoint cluster region (MBR) in 70 % and the minor cluster region in 10 % of patient's tumors. FISH has been shown to be of higher sensitivity and of equivalent specificity when compared to PCR on paraffin-embedded tissue sections. Solid Tumors Lymphomas Vaandrager et al (2000) Blood 96: Godon et al (2003) Leukemia 17: Weinberg et al (2007) J Mol Diagn 9: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 67 Chr18

68 MALT1 BA Break Apart Probe The MALT1 BA probe is designed as a break apart probe. Its orange labeled part hybridizes proximal to the MALT1 gene at 18q21, the green labeled probe hybridizes to the distal region of MALT1. MALT1 BA hybridized to lymphoid tissue. The normal green-orange fusion signal pattern is observed. This probe is intended for methanol/aceticacid fixed cells and tissue sections. Two green-orange (2GO) fusion signals. One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the MALT1 locus. The MALT1 gene was identified through its involvement in t(11;18)(q21;q21), seen in 30% of cases of mucosa-associated lymphoid tissue (MALT) lymphoma. The t(11;18) (q21;q21) is restricted to MALT lymphomas and has not been detected in nodal or splenic marginal zone lymphomas, diffuse large B-cell lymphomas, or other non- Hodgkin lymphomas. The second most frequent translocation identified in MALT lymphoma is the t(14;18)(q32;q21) IGH/MALT1. The t(14;18)(q32;q21) IGH/MALT1 is found most often in MALT lymphomas arising at non-gastric sites, and is identified in 5-25% of cases arising in the ocular adnexa, lung, salivary gland and skin. The oncogenic activity of MALT1 is linked to it's involvement of the CARMA1-BCL10- MALT1 (CBM) complex in antigen receptor-mediated activation of the transcription factor NF-kB, which controls the expression of numerous anti-apoptotic and proliferation-promoting genes. Solid Tumors Lymphomas Streubel et al (2003) Blood 101: Murga Penas et al (2003) Leukemia 17: Bacon et al (2007) J Clin Pathol 60: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 68 Chr18

69 E2A Break Apart Probe The E2A probe is designed as a break apart probe with two probes juxtaposed and differently labeled. The orange labeled probe hybridizes proximal and the green labeled probe hybridizes distal to the E2A (=TCF3) breakpoint in 19p13. E2A hybridized to lymphocytes. One normal interphase is shown. Two green-orange fusion signals (2GO). One green-orange fusion signal (1GO), one separate green (1G) and one orange (1O) signal each resulting from a chromosome break in the relevant locus. Acute Lymphoblastic Leukemia (ALL) is the most common type of leukemia in children, representing almost 25 % of pediatric cancer. The majority of patients with ALL demonstrate an abnormal karyotype, either in chromosome number or as structural changes such as translocations, inversions, or deletions. E2A (also termed TCF3) is the target of three known recurrent genomic rearrangements in ALL. The t(1;19)(q23;p13.3) occurs in approximately 5 % of cases and is the second most common translocation in ALL. The t(17;19)(q22;p13) occurs in about 1 % of ALLs and fuses E2A to the chromosome 17 gene HLF. A recently described cryptic inversion of chromosome 19 fuses E2A to the 19q13.4 gene FB1. ALL Boomer et al (2001) Leukemia 15: Van der Burg et al (2004) Leukemia 18: Kager et al (2007) Haematologica 92: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 69 Chr19

70 20q12 / 20qter Deletion Probe The 20q12/20qter locus-specific probe detects deletions in the long arm of chromosome 20. The orange labeled probe hybridizes to a specific region at 20q12, and the green labeled probe hybridizes to the subtelomeric region of the q-arm of chromosome 20. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating a deletion in 20q12. 20q12/20qter hybridized to lymphocytes. One normal interphase and metaphase are shown. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3). A chromosome 20q deletion is associated with about 5 % of primary MDS. The majority of cases has an interstitial deletion between 20q11.2 and q13.3. Isochromosome of the long arm of chromosome 20 with loss of interstitial material [ider(20q)] is a variant of deletion of chromosome 20q. Amplification of genes included in retained regions associated with loss of tumor suppressor genes in deleted regions could explain cell tumor progression and possibly the less favorable prognosis of ider(20q) compared with del(20q). MDS AML Saunders et al (2005) Cancer Genet Cytogenet 156: Smoley et al (2006) Cancer Genet Cytogenet 173: Douet-Gilbert et al (2008) Br J Haematol 143: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 70 Chr20

71 Del(20q) Deletion Probe Del(20q) hybridized to lymphocytes. One normal Interphase and one normal partial metaphase are shown The Del(20q) detects deletions which occur in the long arm of chromosome 20. The probe mixture includes two probes: an orange labeled one which hybridizes to 20q12 and includes the proximal part of PTPRT, and a green labeled probe which hybridizes to 20q13 and includes the MYBL2 locus. Two green (2G) and two orange (2O) signals. Two green (2G) and one orange (1O) signal, indicating the deletion of a PTPRT locus at 20q12. The myelodysplastic syndromes and myeloproliferative disorders are associated with deregulated production of myeloid cells. According to WHO classification (2008) cytogenetic aberrations are observed in about 50 % of MDS cases. The most common aberrations are 5q-, 7/7q-, trisomy 8, del(20q), and inv(3) or t(3;3). A chromosome 20q deletion is associated with about 5 % of primary MDS. The majority of cases have an interstitial deletion between 20q11.2 and q13.3. As a single anomaly, the del(20q) has a favorable prognosis. One green (1G) and two orange (2O) signals, indicating a deletion of MYBL2 at 20q13. One green (1G) and one orange (1O) signal, indicating deletions of both loci, PTPRT at 20q12 and MYBL2 at 20q13. MDS AML Bench et al (2000) Oncogene 19: Wang et al (2000) Genomics 67:28-39 Saunders et al (2005) Cancer Genet Cytogenet 15: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 71 Chr20

72 RUNX1 Break Apart Probe The RUNX1 (formerly AML1) is designed as a break apart probe with two probes juxtaposed and differently labeled. The proximal probe is labeled in orange and a green labeled probe is designed to hybridize distal to the breakpoint in 21q22. RUNX1 was hybridized to lymphocytes. One normal interphase and partial metaphase are shown. Two green-orange fusion signals (2GO). One green (1G), one orange (1O), and one greenorange (1GO) fusion signal, indicating a chromosome break in the RUNX1 locus. Several recurrent balanced translocations and inversions, and their variants, are recognized in the WHO category acute myeloid leukemia (AML) with recurrent genetic abnormalities. Furthermore, several cytogenetic abnormalities are considered sufficient to establish the WHO diagnosis of AML with myelodysplasiarelated features when 20% or more blood or marrow blasts are present. The RUNX1 gene, located on chromosome 21q22.3, is crucial for the establishment of definite hematopoiesis and the generation of hematopoietic stem cells in the embryo. The most common translocations involving RUNX1 are the t(8;21) RUNX1T1/ RUNX1 in AML and t(12;21) ETV6/RUNX1 in ALL, both associated with a more favorable diagnosis. More than 40 different translocation partners have currently been identified making the RUNX1 break apart probe a valuable tool in molecular cytogenetics. ALL AML Levanon et al (2001) Gene 262: Zhang et al (2002) Proc Natl Acad Sci USA 99: De Braekeleer et al (2009) 29: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 72 Chr21

73 IGL Break Apart Probe IGL hybridized to normal lymphocytes. Two normal interphases are shown. The IGL probe is designed as a break apart probe with two probes juxtaposed and differently labeled. An orange labeled probe hybridizes proximal to the Variable Region of IGL in 22q11, while a green labeled probe hybridizes distal to the breakpoint and includes BCR. Two green-orange fusion signals (2GO). One green-orange fusion signal (1GO) and one green (1G), one orange (1O) indicating a chromosome break in the IGL locus. Primary karyotypic changes in lymphoid neoplasms commonly juxtapose oncogenes to the potent transcriptional enhancers associated with IG and TCR loci in B and T cells, respectively, often resulting in elevated levels of protein expression and loss of normal mechanisms of control. Less commonly, fusion genes are created that encode novel hybrid proteins. Variant translocations involving the IG lambda (IGL) locus in 22q11 or the IG kappa (IGK) locus in 2p11.2 occur recurrently in B-cell neoplasias. The different translocations involving immunoglobulin genes have a diagnostic value and can be used to monitor the clinical course of the disease. NHL Martin-Subero et al (2002) Int J Cancer 98: Einerson et al (2006) Leukemia 10: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 73 Chr22

74 21q22 / XCP 21 The 21q22/XCP 21 is a combination of a whole chromosome paint 21 in green with an orange labeled locus-specific probe for 21q22. This probe allows analysis of copy numbers and structural aberrations of chromosome 21 on metaphase chromosomes. 21q22/XCP21 was hybridized to normal lymphocytes. A metaphase with chromosomes 21 painted in green and orange signals at 21q22 is shown. This probe is not intended for use to analyze trisomy 21 in prenatal diagnosis. 21q22/XCP 21 hybridized to normal human metaphase spreads will result in green signals along the entire length of chromosome 21 combined with orange signals at 21q22 (Down Syndrome Critical Region 4). A translocation with involvement of chromosome 21 will result in a split of a green signal. In this case the green signal will be partially visible on the der(21) and the respective partner chromosome of the translocation. Depending on the localization of the breakpoint on the der(21), the signal of the locus-specific probe remains on the der(21) or will be observed on the translocation partner. Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (50 µl / 5 Tests) 74

75 Acro-p The Acro-p probe contains sequences which specifically hybridize to the short (p) arm of all human acrocentric chromosomes. The Acro-p FISH probe may replace conventional silver staining used to stain the NOR regions. Acro-p was hybridized to normal lymphocytes. A metaphase with orange signals at band p12 of all acrocentric chromosomes (13, 14, 15, 21 and 22) is shown. Variations in length of stalks and satellites of human acrocentric chromosomes are considered as normal variable chromosome features. However, cryptic translocations can result in unbalanced karyotypes but might be misinterpreted as common acrocentric short arm polymorphisms. Benzacken et al (2001) Prenat Diagn21:96-98 Map components not to scale. Reference Number: D OR (50 µl / 5 Tests) 75

76 76

77 XA XCyting Aneusomy 77

78 XA 13 / 21 Aneusomy Probe XA XCyting Aneusomy The XA 13/21 mix of specific probes allows detecting copy number variations for chromosomes 13 and 21. The green labeled probe hybridizes to a region at 13q14 including the RB1 locus and the orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). Two green (2G), two orange (2O) signals. Aberrant Cell: Trisomy 13 Three green (3G) and two orange (2O) signals. XA 13/21 was hybridized to normal lymphocytes. Interphase nuclei with two orange and two green signals each are shown. Numerical aberrations of autosomes 13, 18, 21, and sex chromosomes X and Y account for 95 % of birth defects in newborns. FISH applied to uncultured amniocytes provides a method to identify those aberrations much faster than conventional chromosome analysis. It has become a standard to provide preliminary results for the detection of anomalies in less than 12 hours. Aberrant Cell: Trisomy 21 Two green (2G) and three orange (3O) signals. Duplications of chromosome bands 21q22.13-q22.2 have been shown to define the smallest region implicated in the causation of Down syndrome. Trisomy 13 syndrome is a rare chromosomal disorder in which all or a portion of chromosome 13 appears three times (trisomy). Based on molecular results a region from 13q14-13qter has been found to be critically involved in Patau syndrome. Bryndorf et al (1996) Am J Hum Genet 59: Tepperberg et al (2001) Prenat Diagn 21: Stumm et al (2006) Cytogenet Genome Res 114: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 78

79 XA 13 / 18 / 21 Aneusomy Probe XA XCyting Aneusomy The XA 13/18/21 mix of specific probes allows detecting copy number variations of chromosomes 13, 18, and 21. The green labeled probe hybridizes to a region at 13q14 including the RB1 locus, the blue (aqua) labeled probe hybridizes to a locus at 18q21, and the orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). Two green (2G), two orange (2O), and two blue (2B) signals. Aberrant Cell: Trisomy 13 Three green (3G), two orange (2O), and two blue (2B) signals. XA 13/18/21 hybridized to cultured amniocytes. A normal signal constellation is observed for 13q14 and 21q22, two green and two orange, respectively. For the 18q21 locus-specific probe three blue signals are shown. Numerical aberrations of autosomes 13, 18, 21, and sex chromosomes X and Y account for 95 % of birth defects in newborns. FISH applied to uncultured amniocytes provides a method to identify those aberrations much faster than conventional chromosome analysis. It has become a standard to provide preliminary results for the detection of anomalies in less than 12 hours. Duplications of chromosome bands 21q22.13-q22.2 have been shown to define the smallest region implicated in the causation of Down syndrome. Trisomy 13 syndrome is a rare chromosomal disorder in which all or a portion of chromosome 13 appears three times (trisomy). Based on molecular results a region from 13q14-13qter has been found to be critically involved in Patau syndrome. Most of the features of Edwards syndrome have been shown to be associated with duplication of the region 18q12.3-q22.1. A locus-specific probe for 18q21 gives clearer signals and provides less ambiguous results compared to a centromeric probe for chromosome 18. Aberrant Cell: Trisomy 21 Two green (2G), three orange (3O), and two blue (2B) signals. Aberrant Cell: Trisomy 18 Two green (2G), two orange (2O), and three blue (3B) signals. Bryndorf et al (1996) Am J Hum Genet 59: Tepperberg et al (2001) Prenat Diagn 21: Stumm et al (2006) Cytogenet Genome Res 114: Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 79

80 XA AneuScore I Aneusomy Probe XA XCyting Aneusomy The XA AneuScore I Probe Kit contains different probe mix, provided in separate test vials, for assessing chromosomal aneuploidies for Chromosomes 13, 18, 21, X, and Y. Please refer to XA 13/21 (D OG) and XA X/Y/18 (D TC) for signal pattern. XA AneuScore I probe kit hybridized to normal lymphocytes. XA X/Y/18 (up) shows signals at the centromeric regions of the X chromosme in green, the Y chromosme in orange, and chromosme 18 in blue. The XA 13/21 (down) shows orange signals at 21q22 and green signals at 13q14. XA 13/21 (D OG): The XA 13/21 mix of specific probes allows detecting copy number variations for chromosomes 13 and 21. The green labeled probe hybridizes to a region at 13q14 including the RB1 locus and the orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). XA X/Y/18 (D TC): The XA X/Y/18 mix of specific probes allows detecting copy number variations for chromosomes X, Y, and 18. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in green, Y in orange, and 18 in blue (aqua). Numerical aberrations of autosomes 13, 18, 21, and sex chromosomes X and Y account for 95% of birth defects in newborns. FISH applied to uncultured amniocytes provides a method to identify those aberrations much faster than conventional chromosome analysis. It is nowadays widely accepted to provide preliminary results for the detection of anomalies in less than 12 hours. Available in two package sizes: D TC XA AneuScore I, 10 Tests D TC XA AneuScore I, 50 Tests Bryndorf et al (1996) Am J Hum Genet 59: Tepperberg et al (2001) Prenat Diagn 21: Stumm et al (2006) Cytogenet Genome Res 114: Map components not to scale. Reference Number: D TC (2x 100 µl / 2x 10 Tests) 80

81 XA AneuScore II Aneusomy Probe XA XCyting Aneusomy The XA AneuScore II Probe Kit contains different probe mix, provided in separate tests vials, for assessing chromosomal aneuploidies for Chromosomes 13, 18, 21, X, and Y. Please refer to the expected results of D TC XA 13/18/21 and D OG XA X/Y. XA 13/18/21 and XA X/Y hybridized to uncultured amniocytes. One interphase and one metaphase are shown for each probe mix. XA 13/18/21 (D TC): The XA 13/18/21 mix of specific probes allows detecting copy number variations of chromosomes 13, 18, and 21. The green labeled probe hybridizes to a region at 13q14 including the RB1 locus, the blue (aqua) labeled probe hybridizes to a locus at 18q21, and the orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). XA X/Y (D OG): The XA X/Y mix of specific probes allows detecting copy number variations for chromosomes X and Y. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in green and Y in orange. Numerical aberrations of autosomes 13, 18, 21, and sex chromosomes X and Y account for 95% of birth defects in newborns. FISH applied to uncultured amniocytes provides a method to identify those aberrations much more fast than conventional chromosome analysis. It is nowadays widely accepted to provide preliminary results for the detection of anomalies in less than 12 hours. Available in two package sizes: D TC XA AneuScore II, 10 Tests D TC XA AneuScore II, 50 Tests Bryndorf et al (1996) Am J Hum Genet 59: Tepperberg et al (2001) Prenat Diagn 21: Stumm et al (2006) Cytogenet Genome Res 114: Map components not to scale. Reference Number: D TC (2x 100 µl / 2x 10 Tests) 81

82 XA 21q22 Aneusomy Probe XA XCyting Aneusomy The XA 21q22 specific probe allows detecting copy number variations for chromosomes 21. The orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). Two orange (2O) signals indicating a chromosome 21 each. Aberrant Cell: Three orange (3O) signals. XA 21q22 was hybridized to normal lymphocytes. A metaphase is shown with orange signals hybridized to 21q22. Numerical aberrations of autosomes 13, 18, 21, and sex chromosomes X and Y account for 95 % of birth defects in newborns. FISH applied to uncultured amniocytes provides a method to identify those aberrations much faster than conventional chromosome analysis. It has become a standard to provide preliminary results for the detection of anomalies in less than 12 hours. Duplications of chromosome bands 21q22.13-q22.2 have been shown to define the smallest region implicated in the causation of Down syndrome. Tepperberg et al (2001) Prenat Diagn 21: Ronan et al (2007) J Med Genet 44: Korbel et al (2009) Proc Natl Acad Sci USA 106: Map components not to scale. Reference Number: D OR (100 µl / 10 Tests) 82

83 XA X / Y Aneusomy Probe XA XCyting Aneusomy The XA X/Y mix of specific probes allows detecting copy number variations for chromosomes X and Y. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in green and Y in orange. Normal Cell female: Two green (2G) signals. Normal Cell male: One green (1G) and one orange (1O) signal. XA X/Y was hybridized to normal uncultured amniocytes from a male fetus. Numerical aberrations of autosomes 13, 18, 21, and sex chromosomes X and Y account for 95 % of birth defects in newborns. FISH applied to uncultured amniocytes provides a method to identify those aberrations much faster than conventional chromosome analysis. It has become a standard to provide preliminary results for the detection of anomalies in less than 12 hours. Aberrant Cell 45, X0: One green (1G) signal. Aberrant Cell 47, XXY: Two green (2G) and one orange (1O) signal. Repetitive sequences around the centromeric regions of chromosomes X and Y can reliably identify Klinefelter syndrome (47,XXY), Triple-X syndrome (47,XXX), Turner syndrome (45,X), and 47,XYY. Bryndorf et al (1996) Am J Hum Genet 59: Tepperberg et al (2001) Prenat Diagn 21: Stumm et al (2006) Cytogenet Genome Res 114: Map components not to scale. Reference Number: D OG (100 µl / 10 Tests) 83

84 XA X / Y / 18 Aneusomy Probe XA XCyting Aneusomy The XA X/Y/18 mix of specific probes allows detecting copy number variations for chromosomes X, Y, and 18. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in green, Y in orange, and 18 in blue (aqua). XA X/Y/18 hybridized to normal uncultured amniocytes. A normal signal constellation with 1 orange (Y centromere-specific), 1 green (X centromere-specific) and 2 blue (18 centromere-specific) is observed. Numerical aberrations of autosomes 13, 18, 21, and sex chromosomes X and Y account for 95 % of birth defects in newborns. FISH applied to uncultured amniocytes provides a method to identify those aberrations much faster than conventional chromosome analysis. It has become a standard to provide preliminary results for the detection of anomalies in less than 12 hours. Repetitive sequences around the centromeric region of chromosomes 18 can reliably determine Edward's syndrome, while chromosome X and Y specifically detect Klinefelter syndrome (47,XXY), Triple-X syndrome (47,XXX), Turner syndrome (45,X), and 47,XYY. Normal cell male: One green (1G), one orange (1O), and two blue (2B) signals. Normal cell female: Two green (2G) and two blue (2B) signals. Aberrant cell male: 47, XXY Two green (2G), one orange (1O) and two blue (2B) signals. Aberrant cell male: Trisomy 18 One green (1G), one orange (1O) and three blue (3B) signals. Aberrant cell female: Trisomy 18 Two green (2G) and three blue (3B) signals. Aberrant cell female: 45, X0 One green (1G) and two blue (2B) signals. Trepperberg et al (2001) Prenat Diagn 21: Stumm et al (2006) Cytogenet Genome Res 114: Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 84

85 XA TriScore (X / Y / 21) Aneusomy Probe XA XCyting Aneusomy The XA TriScore (X/Y/21) mix of specific probes allows detecting copy number variations for chromosomes X, Y, and 21. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in blue (aqua) and Y in green. The orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). Normal cell male: One green (1G), two orange (2O), and one blue (1B) signal. Normal cell female: No green (0G), two orange (2O), and two blue (2B) signals. XA TriScore (X/Y/21) was hybridized to normal uncultured amniocytes. A normal signal constellation on a male cell with 1 green (Y centromere-specific), 1 blue (X centromerespecific) and 2 orange (21q22 specific) signals are observed. Numerical aberrations of autosomes 13, 18, 21, and sex chromosomes X and Y account for 95 % of birth defects in newborns. FISH applied to uncultured amniocytes provides a method to identify those aberrations much faster than conventional chromosome analysis. It has become a standard to provide preliminary results for the detection of anomalies in less than 12 hours. Duplications of chromosome bands 21q22.13-q22.2 have been shown to define the smallest region implicated in the causation of Down syndrome. Repetitive sequences around the centromeric region of the X and Y chromosomes can reliably determine Klinefelter syndrome (47,XXY), Triple-X syndrome (47,XXX), Turner syndrome (45,X), and 47,XYY. This probe allows also to differentiate male fetal cells from maternal cells in blood contaminated amniocyte samples. Aberrant cell male: Trisomy 21 One green (1G), three orange (3O), and one blue (1B) signal. Aberrant cell female: Trisomy 21 No green (0G), three orange (3O), and two blue (2B) signals. Bryndorf et al (1996) Am J Hum Genet 59: Tepperberg et al (2001) Prenat Diagn 21: Stumm et al (2006) Cytogenet Genome Res 114: Map components not to scale. Reference Number: D TC (100 µl / 10 Tests) 85

86 AneuScore Overview XCyting Aneusomy Probe XA XCyting Aneusomy Product Reference No. Package Size Product Details XA 21q22 D OR 100 µl XA 13/21 D OG 100 µl The XA 21q22 specific probe allows detecting copy number variations for chromosomes 21. The orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). The XA 13/21 mix of specific probes allows detecting copy number variations for chromosomes 13 and 21. The green labeled probe hybridizes to a region at 13q14 including the RB1 locus and the orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). XA X/Y/21 TriScore D TC 100 µl The XA TriScore (X/Y/21) mix of specific probes allows detecting copy number variations for chromosomes X, Y, and 21. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in blue (aqua) and Y in green. The orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). XA X/Y/18 D TC 100 µl XA 13/18/21 D TC 100 µl XA X/Y D OG 100 µl The XA X/Y/18 mix of specific probes allows detecting copy number variations for chromosomes X, Y, and 18. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in green, Y in orange, and 18 in blue (aqua). The XA 13/18/21 mix of specific probes allows detecting copy number variations of chromosomes 13, 18, and 21. The green labeled probe hybridizes to a region at 13q14 including the RB1 locus, the blue (aqua) labeled probe hybridizes to a locus at 18q21, and the orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). The XA X/Y mix of specific probes allows detecting copy number variations for chromosomes X and Y. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in green and Y in orange. The XA AneuScore I Probe Kit contains different probe mix, provided in separate test vials, for assessing chromosomal aneuploidies for Chromosomes 13, 18, 21, X, and Y. XA AneuScore I (XA 13/21 + XA X/Y/18) D TC D TC µl µl XA 13/21 (D OG): The XA 13/21 mix of specific probes allows detecting copy number variations for chromosomes 13 and 21. The green labeled probe hybridizes to a region at 13q14 including the RB1 locus and the orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). XA X/Y/18 (D TC): The XA X/Y/18 mix of specific probes allows detecting copy number variations for chromosomes X, Y, and 18. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in green, Y in orange, and 18 in blue (aqua). The XA AneuScore II Probe Kit contains different probe mix, provided in separate tests vials, for assessing chromosomal aneuploidies for Chromosomes 13, 18, 21, X, and Y. XA AneuScore II (XA 13/18/21 + XA X/Y) D TC D TC µl µl XA 13/18/21 (D TC): The XA 13/18/21 mix of specific probes allows detecting copy number variations of chromosomes 13, 18, and 21. The green labeled probe hybridizes to a region at 13q14 including the RB1 locus, the blue (aqua) labeled probe hybridizes to a locus at 18q21, and the orange labeled probe hybridizes to a region at 21q22 including the DSCR4 (Down syndrome critical region 4). XA X/Y (D OG): The XA X/Y mix of specific probes allows detecting copy number variations for chromosomes X and Y. The probe mix is composed of repetitive sequences which hybridize to the centromeric region of chromosomes X in green and Y in orange. 86

87 XCE XCyting Centromere Enumeration 87

88 XCE XCyting Centromere Enumeration Probe XCE XCyting Centromere Enumeration The XCE DNA probes hybridize to human highly repetitive sequences (also called Satellite DNA) located at and around the centromeric region of chromosomes. The XCE probes produce sharp and bright signals allowing for rapid and precise identification and enumeration of human chromosomes in metaphase and interphase cells on various sample types. XCE 7 green, XCE 8 blue and XCE 12 orange were combined and hybridized to normal lymphocytes. A metaphase spread and two interphase cells are shown. XCE probes are provided premixed in hybridization buffer but allow easy mixing of up to four XCE probes. They are directly labeled with either blue (aqua), green, or orange fluorochromes. Chromosome Product Package Size Localization Reference No. / Label Green Orange Blue 1 XCE 1 50 µl 1q12 D FI D OR - 2 XCE 2 50 µl 2p11.1-q11.1 D FI D OR - 3 XCE 3 50 µl 3p11.1-q11.1 D FI D OR - 4 XCE 4 50 µl 4p11.1-q11.1 D FI D OR - 5/19 XCE 5/19 50 µl 5p11.1-q p11.1-q11.1 D FI D OR - 6 XCE 6 50 µl 6p11.1-q11.1 D FI D OR D BL 7 XCE 7 50 µl 7p11.1-q11.1 D FI D OR D BL 8 XCE 8 50 µl 8p11.1-q11.1 D FI D OR D BL 9 XCE 9 50 µl 9p11.1-q11.1 D FI D OR - 10 XCE µl 10p11.1-q11.1 D FI D OR - 11 XCE µl 11p11.1-q11.1 D FI D OR D BL 12 XCE µl 12p11.1-q11.1 D FI D OR D BL 15 XCE µl 15p11.1-q11.1 D FI D OR - 17 XCE µl 17p11.1-q11.1 D FI D OR - 18 XCE µl 18p11.1-q11.1 D FI D OR D BL 20 XCE µl 20p11.1-q11.1 D FI D OR - X XCE X 50 µl Xp11.1-q11.1 D FI D OR - Y XCE Y 50 µl Yp11.1-q11.1 D FI D OR D BL Chromosomes Product Package Size Reference No. / Label X/Y XCE X/Y 50 µl D OG Green / Orange X/Y XCE X/Y 4 50 µl D OG Green / Orange 7/8 XCE 7/8 50 µl D OG Orange / Green 3/7/17 XCE 3/7/17 50 µl D TC Orange / Green / Blue 4/10/17 XCE 4/10/17 50 µl D TC Orange / Green / Blue 88

89 XCE X/Yqh XCyting Centromere Enumeration Probe XCE XCyting Centromere Enumeration The XCE X/Yqh DNA probe contains a mix of repetitive sequences specific for the chromosome X centromeric region in orange and chromosome Yqh in green which is located in the heterochromatic region at Yq12. 46, XX Two orange (2O) signals. 46, XY One green (1G) and one orange (1O) signal. XCE X/Yqh hybridized to lymphocytes. One normal interphase and metaphase are shown. Following allogeneic bone marrow transplantation (BMT) careful monitoring of engraftment is important, as the presence of residual host cells can precede the reappearance of the abnormal hematopoietic clone. FISH allows the rapid screening of large number of cells and has become a powerful tool for monitoring engraftment with a high sensitivity and low false positivity rate in patients undergoing BMT from sex-mismatched donors. FISH-analysis of residual cells after sex-mismatched transplantations is based on simultaneous labeling of the centromeres of the X- and Y-chromosomes. Because the cytogenetic status of either donor or recipient is known also a non-centromeric repeat at Yq12 can be chosen due to its more pronounced signals. Aberrant Cell: 45, X0 One orange (1O) signal. Aberrant Cell: 47, XXY One green (1G) and two orange (2O) signals. Dewald et al (1993) Bone Marrow Trans 12: Najfeld et al (1997) Bone Marrow Trans 19: Probe map details based on UCSC Genome Browser GRCh37/hg19. Map components not to scale. Reference Number: D OG (50 µl / 5 Tests) 89

90 90

91 XCP XCyting Chromosome Paints 91

92 XCP Green XCyting Chromosome Paint XCP XCyting Chromosome Paints XCyting Chromosome Paints are chromosomespecific and cover the entire chromosome. These XCPs are labeled in green. XCP 3 Green hybridized to lymphocytes. A normal metaphase is shown. Chromosomes Product Package Size / Reference No. 1 XCP 1 Green 50 µl D FI 2 50 µl D FI 2 XCP 2 Green 50 µl D FI 2 50 µl D FI 3 XCP 3 Green 50 µl D FI 2 50 µl D FI 4 XCP 4 Green 50 µl D FI 2 50 µl D FI 5 XCP 5 Green 50 µl D FI 2 50 µl D FI 6 XCP 6 Green 50 µl D FI 2 50 µl D FI 7 XCP 7 Green 50 µl D FI 2 50 µl D FI 8 XCP 8 Green 50 µl D FI 2 50 µl D FI 9 XCP 9 Green 50 µl D FI 2 50 µl D FI 10 XCP 10 Green 50 µl D FI 2 50 µl D FI 11 XCP 11 Green 50 µl D FI 2 50 µl D FI 12 XCP 12 Green 50 µl D FI 2 50 µl D FI 13 XCP 13 Green 50 µl D FI 2 50 µl D FI 14 XCP 14 Green 50 µl D FI 2 50 µl D FI 15 XCP 15 Green 50 µl D FI 2 50 µl D FI 16 XCP 16 Green 50 µl D FI 2 50 µl D FI 17 XCP 17 Green 50 µl D FI 2 50 µl D FI 18 XCP 18 Green 50 µl D FI 2 50 µl D FI 19 XCP 19 Green 50 µl D FI 2 50 µl D FI 20 XCP 20 Green 50 µl D FI 2 50 µl D FI 21 XCP 21 Green 50 µl D FI 2 50 µl D FI 22 XCP 22 Green 50 µl D FI 2 50 µl D FI X XCP X Green 50 µl D FI 2 50 µl D FI Y XCP Y Green 50 µl D FI 2 50 µl D FI Chromosomes Product Package Size / Reference No. 1-22, X, Y Kit with 24 XCPs green 24 50µl D FI 1-12 Kit with 12 XCPs green 12 50µl D FI 13-22, X, Y Kit with 12 XCPs green 12 50µl D FI 92

93 XCP Orange XCyting Chromosome Paint XCP XCyting Chromosome Paints XCyting Chromosome Paints are chromosomespecific and cover the entire chromosome. These XCPs are labeled in orange. XCP 9 Orange hybridized to lymphocytes. A normal metaphase is shown. Chromosome Product Package Size / Reference No. 1 XCP 1 Orange 50 µl D OR 2 50 µl D OR 2 XCP 2 Orange 50 µl D OR 2 50 µl D OR 3 XCP 3 Orange 50 µl D OR 2 50 µl D OR 4 XCP 4 Orange 50 µl D OR 2 50 µl D OR 5 XCP 5 Orange 50 µl D OR 2 50 µl D OR 6 XCP 6 Orange 50 µl D OR 2 50 µl D OR 7 XCP 7 Orange 50 µl D OR 2 50 µl D OR 8 XCP 8 Orange 50 µl D OR 2 50 µl D OR 9 XCP 9 Orange 50 µl D OR 2 50 µl D OR 10 XCP 10 Orange 50 µl D OR 2 50 µl D OR 11 XCP 11 Orange 50 µl D OR 2 50 µl D OR 12 XCP 12 Orange 50 µl D OR 2 50 µl D OR 13 XCP 13 Orange 50 µl D OR 2 50 µl D OR 14 XCP 14 Orange 50 µl D OR 2 50 µl D OR 15 XCP 15 Orange 50 µl D OR 2 50 µl D OR 16 XCP 16 Orange 50 µl D OR 2 50 µl D OR 17 XCP 17 Orange 50 µl D OR 2 50 µl D OR 18 XCP 18 Orange 50 µl D OR 2 50 µl D OR 19 XCP 19 Orange 50 µl D OR 2 50 µl D OR 20 XCP 20 Orange 50 µl D OR 2 50 µl D OR 21 XCP 21 Orange 50 µl D OR 2 50 µl D OR 22 XCP 22 Orange 50 µl D OR 2 50 µl D OR X XCP X Orange 50 µl D OR 2 50 µl D OR Y XCP Y Orange 50 µl D OR 2 50 µl D OR Chromosomes Product Package Size / Reference No. 1-22, X, Y Kit with 24 XCPs orange 24 50µl D OR 1-12 Kit with 12 XCPs orange 12 50µl D OR 13-22, X, Y Kit with 12 XCPs orange 12 50µl D OR 93

94 XCP-Mix #1O-#2G-#4GO XCyting Chromosome Paint XCP XCyting Chromosome Paints The XCP-Mix #1O-#2G-#4GO probe mix contains whole chromosome paints (XCP) specific for chromosome 1 labeled with an orange emitting fluorophore, chromosome 2 with a green emitting fluorophore, and chromosome 4 with a combination of those 2 fluorophores. XCP-Mix #1O-#2G-#4GO hybridized to lymphocytes. One normal metaphase is shown. XCP1 orange, XCP2, green and XCP 4 yellow (green-orange). Ionizing radiation exposure gives rise to a variety of lesions in DNA that result in genetic instability and potentially tumorgenesis or cell death. At present, a particular interest of biological dosimetry is to establish a methodology to indicate interindividual sensitivity of people to ionising radiation. Current dose and risk estimates derived using cytogenetic methods and adequate calibration curves, are based on the assumption that all individuals respond equally to radiation. However, this is not necessarily the case. Individual increased radio sensitivity has been highly associated with susceptibility to cancer; therefore it is of particular interest to elucidate the mechanisms leading to such genetic changes. Terzoudi et al (2006) Radiat Prot Disom 122: Pouzoulet et al (2007) J Radiat Res 48: Huber et al (2011) Radiat Oncol 6:32- Reference Number: D MC (200 µl / 20 Tests) 94

95 mfish XCyting Multicolor FISH 95

96 24XCyte Human Multicolor FISH Probe mfish XCyting Multicolor FISH 24 painting probes specific for the 24 different human chromosomes, labeled with different fluorochromes. The excitation/emission spectra of the fluorochromes are compatible to FITC, Spectrum Orange, TexasRed, DEAC (Diethylamino-coumarin), and Cy5. Also available as 120µl (2x60µl) D DI and as 600µl (10x60µl) D DI. 24XCyte hybridized to lymphocytes. Multiple translocations can be identified by conjunction of differently labeled chromosomal fragments. The principle of mfish is based on combinatorial labeling of whole chromosome paints. For each chromosome the different fluorochromes are mixed resulting in a unique color combination (see labeling scheme). The analysis is carried out after capturing grey scale images of each fluorochrome. For best separation of the different colors the filter sets used need to be highly selective assuring that cross-talk is reduced to a minimum. Isis-mFISH supports the analysis by applying appropriate algorithms which leads to pseudo coloring of the different chromosome classes (color combinations). Each chromosome class will be displayed in a unique color. Translocations show up as color changes on individual chromosomes. Complex chromosomal aberrations Speicher MR et al (1996) Nat Genet. 12: Fauth C and Speicher MR (2001) Cytogenet Cell Genet 93:1-10 Schoch C et al(2002)genes Chromosomes Cancer 35:20-29 Reference Number: D DI (60 µl / 6 Tests) 96

97 mband XCyting Multicolor Banding 97

98 XCyte mband Human mband mband XCyting Multicolor FISH XCyte 18 was hybridized to a cell line with a ring chromosome 18. On the left hand side the mband image of the normal chromosome 18 is shown. The mband image of the ring chromosome 18 is shown right to it. The mband technique is based on a series of partial chromosome paints for sequential partially overlapping chromosome regions of a single chromosome. For labeling the same 5 fluorochromes as in the 24XCyte probe are used. The characteristic multicolor banding pattern of mband is generated by quantifying the fluorescence intensity ratios along the chromosome. These ratios are unique and visualized as band-specific pseudo colors. mband provides information that allows for a precise analysis of even highly complex inter- and intrachromosomal aberrations. The mband technique is protected by international patents (e.g. US 7,050,911, EP , EP ). Chudoba I et al (1999) Cytogenet Cell Genet, 84: Johannes C et al (1999) Chromosome Res. 7: MacKinnon RN and Campbell LJ (2005) Cancer Genet Cytogenet 163: Chromosome Product Package Size / Reference No. 1 XCyte 1 30 µl D DI 2x30 µl D DI 4 30 µl D DI 2 XCyte 2 30 µl D DI 2x30 µl D DI 4 30 µl D DI 3 XCyte 3 30 µl D DI 2x30 µl D DI 4 30 µl D DI 4 XCyte 4 30 µl D DI 2x30 µl D DI 4 30 µl D DI 5 XCyte 5 30 µl D DI 2x30 µl D DI 4 30 µl D DI 6 XCyte 6 30 µl D DI 2x30 µl D DI 4 30 µl D DI 7 XCyte 7 30 µl D DI 2x30 µl D DI 4 30 µl D DI 8 XCyte 8 30 µl D DI 2x30 µl D DI 4 30 µl D DI 9 XCyte 9 30 µl D DI 2x30 µl D DI 4 30 µl D DI 10 XCyte10 30 µl D DI 2x30 µl D DI 4 30 µl D DI 11 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 12 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 13 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 14 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 15 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 16 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 17 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 18 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 19 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 20 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 21 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI 22 XCyte µl D DI 2x30 µl D DI 4 30 µl D DI X XCyte X 30 µl D DI 2x30 µl D DI 4 30 µl D DI Y XCyte Y 30 µl D DI 2x30 µl D DI 4 30 µl D DI 98

99 Non-Human DNA Chromosome Paints and mfish Kits for Mouse, Rat and Chinese Hamster 99

100 XMP XCyting Mouse Chromosome Paint XMP XCyting Mouse Chromosome Paints XMP are chromosome-specific and comprise mouse whole chromosome painting probes which are directly labeled with a green or orange emitting fluorochrome, respectively. Example image is shown in which XMP 4 green is hybridized to a metaphase spread showing two normal chromosomes 4. Mouse Chromosome Product Package Size Reference No. / Label Green Orange 1 XMP 1 50 µl D FI D OR 2 XMP 2 50 µl D FI D OR 3 XMP 3 50 µl D FI D OR 4 XMP 4 50 µl D FI D OR 5 XMP 5 50 µl D FI D OR 6 XMP 6 50 µl D FI D OR 7 XMP 7 50 µl D FI D OR 8 XMP 8 50 µl D FI D OR 9 XMP 9 50 µl D FI D OR 10 XMP µl D FI D OR 11 XMP µl D FI D OR 12 XMP µl D FI D OR 13 XMP µl D FI D OR 14 XMP µl D FI D OR 15 XMP µl D FI D OR 16 XMP µl D FI D OR 17 XMP µl D FI D OR 18 XMP µl D FI D OR 19 XMP µl D FI D OR X XMP X 50 µl D FI D OR Y XMP Y 50 µl D FI D OR 100

101 XRP XCyting Rat Chromosome Paint XRP XCyting Rat Chromosome Paints XRP are chromosome-specific and comprise rat whole chromosome painting probes which are directly labeled with a green or orange emitting fluorochrome, respectively. Example image is shown in which XRP X green is hybridized to a normal metaphase from a male. Rat Chromosome Product Package Size Reference No. / Label Green 1 XRP 1 50 µl please inquire 2 XRP 2 50 µl please inquire 3 XRP 3 50 µl please inquire 4 XRP 4 50 µl please inquire 5 XRP 5 50 µl please inquire 6 XRP 6 50 µl please inquire 7 XRP 7 50 µl please inquire 8 XRP 8 50 µl please inquire 9 XRP 9 50 µl please inquire 10 XRP µl please inquire 12 XRP µl please inquire 13 XRP µl please inquire 16 XRP µl please inquire 17 XRP µl please inquire 18 XRP µl please inquire 19 XRP µl please inquire 20 XRP µl please inquire Orange X XRP X 50 µl D FI D OR Y XRP Y 50 µl D FI D OR 101

102 mfish-non-human Multicolor FISH for Mouse, Rat and Chinese Hamster Chromosomes mfish XCyting Multicolor FISH mfish probes are comprised of whole chromosome painting probes which are labeled with a total of five fluorochromes. The combinations of the fluorochromes for the different chromosomal paints result in an individual color signature for each chromosome class. The excitation/emission spectra of the fluorochromes are compatible to FITC, Spectrum Orange, TexasRed and DEAC (Diethylamino-coumarin) and Cy 5. 12XCHamster was hybridized to cells from a cell line derived from Chinese hamster tissue. The karyogram shows additional copies of a derivative chromosome 3. Beside the human mfish probes MetaSystems offers additional specific mfish probes for three different species: Mouse, Rat, and Chinese Hamster. Probe Kit Family Product Package Size / Reference No. Multicolor FISH Probe Kit for Mouse Chromosomes 21XMouse 60 µl D DI 2 60 µl D DI Multicolor FISH Probe Kit for Rat Chromosomes 22XRat* 60 µl D DI 2 60 µl D DI Multicolor FISH Probe Kit for Chinese Hamster Chromosomes 12XCHamster 60 µl D DI - - *Chr 13 and 14 show an identical labeling scheme and are not distinguishable with 22XRat

103 Addendum 103

104 DAPI/Antifade General Reagents Chromosome counterstain in a buffer containing anti-photobleaching (antifade) reagent. 250ng/ml, 500µl MetaSystems DAPI/Antifade contains a blue fluorescent stain at 250 ng/ml that intercalates into the minor groove of double stranded DNA. It is mixed with an anti-photobleaching, non-hardening solution. DAPI/Antifade is intended for use on cytogenetic preparations and on formalin-fixed, paraffin embedded tissue sections suitable for FISH. Reference Number: D DA (500 µl / 50 Tests) 104

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106 Image Analysis Systems Excellence in Automated Life Science Imaging MetaSystems Portfolio of Imaging Systems For three decades, MetaSystems has been providing high-performance systems for automated imaging in microscopy. After having introduced a metaphase finder as the first product in 1986, MetaSystems portfolio today encompasses systems for many different applications in cytogenetics, pathology, oncology, toxicology, forensics, and radiation biology. To date, MetaSystems renowned products are being used in more than 2,000 labs in 92 countries worldwide. Neon Neon is a brand-new platform for case and image data organization, and it is the basis of all MetaSystems imaging systems. MetaSystems solutions are designed to address particular imaging and image analysis tasks. Neon collects the data from any imaging job and also from external sources and presents them in a comprehensive and versatile case management dashboard. Hence, Neon always has the most relevant information for the user at hand; fast, secure, and no matter from where the information originates. Strong data management algorithms, several convenient display modes, and many options for selecting and filtering content make Neon the perfect basis to organize large quantities of heterogeneous information. In laboratories, data are usually generated from many different, sometimes unrelated sources. Patient data may originate from a central lab information system, samples may be identified by bar codes, and images may come from the automated scanning system or from a manual capture station. Neon was made to collect data from all different sources, and to unite them to form an efficient and well structured workflow. Neon reliably manages cases, images, and results of single workstations, as well as of large multi-user installations. It guarantees that all relevant information is visible whenever and wherever it is needed. Neon s elaborated and flexible workflow settings facilitate seamless integration with existing routines and allow for the use of a variety of different imaging applications. Ikaros Karyotyping Platform Ikaros is the karyotyping system of MetaSystems. The highly convenient software helps karyotyping metaphases which can either be acquired locally, or be provided by a Metafer system. Ikaros offers many very helpful tools for metaphase and chromosome imaging, and karyotypes are done in no time. Ikaros also does fluorescence, so that G-banded, R-banded, Q-banded, and DAPI-banded chromosomes are fully supported. The software supports many different banding techniques and resolutions. Numerous pre-defined karyogram and idiogram forms for human, animal, and plant chromosomes are available. The integrated karyogram form editor makes Ikaros applicable to many different fields of research. The possibility to run chromosome comparisons by chromosome classes or by karyograms facilitates the on-screen analysis of chromosome. Aberrant chromosomes can be easily illustrated with the Cut and Join function for idiograms. 106

107 Image Analysis Systems Excellence in Automated Life Science Imaging Isis Fluorescence Imaging Platform Isis combines ease of use and a functionality meeting the requirements of even the most demanding research and routine applications. With the help of automatic exposure time adjustment, and with the support of most of the common motorized microscopes, it reliably acquires fluorescence images with up to 12 color channels. For image processing, Isis provides a variety of tools to enhance, edit, annotate, archive, measure, and print the images. The optimized user interface guarantees rapid results in research and routine. Isis can be either installed as a stand-alone system, or it can be seamlessly integrated into Ikaros karyotyping stations, the Metafer slide scanning workstation, or any multi-user workplace with networked stations. Options for color karyotyping, comparative genomic hybridization (CGH), multicolor FISH (mfish), multicolor fluorochrome banding (mband), and for automatic telomere measurement are available. Professional imaging of fluorescently labeled samples requires images of highest quality. The combination of state-of-theart image acquisition hardware and software tools for automated control of imaging parameters guarantees perfect raw images. Many image enhancement tools can be used automatically, thus matching the requirements of routine diagnostics and providing a streamlined workflow. The integrated focus stack function (most conveniently in combination with a motorized microscope) is a simple and effective tool to visualize and analyze 3D objects. Captured images from different focus planes can be combined generating an extended focus image. All signals are clearly detectable, while unspecific background is removed. Metafer: Metaphase Finder and Automated Image Acquisition With the automated metaphase finder and the image acquisition software both based on the slide scanning platform Metafer, tedious steps in cytogenetic imaging can be fully automated. The metaphase finder detects metaphases on up to 800 slides unattended (with the SlideFeeder x80; slides can also be bar coded) and subsequently generates high-quality images. An automated immersion oil dispenser facilitates changing from low power magnification for metaphase finding to high power magnification for image capture. Metaphases can be automatically ranked by quality, so that Metafer can be set to acquire only the best metaphases from the list. Due to the concept of trainable classifiers, the system can be used for an unlimited number of different samples and, of course, also for fluorescent specimen such as mfish or mband metaphases. The metaphase finder is also capable of detecting colonies on clonal samples, and of assigning the metaphase to their respective colony. Once a slide is acquired, images are automatically sent to the server allowing for immediate review with any connected Isis FISH imaging or Ikaros karyotyping station in the network. 107

108 Image Analysis Systems Excellence in Automated Life Science Imaging Metafer: Fluorescence Imaging Automation The analysis of fluorescence signal patterns / FISH spots in cells or cell nuclei is the basis for many assays in hematology and cancer genetics. With the automated fluorescence signal analysis system based on the Metafer platform (MetaCyte), these patterns are analyzed automatically, precisely, and reproducibly. Results are stored together with the cell or nuclei images, and they can be displayed in the image gallery, in histograms and scatter plots, or as a summary table in one of Neon s beautiful reports. Metafer does a lot more than simply counting signals: for example it is also able to identify and count fusions of signals from different color channels. In this way the software has the capability to analyze all signal patterns found in samples hybridized with MetaSystems locus-specific probes. With Rapid Score MetaSystems created a novel workflow for analyzing FISH signals which combines manual scoring strategies with the advantages of automated scoring. RS uses Metafer to automatically score cell signal patterns. All analyzed cells are displayed in a gallery. Signal patterns are summarized in a convenient graph and a table. Immediately after the scan technicians can begin categorizing cells with doubtful results. Categories are assigned to each cell using an external keypad, and new categories (groups of cells) can be added any time. An empty scoring sheet displayed left of the automated results dynamically displays the manual results while the categorization is proceeding. An enlarged image of the unprocessed cell in question facilitates evaluation of signal patterns. Metafer: Tissue Imaging MetaSystems has designed a system of hybridization and imaging tools to be integrated in the routine workflow of the pathology lab. Core of this system is the combination of dedicated DNA probes for tissue sections with the innovative platform Metafer, a flexible and robust slide scanning system with many options. MetaSystems provides a range of locus-specific DNA probes for tissue FISH to detect gene amplifications, deletions, or translocations in solid tumors. Intense signals aid with the interpretation on tissue sections. The Metafer scanning platform automatically generates virtual slides in brightfield and fluorescence, acquires high resolution FISH images and provides an automatic score. Equipped with an automated bar code reader and the robust SlideFeeder x80 for up to 800 samples, it can be operated in a 24/7 mode. 1. As initial step a digital brightfield, e.g. H&E slide is generated by Metafer. The pathologist calls up the digital slide and selects on screen the tumor region on the virtual slide that needs to be FISH-scored. 2. Next, the FISH slide (from a subsequent section of the same block) is being scanned at low magnification to generate an overview. Displayed side by side to the marked digital H&E image the tumor region can easily be transferred to the FISH slide. 3. Neon Metafer now has all the information to start automatic image acquisition of the FISH slide at higher magnification. Cell nuclei that are isolated or slightly connected will be separated automatically and spot-counted. Manual tools for segmentation help to separate touching nuclei for immediate automatic scoring until the preset number of cells to be analyzed has been reached. The software module can be easily set up to match the individual analysis standards. For instance, it is possible to define a minimum number of cells to be analyzed, and also to define a number of independent readers. 4. For final review the system presents a full synopsis to the pathologist, comprising the cell gallery with the scoring results, the virtual DAPI slide showing the positions of analyzed cells, and the corresponding H&E virtual slide. Every cell can be traced back to the tissue section to confirm its location within the preselected tumor region. 5. Final results can either be exported as raw data, e.g. for subsequently being processed by external software, or can be summarized in comprehensive, user-adaptable reports. Due to Metafer s modularity and its flexible architecture it is applicable to a large variety of imaging tasks. Around 1,500 Metafer scanning platforms are in use worldwide as metaphase finders, FISH signal counters, toxicology workstations, sample digitizers, and more. Please contact MetaSystems or visit for more information on Metafer. 108