DIRECTORY OF SERVICES

Transcription

1 DIRECTORY OF SERVICES

2 1916 Patterson Street, Suite 400 Nashville, TN (615) (800)331-GENE GENETICS ASSOCIATES, Inc Patterson Street, Suite 400 Nashville, TN Business Hours Monday through Friday 7:00 a.m. to 6:00 p.m. (CST) Saturday 8:00 a.m. to 2:00 p.m. (CST) *After hours, calls are answered by a licensed technologist Office Phone: Office Fax: Toll Free:

3 TABLE of CONTENTS Genetics Associates, Inc. o History of Genetics Associates, Inc. o Our Mission o Licensure & Certification Specimen Collection o Specimen Requirements o Specimen Collection o Turn Around Time o Requisition Instructions o Additional Forms o CPT Codes Shipping o Order Shipping Supplies o Specimen Pickup / Shipping o Specimen Packaging Guidelines Contact Information o Executive Team o Administrative Team o Laboratory Team o Sales & Marketing Team o Client Services Team / IT Team o Directors Cancer / Leukemia o Chromosome Analysis o Fluorescence in situ Hybridization (FISH) o Polymerase Chain Reaction (PCR) o Fluorescence in situ Hybridization (FISH) Panels o Individual FISH probes (numerically) Constitutional (Including Prenatal) o Peripheral Blood Chromosome Analysis o Prenatal Chromosome Analysis o Fluorescence in situ Hybridization (FISH) o Polymerase Chain Reaction (PCR) o Microarray o FISH for Microdeletion Syndromes Abbreviations o Cancer/Leukemia Terminology o Cytogenetic Terminology

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5 History of Genetics Associates, Inc. Genetics Associates, Inc. was established in 1990, with the goal of providing high quality, efficient, economical, and state of the art cytogenetic diagnostic services. GAI believes in building relationships by paying close attention to the needs of our clients. We provide a fullrange of clinical cytogenetic services to private physicians, hospitals and laboratories throughout the United States. Located in Nashville, Tennessee, our reputation is built on high quality banding, expert chromosome analysis and rapid turn-around times. Our laboratory is College of American Pathology (CAP) and CLIA certified and is licensed by the states of Tennessee, California, Florida, and Rhode Island. Genetics Associates Inc. specializes in standard and molecular cytogenetics, including FISH and microarray analysis. OUR MISSION To be the cytogenetic laboratory and information resource of choice for physicians who demand accurate, timely, and state of the art cytogenetic diagnostic services for their patients. To grow and expand our services while maintaining the excellence in quality that is expected by our physicians, patients, and staff. To provide our staff with environment that promotes growth, education, fairness, security, and a sense of well-being through leadership, discipline, and belief in our fellow employees.

6 LICENSURE AND CERTIFICATION College of American Pathologists License # Clinical Laboratory Improvements Amendments License # 44D State of TN Board of Health License # State of CA Dept. of Public Health License # COS State of FL Agency for Health Care Administration License # Maryland Dept. of Health & Mental Hygiene Permit # 1353 Office of Health Care Quality -Medical Laboratory Pennsylvania Clinical Laboratory Permit Permit # 29942A Rhode Island & Prov. Plantations Dept. of Health License # LCO 00272

7 SPECIMEN COLLECTION

8 SPECIMEN REQUIREMENTS Precautions: POC/Tissue -- DO NOT place in formalin Do not freeze specimens There are two types of heparin tubes---make sure to use Sodium Heparin *Please refer to specimen collection chart on the following page. This chart is also located on the reverse side of each requisition. Requisitions A requisition must be completed and submitted with each specimen sent to Genetics Associates. Please complete the requisition with the following information: o o o o o o o o o o Patient Name Date of Birth Referring Physician Facility Facility Contact Information (Phone & Fax) Date of Collection Type of Specimen ICD 10 Code (Referring Diagnosis) Test Order (Chromosome Analysis, FISH, PCR, Microarray, etc.) Billing Information (Client Bill, Insurance Bill, etc.) Contact Client Services for preprinted requisitions. Requisitions are also available at on the For Physicians page.

9 SPECIMEN COLLECTION SPECIMEN COLLECTION Test Specimen Type Volume Container Storage Conditions Special Instructions Chromosome Analysis & FISH Peripheral Blood Adult/Child: 2-5 ml Newborn: 1-2 ml Sodium Heparin Green-top Tube Room Temperature Do Not Freeze Bone Marrow Adult/Child: 2-5 ml Newborn: 1-2 ml Paraffinembedded Tissue Solid Tissue Biopsy Fine Needle Aspirate Positively charged 3-4μ thick, 2 slides per probe minimum Sterile Saline/RPMI Media Sterile Saline/RPMI Media Sodium Heparin Green-top Tube Room Temperature Do Not Freeze Slide Mailer Room Temperature Include H&E Slide Mark Area of Interest Sterile Specimen Cup Sterile Centrifuge Tube with RPMI Pleural Fluid Whole Fluid Sterile Centrifuge Tube ml Urine 33 ml Mix the urine at a 2:1 ratio with either Carbowax or PreservCyt. PCR Bone Marrow Adult/Child: 2-5 ml Peripheral Blood Adult/Child: 2-5 ml Paraffinembedded Tissue Positively charged 3-4μ thick, 4 Slide Minimum EDTA Purple-top Tube EDTA Purple-top Tube Room Temperature or Refrigerate Room Temperature Room Temperature Refrigerate Refrigerate immediately Refrigerate immediately Do Not Freeze Do Not Add Formalin Do Not Freeze Do Not Add Formalin Do Not Freeze Do Not Freeze Do Not Freeze Specimen Must be received in lab within 48 hours of collection Do Not Freeze Specimen Must be received in lab within 48 hours of collection Slide Mailer Room Temperature Include H&E Slide Mark Area of Interest Please place Cool Packs in Specimen Kit when shipping during the warm months.

10 SPECIMEN COLLECTION SPECIMEN COLLECTION Test Specimen Type Volume Container Storage Conditions Chromosome Analysis & FISH Amniotic Fluid ml of whole fluid Sterile Centrifuge Tube Chorionic Villi >10 mg of Villi Sterile Centrifuge Tube with Transport Media (RPMI) Paraffinembedded Positively charged 3- Slide Mailer 4μ thick, 2 slides per Tissue probe minimum Peripheral Blood Products of Conception Adult/Child: 2-5 ml Newborn: 1-2 ml PUBS: 1-2 ml >10 mg of Villi, Placenta, Placental Membrane, or Fetal Tissue Sodium Heparin Green-top Tube Sterile Specimen Cup or Centrifuge Tube with Sterile Saline or Transport Media (RPMI) Tissue Biopsy 3mmᶟ Sterile Specimen Cup or Centrifuge Tube with Sterile Saline or Transport Media (RPMI) SNP Microarray Amniotic Fluid 10 ml of additional Sterile Centrifuge whole fluid Tube Chorionic Villi Peripheral Blood Products of Conception >10 mg of additional Villi Adult/Child: 2-5 ml Newborn: 1-2 ml PUBS: 1-2 ml >10 mg of Villi, Placenta, Placental Membrane, or Fetal Tissue Sterile Centrifuge Tube With Transport Media EDTA (Sodium Heparin acceptable) Sterile Specimen Cup or Centrifuge Tube with Sterile Saline or Transport Media (RPMI) Room Temperature Room Temperature Room Temperature Room Temperature or Refrigerate Room Temperature or Refrigerate Room Temperature or Refrigerate Room Temperature Room Temperature Room Temperature or Refrigerate Room Temperature or Refrigerate Special Instructions Do Not Freeze Do Not Freeze Do Not Freeze Do Not Freeze Do Not Add Formalin Do Not Freeze Do Not Add Formalin Do Not Freeze Do Not Freeze Do Not Freeze Do Not Freeze Do Not Add Formalin Please place Cool Packs in Specimen Kit when shipping during the warm months.

11 TURN AROUND TIME Leukemic Bloods Bone Marrows Lymph Nodes Urovysion Peripheral Bloods Newborn Bloods hour prelims Paraffin-embedded Slides PCR ICP CVS POC Amniotic Fluid Microarray Mass Tissue 3 Days 3 Days 3 Days 3 Days 4 Days 4 Days 4 Days 4 Days 5 Days 7 Days 7 Days 7 Days 7 Days 10 Days 10 Days

12 REQUISITION INSTRUCTIONS

13 Required Information *Current requisitions may be printed at Patient Name, Date of Birth, Sex, and additional ID (MR#, SS#, Hospital#) Referring Physician & Facility Contact Information (Phone, Cell, Fax, etc.) Collection Date/Time Specimen Info (Transplant, Donor, WBC) Specimen Type (Bone Marrow, Peripheral Blood, Mass, etc.) ICD-10/Diagnosis Test Requested (Chromosome Analysis, FISH, PCR, etc.) Paraffin slide prep: Positively charged 3-4μ thick (2 slides per probe minimum) with accompanying marked H & E slide Please include a copy of insurance information

14 ADDITIONAL FORMS: TEST AUTHORIZATION Genetics Associates will send this form when additional tests are requested. Please complete patient information Check all applicable boxes for add-on testing Sign

15 ADDITIONAL FORMS: PATIENT DATA VERIFICATION When additional information is needed, GAI will send this for verification. Please enter the correct information Sign

16 ONCOLOGY TEST CPT CODES Chromosome Analysis Bone Marrow x 2, 88264, x 3, Chromosome Analysis Bone Marrow Core x 2, 88264, x 3, Chromosome Analysis Leukemic Blood x 2, 88264, x 3, Chromosome Analysis Mass/Solid Tumor x 2, 88264, x 3, Fluorescence in Situ Hybridization Single (per probe), (per probe), Fluorescence in Situ Hybridization Multi FISHnet / ifish (enrichment only) x 2 (per probe), (per probe), (FISH codes will also apply see above) Microarray (SNP) PCR JAK BCR/ABL p210 BKPT BCR/ABL P190 BKPT *Please note, codes are report dependent.

17 CONSTITUTIONAL TEST CPT CODES Chromosome Analysis Amniotic Fluid X 2, 88267, 88261, 88280, Chromosome Analysis CVS X 2, 88267, 88261, 88280, 88172, Chromosome Analysis Peripheral Blood x 2, 88262, 88280, Chromosome Analysis POC 88305, 88233x2, 88261, 88267, Chromosome Analysis Tissue x 2, 88264, x 3, FISH (Microdeletion) 88271, 88273, Aneuvysion FISH x 5, 88275, POC FISH x 8, X 2, ICP FISH X 24, x 2, Microarray (SNP) *Please note, codes are report dependent.

18 SHIPPING

19 FEDERAL EXPRESS SUPPLIES GAI supplies shipping supplies for our clients, unless other arrangements are made. Clients may request the following supplies by calling or GENE (4363). 1. Shipping kits and supplies 2. Requisitions 3. POC & CVS transport media Please note that Federal Express does not deliver on Sunday or holidays. COURIER SERVICES GAI provides courier services to the Nashville Metropolitan area. A Better Courier Service (ABC) couriers are utilized in a 100 mile radius of Nashville, TN.

20 Specimen Packaging Guidelines 1. Use the Genetics Associates, Inc. (GAI) Cytogenetic Specimen box with the Styrofoam insert and lid to send samples. 2. To be compliant with federal regulations, the box must have a UN3373 diamond and should read Biological Substance Category B. Do not place stickers or labels on the outside of the box or cover up these required logos. 3. Always use TWO SMALL OR ONE LARGE REFRIGERATED GEL PACKS. NOT frozen or room temperature, 4. Make sure the specimen collection tube/container is fully closed. 5. Place the specimen collection tube in one of the pockets of the included absorbent material (see image below). 6. Insert the tubes and absorbent material in the enclosed 95kpa specimen bag. Seal the bag by removing the tape and pressing down firmly. a. If you are sending 5-7ml vacutainers, one GAI specimen box will hold up to 10 tubes. b. If you are sending 8-10ml vacutainers, one GAI specimen box will hold up to 6 tubes. c. If you are sending 15ml centrifuge tubes, one GAI specimen box will hold up to 6 tubes. d. If you are sending 50ml conical tubes, one GAI specimen box will hold up to 3 tubes. 7. Different patient specimens may be included in the same box. Make sure each patient s paperwork is included in the same box as the specimen. Note: One patient s specimens are not to be divided between different boxes. 8. Patient test requisitions and corresponding insurance paperwork must be folded and inserted into the pouch at the back of the specimen bag. Fold the paperwork to ensure patient information is not visible. 9. Fold the specimen bag above the tubes and lay flat on the gel pack (see image below). 10. Close the box by inserting the tabs on top lid into side slots. 11. Place in the orange FedEx biological substance shipping pak. a. Seal the pak by removing the tape and pressing down firmly. 12. Apply the proper FedEx airbill marked from your facility to GAI. 13. Call GENE (4363) to inform GAI of the package s shipment and corresponding tracking number.

21 CONTACT INFORMATION

22 Executive Team David Murray, Chief Executive Officer Brenda Neal, Chief Operating Officer Jesse Gore, Chairman of the Board/Owner V. G. Dev, Executive Director/Owner

23 Administrative Team Jeanne Ragland, Office Manager Kristie Anderson, Billing Specialist Ida Settlemires, Administrative Assistant Catherine Foreman, Accounts Receivable Supervisor

24 Laboratory Team Ronda Moseley Eppinger, Quality Control Director Leigh Ann Sheffield, Laboratory Manager Tom Byrne, Laboratory Supervisor Mingya Liu, FISH Supervisor Elizabeth Holland, Laboratory Supervisor, Cookeville

25 Sales & Marketing Team Gary Deitelhoff, Sales Director, Northern U.S. Melissa Jones, Sales Manager Client Services Team Francesca Mims, Client Services Manager Ewellonda Rowley, Client Services Representative William Stephenson, Specimen Distribution Representative

26 IT Team Steven Gore, IT Manager Reed Chamberlin, WindoPath Administrator

27 Laboratory Directors V.G. Dev, Ph.D. Founding Fellow of the American College of Medical Genetics and Genomics Diplomate of the ABMGG Clinical Cytogenetic Diplomate of the ABMGG Clinical Cytogenetics Eric Crawford, Ph.D. Fellow of the American College of Medical Genetics and Genomics Diplomate of the ABMGG Clinical Cytogenetics Diplomate of the ABMGG Clinical Molecular Genetics S. Dwanna Stewart, Ph.D. Fellow of the American College of Medical Genetics and Genomics Diplomate of the ABMGG Clinical Cytogenetics

28 Leticia Miravalle, Ph.D. Fellow of the American College of Medical Genetics and Genomics Diplomate of the ABMGG Clinical Cytogenetics Diplomate of the ABMGG Clinical Molecular Genetics Diplomate of the American Board of Clinical Chemistry Molecular Guangyu Gu, M.D. Fellow of the American College of Medical Genetics and Genomics Diplomate of the ABMGG Clinical Cytogenetics

29 CANCER/LEUKEMIA

30 Bone Marrow & Leukemic Blood Chromosome Analysis Bone marrow and leukemic blood samples which contain spontaneously dividing cells are usually cultured short term without mitogens. Some specimens with B-cell conditions are stimulated with mitogens. Chromosome analysis of the dividing cells is useful in the diagnosis of malignancy and in the classification of hematological malignancies.

31 Fluorescence in Situ Hybridization (FISH) Fluorescence in situ hybridization (FISH) utilizes molecular biology techniques to detect the presence or absence of and enumerate specific region of the genome using fluorescently labeled pieces of DNA (probes). Unlike most other techniques used to study chromosomes, FISH does not require actively dividing cells. This adds flexibility and increases the ability to identify and characterize cytogenetic abnormalities. FISH has applications in all aspects of clinical cytogenetics including: prenatal aneuploidy screening and sex determination; diagnosis of microdeletion syndromes; investigation of unexplained mental disability; and malignancy diagnosis, prognosis, and remission status. Probes may be used alone or in combinations of genes and/or regions specific to a particular disease. FISH offers limited information specific to the DNA sequence contained in the probe. Currently, FISH is routinely used in clinical practice for diagnosis, prognosis and to select appropriate therapies for patients with diseases such as hematologic malignancies. Polymerase Chain Reaction (PCR) The polymerase chain reaction (PCR) is a molecular method that enables the detection and analysis of specific gene sequences in a patient's sample. Our molecular testing involves both the diagnosis and monitoring of hematologic malignancies and solid tumors, and is performed on a variety of specimen types including peripheral blood, bone marrow, and paraffin embedded tissue. PCR is routinely used in clinical practice for diagnosis, prognosis, monitoring patient response to treatment, and to select appropriate therapies for patients with hematologic malignancies.

32 Fluorescence in situ Hybridization (FISH) Panels Please note, FISH probes may be ordered individually or as panel. Adult B-Cell ALL profile del(9p) CDKN2A del(6q) CCND3/SEC63/MYB t(9;22) BCR/ABL1/ASS1 11q23 KMT2A (MLL) rearrangements t(1;19) TCF3/PBX1 14q32 IGH rearrangements Adult T-Cell ALL profile 14q11.2 TRA rearrangements 7q34 TRB rearrangements 10q24 TLX1 5q35 TLX3 11q23 KMT2A (MLL) rearrangements del(9p) CDKN2A Pediatric ALL profile t(12;21) ETV6/RUNX1 11q23 KMT2A (MLL) rearrangements t(9;22) BCR/ABL1/ASS1 trisomy 4,10,17 Additional probes t(1;19) TCF3/PBX1 14q32 IGH rearrangements

33 Acute Myelogenous (AML) profile t(15;17) PML/RARA t(9;22) BCR/ABL1/ASS1 t(8;21) RUNX1T1/RUNX1 11q23 KMT2A (MLL) rearrangements inv(16), t(16;16) CBFB rearrangements inv(3) MECOM rearrangements 17q RARA rearrangements Chronic Lymphocytic (CLL) profile del(11q) ATM trisomy 12 del(13q) 13q14/13q34 del(17p) TP53 Additional probes t(11;14) CCND1/IGH del(6q) CCND3/SEC63/MYB Chronic Myelogenous (CML) profile t(9;22) BCR/ABL1/ASS1 Additional probes trisomy 8 i(17q)

34 Lymphoma probes t(8;14) MYC/IGH (Burkitt or Follicular) 8q24 MYC rearrangements t(11;14) CCND1/IGH (Mantle Cell) t(11;18) BIRC3/MALT1 18q21 BCL2 rearrangements 18q21 MALT1 rearrangements t(14;18) IGH/BCL2 (Follicular or Diffuse Large B-Cell) 3q27 BCL6 rearrangements (Diffuse Large B-Cell, Follicular, Marginal Zone B-cell) T-cell Leukemia/Lymphoma probes 2p23 ALK (Anaplastic) rearrangements 14q11.2 TRA rearrangements 7q34 TRB rearrangements i(7q) 7cen/7q22/7q31 14q32 TCL1A 10q24 TLX1 5q35 TLX3

35 Multiple Myeloma CD138 Enriched (MM) profile (FISHnet ) 1p32.3/1q21 CDKN2C/CKS1B del(13q) 13q14/13q34 del(17p) TP53 t(11;14) CCND1/IGH t(4;14) FGFR3/IGH t(14;16) IGH/MAF Additional probes trisomy 5 trisomy 7 t(6;14) CCND3/IGH t(14;20) IGH/MAFB Myelodysplastic (MDS) profile del(5q) EGR1 del(7q) / monosomy 7 trisomy 8 del(20q) Additional probes 11q23 KMT2A (MLL) rearrangements t(9;22) BCR/ABL1/ASS1

36 Myeloproliferative (MPN) profile del(5q) EGR1 del(7q) / monosomy 7 trisomy 8 del(20q) t(9;22) BCR/ABL1/ASS1 Additional probes 4q12 FIP1L1/CHIC2/PDGFRA 5q33 PDGFRB rearrangements 8p11 FGFR1 rearrangements Solid Tumor probes EWSR1 Ewing Sarcoma FOXO1 Alveolar Rhabdomyosarcoma DDIT3 (CHOP) Myxoid Liposarcoma LOH 1p/19q Glioma MYCN 2p24.1 Neuroblastoma SS18 Synovial Sarcoma UroVysion Transplant XX/XY for sex mismatched transplant

37 Individual FISH Probes (Numerically by Chromosome) Probe 1p32.3/1q21 CDKN2C/CKS1B t(1;19) TCF3/PBX1 t(1;19) TCF3/PBX1 1p/19q LOH (Glioma) Location on Cancer Requisition Multiple Myeloma Profile Adult B-Cell ALL profile Pediatric ALL profile Solid Tumor probes 2p23 ALK (Anaplastic) rearrangements T-cell Leukemia/Lymphoma probes 2p24.1 MYCN (Neuroblastoma) Solid Tumor probes inv(3) MECOM rearrangements 3q27 BCL6 rearrangements (Diffuse Large B-Cell, Follicular, Acute Myelogenous (AML) profile Lymphoma probes Marginal Zone B-cell) trisomy 4,10,17 4q12 FIP1L1/CHIC2/PDGFRA t(4;14) FGFR3/IGH Pediatric ALL profile Myeloproliferative (MPN) profile Multiple Myeloma Profile trisomy 5 del(5q) EGR1 del(5q) EGR1 5q33 PDGFRB rearrangements 5q35 TLX3 Multiple Myeloma Profile Myelodysplastic (MDS) profile Myeloproliferative (MPN) profile Myeloproliferative (MPN) profile Adult T-Cell ALL profile

38 del(6q) CCND3/SEC63/MYB del(6q) CCND3/SEC63/MYB t(6;14) CCND3/IGH Adult B-Cell ALL profile Chronic Lymphocytic (CLL) profile Multiple Myeloma Profile trisomy 7 del(7q) / monosomy 7 del(7q) / monosomy 7 i(7q) 7cen/7q22/7q31 7q34 TRB rearrangements 7q34 TRB rearrangements Multiple Myeloma Profile Myelodysplastic (MDS) profile Myeloproliferative (MPN) profile T-cell Leukemia/Lymphoma probes Adult T-Cell ALL profile T-cell Leukemia/Lymphoma probes trisomy 8 trisomy 8 trisomy 8 8p11 FGFR1 rearrangements 8q24 MYC rearrangements t(8;14) MYC/IGH (Burkitt or Follicular) t(8;21) RUNX1T1/RUNX1 Chronic Myelogenous (CML) profile Myelodysplastic (MDS) profile Myeloproliferative (MPN) profile Myeloproliferative (MPN) profile Lymphoma probes Lymphoma probes Acute Myelogenous (AML) profile del(9p) CDKN2A del(9p) CDKN2A t(9;22) BCR/ABL1/ASS1 t(9;22) BCR/ABL1/ASS1 t(9;22) BCR/ABL1/ASS1 t(9;22) BCR/ABL1/ASS1 Adult B-Cell ALL profile Adult T-Cell ALL profile Adult B-Cell ALL profile Pediatric ALL profile Acute Myelogenous (AML) profile Chronic Myelogenous (CML) profile

39 t(9;22) BCR/ABL1/ASS1 t(9;22) BCR/ABL1/ASS1 Myelodysplastic (MDS) profile Myeloproliferative (MPN) profile 10q24 TLX1 10q24 TLX1 Adult T-Cell ALL profile T-cell Leukemia/Lymphoma probes del(11q) ATM 11q23 KMT2A (MLL) rearrangements 11q23 KMT2A (MLL) rearrangements 11q23 KMT2A (MLL) rearrangements 11q23 KMT2A (MLL) rearrangements 11q23 KMT2A (MLL) rearrangements t(11;14) CCND1/IGH t(11;14) CCND1/IGH (Mantle Cell) t(11;14) CCND1/IGH t(11;18) BIRC3/MALT1 Chronic Lymphocytic (CLL) profile Myelodysplastic (MDS) profile Adult B-Cell ALL profile Adult T-Cell ALL profile Pediatric ALL profile Acute Myelogenous (AML) profile Chronic Lymphocytic (CLL) profile Lymphoma probes Multiple Myeloma Profile Lymphoma probes trisomy 12 12q13 DDIT3 (CHOP) Myxoid Liposarcoma t(12;21) ETV6/RUNX1 Chronic Lymphocytic (CLL) profile Solid Tumor probes Pediatric ALL profile del(13q) 13q14/13q34 del(13q) 13q14/13q34 Chronic Lymphocytic (CLL) profile Multiple Myeloma Profile 13q14.1 FOXO1 Alveolar Rhabdomyosarcoma Solid Tumor probes

40 14q11.2 TRA rearrangements Adult T-Cell ALL profile 14q11.2 TRA rearrangements T-cell Leukemia/Lymphoma probes 14q32 IGH rearrangements 14q32 IGH rearrangements 14q32 TCL1A t(14;16) IGH/MAF t(14;18) IGH/BCL2 (Follicular or Diffuse Large B-Cell) t(14;20) IGH/MAFB Adult B-Cell ALL profile Pediatric ALL profile T-cell Leukemia/Lymphoma probes Multiple Myeloma Profile Lymphoma probes Multiple Myeloma Profile t(15;17) PML/RARA Acute Myelogenous (AML) profile inv(16), t(16;16) CBFB rearrangements Acute Myelogenous (AML) profile del(17p) TP53 del(17p) TP53 i(17q) 17q RARA rearrangements Chronic Lymphocytic (CLL) profile Multiple Myeloma Profile Chronic Myelogenous (CML) profile Acute Myelogenous (AML) profile 18q11.2 SS18 Synovial Sarcoma Solid Tumor probes 18q21 BCL2 rearrangements 18q21 MALT1 rearrangements Lymphoma probes Lymphoma probes del(20q) del(20q) Myelodysplastic (MDS) profile Myeloproliferative (MPN) profile

41 22q12.2 EWSR1 Ewing Sarcoma Solid Tumor probes UroVysion Solid Tumor probes Xcen/Yq12 CEPXY (XX/XY for sex mismatched transplant) Transplant

42 CONSTITUTIONAL (Including Prenatal)

43 Peripheral Blood Chromosome Analysis Chromosome analysis (karyotyping) is the microscopic evaluation of metaphase chromosomes for numerical and structural abnormalities associated with disease. The chromosomes are banded using enzymes (trypsin or pancreatin) and stain (Giemsa, Wright's, etc.) to produce G- bands. G-bands create a unique light and dark banding pattern on each chromosome. A cytogenetic technologist analyzes the banded chromosomes at a microscope. Typically, twenty metaphase cells which contain the chromosomes are viewed at the microscope. Photographic images of a few representative cells are captured, and the chromosomes contained in these cells are arranged in a standard format known as a karyogram. The karyograms along with the patient's history are reviewed by a board-certified clinical cytogeneticist. Prenatal Chromosome Analysis Amniotic fluid (AF) cells surround the fetus and contain fetal cells. The chromosomal constitution of the fetus can be accurately determined by studying the chromosomes of the amniotic fluid cells. Fetal cells from epidermal, respiratory, gastrointestinal and genitourinary surfaces are obtained by transabdominal amniocentesis. Chromosome studies of the fetus are indicated when there is a significant risk for a chromosome abnormality, e.g. advanced maternal age (over 35), parent is a translocation carrier or mosaic.

44 Fluorescence in Situ Hybridization (FISH) Fluorescence in situ hybridization (FISH) utilizes molecular biology techniques to detect the presence or absence of and enumerate specific region of the genome using fluorescently labeled pieces of DNA (probes). Unlike most other techniques used to study chromosomes, FISH does not require actively dividing cells. This adds flexibility and increases the ability to identify and characterize cytogenetic abnormalities. FISH has applications in all aspects of clinical cytogenetics including: prenatal aneuploidy screening and sex determination; diagnosis of microdeletion syndromes; investigation of unexplained mental disability; and malignancy diagnosis, prognosis, and remission status. Probes may be used alone or in combinations of genes and/or regions specific to a particular disease. FISH offers limited information specific to the DNA sequence contained in the probe. Currently, FISH is routinely used in clinical practice for diagnosis, prognosis and to select appropriate therapies for patients with diseases such as hematologic malignancies. Polymerase Chain Reaction (PCR) The polymerase chain reaction (PCR) is a molecular method that enables the detection and analysis of specific gene sequences in a patient's sample.

45 Microarray Genetics Associates is proud to announce that array comparative genomic hybridization (acgh) testing is now available at our laboratory. acgh, also called microarray analysis, is a new molecular cytogenetic technology that evaluates areas of the human genome for gains or losses of chromosome segments at a higher resolution than traditional karyotyping. The test targets areas of the human genome that, when deleted or duplicated, are known or highly suspected to cause well-characterized genetic conditions with mental disabilities and/or birth defects including loci of known microdeletion/microduplication syndromes, subtelomeric regions, and pericentromeric regions. Due to the small size, many of these DNA imbalances may not be detected by standard cytogenetics. Array CGH will also identify marker chromosomes, some cases of mosaicism, and aneuploidy. The American College of Medical Genetics includes acgh as an adjunct to standard cytogenetics for patients with developmental delay (DD) or mental disabilities (MD) when no chromosomal or molecular cytogenetic abnormalities are detected and the results of fragile X testing are negative. Recent studies indicate that MD/DD-targeted CGHbased assays can detect clinically relevant genomic alterations in roughly 5.6% to 11% of patients with idiopathic developmental conditions. A microarray slide contains thousands of different copies of DNA sequences attached to a glass slide in an organized fashion or array. Fluorescently labeled DNA from both patient and a normal control are applied to the slide and compete to attach or hybridize to their corresponding DNA segments. Computer software analyzes the fluorescent signals for areas of unequal hybridization of patient versus control DNA, signifying a DNA dosage alteration (deletion or duplication). Any abnormal finding is verified by FISH visualization, which is essential for accurate diagnosis and recurrence risk estimation. The performance characteristics of this test, including sensitivity and specificity, have been determined by Genetics Associates, Inc. All results are interpreted by the board certified and Tennessee licensed cytogenetics directors at our laboratory who, are available to discuss results and offer clinical advice. Appropriate candidates for this testing are patients who have: mental disability of unknown etiology; autism; congenital anomalies; dysmorphic features; a suspected syndrome with normal chromosomes/subtelomere. Complete patient demographic and clinical information is required to ensure that the most appropriate testing is performed. Limitations of array CGH are as follows: balanced chromosome rearrangements; balanced inversions; alterations in chromosome structure at areas of the genome not covered by the array; sequence alterations or single-base pair mutations; mosaicism at a level lower than 20%; some types of polyploidy, such as triploidy.

46 FISH for Microdeletion Syndromes (Listed Alphabetically) Angelman (15q12) Cri-du-Chat (5p15.3) DiGeorge (22q11.2) DiGeorge II (10p14) Kallman (Xp22.3) Miller-Dieker (17p13.3) Pallister-Killian/Tetrasomy 12p Phelan-McDermid (22q13) Prader-Willi (15q12) Saethre-Chotzen (7p21.1) Smith-Magenis (17p11.2) Sotos (5q35.3) Steroid Sulfatase Deficiency (Xp22.3) Williams (7q11.23) Wolf-Hirschhorn (4p16.3) 1p36 microdeletion

47 ABBREVIATIONS

48 ABBREVIATIONS and ACRONYMS FISH Fluorescence in situ hybridization. This is a methodology used to detect chromosome abnormalities in cells. FL FXS GVHD GVL HCL HCT Follicular lymphoma Fragile X syndrome Graft vs host disease Graft vs leukemia or graft vs lymphoma Hairy cell leukemia Hematocrit; the percentage of red blood cells in the blood. A low hematocrit measurement indicates anemia. HD HDC Hem/Onc HGB HLA Hodgkin disease High-dose chemotherapy Hematologist/Oncologist Hemoglobin Human leukocyte antigen test; a special blood test used to match a blood or bone marrow donor to a recipient for transfusion or transplant. Ig ITP IV LB LPL MALT Mab MCL MDS MM MS Immunoglobulin (IgA, IgD, IgE, IgG, IgM) Idiopathic thrombocytopenia purpura Intravenous Leukemic blood Lymphoplasmacytic lymphoma Mucosa associated lymphoid tissue Monoclonal antibodies Mantle cell lymphoma Myelodysplastic syndrome Multiple myeloma Multiple sclerosis

49 MPD Myeloproliferative disease MUD MZL NHL OR OS PD PB PLL PMF PR PV RARS RBC Rx SB SBMT SLE SLVL SMA SMCD-eos SMS SPS SRBCT T-ALL t-aml TTP TAT Matched unrelated donor of bone marrow Marginal zone lymphoma Non-Hodgkin lymphoma Overall remission Overall survival Parkinson s Disease Peripheral blood Prolymphocytic leukemia Primary myelofibrosis Partial remission Polycythemia vera Refractory anemia with ringed sideroblasts Red Blood count Prescribed medication Spina bifida Syngeneic bone marrow transplantation (identical twin transplant) Systemic lupus erythematosus Splenic lymphoma with villous lymphocytes Spinal muscular atrophy Systemic mast cell disease with eosinophillia Smith Magenis syndrome Stiff Person syndrome Small round blue cell tumor T-cell acute lymphoblastic leukemia Therapy-related acute myeloid leukemia Thrombotic thrombocytopenia purpura Turnaround time

50 VCFS Velocardiofacial syndrome VHL WBC WD WM WS XRT XP Von Hippel-Lindau disease White Blood cell Well differentiated Waldenstrom s macroglobulinemia Williams syndrome External radiation therapy Xeroderma pigmentosa

51 CYTOGENETIC ABBREVIATIONS AI AII Ace add amp First meiotic anaphase Second meiotic anaphase Acentric fragment Additional material of unknown origin Denotes an amplified signal (~) Approximate sign denotes intervals and boundaries of a chromosome segment or number of chromosomes, fragments, or markers; denotes a range of number of copies of a chromosome region when the exact number cannot be determined arr b Microarray Break (< >) Brackets, angle; surround the ploidy level ([ ]) Brackets, square; surround number of cells or genome build c cen cgh chi chr cht Constitutional anomaly Centromere Comparative genomic hybridization Chimera Chromosome Chromatid (:) Colon, single; break, in detailed system (::) Colon, double; break and reunion, in detailed system (,) Comma; separates chromosome numbers, sex chromosomes, chromosome abnormalities con cp cth Connected signals Composite karyotype Chromothripsis ({}) Curly braces; indicates differences in the altered segment compared to the reference sequence in duplications, in versions, conversions, insertions, etc. cx Complex rearrangements (.) Decimal point; denotes sub-bands

52 del der dia dic dim dip dis dit dmin dn dup e end enh Deletion Derivative chromosome Diakinesis Dicentric Diminished Diplotene Distal Dictyotene Double minute de novo; designates a chromosome abnormality that has not been inherited Duplication Exchange Endoreduplication Enhanced (=) Equal sign; number of chiasmata fem fib fis fra g GRCh h hmz hsr htz i idem Female Extended chromatin/dna fiber Fission, at the centromere Fragile site Gap Genome Reference Consortium human; human genome build or assembly Heterochromatin, constitutive Homozygous, homozygosity; used when one or two copies of a genome are detected, but previous, known heterozygosity has been reduced to homozygosity through a variety of mechanisms, e.g. loss of heterozygosity (LOH) Homogeneously staining region Heterozygous; heterozygosity Isochromosome Denotes the stemline karyotype in a subclone

53 ider inc inh ins inv ish lep MI MII mal mar mat med min Isoderivative chromosome Incomplete karyotype Inherited Insertion Inversion In Situ hybridization Leptotene First meiotic metaphase Second meiotic metaphase Male Marker chromosome Maternal origin Medial Minute acentric fragment (-) Minus sign/loss mos (x) neg neo nuc oom or p PI pac Mosaic Multiplication sign; multiple copies of rearranged chromosomes No presence of the rearrangement for which testing was conducted Neocentromere Nuclear or interphase Oogonial metaphase Alternative interpretation Short arm of chromosome First meiotic prophase Pachytene () Parentheses; surround structurally altered chromosomes and breakpoints pat pcc Paternal origin Premature chromosome condensation

54 pcd pcp Premature centromere division Partial chromosome paint (.) Period; separates various techniques Ph Philadelphia chromosome (+) Plus sign; additional normal or abnormal chromosome; increase in length; locus present on a specific chromosome (++) Plus sign, double; two hybridization signals or hybridization regions on a specific chromosome pos prx ps psu pter pvz q qdp qr qs qter Detection of a rearrangement for which testing was conducted Proximal Satellited short arm of chromosome Pseudo- Terminal end of the short arm Pulverization Long arm of chromosome Quadruplication Quadriradial Satellited long arm of chromosome Terminal end of the long arm (?) Question mark; questionable identification of a chromosome or chromosome structure r rec rev rob I-IV rsa s sce sdl Ring chromosome Recombinant chromosome Reverse, including comparative genomic Robertsonian translocation Roman numerals; indicate univalent, bivalent, trivalent, and quadrivalent structures Region-specific assay Satellite Sister chromatid exchange Sideline

55 (;) Semicolon; separates altered chromosomes and breakpoints in structural rearrangements involving more than one chromosome; separates probes on different derivative chromosomes sep seq sl Separate signals Sequencing Stemline (/) Slant line, single; separates clones or contiguous probes (//) Slant line, double: separates chimeric clones spm stk subtel t tas ter tr trc trp Spermatogonial metaphase Satellite stalk Subtelomeric region Translocation Telomeric association Terminal (end of chromosome) or telomere Triradial Tricentric chromosome Triplication underline (single) Used to distinguish homologous chromosomes (_) upd var wcp xma zyg Underscore; used to indicate range of nucleotide positions Uniparental disomy Variant or variable region Whole chromosome paint Chiasma(ta) Zygotene