MRC-Holland MLPA. Description version 12; 13 January 2017

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1 SALSA MLPA probemix P219-B3 PAX6 Lot B3-0915: Compared to version B2 (lot B2-1111) two reference probes have been replaced and one additional reference probe has been added. In addition, one flanking probe has been removed. In the human eye morphogenesis a molecular genetic cascade is involved. A number of developmental genes interact in a highly organized process during the embryonic period, to produce functional ocular structures. During the early stages of eye development, PAX6 induces the differentiation of progenitor cells into neurons in the retina, as well as the expression of crystallins in lens epithelial cells. PAX6 mutations lead to a variety of hereditary ocular malformations of the anterior and posterior segment that includes aniridia, coloboma of the iris, keratitis, congenital cataracts, Peter s anomaly, and optic nerve defects. WT1 is required for at least two critical functions during retinogenesis: proliferation of the progenitor cells and development of the retinal ganglion cells. The WT1 gene is often co-deleted with PAX6 in patients with WAGR syndrome. The SOX2 gene encodes a transcription factor involved in the regulation of embryonic development. Mutations in this gene have been associated with optic nerve hypoplasia and with syndromic microphthalmia, a severe form of structural eye malformation. The PAX6 gene (13 exons) spans ~26.6 kb of genomic DNA and is located on chromosome 11p13, ~31.8 Mb from the p-telomere. The WT1 gene (11 exons) spans ~47.8 kb of genomic DNA and is located on chromosome 11p13, ~32.4 Mb from the p-telomere. The SOX2 gene (1 exon) spans ~2.5 kb of genomic DNA and is located on chromosome 3q26, ~182.9 Mb from the p-telomere. The P219 probemix contains one probe for each exon of the PAX6 gene with the exception of exon 11. Also present are two probes for exon 1, and two probes for the sequence upstream of the PAX6 main transcript. This probemix furthermore contains several probes for WT1 exons, as well as probes for two hypothetical genes, LOC and LOC646008, and the gene RCN1, which are all located in the region between PAX6 and WT1. The probemix also includes probes for the genes BDNF, FSHB, DCDC1, and ELP4 flanking PAX6 telomeric, and probes for the genes HIPK3, LMO2, and CD44 centromeric of WT1. Furthermore, three probes are present for the SOX2 gene. In addition, 9 reference probes are included in this probemix, detecting several different autosomal chromosomal locations. This SALSA probemix is designed to detect deletions/duplications of one or more sequences in the aforementioned genes in a DNA sample. Heterozygous deletions of recognition sequences should give a 35-50% reduced relative peak height of the amplification product of that probe. Note that a mutation or polymorphism in the sequence detected by a probe can also cause a reduction in relative peak height, even when not located exactly on the ligation site! In addition, some probe signals are more sensitive to sample purity and small changes in experimental conditions. Therefore, deletions and duplications detected by MLPA should always be confirmed by other methods. Not all deletions and duplications detected by MLPA will be pathogenic; users should always verify the latest scientific literature when interpreting their findings. We have no information on what percentage of defects in these genes is caused by deletions/duplications of complete exons. Finally, note that most defects in these genes are expected to be small (point) mutations, most of which will not be detected by this SALSA test. SALSA probemixes and reagents are sold by for research purposes and to demonstrate the possibilities of the MLPA technique. They are not CE/FDA certified for use in diagnostic procedures. Purchase of the SALSA test probemixes and reagents includes a limited license to use these products for research purposes. The use of a SALSA probemix and reagents requires a thermocycler with heated lid and sequence type electrophoresis equipment. Different fluorescent PCR primers are available. The MLPA technique has been first described in Nucleic Acid Research 30, e57 (2002). SALSA probemix P219 PAX6 Page 1 of 6

2 More information Website : info@mlpa.com (information & technical questions); order@mlpa.com (for orders) Mail : bv; Willem Schoutenstraat 1, 1057 DL Amsterdam, the Netherlands Related SALSA probemixes P229 OPA1: Contains probes for OPA1, involved in optic atrophy type 1. P118 WT1: Contains more probes for WT1. Data analysis The P219-B3 PAX6 probemix contains 44 MLPA probes with amplification products between 130 and 463 nt. In addition, it contains 9 control fragments generating an amplification product smaller than 120 nt: four DNA Quantity fragments (Q-fragments) at nt and three DNA Denaturation control fragments (D-fragments) at nt, one X-fragment at 100 nt and one Y-fragment at 105 nt. More information on how to interpret observations on these control fragments can be found in the MLPA protocol. Data generated by this probemix can first be normalised intra-sample by dividing the peak height of each probe s amplification product by the total peak height of only the reference probes in the probemix (block normalisation). Secondly, inter-sample normalisation can be achieved by dividing the intra-normalised probe ratio in a sample by the average intra-normalised probe ratio of all reference samples. Please note that this type of normalisation assumes no changes occurred in the genomic regions recognised by the reference probes. Data normalisation should be performed within one experiment. Only samples purified by the same method should be compared. Confirmation of most exons deletions and amplifications can be done by e.g. Southern blotting, long range PCR, qpcr, FISH. Note that Coffalyser, the MLPA analysis tool developed at, can be downloaded free of charge from our website Many copy number alterations in healthy individuals are described in the database of genomic variants: For example, a duplication of a complete gene might not be pathogenic, while a partial duplication or a deletion may result in disease. For some genes, certain in-frame deletions may result in a very mild, or no disease. Copy number changes of reference probes are unlikely to be the cause of the condition tested for. Users should always verify the latest scientific literature when interpreting their findings. This probemix was developed at. Info/remarks/suggestions for improvement: info@mlpa.com. SALSA probemix P219 PAX6 Page 2 of 6

3 Table 1. SALSA MLPA P219-B3 PAX6 probemix Length Chromosomal position SALSA MLPA probe (nt) reference other PAX Q-fragments: DNA quantity; only visible with less than 100 ng sample DNA D-fragments: Low signal of 88 or 96 nt fragment indicates incomplete denaturation 100 X-fragment: Specific for the X chromosome 105 Y-fragment: Specific for the Y chromosome 130 Reference probe L q PAX6 probe L07190 Exon DCDC1 probe L07345 Exon ELP4 probe L06707 Exon PAX6 probe L07191 Exon SOX2 probe L06702 Exon FSHB probe L06704 Exon DCDC1 probe L06706 Exon WT1 probe L04733 Exon Reference probe L q «LMO2 probe L00083 Exon HIPK3 probe L07192 Exon BDNF probe L07193 Exon FSHB probe L06703 Exon PAX6 probe L02690 Exon RCN1 probe L06712 Exon * Reference probe L p PAX6 probe L07346 Exon WT1 probe L02204 Upstream 256 SOX2 probe L07347 Exon CD44 probe L01731 Exon WT1 probe L04739 Exon Reference probe L q PAX6 probe L21437 Exon * Reference probe L q PAX6 probe L14006 Exon PAX6 probe (DKFZp686K1684) L06709 Upstream 319 PAX6 probe L03208 Exon PAX6 probe L21498 Exon SOX2 probe L06700 Exon RCN1 probe L06711 Intron PAX6 probe L02492 Exon WT1-area probe (LOC646008) L06713 Downstream 373 Reference probe L p «PAX6 probe L07348 Exon PAX6 probe L05486 Exon * Reference probe L q PAX6 probe L07349 Exon PAX6 probe (DKFZp686K1684) L06710 Upstream 427 PAX6 probe L05485 Exon Reference probe L q WT1-area probe (LOC646008) L06714 Downstream 454 BDNF probe L03996 Exon Reference probe L p14 * New in version B3 (from lot B onwards). Flanking probe. Included to facilitate the determination of the extent of a deletion/duplication. Copy number alterations of flanking and reference probes are unlikely to be related to the condition tested. «This probe is located within, or close to, a very strong CpG island. A low signal of this probe can be due to incomplete sample DNA denaturation, e.g. due to the presence of salt in the sample DNA. The PAX6 and BDNF exon numbering has changed. From description version 11 onwards, we have adopted the NCBI exon numbering that is present in the NM_ sequences for this gene. This exon numbering SALSA probemix P219 PAX6 Page 3 of 6

4 used here may differ from literature! The exon numbering used in previous versions of this product description can be found between brackets in Table 2. Table 2. P219 probes arranged according to chromosomal location Table 2a. 11p13-14 Length (nt) SALSA MLPA probe L L07193 Gene / Exon BDNF Exon 2 (11d) BDNF Exon 1 (8) Ligation site Partial sequence (24 nt adjacent to ligation site) Distance to next probe NM_ ; CCCAATGAAGAA-AACAATAAGGAC 41.2 kb NM_ ; ~22 kb after exon 1; NM_ ; TCCAGGGAAGTT-AAGAGTTTTGAC kb L06703 FSHB Exon 2 NM_ ; GCATCAACACCA-CTTGGTGTGCTG 2.1 kb L06704 FSHB Exon 3 NM_ ; GAACTAACTGCA-GCAGTCTTCTGG kb L06706 DCDC1 Exon 4 NM_ ; CAGCAGTATCAG-AAGGGTCAGGAC 61.9 kb L07345 DCDC1 Exon 1 NM_ ; TGGAGTGGCGTT-TACTACCAGTAA kb L06707 ELP4 Exon 9 NM_ ; reverse TCACAGATCAAG-TTATTAAGCCGA kb PAX6 gene NM_ stop codon (ex 13) L14006 Exon 13 (15) CCTGGTGTGTCA-GTTCCAGTTCAA 0.7 kb L05486 Exon 12 (14) 13 nt after exon 12 TGAGCCACTGCT-TTCTGCAGGCTG 3.0 kb No probe Exon L02492 Exon 10 (12) AGTCATATTCCT-ATCAGCAGTAGT 0.4 kb L05485 Exon 9 (11) reverse TGGATAATGGGT-TCTCTCAAACTC 0.6 kb L21498 Exon 8 (10) AGTTCCAACGGA-GAAGATTCAGAT 6.1 kb L07346 Exon 7 (9) TCTTCGCAACCT-GGCTAGCGAAAA 0.8 kb L21437 Exon 6 (8) TGGGAAATCCGA-GACAGATTACTG 1.2 kb L02690 Exon 5 (6) GTGAATCAGCTC-GGTGGTGTCTTT 3.6 kb L07190 Exon 4 (5) 18 nt after exon 4 GCCTCTGGTCTT-TCTGGGACTTCG 0.5 kb 383 «03091-L07348 Exon 3 (4) reverse GTCCACTCTCAC-AATAAAAGGCCT 4.1 kb L07191 Exon 2 (3) AAACTCTCACCA-GCAACTCCTTTA 0.3 kb L03208 Exon 1 (2a) GTTCAGGCGCAG-GAGGAAGTGTTT 0.1 kb L07349 Exon 1 (2a) 49 nt before exon 1 TCGGCTGGCGCG-AGGCCCCGGCGC 5.2 kb start codon (ex 4) L06709 PAX6 Upstream NM_ ; ~52 kb before exon 1 NM_ ; 1264 nt CCTTCTCCTCCA-GTCATAAATCAA 69.1 kb after exon L06710 PAX6 Upstream NM_ ; ~74 kb upstream from PAX6 TGTGCTAGGGCT-ATCGCGATTTGC kb L06711 NM_ ; 1083 nt after RCN1 Intron 1 exon 1 GGAGGATTTTGA-CTTGGGCTGTTA 11.3 kb L06712 RCN1 Exon 5 NM_ ; 307 nt after exon 5 GTTGCCCTAGGA-TCAGCTTATTTA kb L06714 WT1-area AL ; ; Downstream 158 kb downstream WT1 CCATTCCTTGGT-TACATCATCAAA 88.1 kb L06713 WT1-area AL ; , Downstream 70 kb downstream of WT1 GCTTGTAGATCT-GTCCCTTGGCCT 70.2 kb L04739 WT1 Exon 11 NM_ ; GTCAGCCAGGCT-GCTAACCTGGAA 29.1 kb L04733 WT1 Exon 5 NM_ ; CATCCCAGCTTG-AATGCATGACCT 18.1 kb L02204 NM_ ; 221 nt before WT1 Upstream exon 1 CACCGGCCAGCT-GAGAGCGCGTGT kb L07192 HIPK3 Exon 17 NM_ ; CAGCATCCAACT-TATAATATCTCC kb 193 «00486-L00083 LMO2 Exon 5 NM_ ; AAGCGGATTCGT-GCCTATGAGATG kb L01731 CD44 Exon 1 NM_ ; CCCGCGCCCTCC-GTTCGCTCCGGA SALSA probemix P219 PAX6 Page 4 of 6

5 Flanking probe. Included to facilitate the determination of the extent of a deletion/duplication. Copy number alterations of flanking and reference probes are unlikely to be related to the condition tested. «This probe is located within, or close to, a very strong CpG island. A low signal of this probe can be due to incomplete sample DNA denaturation, e.g. due to the presence of salt in the sample DNA. The NM_ sequence represents transcript variant 2 and is a reference standard in the NCBI RefSeqGene project. Table 2b. 3q26 Length (nt) SALSA MLPA probe SOX2 Exon Ligation site NM_ Partial sequence (24 nt adjacent to ligation site) Distance to next probe start codon (ex 1) L06700 Exon reverse CCCCCTTTTGCA-AACACTCTCTTC 0.7 kb L07347 Exon CACCCGGATTAT-AAATACCGGCCC 0.2 kb L06702 Exon GGACAGTTACGC-GCACATGAACGG stop codon (ex 1) The NM_ sequence is a reference standard in the NCBI RefSeqGene project. The PAX6 and BDNF exon numbering has changed. From description version 11 onwards, we have adopted the NCBI exon numbering that is present in the NM_ sequences for this gene. This exon numbering used here may differ from literature! The exon numbering used in previous versions of this product description can be found between brackets in Table 2. Complete probe sequences are available on request: info@mlpa.com. Please notify us of any mistakes: info@mlpa.com. SALSA MLPA probemix P219-B3 PAX6 sample picture Figure 1. Capillary electrophoresis pattern of a sample of approximately 50 ng human male control DNA analysed with SALSA MLPA probemix P219-B3 PAX6 (lot B3-0915). SALSA probemix P219 PAX6 Page 5 of 6

6 Implemented Changes compared to the previous product description versions Version January 2017 (55) - Warning added in Table 1 and Table 2, 383 nt probe L07348 and 193 nt probe L Several minor textual changes on page 1. Version December 2015 (55) - Product description adapted to a new product version (version number changed, lot number added, changes in Table 1 and Table 2, new picture included). - Exon numbering of PAX6 and BDNF adjusted according to RefSeq sequence. - Ligation sites of PAX6 and SOX2 adjusted according to RefSeq sequence. - Peak area replaced with peak height. - Update link for Database of Genomic Variants. - Manufacturer s address adjusted. Version June 2015 (48) - Electropherogram pictures of the old buffer (introduced Dec. 2012) removed. Version 09 (48) - Electropherogram pictures using the new MLPA buffer (introduced in December 2012) added. Version 08 (48) - Product description adapted to a new product version (version number changed, lot number added, changes in Table 1 and Table 2, new picture included). - New references added on page 1. - Various minor textual changes. - Ligation sites of the probes targeting the PAX6, RCN1, WT1 genes updated according to new version of the NM_reference sequence. - Small changes of probe lengths in Table 1 and 2 in order to better reflect the true lengths of the amplification products. Version 07 (46) - Remark on RefSeqGene standard and transcript variant added below Table 2. - DCDC1 gene added to the note regarding exon numbering change. Version 06 (46) - Exon numbering of the PAX6, WT1, LMO2, and BDNF genes has been changed on page 3 and 4. - Ligation sites of the probes targeting the BDNF, PAX6, RCN1, WT1HIPK3, LMO2, EHF, CD44 genes updated according to new version of the NM_reference sequence. - Small changes of probe lengths in Table 1 and 2 in order to better reflect the true lengths of the amplification products. - Warning added about variability of EHF probe L Data analysis method has been modified. - Various minor textual changes on page 1. - Various minor layout changes. SALSA probemix P219 PAX6 Page 6 of 6

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