Table 1.
SALSA MLPA Probemix P245 Microdeletion Syndromes-1A probe sequences used for CNVs analysis
| Syndrome | Gene | Partial sequence (24 nt adjacent to ligation site) |
|---|---|---|
| 1p36 deletion syndrome | TNFRSF18 | CGGGTTTCTCAC-TGTGTTCCCTGG |
| TNFRSF4 | GCCGGCCAGCAA-TAGCTCGGACGC | |
| GNB1 | CTAAGATCGGAA-GATGAGTGAGCT | |
| GABRD | CGGCGACTACGT-GGGCTCCAACCT | |
|
| ||
| 2p16.1p15 microdeletion syndrome | REL | TATCACAGAACC-CGTAACAGTAAA |
| PEX13 | TGAGGATGACCA-TGTAGTTGCCAG | |
|
| ||
| 2q23.1 microdeletion/microduplication syndrome | MBD5 | CCAGCTATACAA-GTTCCTGTGGGT |
| MBD5 | CTGGAGATCTTC-CTCCTCTTGGGT | |
|
| ||
| Glass syndrome (2q32q33 microdeletion syndrome) | SATB2 | TGCCATTTATGA-CGAGATCCAACA |
| SATB2 | AGAGAAGAACAC-GCCGAGTTTGTC | |
|
| ||
| 3q29 microdeletion/microduplication syndrome | DLG1 | CTATGAAAGACA-GGATAAATGATG |
| DLG1 | CAGCTCAGAAGT-TCCATAGAACGG | |
| BDH1 | GAACTGGGCCAT-TCTAACACCCGT | |
| KIAA0226 | GCTGGAGGACAG-ATGTGCCGTCTT | |
|
| ||
| Wolf-Hirschhorn syndrome, 4p16.3 | PIGG | AAAAGCATTCAG-GCTAGATGGTGG |
| PIGG | GAGTGTGACGTA-GTCCTTCTGCTC | |
| LETM1 | CCTGTGTACACA-TCCTCCAGAGGC | |
| WHSC1 | GTGGGCATTTAT-TTTCCCTTAATG | |
|
| ||
| Cri-du-Chat syndrome, 5p15 | CCDC127 | ACGCCATGATCT-CAGAAAATCGGC |
| PDCD6 | AGGTGTCGTACG- AACAGTACCTGT | |
| TERT | TCTTTCTTTTAT-GTCACGGAGACC | |
| SEMA5A | ACTTGGGCTGGA-GTGCCCACGTGG | |
|
| ||
| Sotos syndrome, 5q35.3 | NSD1 | ACCCACCCACTG-TTATGCAGAACA |
| NSD1 | GGAAAGACTGTT-TGCAAATGTGGA | |
|
| ||
| Williams-Beuren duplication syndrome, 7q11.23 | ELN | TTTCCCGGCTTT-GGTGTCGGAGTC |
| ELN | ACCTCATCAACG-TTGGTGCTACTG | |
|
| ||
| Langer-Giedion syndrome, 8q24.11q24.13 | TRPS1 | |
| CTCIIIIIIGGT-GCTGCTGGIIIC | ||
| EXT1 | GGTGATAATGTT-AAACCCACTTAA | |
|
| ||
| 9q22.3 microdeletion syndrome | FANCC | GATAACTCACGA-GATCATTGGCTT |
| PTCH1 | GTTAATGACTCC-CAAGCAAATGTA | |
|
| ||
| DiGeorge syndrome-2, 10p13p14 | GATA3 | GAGCAACGCAAT-CTGACCGAGCAG |
|
| ||
| Prader-Willi/Angelman syndrome, 15q11.2 | MKRN3 | GGCTGCAGACCT-TGCACCCCATGG |
| NDN | ACACTGCTGCGA-GGGTAGTGGGCA | |
| SNRPN | ACCACCACCTGA-TGAAAGATACAC | |
| SNRPN | GATTCCTCGCTA-CTCCAATATGGC | |
| UBE3A | AGTGTTATTGGA-AGTGAGCCACCA | |
|
| ||
| Witteveen-Kolk syndrome/15q24 microdeletion syndrome | SEMA7A | TACCCACAGAGA-CCTTCCAGGTGG |
| CYP1A1 | GTCAACCTGAAT-AATAATTTCGGG | |
|
| ||
| Rubinstein-Taybi syndrome, 16p13.3 | CREBBP | AGCAGGTGAAAA-TGGCTGAGAACT |
|
| ||
| Miller-Dieker syndrome/lissencephaly-1, 17p13.3 | PAFAH1B1 | TGTAGGCACTCT-ATAGATCAAGCT |
| PAFAH1B1 | CCAGAAAAATAT-GCATTGAGTGGT | |
|
| ||
| Smith-Magenis syndrome/Potocki-Lupski syndrome, 17p11.2 | RAI1 | CCAAGGATCTCA-TCTGGCCACCGC |
| DRC3 | CGGATCTCCAAG-ATCGACTCCCTG | |
| LLGL1 | CAGCAGTCTGCA-TCTCTGGGAGAT | |
|
| ||
| NF1 microdeletion syndrome, 17q11.2 | NF1 | GGATCATGAAGA-ATTACTACGTAC |
| NF1 | TCTTGTTGTCTT-TGGGTGTATTAG | |
|
| ||
| Koolen-de Vries syndrome/17q21.31 microduplication syndrome | MAPT | GTCGCCAGTGGT-GTCTGGGGACAC |
| KANSL1 | CCGCTTCTTACA-GCTCAGTACAGG | |
|
| ||
| DiGeorge/22q11.2 duplication/distal 22q11.2 deletion syndrome | IL17RA | GCAGAGTTATCT-GTCCTGCAGCTG |
| BID | CTACTGGTGTTT-GGCTTCCTCCAA | |
| CLDN5, region AB | TTCGCCAACATT-GTCGTCCGCGAG | |
| GP1BB, region AB | CACAACCGAGCT-GGTGCTGACCGG | |
| SNAP29, region CD | GTATCCACTTAC-CTGTATCATCCA | |
| PPIL2, distal 22q11 | GAAGAGCCCTCA-ACCAGTGCCACT | |
| RTDR1, distal 22q11 | GGTGTGTCATTT-TGACGTCATCCC | |
|
| ||
| Phelan-McDermid syndrome, 22q13 | ARSA | GGAGGATCAGAT-CTCCGCTCGAGA |
| SHANK3 | AAGCGGCGAGTT-TATGCCCAGAAC | |
| RABL2B | AATACACAAGCC-GTAAAATCGAGT | |
|
| ||
| X chromosome copy number changes | DMD | AAACTCATAGAT-TACTGCAACAGT |
|
| ||
| Rett syndrome/MECP2 duplication syndrome, Xq28 | MECP2, exon 1 | CATTAATCCTTA-ACATTCAAATTC |
| MECP2, exon 3 | ACTTGTTCTGCA-GACTGGCATGTT | |
| MECP2, exon 4 | TTTCATCCTCCA-TGCCAAGGCCAA | |