Table 1B.
Copy number variation in SUDEP proband (IE124) compared to parental profiles using a clinical diagnostic microarray and a custom high density ion channel comparative hybridization array.
| Clinical aCGH Diagnostic Array (BCM Molecular Diagnostics Core - Director Dr. Ankita Patel)
| |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CNV# | Chromosome | CytoBand |
Start Position (Hg19) |
End Position (Hg19) |
Gain/Loss |
Number of Probes |
Length of CNV |
Known CNV* |
Number of Genes |
RefSeq (HUGO) Gene Names |
In Proband (IE124) |
In Mother (IE125) |
In Father (IE126) |
| 1 | chr1 | p21.1 | 104012051 | 104012498 | Loss | 8 | 447 | N(1,2,4) | y | n | y | ||
| 2 | chr4 | q12 | 57746415 | 57988228 | Gain | 9 | 241813 | N(1,2,3) | y | n | y | ||
| 3 | chr8 | p11.23 | 39369942 | 39499498 | Gain | 8 | 129556 | N(1,2,3) | 2 | ADAM5P, ADAM3A | y | y | y |
| 4 | chr10 | q11.22 | 46384979 | 46506801 | Gain | 4 | 121822 | N(1,2,3,4) | 3 | SYT15,GPRIN2,PPYR1 | y | y | y |
| 5 | chr14 | q11.2 | 21609644 | 22028409 | Loss | 14 | 418765 | N(1,2,3) | y | y | y | ||
| 6 | chr14 | q11.2 | 18864561 | 19459230 | Gain | 3 | 594669 | N(1,2,3) | 6 | P704P, OR4Q3, OR4M1, OR4N2, OR4K2, OR4K5 | y | y | y |
| 7 | chr15 | q11.2 | 19108763 | 19464920 | Loss | 113 | 356157 | N(1,2,3,4) | 3 | LOC646214, CXADRP2, POTEB | y | y | y |
| 8 | chr16 | p11.2 | 32481308 | 33528443 | Gain | 106 | 1047135 | N(1,2,3,4) | 5 | ZNF267, HERC2P4, LOC729355, TP53TG3, SLC6A10P | y | n | y |
| Ion Channel Comparative Hybridization (ICCH) Custom High Density aCGH Array (Translational Neurogenetics in Epilepsy Laboratory - Director Dr. Alica Goldman)
| |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| CNV# | Chromosome | CytoBand |
Start Position (Hg18) |
End Position (Hg18) |
Gain/Loss |
Number of Probes |
Length of CNV |
Known CNV* |
Number of Genes |
RefSeq (HUGO) Gene Names |
In Proband (IE124) |
In Mother (IE125) |
In Father (IE126) |
| 1 | chr1 | q43 | 235879084 | 235879144 | Gain | 1 | 60 | N | 1 | RYR2 (intron 49/50) NM_001035.2 | y | n | n |
| 2 | chr1 | q43 | 236028304 | 236028634 | Gain | 3 | 330 | N(1,2) | 1 | RYR2 (intron 97/98) NM_001035.2 | y | n | n |
| 3 | chr1 | q43 | 19864621 | 19864666 | Gain | 2 | 45 | N | 1 | HTR6 (exon 1 5′UTR) NM_000871.1 | y | y | n |
| 4 | chr7 | q36.1 | 150285908 | 150285968 | Gain | 1 | 60 | N(1,2) | 1 | KCNH2 (intron 4/5) iso1 NM_000238.3 | y | n | y |
| 5 | chr12 | p13.33 | 2117163 | 2123823 | Gain | 3 | 6660 | N(1,2) | 1 | CACNA1C (intron 2/3) iso1 NM_199460.2 | y | n | y |
| 6 | chr12 | P13.32 | 4892174 | 4892251 | Gain | 2 | 77 | N | 1 | KCNA1 (exon 2): NM_000217.2 | y | n | n |
| 7 | chr15 | q12 | 24568642 | 24569014 | Gain | 3 | 372 | N(1) | 1 | GABRB3 (exon 2–3) iso1 NM_000814.5 | y | y | y |
| 8 | chr15 | q12 | 25052658 | 25055717 | Gain | 2 | 3059 | N(2) | 1 | GABRG3 (intron 3/4) iso1 NM_033223.4 | y | n | n |
| 9 | chr19 | P13.13 | 13178788 | 13179169 | Gain | 3 | 381 | N | 1 | CACNA1A (exon 47 3′UTR) iso1 NM_000068.3 | y | y | y |
| 10 | chr19 | p13.13 | 13478014 | 13478059 | Gain | 1 | 45 | N(2) | 1 | CACNA1A (exon 1) NM_000068.3 | y | Y | y |
| 11 | chr19 | p13.3 | 565234 | 565928 | Gain | 5 | 694 | N(1,2) | 1 | HCN2 (intron 3/4) NM_001194.3 | y | y | y |
*
Known aberrations Toronto DGV (1 = region has reported gain; 2 = region has reported loss; 3 = region has reported indels; 4 = region has reported inversions)