Table 2.
Overview of the “new” TSC1 and TSC2 variants
| Individual I | HaloPlex (% minor allele) | Validation (PCR-Sanger sequencing) | |||
| Index | Father | Mother | |||
| chr9 g.135804394A > G; TSC1 c.80-55 T > C (intron 3) | +/− | +/− | +/− | −/− | |
| chr9 g.135798153C > T; TSC1 c.508 + 582G > A (intron 6) | +/− | +/− | −/− | +/− | |
| chr9 g.135791383 T > C; TSC1 c.738-3539A > G (intron 8) | +/− | +/− | −/− | +/− | |
| chr9 g.135765655 T > C; TSC1 c.*5967A > G (exon 23; 3′UTR) | +/− | +/− | −/− | +/− | |
| chr 16 g.2108070C > A; TSC2 c.849-678C > A (intron 9) | +/− | +/− | −/− | +/− | |
| chr 16 g.2119403C > T; TSC2 c.1717-1054C > T (intron 16) | +/− | +/− | −/− | +/− | |
| chr 16 g.2124981C > G; TSC2 c.2545 + 591C > G (intron 22) | +/− (20%) | −/−* | −/− | −/− | |
| chr 16 g.2125962C > T; TSC2 c.2639 + 69C > T (intron 23) | +/− | +/− | −/− | +/− | |
| chr 16 g.2131815insC; TSC2 c.3814 + 19dup (intron 31) | +/− (18%) | −/−* | −/− | −/− | |
| Individual II | HaloPlex (% minor allele) | Validation (PCR-Sanger sequencing) | |||
| Index | Sibling | Father | Mother | ||
| chr9 g.135801283C > T; TSC1 c.211-157G > A (intron 4) | +/− (31%) | +/− | +/− | +/− | −/− |
| chr9 g.135775735 T > C; TSC1 c.2625 + 367A > G (intron 20) | +/− | +/− | +/− | −/− | +/− |
| chr 9 g.135775718insA (rs36000704); TSC1 c.2625 + 383dup (intron 20) | +/− | ? | ? | ? | ? |
| chr 9 g.135775530 T > C (rs2284902); TSC1 c.2625 + 572 (intron 20) | +/− | +/− | +/− | +/− | −/− |
| chr9 g.135775415dup (rs200047376); TSC1 c.2625 + 687dup (intron 20) | +/− (35%) | +/− | +/− | +/− | −/− |
| chr9 g.135775427 T > C (rs6597584); TSC1 c.2625 + 675 T > G (intron 20) | +/− | +/− | +/− | +/− | −/− |
| Individual III | HaloPlex (% minor allele) | Validation (alle-specific PCR) | |||
| Index | Father | Mother | |||
| chr16 g.2129165, rs45464800; TSC2 c.3099C > G (exon 16) | +/− (9%) | +/− | −/− | −/− | |
| Individual IV | HaloPlex | Validation (PCR-Sanger sequencing) | |||
| Index | Father | Mother | |||
| chr16 g.2100489 T > A; TSC2 c.225 + 2 T > A (intron 3) | +/− | +/− | −/− | −/− | |
| chr16 g.2102256del10, rs140492671; TSC2 c.226-1086del10 (intron 3) | +/+ | +/+ (ins Alu) | +/− (ins Alu) | +/+ (ins Alu) | |
| Individual V | HaloPlex | Validation (PCR-Sanger sequencing) | |||
| Index | Father | Mother | |||
| chr9 g.135820146delACTCATA; TSC1 c.-15894_-15888del | +/− | +/− | −/− | +/− | |
| chr9 g.135763459 T > A; 3′ TSC1 exon 23 | +/− | +/− | −/− | +/− | |
| Individual VI | HaloPlex (% minor allele) | Validation (alle-specific PCR) | |||
| Index | Father | Mother | |||
| chr16 g.2127477G > A; TSC2 c.2838-122G > A (intron 25) | +/− (12%) | +/− | −/− | −/− | |
| Individual VII | HaloPlex (% minor allele) | Validation (PCR-Sanger sequencing) | |||
| chr16 g.2101947C > T, rs139385485; TSC2 c.226-1396 T > C (intron 3) | +/− (18%) | +/− | |||
| chr16 g.2102256del10, rs140492671; TSC2 c.226-1086del10 (intron 3) | +/− (10%) | +/− (ins Alu) | |||
| chr16 g.2105289 T > C, rs77037371; TSC2 c.482-114 T > C (intron 5) | +/− (70%) | +/− | |||
| chr16 g.2105335C > G, rs2516734; TSC2 c.482-68C > G (intron 5) | +/− (70%) | +/− | |||
| chr16 g.2113125A > G; TSC2 c.1443 + 71A > G (intron 14) | +/− | +/− | |||
| chr16 g.2113464C > T; TSC2 c.1443 + 410C > T (intron 14) | +/− | +/− | |||
| chr16 g.2120785C > T; TSC2 c.1839 + 206C > T (intron 17) | +/− | +/− | |||
| chr16 g.2130697G > A; TSC2 c.3610 + 319G > A (intron 30) | +/− | +/− | |||
Variants identified by HaloPlex custom capture NGS without an rs-number in dbSNP132 are listed per individual. The results of the subsequent PCR-Sanger sequencing and/or allele-specific PCR validation are shown for the relevant individual and any available family members. Results for variants identified with a skewed allelic ratio (minor allele detected in <40% or >60% of the sequence reads) are also shown. * indicates a discrepancy between the HaloPlex result and the validation experiment. ? indicates that the nucleotide change identified by HaloPlex could not be confirmed by Sanger sequencing due to the presence of polyA:T stretches. Pathogenic mutations are indicated in bold.