Table 2 Complex indels detected by INDELseek in human clinical samples
From: INDELseek: detection of complex insertions and deletions from next-generation sequencing data
Sample | Gene | Mutation | Allele frequency | Sequencing depth (X) | NGS method | Orthogonal validation |
|---|---|---|---|---|---|---|
Germline pathogenic mutations in hereditary breast and/or ovarian cancers | ||||||
1 | BRCA1 | c.4046_4047delinsA p.Thr1349Lysfs*17 | 37.9% | 730 | * | † |
2 | BRCA2 | c.4467_4474delinsTGTTTTT p.Lys1489Asnfs*15 | 74.9% | 1272 | * | † |
3 | BRCA2 | c.8400_8402delinsAAAA p.Phe2801Lysfs*11 | 33.6% | 4141 | * | † |
Somatic pathogenic mutations in myeloid neoplasms | ||||||
4 | CALR | c.1102_1136delinsT p.Lys368Trpfs*51 | 40.8% | 2274 | ‡ | † |
5 | CALR | c.1154delAinsCTTGTC p.Lys385Thrfs*47 | 31.9% | 2998 | ‡ | † |
6 | CALR | c.1129_1154delinsTGTC p.Lys377Cysfs*46 | 73.6% | 2159 | ‡ | † |
7 | CALR | c.1118_1125delinsCTTG p.Asp373Alafs*56 | 15.3% | 3603 | ‡ | § |
8 | JAK2 | c.1620_1627delinsGA p.Ile540_Glu543delinsMetLys | 57.7% | 4629 | ‡ | † |
9 | KIT | c.1248_1257delinsTTGG p.Thr417_Asp419delinsTrp | 39.0% | 11109 | ‡ | * |
10 | KIT | c.1248_1256delinsTTTCCG p.Thr417_Asp419delinsPheArg | 2.9% | 13724 | ‡ | * |
KIT | c.1249_1258delinsGGATGGAACT p.Thr417_Arg420delinsGlyTrpAsnTrp | 3.3% | 13651 | ‡ | * | |
KIT | c.1250_1258delinsAACCTC p.Thr417_Asp419delinsLysPro | 11.9% | 13525 | ‡ | * | |
KIT | c.1251_1258delinsCTCCT p.Tyr418_Arg420delinsSerTrp | 2.1% | 13376 | ‡ | * | |
11 | KIT | c.1250_1256delinsT p.Thr417_Asp419delinsIle | 5.7% | 7326 | ‡ | § |
KIT | c.1251_1257delinsAACA p.Tyr418_Asp419delinsThr | 2.2% | 7416 | ‡ | § | |
12 | KIT | c.1251_1256delinsGGG p.Tyr418_Asp419delinsGly | 2.7% | 14829 | ‡ | * |
13 | KIT | c.1253_1258delinsCCG p.Tyr418_Arg420delinsSerGly | 40.7% | 68180 | ‡ | * |
14 | KIT | c.1256_1257delinsGTCTA p.Asp419delinsGlyLeu | 17.9% | 19042 | ‡ | * |