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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 *
  1. *Microfluidic PCR and MiSeq sequencing
  2. †Sanger sequencing
  3. ‡Probe extension/ligation and MiSeq sequencing
  4. §PCR fragment analysis