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Table 1 Evaluation of INDELseek complex indel detection performance

From: INDELseek: detection of complex insertions and deletions from next-generation sequencing data

Dataset Sample count and description Sensitivity Specificity
Real NGS data
 1. Protein-coding and flanking regions from whole-genome sequencing (random fragments) 1 (NA12878) 100% 100%
160 putative complex indels
26 negative control loci
 2. Hereditary breast and/or ovarian cancer panel (amplicons) 239 100% 100%
3 positive samples (BRCA1 n = 1, BRCA2 n = 2)
236 negative samples
 3. Myeloid neoplasm panel (amplicons) 23 100% 100%
5 positive samples (CALR n = 4, JAK2 n = 1)
18 negative samples (NA12878 and 17 healthy controls)
Semi-simulated data by engineering mutations to real NGS data
 1. Whole-genome sequencing (random fragments) 8671 collected from COSMIC and dbSNP 93.7% N/A
 2. Hereditary breast and/or ovarian cancer panel (amplicons) 237 collected from COSMIC and dbSNP 96.2% N/A
 3. Myeloid neoplasm panel (amplicons) 576 collected from COSMIC and dbSNP 94.6% N/A
  1. N/A Not applicable