Of the subset of inspected putative variant calls ( n=223) in genomic regions that were not intronic or intergenic, 68 variants (30%) were deemed valid after visual inspection. Visual validation of 434 called variants was performed, and performance of the methods assessed individually and in combination. We used MuTect, Varscan2, IONT’s proprietary Ion Reporter, and a simple subtraction we called “Poor Man’s Caller.” Together these produced calls at 637 loci across all samples. Using IONT, we surveyed variants from the 409-gene Comprehensive Cancer Panel in whole-section tumors, intra-tumoral biopsies and matched normal samples obtained from frozen tissues and blood from four early-stage non-small cell lung cancer (NSCLC) patients. We compared various computational variant-calling methods to derive a variant identification pipeline that may improve the molecular diagnostic and research utility of IONT. However, identifying mutations from IONT deep sequencing with high confidence has remained a challenge. The Ion Torrent-based (IONT) platform is among NGS technologies employed in clinical, research and diagnostic settings. ‘Next-generation’ (NGS) sequencing has wide application in medical genetics, including the detection of somatic variation in cancer.
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