Reliability of algorithmic somatic copy number alteration detection from targeted capture data.

ABSTRACT:

Motivation

Whole exome and gene panel sequencing are increasingly used for oncological diagnostics. To investigate the accuracy of SCNA detection algorithms on simulated and clinical tumor samples, the precision and sensitivity of four SCNA callers were measured using 50 simulated whole exome and 50 simulated targeted gene panel datasets, and using 119 TCGA tumor samples for which SNP array data were available.

Results

On synthetic exome and panel data, VarScan2 mostly called false positives, whereas Control-FREEC was precise (>90% correct calls) at the cost of low sensitivity (<40% detected). ONCOCNV was slightly less precise on gene panel data, with similarly low sensitivity. This could be explained by low sensitivity for amplifications and high precision for deletions. Su

SUBMITTER: Rieber N 

PROVIDER: S-EPMC5870863 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature