False-negative errors in next-generation sequencing contribute substantially to inconsistency of mutation databases
Fig 2
Estimation of error rates in mutation calls from CCLE and GDSC.
A. Comparison of mutation calls between CCLE and GDSC for 151 genes in 35 cell lines. The consistency between GDSC and CCLE was 61.5%. B. Mutation detection rates in consistent and inconsistent mutation calls between GDSC and CCLE for 151 genes in 35 cell lines. Almost all of the consistent calls (“Consistent” on X-axis, 95.3%) and 76.5% of the inconsistent calls (“Inconsistent” on X-axis) between the two databases were positive (P-TP) in our T-NGS. C. P-FP call rates in GDSC and CCLE databases along with combined data from GDSC and CCLE databases (GDSC/CCLE). D. P-FP and P-FN mutation call rates in CCLE, GDSC, and combined data from GDSC and CCLE (GDSC/CCLE). E. P-FP and P-FN mutation call rates in later versions of CCLE (nCCLE) and GDSC (nGDSC), or in the combined data from later versions of GDSC and CCLE (nGDSC/nCCLE). P-TP, possibly true positive; P-FP, possibly false positive; P-FN, possibly false negative.