In silico error correction improves cfDNA mutation calling.

ABSTRACT:

Motivation

Circulating-free DNA (cfDNA) profiling by sequencing is an important minimally invasive protocol for monitoring the mutation profile of solid tumours in cancer patients. Since the concentration of available cfDNA is limited, sample library generation relies on multiple rounds of PCR amplification, during which the accumulation of errors results in reduced sensitivity and lower accuracy.

Results

We present PCR Error Correction (PEC), an algorithm to identify and correct errors in short read sequencing data. It exploits the redundancy that arises from multiple rounds of PCR amplification. PEC is particularly well suited to applications such as single-cell sequencing and circulating tumour DNA (ctDNA) analysis, in which many cycles of PCR are used to generate suffici

SUBMITTER: Kim CS 

PROVIDER: S-EPMC6612818 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature