ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA.

ABSTRACT:

Motivation

The use of liquid biopsies for cancer patients enables the non-invasive tracking of treatment response and tumor dynamics through single or serial blood drawn tests. Next-generation sequencing assays allow for the simultaneous interrogation of extended sets of somatic single-nucleotide variants (SNVs) in circulating cell-free DNA (cfDNA), a mixture of DNA molecules originating both from normal and tumor tissue cells. However, low circulating tumor DNA (ctDNA) fractions together with sequencing background noise and potential tumor heterogeneity challenge the ability to confidently call SNVs.

Results

We present a computational methodology, called Adaptive Base Error Model in Ultra-deep Sequencing data (ABEMUS), which combines platform-specific genetic knowledge and

SUBMITTER: Casiraghi N 

PROVIDER: S-EPMC7203757 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature