Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection.

ABSTRACT:

Background

Circulating tumour DNA (ctDNA) is a subset of cell free DNA (cfDNA) released by tumour cells into the bloodstream. Circulating tumour DNA has shown great potential as a biomarker to inform treatment in cancer patients. Collecting ctDNA is minimally invasive and reflects the entire genetic makeup of a patient's cancer. ctDNA variants in NGS data can be difficult to distinguish from sequencing and PCR artefacts due to low abundance, particularly in the early stages of cancer. Unique Molecular Identifiers (UMIs) are short sequences ligated to the sequencing library before amplification. These sequences are useful for filtering out low frequency artefacts. The utility of ctDNA as a cancer biomarker depends on accurate detection of cancer variants.

Results

In this stud

SUBMITTER: Maruzani R 

PROVIDER: S-EPMC11370058 | biostudies-literature | 2024 Sep

REPOSITORIES: biostudies-literature