Detecting Somatic Mutations Without Matched Normal Samples Using Long Reads.

ABSTRACT: DNA sequencing of tumours to identify somatic mutations has become a critical tool to guide the type of treatment given to cancer patients. The gold standard for mutation calling is comparing sequencing data from the tumour to a matched normal sample to avoid mis-classifying inherited SNPs as mutations. This procedure works extremely well, but in certain situations only a tumour sample is available. While approaches have been developed to find mutations without a matched normal, they have limited accuracy or require specific types of input data (e.g. ultra-deep sequencing). Here we explore the application of single molecule long read sequencing to calling somatic mutations without matched normal samples. We develop a simple theoretical framework to show how haplotype phasing is an importan

SUBMITTER: Simpson JT 

PROVIDER: S-EPMC10925087 | biostudies-literature | 2024 Feb

REPOSITORIES: biostudies-literature