Tangent normalization for somatic copy-number inference in cancer genome analysis.

ABSTRACT:

Motivation

Somatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas, the Broad Institute Genome Characterization Center developed the Tangent normalization method to generate copy-number profiles using data from single-nucleotide polymorphism (SNP) arrays and whole-exome sequencing (WES) technologies for over 10 000 pairs of tumors and matched normal samples. Here, we describe the Tangent method, which uses a unique linear combination of normal samples as a reference for each tumor sample, to subtract systematic errors that vary across samples. We also describe a modification of Tangent, c

SUBMITTER: Gao GF 

PROVIDER: S-EPMC9563697 | biostudies-literature | 2022 Oct

REPOSITORIES: biostudies-literature