Chromosomal imbalances detected via RNA-sequencing in 28 cancers.

ABSTRACT:

Motivation

RNA-sequencing (RNA-seq) of tumor tissue is typically only used to measure gene expression. Here, we present a statistical approach that leverages existing RNA-seq data to also detect somatic copy number alterations (SCNAs), a pervasive phenomenon in human cancers, without a need to sequence the corresponding DNA.

Results

We present an analysis of 4942 participant samples from 28 cancers in The Cancer Genome Atlas (TCGA), demonstrating robust detection of SCNAs from RNA-seq. Using genotype imputation and haplotype information, our RNA-based method had a median sensitivity of 85% to detect SCNAs defined by DNA analysis, at high specificity (∼95%). As an example of translational potential, we successfully replicated SCNA features associated with breast cancer subtyp

SUBMITTER: Ozcan Z 

PROVIDER: S-EPMC8896613 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature