Dataset Information

Chromosomal imbalances detected via RNA-sequencing in 28 cancers.

ABSTRACT:

Motivation

RNA sequencing of tumor tissue is typically only used to measure gene expression. Here, we present a statistical approach that leverages existing RNA sequencing data (RNA-seq) 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, 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 subtypes. Our results credential haplotype-based inference based on RNA-seq to detect SCNAs in clinical and population-based settings.

Availability of data and materials

The analyses presented use the data publicly available from The Cancer Genome Atlas Research Network (http://cancergenome.nih.gov/). See Methods for details regarding data downloads. hapLOHseq software is freely available under The MIT license and can be downloaded from http://scheet.org/software.html.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Ozcan Z

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

REPOSITORIES: biostudies-literature

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Publications

Chromosomal imbalances detected via RNA-sequencing in 28 cancers.

Ozcan Zuhal Z San Lucas Francis A FA Wong Justin W JW Chang Kyle K Stopsack Konrad H KH Fowler Jerry J Jakubek Yasminka A YA Scheet Paul P

Bioinformatics (Oxford, England) 20220301 6

<h4>Motivation</h4>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.<h4>Results</h4>We present an analysis of 4942 participant samples from 28 cancers in The Cancer Genome Atlas (TCGA), demonstrating robust detection of SCNAs from RNA ...[more]

PMID: 34999743

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Dataset Information

Chromosomal imbalances detected via RNA-sequencing in 28 cancers.

Motivation

Results

Availability of data and materials

Supplementary information

Publications

Chromosomal imbalances detected via RNA-sequencing in 28 cancers.

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