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Article

Discovery of regulatory noncoding variants in individual cancer genomes by using cis-X.

Nature genetics - 1 Aug 2020

Liu Yu, Li Chunliang, Shen Shuhong, Chen Xiaolong, Szlachta Karol, Edmonson Michael N, Shao Ying, Ma Xiaotu, Hyle Judith, Wright Shaela, Ju Bensheng, Rusch Michael C, Liu Yanling, Li Benshang, Macias Michael, Tian Liqing, Easton John, Qian Maoxiang, Yang Jun J, Hu Shaoyan, Look A Thomas, Zhang Jinghui

Abstract excerpt

We developed cis-X, a computational method for discovering regulatory noncoding variants in cancer by integrating whole-genome and transcriptome sequencing data from a single cancer sample. cis-X first finds aberrantly cis-activated genes that exhibit allele-specific expression accompanied by an elevated outlier expression. It then searches for causal noncoding variants that may introduce aberrant transcription...

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Identifiers

PMID: 32632335
DOI: 10.1038/s41588-020-0659-5
PMCID: PMC7679232

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