A Comprehensive Transcriptional Portrait of Human Cancer Cell Lines

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2014 Dec 9

PMID 25485619

Citations 370

Authors

Christiaan Klijn

Steffen Durinck

Eric W Stawiski

Peter M Haverty

Zhaoshi Jiang

Hanbin Liu

Jeremiah Degenhardt

Oleg Mayba

Florian Gnad

Jinfeng Liu

Gregoire Pau

Jens Reeder

Yi Cao

Kiran Mukhyala

Suresh K Selvaraj

Mamie Yu

Gregory J Zynda

Matthew J Brauer

Thomas D Wu

Robert C Gentleman

Gerard Manning

Robert L Yauch

Richard Bourgon

David Stokoe

Zora Modrusan

Richard M Neve

Frederic J de Sauvage

Jeffrey Settleman

Somasekar Seshagiri

Zemin Zhang

Affiliations

Soon will be listed here.

Abstract

Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic responses. Although substantial effort has been made to define the genomic constitution of cancer cell line panels, the transcriptome remains understudied. Here we describe RNA sequencing and single-nucleotide polymorphism (SNP) array analysis of 675 human cancer cell lines. We report comprehensive analyses of transcriptome features including gene expression, mutations, gene fusions and expression of non-human sequences. Of the 2,200 gene fusions catalogued, 1,435 consist of genes not previously found in fusions, providing many leads for further investigation. We combine multiple genome and transcriptome features in a pathway-based approach to enhance prediction of response to targeted therapeutics. Our results provide a valuable resource for studies that use cancer cell lines.

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