Journal article

Exon-Level Microarray Analyses Identify Alternative Splicing Programs in Breast Cancer

Anna Lapuk, Henry Marr, Lakshmi Jakkula, Helder Pedro, Sanchita Bhattacharya, Elizabeth Purdom, Zhi Hu, Ken Simpson, Lior Pachter, Steffen Durinck, Nicholas Wang, Bahram Parvin, Gerald Fontenay, Terence Speed, James Garbe, Martha Stampfer, Hovig Bayandorian, Shannon Dorton, Tyson A Clark, Anthony Schweitzer Show all

MOLECULAR CANCER RESEARCH | AMER ASSOC CANCER RESEARCH | Published : 2010

Abstract

Protein isoforms produced by alternative splicing (AS) of many genes have been implicated in several aspects of cancer genesis and progression. These observations motivated a genome-wide assessment of AS in breast cancer. We accomplished this by measuring exon level expression in 31 breast cancer and nonmalignant immortalized cell lines representing luminal, basal, and claudin-low breast cancer subtypes using Affymetrix Human Junction Arrays. We analyzed these data using a computational pipeline specifically designed to detect AS with a low false-positive rate. This identified 181 splice events representing 156 genes as candidates for AS. Reverse transcription-PCR validation of a subset of p..

View full abstract

University of Melbourne Researchers

Grants

Awarded by U.S. Department of Energy


Awarded by NIH


Awarded by FCT SFRH/BD


Awarded by NATIONAL CANCER INSTITUTE


Awarded by NATIONAL HEART, LUNG, AND BLOOD INSTITUTE


Funding Acknowledgements

Director, Office of Science, Office of Biological & Environmental Research, of the U.S. Department of Energy under contract no. DE-AC02-05CH11231, USAMRMC W81XWH-07-1-0663 and NIH grants CA58207, CA112970, and CA 126477 (J.G. Conboy) by NIH grant HL045182 (J.W. Gray); and by the FCT SFRH/BD 33203 2007 (H. Pedro).