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Nucleic Acids Res. 2015 Feb 18;43(3):1332-44. doi: 10.1093/nar/gku1290. Epub 2015 Jan 12.

Sparse expression bases in cancer reveal tumor drivers.

Author information

1
Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA Sage Bionetworks, Seattle, WA, 98109, USA.
2
Center for Cancer Systems Biology, Department of Radiology, Stanford University, CA, 94305, USA.
3
Department of Medicine/Hematology, Center for Cancer Innovation, University of Washington, Seattle, WA, 98195, USA.
4
Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA Department of Computer Science & Engineering, University of Washington, Seattle, WA, 98195, USA suinlee@cs.washington.edu.

Abstract

We define a new category of candidate tumor drivers in cancer genome evolution: 'selected expression regulators' (SERs)-genes driving dysregulated transcriptional programs in cancer evolution. The SERs are identified from genome-wide tumor expression data with a novel method, namely SPARROW ( SPAR: se selected exp R: essi O: n regulators identified W: ith penalized regression). SPARROW uncovers a previously unknown connection between cancer expression variation and driver events, by using a novel sparse regression technique. Our results indicate that SPARROW is a powerful complementary approach to identify candidate genes containing driver events that are hard to detect from sequence data, due to a large number of passenger mutations and lack of comprehensive sequence information from a sufficiently large number of samples. SERs identified by SPARROW reveal known driver mutations in multiple human cancers, along with known cancer-associated processes and survival-associated genes, better than popular methods for inferring gene expression networks. We demonstrate that when applied to acute myeloid leukemia expression data, SPARROW identifies an apoptotic biomarker (PYCARD) for an investigational drug obatoclax. The PYCARD and obatoclax association is validated in 30 AML patient samples.

PMID:
25583238
PMCID:
PMC4330344
DOI:
10.1093/nar/gku1290
[Indexed for MEDLINE]
Free PMC Article

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