Identification of cancer genomic markers via integrative sparse boosting

Yuan Huang; Jian Huang; Ben-Chang Shia; Shuangge Ma

doi:10.1093/biostatistics/kxr033

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Identification of cancer genomic markers via integrative sparse boosting

Journal article

Open access

Peer reviewed

Identification of cancer genomic markers via integrative sparse boosting

Yuan Huang, Jian Huang, Ben-Chang Shia and Shuangge Ma

Biostatistics (Oxford, England), Vol.13(3), pp.509-522

07/2012

DOI: 10.1093/biostatistics/kxr033

PMCID: PMC3577103

PMID: 22045909

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https://doi.org/10.1093/biostatistics/kxr033View

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Abstract

In high-throughput cancer genomic studies, markers identified from the analysis of single data sets often suffer a lack of reproducibility because of the small sample sizes. An ideal solution is to conduct large-scale prospective studies, which are extremely expensive and time consuming. A cost-effective remedy is to pool data from multiple comparable studies and conduct integrative analysis. Integrative analysis of multiple data sets is challenging because of the high dimensionality of genomic measurements and heterogeneity among studies. In this article, we propose a sparse boosting approach for marker identification in integrative analysis of multiple heterogeneous cancer diagnosis studies with gene expression measurements. The proposed approach can effectively accommodate the heterogeneity among multiple studies and identify markers with consistent effects across studies. Simulation shows that the proposed approach has satisfactory identification results and outperforms alternatives including an intensity approach and meta-analysis. The proposed approach is used to identify markers of pancreatic cancer and liver cancer.

Biomarkers, Tumor - genetics

Computer Simulation

Data Interpretation, Statistical

Gene Expression Profiling - methods

Humans

Liver Neoplasms - diagnosis

Liver Neoplasms - genetics

Models, Statistical

Pancreatic Neoplasms - diagnosis

Pancreatic Neoplasms - genetics

Details

Title: Subtitle: Identification of cancer genomic markers via integrative sparse boosting
Creators: Yuan Huang - Pennsylvania State University
Jian Huang - University of Iowa
Ben-Chang Shia - Fu Jen Catholic University
Shuangge Ma - Yale University
Resource Type: Journal article
Publication Details: Biostatistics (Oxford, England), Vol.13(3), pp.509-522
DOI: 10.1093/biostatistics/kxr033
PMID: 22045909
PMCID: PMC3577103
ISSN: 1465-4644
eISSN: 1468-4357
Grant note: LM009828 / NLM NIH HHS R01 CA142774 / NCI NIH HHS CA142774 / NCI NIH HHS CA120988 / NCI NIH HHS CA152301 / NCI NIH HHS
Language: English
Date published: 07/2012
Academic Unit: Statistics and Actuarial Science; Biostatistics
Record Identifier: 9984257626602771

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