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A new gene-based association test for genome-wide association studies.

ABSTRACT: Genome-wide association studies are widely used today to discover genetic factors that modify the risk of complex diseases. Usually, these methods work in a SNP-by-SNP fashion. We present a gene-based test that can be applied in the context of genome-wide association studies. We compare both strategies, SNP-based and gene-based, in a sample of cases and controls for rheumatoid arthritis.We obtained different results using each strategy. The SNP-based test found the PTPN22 gene while the gene-based test found the PHF19-TRAF1-C5 region. That suggests that no single strategy performs better than another in all cases and that a certain underlying genetic architecture can be delineated more easily with one strategy rather than with another.

SUBMITTER: Buil A

PROVIDER: S-EPMC2795904 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

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A new gene-based association test for genome-wide association studies.

Buil Alfonso A Martinez-Perez Angel A Perera-Lluna Alexandre A Rib Leonor L Caminal Pere P Soria Jose Manuel JM

BMC proceedings 20091215

Genome-wide association studies are widely used today to discover genetic factors that modify the risk of complex diseases. Usually, these methods work in a SNP-by-SNP fashion. We present a gene-based test that can be applied in the context of genome-wide association studies. We compare both strategies, SNP-based and gene-based, in a sample of cases and controls for rheumatoid arthritis.We obtained different results using each strategy. The SNP-based test found the PTPN22 gene while the gene-bas ...[more]

PMID: 20017997

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