A data-adaptive sum test for disease association with multiple common or rare variants

Fang Han, Wei Pan

Research output: Contribution to journalArticle

Abstract

Since associations between complex diseases and common variants are typically weak, and approaches to genotyping rare variants (e.g. by next-generation resequencing) multiply, there is an urgent demand to develop powerful association tests that are able to detect disease associations with both common and rare variants. In this article we present such a test. It is based on data-adaptive modifications to a so-called Sum test originally proposed for common variants, which aims to strike a balance between utilizing information on multiple markers in linkage disequilibrium and reducing the cost of large degrees of freedom or of multiple testing adjustment. When applied to multiple common or rare variants in a candidate region, the proposed test is easy to use with 1 degree of freedom and without the need for multiple testing adjustment. We show that the proposed test has high power across a wide range of scenarios with either common or rare variants, or both. In particular, in some situations the proposed test performs better than several commonly used methods.

Original languageEnglish (US)
Pages (from-to)42-54
Number of pages13
JournalHuman Heredity
Volume70
Issue number1
DOIs
StatePublished - Jun 2010
Externally publishedYes

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Linkage Disequilibrium
Costs and Cost Analysis

Keywords

  • Genome-wide association study
  • Logistic regression
  • Multimarker analysis
  • Single nucleotide polymorphism

ASJC Scopus subject areas

  • Genetics(clinical)
  • Genetics
  • Medicine(all)

Cite this

A data-adaptive sum test for disease association with multiple common or rare variants. / Han, Fang; Pan, Wei.

In: Human Heredity, Vol. 70, No. 1, 06.2010, p. 42-54.

Research output: Contribution to journalArticle

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