Tests of association between quantitative traits and haplotypes in a reduced-dimensional space.

Abstract:

:Candidate gene association tests are currently performed using several intragenic SNPs simultaneously, by testing SNP haplotype or genotype effects in multifactorial diseases or traits. The number of haplotypes drastically increases with an increase in the number of typed SNPs. As a result, large numbers of haplotypes will introduce large degrees of freedom in haplotype-based tests, and thus limit the power of the tests. In this study we propose using the principal component method to reduce the dimension, and then construct association tests on the lower-dimensional space to test the association between haplotypes and a quantitative trait using population-based samples. The proposed method allows ambiguous haplotypes. We use simulation studies to evaluate the type I error rate of the tests, and compare the power of the proposed tests with that of the tests without dimension reduction, and the tests with dimension reduction by merging rare haplotypes. The simulation results show that the proposed tests have correct type I error rates and are more powerful than other tests in most cases considered in our simulation studies.

journal_name

Ann Hum Genet

journal_title

Annals of human genetics

authors

Sha Q,Dong J,Jiang R,Zhang S

doi

10.1111/j.1529-8817.2005.00216.x

subject

Has Abstract

pub_date

2005-11-01 00:00:00

pages

715-32

issue

Pt 6

eissn

0003-4800

issn

1469-1809

pii

AHG216

journal_volume

69

pub_type

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