DMCA
Cross Haplotype Sharing Statistic: Haplotype length based method for whole genome association testing
BibTeX
@MISC{A_crosshaplotype,
author = {André R. De Vries A and Ilja M. Nolte B and Geert T. Spijker C and Dumitru Brinza D and Er Zelikovsky D and Gerard J. Te Meerman A},
title = {Cross Haplotype Sharing Statistic: Haplotype length based method for whole genome association testing},
year = {}
}
Share
 |
 |
 |
 |
||
OpenURL
Abstract
We analyzed a dataset of 2,300 SNPs from a region of 10 Mb of chromosome 18q, which had shown linkage evidence for Rheumatoid Arthritis [1]. To test for disease association, a novel method, called the Cross-test, was used, which is based on differences between direct sharing of a patient and a control haplotype and sharing of two patients or two control haplotypes. We found highly significant association at a position ~4,407 kb from the starting SNP and a second less significant one at position ~4,863 kb. These results are supported by a single marker chi-square test and the Haplotype Sharing Statistic, but the Cross-test outperforms them with respect to significance and signal-to-noise ratio. For determining the significances, a sequential randomization procedure is implemented to render the method fast enough and hence practically useful even for whole genome screens with marker densities of 500,000 SNPs/genome. Background With the current advances in genotyping technology, genome wide association studies for detecting genes involved in complex diseases have recently become feasible. However, the computational and statistical methodology for analyzing such studies needs optimization and standardization. Various
Keyphrases
cross haplotype sharing statistic haplotype length whole genome association control haplotype linkage evidence single marker chi-square test wide association study direct sharing rheumatoid arthritis complex disease statistical methodology disease association significant association haplotype sharing statistic signal-to-noise ratio snp genome novel method current advance whole genome screen sequential randomization procedure marker density
