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Single-marker analysis of SNPs from 4 genes on chromosome 22 by PLINK.

By Daniel W. H. Ho (154412), Maurice K. H. Yap (154413), Po Wah Ng (154414), Wai Yan Fung (154415) and Shea Ping Yip (154416)


*<p>The major allele in the control group is designated as allele 1, and the minor allele as allele 2 unless follows allele designation in initial study.</p>†<p>Four genes that showed suggestive significance in set-based test in the discovery sample set (see <a href="" target="_blank">Table 4</a>) were followed up with the replication sample set. Six SNPs within these four genes with nominal <i>P</i><0.05 (marked by ¶) were first chosen for follow-up. Nineteen more SNPs were also selected for follow-up for the following reasons: (i) in LD with these six SNPs (not marked by any symbol); (ii) with potential functional relevance – T for SNP located at predicted transcription factor binding site, and M for SNP located at predicted microRNA binding site); or (iii) forming significantly associated haplotype windows with one of the six chosen SNPs (marked by #) – rs2238754 (#) and rs2800960 (¶) with normal <i>P</i> = 5.19e-13; rs9610583 (#) and rs4616572 (¶) with nominal <i>P</i> = 9.32e-46; and rs1217125 (#), rs2284021 (#) and rs4820254 (¶) with nominal <i>P</i> = 1.06e-07. As such, 13 SNPs that had not been genotyped in the discovery sample set are shown as missing data (−).</p>‡<p>SNPs are listed according to their sequential physical positions on chromosome 22 (NCBI build 37.1).</p>§<p>Empirical <i>P</i> values (<i>P</i><sub>emp</sub>) are estimated based on 10,000,000 permutations. In each round of permutation (swapping of the case-control status), the best <i>original</i> result of every SNP is compared against the best result of the three tests (allelic, dominant and recessive) of that SNP, and also against the best results from all SNPs.</p>+<p>SNPs tested to have significant difference (<i>P</i><0.05) in minor allele frequency (MAF) for control subjects between the discovery and the replication sample sets.</p

Topics: Medicine, Genetics, Biotechnology, Biological Sciences, snps, genes, chromosome, 22
Year: 2012
DOI identifier: 10.1371/journal.pone.0040238.t003
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Provided by: FigShare
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