ADIPOQ Locus SNP Genotyping

Single nucleotide polymorphism (SNP) genotype data from a variety of sources were collected. These included individually genotyped SNPs at the ADIPOQ locus (n=33)(An et al. 2012 (link); An et al. 2013 (link)) which were combined with data from 7497 SNPs in the ADIPOQ region (chr3:161,560,463-197,838,262, hg19, 25 MB proximal and to the distal end of the chromosome) derived from Illumina OmniExpress (GWAS chip) genome-wide genotyping as part of the GUARDIAN Consortium(Goodarzi et al. 2013 ) and data from all chromosome 3 SNPs (n=3428) on the Illumina HumanExome Beadchip(Hellwege et al. 2014 (link)) for a total of 10,958 non-redundant, polymorphic SNPs. Quality control for each group of SNP data has previously been described in detail(An et al. 2012 (link); Hellwege et al. 2014 (link)). All datasets underwent Mendelian error checking using PedCheck(O'Connell and Weeks 1998 (link)).

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Hellwege J.N., Palmer N.D., Brown W.M., Ziegler J.T., An S.S., Guo X., Chen Y.D., Taylor K., Hawkins G.A., Ng M.C., Speliotes E.K., Lorenzo C., Norris J.M., Rotter J.I., Wagenknecht L.E., Langefeld C.D, & Bowden D.W. (2014). Empirical Characteristics of Family-Based Linkage to a Complex Trait: the ADIPOQ Region and Adiponectin Levels. Human genetics, 134(2), 203-213.

Publication 2014

OmniExpress (GWAS chip) HumanExome Beadchip

Chip Chromosome Chromosome 3 Genome Guardian Gwas Polymorphic Single nucleotide polymorphism

Corresponding Organization :

Other organizations : Wake Forest University, The Lundquist Institute, Harbor–UCLA Medical Center, University of Michigan–Ann Arbor, The University of Texas Health Science Center at San Antonio, Colorado School of Public Health, University of Colorado Denver

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Variable analysis

independent variables

Genotype data from individually genotyped SNPs at the ADIPOQ locus (n=33)
Genotype data from 7497 SNPs in the ADIPOQ region (chr3:161,560,463-197,838,262, hg19, 25 MB proximal and to the distal end of the chromosome) derived from Illumina OmniExpress (GWAS chip) genome-wide genotyping as part of the GUARDIAN Consortium
Genotype data from all chromosome 3 SNPs (n=3428) on the Illumina HumanExome Beadchip

dependent variables

Not explicitly mentioned

control variables

Mendelian error checking using PedCheck

Annotations

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