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Multicenter Study
. 2009 Feb;11 Suppl 1(0 1):2-7.
doi: 10.1111/j.1463-1326.2008.00997.x.

Overview of the MHC fine mapping data

W M Brown  1 , J Pierce, J E Hilner, L H Perdue, K Lohman, L Li, R B Venkatesh, S Hunt, J C Mychaleckyj, P Deloukas; Type 1 Diabetes Genetics Consortium
Affiliations
Multicenter Study

Overview of the MHC fine mapping data

W M Brown et al. Diabetes Obes Metab. 2009 Feb.

Abstract

Aim: The aim of this study was to perform quality control (QC) and initial family-based association analyses on the major histocompatibility complex (MHC) single nucleotide polymorphism (SNP) and microsatellite marker data for the MHC Fine Mapping Workshop through the Type 1 Diabetes Genetics Consortium (T1DGC).

Methods: A random sample of blind duplicates was sent for analysis of QC. DNA samples collected from participants were shipped to the genotyping laboratory from several T1DGC DNA Repository sites. Quality checks including examination of plate-panel yield, marker yield, Hardy-Weinberg equilibrium, mismatch error rate, Mendelian error rate and allele distribution across plates were performed.

Results: Genotypes from 2325 families within nine cohorts were obtained and subjected to QC procedures. The MHC project consisted of three marker panels - two 1536 SNP sets (Illumina Golden Gate platform performed at the Wellcome Trust Sanger Institute, Cambridge, UK) and one 66 microsatellite marker panel (performed at deCODE). In the raw SNP data, the overall concordance rate was 99.1% (+/-0.02).

Conclusions: The T1DGC MHC Fine Mapping project resulted in a 2300 family, 9992 genotyped individuals database comprising of two 1536 SNP panels and a 66 microsatellite panel to densely cover the 4 Mb MHC core region for use in statistical genetic analyses.

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References

    1. Fan JB, Oliphant A, Shen R, et al. Highly parallel SNP genotyping. Cold Spring Harb Symp Quant Biol. 2003;68:69–78. - PubMed
    1. O’Connell JR, Weeks DE. PedCheck: a program for identifying marker typing incompatabilities in linkage analysis. Am J Hum Genet. 1998;63:259–266. - PMC - PubMed
    1. McPeek MS, Sun L. Statistical tests for detection of mis-specified relationships by use of genome-screen data. Am J Hum Genet. 2000;66:1076–1094. - PMC - PubMed
    1. Abecasis GR, Cherny SS, Cookson WO, Cardon LR. GRR: graphical representation of relationship errors. Bioinformatics. 2001;17:742–743. - PubMed

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