Genotyping Protocols for Genetic Diversity

Genotyping was carried out using Illumina GoldenGate assays for the exploration stage at the Genomics Core Facility (Technion, Haifa, Israel), and the Biomark system (Fluidigm, South San Francisco, CA) for the replication stage at Biological Services (Weizmann Institute for Science, Rehovot, Israel), according to the manufacturer's protocols.17 (link),18 (link) SNP assays were designed by Illumina or by Fluidigm SNPtype Assays. Subjects with <90% successful genotyping or deviating from the expected European clustering were excluded from the analysis, about 10% of the samples. SNPs with minor allele frequencies (MAF) less than 0.05, or not in Hardy–Weinberg equilibrium, or with GenCall score <0.5 were also excluded from the analysis, about 30% of SNPs.19 (link) Population substructure was determined using principal component analysis and 24 SNPs used to infer population ancestry (genomic control SNPs) (Table2).20 (link) The F_ST score, that is, the contribution by each centre (the S subscript) to the total genetic variance (the T subscript), was about 0.02, which is as expected for a European population, and implies a high degree of similarity among cohorts.21 (link)

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Avidan N., Le Panse R., Harbo H.F., Bernasconi P., Poulas K., Ginzburg E., Cavalcante P., Colleoni L., Baggi F., Antozzi C., Truffault F., Horn-Saban S., Pöschel S., Zagoriti Z., Maniaol A., Lie B.A., Bernard I., Saoudi A., Illes Z., Casasnovas Pons C., Melms A., Tzartos S., Willcox N., Kostera-Pruszczyk A., Tallaksen C., Mantegazza R., Berrih-Aknin S, & Miller A. (2014). VAV1 and BAFF, via NFκB pathway, are genetic risk factors for myasthenia gravis. Annals of Clinical and Translational Neurology, 1(5), 329-339.

Publication 2014

GoldenGate assays Biomark system SNPtype Assays

Assays Biological European Genetic variance Genomic Replication Snps

Corresponding Organization : Carmel Medical Center

Other organizations : Astrophysique, Instrumentation et Modélisation, Institut de Myologie, Centre National de la Recherche Scientifique, Centre de Recherche en Myologie, Sorbonne Université, Inserm, University of Oslo, Fondazione IRCCS Istituto Neurologico Carlo Besta, University of Patras, Weizmann Institute of Science, Universitätsklinikum Erlangen, Oslo University Hospital, University of Pecs, University of Southern Denmark, Odense University Hospital, Bellvitge University Hospital, Pasteur Hellenic Institute, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Medical University of Warsaw

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Variable analysis

independent variables

Genotyping methods (Illumina GoldenGate assays and Biomark system)

dependent variables

Successful genotyping rate
Adherence to European ancestry clustering
Minor allele frequency (MAF)
Hardy-Weinberg equilibrium
GenCall score

control variables

Manufacturer's protocols for Illumina GoldenGate assays and Biomark system
Exclusion criteria (subjects with <90% successful genotyping or deviating from expected European clustering, SNPs with MAF <0.05, not in Hardy-Weinberg equilibrium, or with GenCall score <0.5)
Population substructure determined using principal component analysis and 24 genomic control SNPs
Genetic variance among cohorts (F_ST score ~0.02)

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