Protocol detail

Germline DNA Genotyping and Imputation

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Details of sample collection, genotyping, quality control (QC) and imputation have been reported elsewhere (Schmit et al., 2018 (link)). In brief, genotype data was generated from germline DNA on the Affymetrix Axiom, Illumina 1M/1M-Duo, Omni1 and OncoArray. Standard QC filters were applied to the high-density genotype array data at both the individual participant and SNP levels. Quality-controlled genotype data was imputed to the 1,000 Genomes Project (1KGP) Phase 1 multiethnic reference panel (March 2012 release, N=1,092) using SHAPE-IT/IMPUTE2 (Affymetrix Axiom; Illumina 1M/1M-Duo, and Omni1) (Eyre et al., 2012 (link); Howie, Donnelly, & Marchini, 2009 (link)) or the 1KGP Phase 3 reference panel (Illumina OncoArray) (Amos et al., 2017 (link)). Imputation quality (info score> 0.3) and minor allele frequency filters (MAF ≥ 1%) were imposed on variants prior to the analysis phase. Approximately 44.4% (N=794) of the participants were run on Illumina 1M/1M-Duo while 12.1% (N=217) were on Illumina OncoArray; Affymetrix Axiom and Illumina Omni1 contributed similar proportions (20.5% (N=366) and 23.0% (N=411), respectively).

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Wang J., Asante I., Baron J.A., Figueiredo J.C., Haile R., Levine A.J., Newcomb P.A., Templeton A.S., Schumacher F.R., Louie S.G., Casey G, & Conti D.V. (2019). Genome-wide association study of circulating folate one-carbon metabolites. Genetic epidemiology, 43(8), 1030-1045.

Publication 2019

Axiom Illumina 1M/1M-Duo Omni1

Genomes Genotype Germline Sample collection

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Variable analysis

independent variables

Not explicitly mentioned

dependent variables

Not explicitly mentioned

control variables

Standard QC filters were applied to the high-density genotype array data at both the individual participant and SNP levels.
Imputation quality (info score> 0.3) and minor allele frequency filters (MAF ≥ 1%) were imposed on variants prior to the analysis phase.

positive controls

Not specified

negative controls

Not specified

Annotations

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