All genotyping specifications for the PCOS cohorts have been described earlier in a large genome-wide association study (GWAS) meta-analysis in PCOS patients (Day et al., 2018 (link)). Samples used in this study were selected from the Rotterdam PCOS cohort based on the presence of AMH levels measured by the picoAMH assay [Ansh Labs®, Webster, TX, USA] (Day et al., 2018 (link)). All two-allelic SNPs in the region Chr19:2 245 353–2 250 827 bp (Build 37, hg19) were selected. This region covers 3969 bp of the human AMH promoter and 1505 bp downstream of the protein coding region of AMH, covering the first three exons of the AMH protein. Only SNPs with a minor allele frequency (MAF) >1% and imputation quality (r2) >0.75 were included for the analysis. The quality control check analysis was described previously (Day et al., 2018 (link)). Linkage disequilibrium (LD) between SNPs was calculated using the Ensembl library 1000GENOMES:phase_3:CEU (Zerbino et al., 2018 (link)).
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PCOS Cohort Genotyping Analysis
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Corresponding Organization : Erasmus MC
Other organizations : University Medical Center Utrecht, Utrecht University, Northwestern University, Icahn School of Medicine at Mount Sinai
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Variable analysis
independent variables
- SNPs in the region Chr19:2 245 353–2 250 827 bp (Build 37, hg19) with a minor allele frequency (MAF) >1% and imputation quality (r^2) >0.75
- AMH levels measured by the picoAMH assay
- Samples selected from the Rotterdam PCOS cohort
- No positive or negative controls were explicitly mentioned.
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