Fig. 1: Quality control pipeline for genomic analyses.
From: The genetic architecture of cervical length is shared with spontaneous preterm birth risk
Purified genomic DNA from 5023 patients with available samples were sent for low-pass whole-genome sequencing. Approximately 9.8 million single-nucleotide polymorphisms (SNPs) remained after variant level filtering for genotyping rate (geno <0.05), minor allele frequency (MAF < 0.01), and deviation from Hardy-Weinberg equilibrium (HWE < 0.000001). Samples from 4423 women remained after excluding samples for poor nucleic acid quality (n = 2), missing data (n = 15), duplicates (n = 80), and population stratification (n = 243).
