Baseline: Assessment ⏵ Genomics
Description
This category contains information on genetic data available from baseline samples.Data available to researchers worldwide includes:
Genome-wide genotyping with the Illumina Global Screening Array (GSA) version 2 (see Publication 22)
- Non-filtered dataset (140,831 participants) - 650,381 variants: 619,501 autosomal variants; 30,101 sex chromosome variants; 779 mitochondrial variants.
- Quality controlled dataset (138,511 participants) - 559,923 variants: 539,315 autosomal variants; 19,954 sex chromosome variants; 654 mitochondrial variants.
TOPMed Imputed (see Publication 22)
- Non-filtered dataset (140,831 participants) - 307,624,124 variants: 292,293,083 autosomal variants; 15,331,041 chromosome X variants.
Genetic Risk Score Instruments
Further detail is provided in Category 26.
- Type 2 Diabetes (see Publication 27 and Category 28)
- Adiposity (see Publication 30 and Category 29)
- Blood Pressure (see Publication 28 and Category 30)
- Coronary heart disease (see Publication 29 and Category 31)
Genetic Derived Variables
Further detail is provided in Category 27.
- Genomic ancestry (see Category 32)
- Relatedness (see Category 33)
- Genetic principal components (see Category 34)
Linkage Disequilibrium Scores (see https://www.medrxiv.org/content/10.64898/2026.06.23.26356360v1)
- Covariate-adjusted linkage disequilibrium (LD) scores for 18.8 million variants (MAF >= 0.1%) estimated from whole-genome sequence data in 9,764 MCPS participants using cov-LDSC.
Whole Exome Sequencing (WES) (see Publication 22)
- Non-filtered dataset (141,046 participants) - 13,331,228 variants: 12,957,291 autosomal variants; 368,300 chromosome X variants; 5,637 chromosome Y variants.
Whole Genome Sequencing (WGS) (see Publication 22)
- Non-filtered dataset (9950 participants) - 158,464,363 variants: 151,639,445 autosomal variants; 6,342,270 chromosome X variants; 482,648 chromosome Y variants.
Phased WGS Imputation Reference Panel (MCPS10k) (see Publication 22)
- 9,948 whole genome sequenced phased samples - 134,337,444 variants distributed across 22 autosomes and chromosome X. Data available in four file formats.