Omni genotyping arrays

N85+ participants were genotyped at the age of 85 years using Illumina Omni genotyping arrays. The details of the QC carried out on the genetic data from the N85+ study are available in Deelen et al. (13 (link)). In addition to this QC, all variants with an INFO score of <0.8 were excluded.
In the UKB, 488 377 individuals were genotyped for up to 812 428 variants using DNA extracted from blood samples on either the UK Biobank Axiom array (438 427 participants) or the UK BiLEVE Axiom array (49 950 participants). Variant quality control metrics were provided by UKB as described previously (14 (link)). Samples that did not have genetically determined White British ancestry were excluded. A list of related individuals was provided by UK Biobank and one individual from each related pair was excluded at random. For imputed variants, all variants with an INFO score of <0.8 were excluded.
The KL gene is located at 13:33590571-33640282 (GRCh37.p13) and 214 variants passed QC within ±5 Kb of KL. These were selected for our analyses. Out of the 214 variants that were available for analyses in the UKB, 195 were available in the N85+ study after the aforementioned QC filters (see previous paragraph) were applied.

The Genotype-Tissue Expression (GTEx) dataset was previously described.⁵⁶ (link) We accessed this dataset through NCBI dbGaP (the Database of Genotypes and Phenotypes), deposited under the accession code phs000424.v7.p2 (approved access #82151, May/2020). For SNV analyses, we used high-coverage (30X) Illumina WGS data of n = 652 unrelated individuals in the GTEx dataset. This cohort consisted of n = 561 individuals with self-reported European ancestry, n = 75 of African ancestry, and n = 8, n = 3 and n = 5 of Asian, Amerindian, and unknown ancestry, respectively. For each sample, we downloaded a VCF file containing genotype calls relative to the GRCh37/hg19 reference genome. For haplotype analyses, we used the data of n = 355 individuals, which corresponds to those with NFE ancestry (see “Ancestry admixture analysis” in Method details) and phasing information available. Phased genotypes from GTEx samples (obtained using Illumina Omni genotyping arrays) were downloaded from the accession code phs000424.v7.p2.⁵⁶ (link)