Humanhap550

A total of 9,912 ALSPAC children were genotyped using the Illumina HumanHap550 quad genome-wide SNP genotyping platform. Individuals were excluded from further analysis based on having incorrect gender assignments; minimal or excessive heterozygosity (0.345 for the Sanger data and 0.330 for the LabCorp data); disproportionate levels of individual missingness (>3%); evidence of cryptic relatedness (>10% IBD) and being of non-European ancestry (as detected by a multidimensional scaling analysis seeded with HapMap 2 individuals). The resulting post-quality control dataset contained 8,237 individuals. The post-quality control ALSPAC children were combined with the ALSPAC mothers cohort (described in detail previously [44 (link)]) and imputed together using a subset of markers common to both the mothers and the children. The combined sample was pre-phased using ShapeIT (v2.r644) [45 ] and imputed to the 1000 Genomes reference panel (Phase 1, Version3) [46 (link)] using IMPUTE3 V2.2.2 [47 (link)]. After removing SNPs with MAF (<0.1) and INFO (<0.8), genotype data were available for 8,099,747 SNPs.

Patients’ DNA was extracted from whole blood using a Maxwell 16 PROMEGA® extractor (Promega France, Charbonnières-les-Bains, France). Purity assessment followed the procedures described by the Centre National de Recherche en Génomique Humaine, estimated on a NanoDrop® spectrophotometer. Participants were genotyped using the Infinium PsychArray (PsychArray.html">https://www.illumina.com/products/by-type/microarray-kits/infinium-PsychArray.html). Samples were processed in two stages (2014 and 2017) by Integragen SA® (Evry, France) and genotype files were merged for this study, keeping variants common to both extractions.
Controls’ DNA was extracted and analyzed according to the Wellcome Trust Case-Control Consortium standards. Genotyping was performed with the humanhap550 array (Illumina, San Diego, CA, USA; humanhap550-quad_plus_dna_analysis_kit.html">https://support.illumina.com/array/array_kits/humanhap550-quad_plus_dna_analysis_kit.html).

For replication, we used, as detailed previously [2 (link)], data from TCGA and IARC. Briefly, the TCGA RCC clear cell cases (KIRC study, accession number phs000178.v7.p6) were genotyped using the Affymetrix Genome-Wide Human SNP Array 6.0. For controls we made use of data on healthy individuals from the CGEMS breast and prostate cancer study, genotyped using Illumina HumanHap550 and Phase 1A HumanHap300+Phase 1BHumanHap240 Beadchips respectively. Both cases and controls were formally examined for an overlap with the NCI GWAS samples. Any TCGA or CGEMS sample found to be a duplicate of or related to a sample from the NCI GWAS was removed from the replication dataset. After further checking for relatedness and European ancestry 383 cases and 2,189 controls constituted the TCGA/CGEMS replication series. The International Agency for Research on Cancer (IARC) GWAS consisted of 2,461 RCC cases (including 1,340 CCCs, 95 PCs, 88 other histological subtypes) and 5,081 controls of European background from eight European studies) and has previously been described [7 (link)]. Genotyping of cases and controls was performed using either Illumina HumanHap300, 550 or 610 Quad Beadchips. Data derived from the three arrays were imputed to recover rs3845536 genotype.

ALSPAC children were genotyped using the Illumina HumanHap550 quad chip genotyping platforms (Supplemental Methods). After quality control, 8237 children and 477,482 directly genotyped SNPs were kept within the study.

The 77 SNPs used to compute the PRS [6 ] were genotyped for the eight studies either as part of a GWAS (Illumina, Human Hap550) [34 (link)] or on a custom Illumina iSelect genotyping array comprising 211,155 SNPs (iCOGS, described in [1 (link)]). Quality control was conducted at the study level, as previously described [1 (link), 35 ]; call rates were > 95% for all SNPs. Thus, 77 SNPs associated with breast cancer and their published odds ratios were used to form the PRS.