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.
Vachon C.M., Scott C.G., Tamimi R.M., Thompson D.J., Fasching P.A., Stone J., Southey M.C., Winham S., Lindström S., Lilyquist J., Giles G.G., Milne R.L., MacInnis R.J., Baglietto L., Li J., Czene K., Bolla M.K., Wang Q., Dennis J., Haeberle L., Eriksson M., Kraft P., Luben R., Wareham N., Olson J.E., Norman A., Polley E.C., Maskarinec G., Le Marchand L., Haiman C.A., Hopper J.L., Couch F.J., Easton D.F., Hall P., Chatterjee N, & Garcia-Closas M. (2019). Joint association of mammographic density adjusted for age and body mass index and polygenic risk score with breast cancer risk. Breast Cancer Research : BCR, 21, 68.
Corresponding Organization : Mayo Clinic in Florida
Other organizations :
Mayo Clinic, Harvard University, Brigham and Women's Hospital, University of Cambridge, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen, Curtin University, University of Western Australia, Monash Health, Monash University, University of Washington, University of Melbourne, Cancer Council Victoria, Genome Institute of Singapore, Karolinska Institutet, MRC Epidemiology Unit, Medical Research Council, University of Hawaii System, Cancer Center of Hawaii, University of Hawaiʻi at Mānoa, University of Southern California, Mayo Clinic in Arizona, National Cancer Institute
Genotyping of 77 SNPs associated with breast cancer
dependent variables
Computed Polygenic Risk Score (PRS) for breast cancer
control variables
Call rates > 95% for all 77 SNPs
Quality control conducted at the study level as previously described
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