Protocol detail

Genotyping and Imputation Workflow

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Details on genotyping and imputation have been reported previously(17 (link)–19 (link)). In brief, DNA was mostly obtained from blood samples, with some from buccal swabs. Several platforms, including Affymetrix 500K, Affymetrix Axiom, Illumina 1M, 1M duo, Illumina 300K, Illumina 550K, 550Kduo, 610K, Illumina OmniExpress, Illumina OmniExpressExome, Illumina Oncoarray, Illumina Oncoarray+custom iSelect, were used for genotyping(20 (link),21 (link)). Samples were excluded on the basis of sample call rate, heterozygosity, unexpected duplicates or relative pairs, gender discrepancy and principal component analysis (PCA) outliers. SNPs were excluded on the basis of inconsistency across platforms, call rate, and out of Hardy-Weinberg equilibrium (HWE) in controls(20 (link)). SNPs were imputed using Haplotype Reference Consortium (HRC version r1.0) reference panel (22 (link)), and restricted by imputation accuracy (R²>0.3 for SNPs with MAF>1%, R²>0.5 for SNPs with MAF>0.5% and <1%, and R²>0.99 for SNPs with MAF<0.05%).

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Wang X., Su Y.R., Petersen P.S., Bien S., Schmit S.L., Drew D.A., Albanes D., Berndt S.I., Brenner H., Campbell P.T., Casey G., Chang-Claude J., Gallinger S.J., Gruber S.B., Haile R.W., Harrison T.A., Hoffmeister M., Jacobs E.J., Jenkins M.A., Joshi A.D., Li L., Lin Y., Lindor N.M., Marchand L.L., Martin V., Milne R., Maclnnis R., Moreno V., Nan H., Newcomb P.A., Potter J.D., Rennert G., Rennert H., Slattery M.L., Thibodeau S.N., Weinstein S.J., Woods M.O., Chan A.T., White E., Hsu L, & Peters U. (2020). Exploratory genome-wide interaction analysis of non-steroidal anti-inflammatory drugs and predicted gene expression on colorectal cancer risk. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 29(9), 1800-1808.

Publication 2020

Axiom 1M duo 550Kduo OmniExpress OmniExpressExome Oncoarray

Blood Haplotype Heterozygosity Snps Some

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Variable analysis

independent variables

Genotyping platforms used (Affymetrix 500K, Affymetrix Axiom, Illumina 1M, 1M duo, Illumina 300K, Illumina 550K, 550Kduo, 610K, Illumina OmniExpress, Illumina OmniExpressExome, Illumina Oncoarray, Illumina Oncoarray+custom iSelect)
Imputation using Haplotype Reference Consortium (HRC version r1.0) reference panel

dependent variables

Not explicitly mentioned

control variables

Sample call rate
Heterozygosity
Unexpected duplicates or relative pairs
Gender discrepancy
Principal component analysis (PCA) outliers
Inconsistency across platforms
Call rate
Out of Hardy-Weinberg equilibrium (HWE) in controls
Imputation accuracy (R^2>0.3 for SNPs with MAF>1%, R^2>0.5 for SNPs with MAF>0.5% and <1%, and R^2>0.99 for SNPs with MAF<0.05%)

controls

Not specified
Not specified

Annotations

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