COPDGene Genotyping and Quality Control

COPDGene subjects were of self-reported NHW or African-American ancestry, and genotyped using the HumanOmniExpress array (Illumina) [18 (link)]. Details on the processing of the COPDGene genotype data have been reported [18 (link)]. Briefly, genotyping was performed using the HumanOmniExpress array, and BeadStudio quality control, including reclustering on project samples was performed following Illumina guidelines. Subjects and markers with a call rate of < 95% were excluded. Population stratification exclusion and adjustment on self-reported white subjects was performed using EIGENSTRAT (EIGENSOFT Version 2.0).

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Sun W., Kechris K., Jacobson S., Drummond M.B., Hawkins G.A., Yang J., Chen T.H., Quibrera P.M., Anderson W., Barr R.G., Basta P.V., Bleecker E.R., Beaty T., Casaburi R., Castaldi P., Cho M.H., Comellas A., Crapo J.D., Criner G., Demeo D., Christenson S.A., Couper D.J., Curtis J.L., Doerschuk C.M., Freeman C.M., Gouskova N.A., Han M.K., Hanania N.A., Hansel N.N., Hersh C.P., Hoffman E.A., Kaner R.J., Kanner R.E., Kleerup E.C., Lutz S., Martinez F.J., Meyers D.A., Peters S.P., Regan E.A., Rennard S.I., Scholand M.B., Silverman E.K., Woodruff P.G., O’Neal W.K, & Bowler R.P. (2016). Common Genetic Polymorphisms Influence Blood Biomarker Measurements in COPD. PLoS Genetics, 12(8), e1006011.

Publication 2016

HumanOmniExpress array

African ancestry

Corresponding Organization : University of California, San Francisco

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Variable analysis

independent variables

Self-reported NHW or African-American ancestry

dependent variables

Not explicitly mentioned

control variables

Subjects and markers with a call rate of < 95% were excluded
Population stratification exclusion and adjustment on self-reported white subjects was performed using EIGENSTRAT (EIGENSOFT Version 2.0)

positive controls

Not specified

negative controls

Not specified

Annotations

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