The studies employed SNP arrays available from Illumina or Affymetrix. Using available imputation techniques, each cohort imputed approximately > 37 million variants from 1000 Genomes reference panel (phase 1 version 3) and applied strict quality control checks. Further information on the genotyping and imputation methods is detailed in Supplementary Material, Table S3.Exonic and non-exonic variants were genotyped using the Illumina Infinium HumanExome BeadChip kit. The array covers > 240 000 markers, mostly coding variants discovered through exome sequencing in approximately 12 000 individuals and observed at least three times across at least two existing sequence datasets, and includes nonsynonymous, splicing, stop-altering variants, most of which are rare (http://genome.sph.umich.edu/wiki/Exome_Chip_Design). In order to ensure the accurate identification of variants and to minimize population stratification, exome array data quality control was performed based on Best Practices and Joint Calling of the HumanExome BeadChip: The CHARGE Consortium (61 (link)). Further details on methods employed by each study are outlined in supplementary information.
Portilla-Fernandez E., Klarin D., Hwang S.J., Biggs M.L., Bis J.C., Weiss S., Rospleszcz S., Natarajan P., Hoffmann U., Rogers I.S., Truong Q.A., Völker U., Dörr M., Bülow R., Criqui M.H., Allison M., Ganesh S.K., Yao J., Waldenberger M., Bamberg F., Rice K.M., Essers J., Kapteijn D.M., van der Laan S.W., de Knegt R.J., Ghanbari M., Felix J.F., Ikram M.A., Kavousi M., Uitterlinden A.G., Roks A.J., Danser A.H., Tsao P.S., Damrauer S.M., Guo X., Rotter J.I., Psaty B.M., Kathiresan S., Völzke H., Peters A., Johnson C., Strauch K., Meitinger T., O’Donnell C.J, & Dehghan A. (2022). Genetic and clinical determinants of abdominal aortic diameter: genome-wide association studies, exome array data and Mendelian randomization study. Human Molecular Genetics, 31(20), 3566-3579.
Corresponding Organization : Imperial College London
Other organizations :
Erasmus MC, Massachusetts General Hospital, Harvard University, Broad Institute, Office of Extramural Research, Framingham Heart Study, National Heart Lung and Blood Institute, University of Washington, Universitätsmedizin Greifswald, German Centre for Cardiovascular Research, Helmholtz Zentrum München, Brigham and Women's Hospital, Stanford University, Cornell University, University of California, San Diego, University of Michigan–Ann Arbor, UCLA Medical Center, Harbor–UCLA Medical Center, University of Freiburg, University Medical Center Utrecht, Utrecht University, University of Pennsylvania, Philadelphia VA Medical Center, Ludwig-Maximilians-Universität München, Heinrich Heine University Düsseldorf, Deutsches Diabetes-Zentrum e.V., German Center for Diabetes Research, Johannes Gutenberg University Mainz, University Medical Center of the Johannes Gutenberg University Mainz, Technical University of Munich, VA Boston Healthcare System
Imputation techniques used to impute approximately > 37 million variants from 1000 Genomes reference panel (phase 1 version 3)
Exonic and non-exonic variants genotyped using the Illumina Infinium HumanExome BeadChip kit
dependent variables
Not explicitly mentioned
control variables
Quality control checks applied to ensure accurate identification of variants and minimize population stratification
Best Practices and Joint Calling of the HumanExome BeadChip: The CHARGE Consortium employed to ensure data quality control
positive controls
Not explicitly mentioned
negative controls
Not explicitly mentioned
Annotations
Based on most similar protocols
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