Exome Array Genotyping of Lung Function

All 3487 cases and 1032 GS:SFHS controls were genotyped together using the Illumina Human Exome BeadChip with additional custom content for regions which have previously shown modest association with lung function (description of custom content design in online supplementary methods). The remaining discovery analyses control samples were genotyped separately using the Illumina Human Exome BeadChip.
The UK BiLEVE samples were genotyped using the Affymetrix UK BiLEVE array, which includes rare variants selected from the same sequencing project as the Illumina Human Exome BeadChip alongside additional content.16 (link) Of the 807 411 SNPs included on the Affymetrix UK BiLEVE array, 74 891 were also present on the Illumina Human Exome BeadChip; this subset of SNPs, which were directly genotyped on both arrays, was selected for the discovery meta-analysis.

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Jackson V.E., Ntalla I., Sayers I., Morris R., Whincup P., Casas J.P., Amuzu A., Choi M., Dale C., Kumari M., Engmann J., Kalsheker N., Chappell S., Guetta-Baranes T., McKeever T.M., Palmer C.N., Tavendale R., Holloway J.W., Sayer A.A., Dennison E.M., Cooper C., Bafadhel M., Barker B., Brightling C., Bolton C.E., John M.E., Parker S.G., Moffat M.F., Wardlaw A.J., Connolly M.J., Porteous D.J., Smith B.H., Padmanabhan S., Hocking L., Stirrups K.E., Deloukas P., Strachan D.P., Hall I.P., Tobin M.D, & Wain L.V. (2016). Exome-wide analysis of rare coding variation identifies novel associations with COPD and airflow limitation in MOCS3, IFIT3 and SERPINA12. Thorax, 71(6), 501-509.

Publication 2016

Human Exome BeadChip UK BiLEVE array

Exome Human Lung function Snps

Corresponding Organization : University of Leicester

Other organizations : William Harvey Research Institute, Queen Mary University of London, Queen's Medical Centre, University of Nottingham, University of Bristol, University College London, St George's, University of London, Cochrane, Farr Institute, London School of Hygiene & Tropical Medicine, University of Essex, Nottingham City Hospital, University of Dundee, Southampton General Hospital, University of Southampton, University Hospital Southampton NHS Foundation Trust, NIHR Southampton Respiratory Biomedical Research Unit, NIHR Southampton Biomedical Research Centre, MRC Lifecourse Epidemiology Unit, Victoria University of Wellington, University of Oxford, National Institute for Health Research, Glenfield Hospital, Newcastle Hospitals - Campus for Ageing and Vitality, Newcastle University, Imperial College London, University of Auckland, Edinburgh Cancer Research, University of Glasgow, University of Aberdeen, University of Cambridge, King Abdulaziz University

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Variable analysis

independent variables

Genotyping platform: Illumina Human Exome BeadChip with additional custom content, Affymetrix UK BiLEVE array

dependent variables

Not explicitly mentioned

control variables

Genotyping platform: Illumina Human Exome BeadChip used for all 3487 cases and 1032 GS:SFHS controls, Affymetrix UK BiLEVE array used for UK BiLEVE samples
Subset of 74,891 SNPs directly genotyped on both the Illumina Human Exome BeadChip and Affymetrix UK BiLEVE array were selected for the discovery meta-analysis

controls

Positive control: Not mentioned
Negative control: Not mentioned

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