In BREATH and PAGES, genotypes were determined by using Taqman-based allelic discrimination assays on an ABI 7,700 sequence detection system (Applied Biosystems, Foster City, Calif)4 (link),27 (link) In followMAGICS, samples were genotyped using Illumina Sentrix HumanHap300 BeadChip array (Illumina, Inc.)15 (link) In both GALA II and SAGE, samples were genotyped using the Axiom® LAT1 array (Affymetrix Inc.), and quality control (QC) procedures were performed as described previously.28 (link),29 (link) In PACMAN and ESTATe, samples were genotyped using the Illumina Infinium CoreExome-24 BeadChip (Illumina, Inc.).30 In PASS, genotyping was performed using the Illumina Omni Express 8v1 array (Illumina, Inc.). QC procedures and imputation are described elsewhere.22 (link) In SCSGES, genotyping was conducted using Kompetitive Allele Specific PCR (KASP) genotyping platform (LGC, Inc). QC was performed based on the quality of clustering.23 (link) In the SLOVENIA study, genotyping of 336 samples was performed with the Illumina Global Screening Array-24 v1.0 BeadChip (Illumina). QC procedures and imputation described elsewhere.30
Protocol detail
Genotyping Methods Across Asthma Studies
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ABI 7,700 sequence detection system
Axiom® LAT1 array
Infinium CoreExome-24 BeadChip
KASP) genotyping platform
Allele
Assays
Discrimination
Gala
Corresponding Organization : Ghent University
Other organizations : Amsterdam University Medical Centers, University of Amsterdam, Utrecht University, Universidad de La Laguna, Royal Alexandra Children's Hospital, Brighton and Sussex Medical School, Instituto de Salud Carlos III, University of Liverpool, University of California, San Francisco, Medizinische Hochschule Hannover, National University of Singapore, University of Maribor, Alder Hey Children's Hospital, University of Dundee, Ninewells Hospital, University of Aberdeen, Erasmus MC - Sophia Children’s Hospital
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Variable analysis
independent variables
- Genotyping method (Taqman-based allelic discrimination assays, Illumina Sentrix HumanHap300 BeadChip array, Axiom® LAT1 array, Illumina Infinium CoreExome-24 BeadChip, Illumina Omni Express 8v1 array, Kompetitive Allele Specific PCR (KASP) genotyping platform, Illumina Global Screening Array-24 v1.0 BeadChip)
- Genotypes
- Quality control (QC) procedures
- Positive and negative controls not explicitly mentioned
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