Genome-wide Genotyping and Imputation

Genomic and whole genome amplified DNA were genotyped on the Human-OMNI1-Quad_v1-0_B BeadChip platform (Illumina, San Diego, California). Initially, 1.2 million SNPs were tested, of which over 900,000 (91%) were successfully genotyped. We employed standard quality control thresholds, and included samples and SNPs with > 97% call rate, while excluding minor allele frequencies < 1%. Additionally, 7.2 million SNPs were imputed against the HapMap 3 cosmopolitan reference panel with Impute2.^{20 (link)} All SNP-gene assignments were made based on the UCSC gene tracks within the GRCh37/hg19 genome build.^{22 23 (link)} Genotypes, and a subset of subject information inclusive of key characteristic and outcome phenotype data have been stored, with no identifying links, in the National Human Genome Research Institute Database of Genotypes and Phenotypes (dbGaP Study Accession: phs000353.v1.p1).^{19 20 (link)}.

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Srinivasan L., Page G., Kirpalani H., Murray J.C., Das A., Higgins R.D., Carlo W.A., Bell E.F., Goldberg R.N., Schibler K., Sood B.G., Stevenson D.K., Stoll B.J., Van Meurs K.P., Johnson K.J., Levy J., McDonald S.A., Zaterka-Baxter K.M., Kennedy K.A., Sánchez P.J., Duara S., Walsh M.C., Shankaran S., Wynn J.L, & Cotten C.M. (2017). Genome Wide Association Study of Sepsis in Extremely Premature Infants. Archives of disease in childhood. Fetal and neonatal edition, 102(5), F439-F445.

Publication 2017

Human-OMNI1-Quad_v1-0_B BeadChip

Gene Genome Genotypes Hapmap Human Phenotypes

Corresponding Organization :

Other organizations : Children's Hospital of Philadelphia, University of Pennsylvania, RTI International, University of Iowa, National Institutes of Health, University of Alabama at Birmingham, Duke University, University of Cincinnati, Wayne State University, Lucile Packard Children's Hospital, Stanford University, Children's Healthcare of Atlanta, Emory University, The University of Texas Southwestern Medical Center, University of Miami, Case Western Reserve University, University of Florida

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Variable analysis

independent variables

Genomic and whole genome amplified DNA

dependent variables

Genotypes
Subject information inclusive of key characteristic and outcome phenotype data

control variables

Samples and SNPs with > 97% call rate
Minor allele frequencies > 1%

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