Quality Control Analysis of Add Health GWAS Data Public Deposited

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  • Avery, Christy
    • Affiliation: Carolina Population Center
  • Highland, Heather M.
    • ORCID: https://orcid.org/0000-0002-3583-8239 X
    • Affiliation: Carolina Population Center
  • Harris, Kathleen Mullan
    • Affiliation: Carolina Population Center
  • Duan, Qing
    • Affiliation: Carolina Population Center
  • Li, Yun
    • Affiliation: Carolina Population Center
  • At Wave IV, Add Health collected Oragene saliva samples from consenting participants (96% of n=15,701), and requested a second consent to archive their samples for future genomic studies. Approximately 80% consented to archive and were thus eligible for genome-wide genotyping. Genotyping was completed over three years funded by R01 HD073342 (PI Harris) and R01 HD060726 (PIs Harris, Boardman, and McQueen). Add Health utilized two Illumina platforms for genotyping: the Illumina Human Omni1-Quad BeadChip for the majority of samples and the Illumina Human Omni-2.5 Quad BeadChip for the remainder. The two platforms utilized tag SNP technology to identify and include over 1.1 million and 2.5 million genetic markers respectively from Omni1 and Omni2.5 derived from the International HapMap Project and the most informative markers from the 1000 Genomes Project (1KGP). The genetic markers include known disease-associated SNPs from multiple sources, ancestry-informative markers, sex chromosomes, and ABO blood typing markers. The platforms also included probes for the detection of copy number variation (CNV) covering all common CNV regions and more than 5,000 rare CNV regions. After quality control procedures (described below), genotype data were available for 9,974 individuals: n=7,917 from the Illumina HumanOmni1-Quad chip and for 2,057 individuals from the Illumina HumanOmni2.5-Quad chip (Figure 1). After filtering, the Add Health genotype GWAS data contained n=609,130 single-nucleotide polymorphisms (SNPs) common to both chips to enable joint imputation to the entire Add Health population (see below).
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  • English
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  • National Longitudinal Study of Adolescent to Adult Health (Add Health)
  • 18 pp

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