DENSE GENOTYPIC DATA
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, 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. 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.
|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)||9,974||dbGaP Data Use Agreement|
|2||1,886||Add Health Restricted-Use Data Contract|
|3||1,886||Add Health Restricted-Use Data Contract|
|53||9,129||Add Health Restricted-Use Data Contract|
|23||5,690||Add Health Restricted-Use Data Contract|
|24||2,574||Add Health Restricted-Use Data Contract|
|30||15,701||Add Health Restricted-Use Data Contract|
How to access data
Questions about the Add Health OMICS data?
Post them on Biostars with the “addhealthomics” tag so that other data users or one of our team members can answer questions as they arise.
Click here to access Biostars: https://www.biostars.org/t/addhealthomics/
Add Health GWAS Acknowledgement:
Add Health GWAS data were funded by Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) Grants R01 HD073342 (Harris) and R01 HD060726 (Harris, Boardman, and McQueen). Investigators thank the staff and participants of the Add Health Study for their important contributions.
When GWAS data are combined with Add Health phenotype data, use this acknowledgement:
This research uses data from Add Health, a program project directed by Kathleen Mullan Harris and designed by J. Richard Udry, Peter S. Bearman, and Kathleen Mullan Harris at the University of North Carolina at Chapel Hill, and funded by grant P01 HD31921 from Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), with cooperative funding from 23 other federal agencies and foundations. Add Health GWAS data were funded by NICHD Grants R01 HD073342 (Harris) and R01 HD060726 (Harris, Boardman, and McQueen). Investigators thank the staff and participants of the Add Health Study for their important contributions.