Omics

Omics

“OMICS” – named for the suffix -omics, as in genomics – refers to the collective technologies used to explore the roles, relationships, and actions of molecules that make up the cells of an organism and includes: genomics, the study of genes and their function; proteomics, the study of proteins and their function; metabolomics, the study of molecules involved in cellular metabolism; transcriptomics, the study of RNA molecules and their regulation; and epigenomics, the study of epigenetic modifications on the genetic material of a cell. This page provides tools and resources to enable Add Health users to integrate these unprecedented technological advances into their research agendas.

DENSE GENOTYPIC DATA

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GWAS 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)9,974dbGaP Data Use Agreement

POLYGENIC SCORES

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Wave IV Genetic Risk Score* – BMI

This file contains the BMI genetic risk score* for Add Health twin and full sibling respondents who provided saliva samples at Wave IV. *Polygenic Score
21,886Add Health Restricted-Use Data Contract

Wave IV Genetic Risk Score* – Education

An education genetic risk score* (GRS_EDU) is available for Add Health twin and full sibling respondents who provided saliva samples at Wave IV. This variable is the weighted sum of risk alleles identified in the Rietveld et al. (2013) genome-wide association study. *Polygenic Score
31,886Add Health Restricted-Use Data Contract

Wave IV Polygenic Scores

Thirty constructed polygenic scores (PGS) are available for Add Health respondents who provided archival saliva samples for genetic testing at Wave IV. Scores are available for coronary artery disease, myocardial infarction, plasma cortisol, LDL cholesterol, HDL cholesterol, total cholesterol, triglycerides, type II diabetes (2 measures), BMI, waist circumference, waist-to-hip ratio, height, age at menarche, age at menopause, number of children, age at first birth, ever/current smoker, number of cigarettes per day, extraversion, attention deficit disorder (2 measures), bipolar disorder, major depressive disorder (2 measures), schizophrenia, mental health cross disorder, Alzheimer’s disease, and educational attainment (2 measures).
539,129Add Health Restricted-Use Data Contract

Wave IV Polygenic Scores – SSGAC

Polygenic scores (PGS) constructed by the Social Science Genetic Association Consortium (SSGAC) are available for Add Health respondents who provided archival saliva samples for genetic testing at Wave IV. This data file contains educational attainment, cognitive performance, depression, neuroticism, and subjective well-being scores based on standard GWAS summary statistics and multilevel analysis (2 scores for each construct). Additional multivariate analysis scores for highest level math taken and math ability are also included.
235,690Add Health Restricted-Use Data Contract

CANDIDATE GENES

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Wave III DNA Data

Twin and full siblings interviewed at Wave III were asked to provide saliva samples for DNA analysis. This file contains the genotype values for DAT1 (dopamine transporter), DRD4 (dopamine receptor), and SLC6A4 (serotonin transporter), MAOA_V (monoamine oxidase A-uVNTR), DRD2 (dopamine D2 receptor), and CYP2A6 (cytochrome P450 2A6) from these samples. Also included are values for the following SNPs: rs2304297, rs892413, rs4950, rs13280604.
242,574Add Health Restricted-Use Data Contract

Wave IV DNA Data

Contains genotyping results for all Wave IV respondents who agreed to provide a saliva sample for DNA testing. This dataset has values for DAT1 (dopamine transporter), DRD4 (dopamine receptor), MAOA (monoamine oxidase A-uVNTR), 5HTTLPR (serotonin transporter), HTTLPR La-Lg-S, and triallelic activity bins for the serotonin transporter 5HTTLPR adjusted for rs25531, DRD2, s000005, s000006, DRD5, and MAOCA1
3015,701Add Health Restricted-Use Data Contract

How to access data

Need help accessing the Add Health GWAS data? Interested in accessing a file to link genomic data to phenotype 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/

Acknowledgments

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.