Genetic and Omic Data in WHI

Genetic Data

All genetic studies funded by NIH are now required to deposit the GWAS data into dbGaP. Please refer to the dbGaP website for detailed information on what WHI datasets are currently available, instructions on how to access and download data, searchable FAQs, and dbGaP contact information.

Included in the WHI Investigators' data is a file indicating which participants have genetic data on dbGaP (see the dbGaP Data Dictionary). For genetic data that are not yet available on dbGaP, or for very limited genetic datasets, data may be available from the WHI Clinical Coordinating Center (CCC) as detailed in our policy for accessing WHI genetic data.

GWAS Data on WHI Participants

GWAS has been performed through many WHI ancillary studies with different platforms and different outcomes/exposures of interest. Raw GWAS data from over 42,000 WHI participants is currently available from dbGap.

This is a list of all GWAS that include at least 1,000 WHI participants. Clicking on the study titles will take you to the appropriate page of the dbGaP website.

Study Platform Study Design Ethnicity Total N after QC
Hip Fracture (BA03) Illumina 550K and 610K ​Hip fracture case-control Mostly white 3,690
SHARE (M5) Affymetrix 6.0​ Cohort, minorities Black and Hispanic​ 11,992​
GARNET (M13) Illumina HumanOmni1-Quad v1-0 B Case-control (diabetes, myocardial infarction, stroke, VTE), from hormone therapy trials Mostly White ​4,880
WHIMS+ (W63) HumanOmniExpressExome 8v1_B Cohort, selected from hormone therapy trials White 5,687
​GECCO (AS224) ​Illumina 610 and Cytochip 370K ​Colorectal case-control White and Black​ ​2,493
MOPMAP (AS264) Affymetrix Gene Titan, Axiom Genome-Wide Human CEU I Ventricular ectopy cases and controls selected within Centers, seasons, and visit years of cases White ​3,069
PAGE II (AS349) Illumina MEGA array ​Cohort, minorities Minorities, mostly black and hispanic ​12,439
Oncochip (M18) ​Illumina Oncochip ​Breast cancer cases and controls White 9,553
LLS GWAS (W66) ​Illumina Omin Express/Exome Cohort White, Black, Hispanic 1,446
Note, there is overlap between these GWAS studies, the total sample size is currently ~42,000.

WHI Sequencing Studies

​Study Name (ID) Study Population (synopsis)​ ​Assays
​WHISP (M24)

​N~2,230

​Exome sequencing

TOPMed (AS564) ​N~11,000 VTE, stroke, and controls Whole genome sequencing

*We also have WHI participants genotyped on a variety of other (older) high density arrays, including the MetaboChip, ExomeChip, and CytoChip. Contact the helpdesk if you're interested in this..

Genetic and Omic data

Omic measurements have been performed for various different omic technologies through many WHI ancillary studies with different platforms and different outcomes/exposures of interest. As opposed to genetic studies, for most omic studies there is currently not an NIH requirement to submit the data to dbGaP, though some of the data is on dbGaP anyway (those are linked below under the AS number).

As the details for the processing of each of these omic technologies is different, and also because some of the AS that facilitated these omic measurements were fairly recent, investigators are strongly encouraged to contact the PIs of the AS before submitting paper proposals using this data. For approved proposals the data for these omics studies is available from the WHI Clinical Coordinating Center (CCC) as detailed in our policy for accessing WHI genetic data.

Omic type Study PI Platform Study design Ethnicity Timepoint Total N after QC
MethylationAS311Parveen BhattiInfinium HumanMethylation450Bladder Cancer Cases and ControlsMixedBaseline882
MethylationAS315Eric WhitselInfinium HumanMethylation450CohortHalf white, half minoritiesBaseline2400
MethylationBA23Tim AssimesInfinium HumanMethylation450CVD cases and controlsHalf white, half minoritiesBaseline2151
MethylationAS564 (TOPMed)Charles KooperbergInfinium MethylationEPICCohortMixedLLS1336
MetabolomicsBA24Katherine RexrodeBroad Metabolomics PlatformCHD cases and controlsMixedMostly baseline2129
MetabolomicsAS564 (TOPMed)Charles KooperbergBroad Metabolomics PlatformCohortMixedLLS1336
RNA seqAS564 (TOPMed)Charles Kooperberg CohortMixedLLS1335
ProteomicsAS576Alex ReinerOLINK (6 panels)CohortMixedLLS1336

Limitations on Use in Public Datasets

Summary data may be used for all participants. However, not all participant samples may be used in studies that plan to deposit genetic data into public datasets such as dbGaP or BioLINCC. All genetic studies funded by NIH are now required to deposit the GWAS data into dbGaP. Restrictions apply based on whether the participant signed the WHI Supplemental Use Consent Form - see table below. A participant who previously signed the Supplemental Use Consent and later declines to have her DNA used, will be moved to the Refused category.

​Supplemental Use Consent form ​ ​ ​Post Individual Data on Public Website
​Non-Commercial Use Commercial Use​
​Participant Signed (72.7%) Yes Yes​
​Participant did not respond (8.6%) or died before able to sign (7.2%) ​Yes ​No
​Participant refused to sign (11.4%)
​No ​No