Blood and urine samples collected from WHI participants at the outset of WHI and at various timepoints throughout the study are available for use by Ancillary and Broad Agency Announcement (BAA) Studies based on scientific merit. These samples are maintained in a biorepository in Rockville, MD, under highly controlled conditions. The inventory of samples is tracked via a WHI Specimen Tracking database, which allows for good prediction of sample availability and status. The Specimen Tracking database also stores variables associated with the blood draw, such as number of fasting hours prior to blood draw and number of freeze/thaw cycles.
Useful Biospecimen Links
Baseline: All Clinical Trial (CT) and Observational Study (OS) participants
Year 1: CT participants
Year 6: the same 6% CT subsample*
Year 9: the same 6% CT subsample*
Year ~18: WHI Long Life Study participants (N~8,000; collected between 2/2012 and 2/2013)
*Buffy coat (DNA) was not collected for the 6% CT subsample at Years 3,6, and 9
Collected from participants at the 3 WHI Field Centers specializing in Bone Mineral Density
Baseline: All CT and OS participants
Year 1: CT participants
Year 3: CT and OS participants
Year 6: CT participants; first 25% of the OS participants recruited
Year 9: CT subsample
Types of Biospecimen Available
Serum, Plasma, Red Blood Cells, and Urine:
DNA: DNA has been extracted from a buffy coat sample for nearly all Hormone Trial participants and for many Observational Study participants with a primary WHI outcome. By April 2013, the WHI Long Life Study participants will have extracted DNA available from the buffy coat collected in 2012-2013.
· DNA Extraction methods: DNA was extracted from buffy coat samples using the methods below. The current ‘Five Prime’ extraction method was developed by the FHCRC using Qiagen reagents in a method designed to maximize both the quality and yield of extracted DNA. DNA extracted using this method has performed very well in a variety of genotyping, telomere, and DNA methylation assays. An AS may receive a mix of DNA extracted by these different methods, as well as DNA from samples that still need to be extracted. Extraction method is tracked in the WHI Specimen Tracking System.
o 2000 – 2003 Qiagen/Bioserve
o 2004 – 2005 Salt-precipitation
o 2005 – 2007 Phenol Chloroform
o 2007 to present Qiagen/ Five Prime
· DNA concentration assessment: Before July 2007, the concentration of DNA was assessed using the 260/280 OD ratio. Beginning in August, 2007, DNA concentration was assessed using picogreen. Concentration assessment method is tracked in the WHI Specimen Tracking System.
· DNA plating: Plating of DNA is available through the WHI CCC at an extra cost to investigators. It is preferred that investigators make arrangements for their labs to plate the DNA.
Limits on Biological Samples Available for Ancillary and BAA Studies
Without significant scientific justification, Ancillary and BAA Study proposals are limited to the following sample volumes (including any necessary dead volume) from a given specimen collection timepoint:
0.25 ml serum
0.25 ml EDTA plasma
0.25 ml citrated plasma
0.25 ml red blood cells (lysed)
0.50 ml urine
1 ug DNA for SNP or candidate gene studies, 2 ug for GWAS studies
0.5 ug RNA (only available on WHI Long Life Study participants)
Buffy coat: not available
Whole blood: not available
Note that samples are available for almost all study participants, though for some outcomes particular sample types may be more limited. For BAAs, see BAA – Blood Remaining. For Ancillary Studies, for ASs, see Blood and DNA Available to AS. Parsimonious use of sample will be an important factor in a study’s technical evaluation. Whenever possible, multiplex assays should be considered.
Limitations on Use of Biospecimen Data 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; and all GWAS studies funded by NIH are required to deposit the GWAS data into dbGaP. Restrictions apply based on whether the participant signed the WHI Supplemental Use Consent Form - see the table below. For example, samples from participants who signed the Supplemental Use Consent may be used for GWAS studies for both commercial and non-commercial studies and must be sent to dbGaP for posting. A participant who previously signed the Supplemental Use Consent later declines to have her DNA use, will be moved to the Refused category.
Post Individual Data on Public Website
Ppt Signed (72.7%)
Ppt did not respond (8.6%) and/or deceased before able to sign (7.2%)
Ppt refused to sign (11.4%)
Blood Assay Quality Control
WHI includes quality control samples in all sample pulls, as follows:
· DNA Genetic Testing Quality Control: Studies requesting DNA samples are required to include quality control samples: 5% of the total number of participant samples (2.5% blind duplicate pairs). For smaller genotyping studies (e.g., candidate genes, limited SNPs), the WHI-CCC will produce a SNP concordance report that assesses the study’s (1) correct identification of the blind duplicates, (2) failure to identify the blind duplicates, and (3) any unexpected duplicates among all samples provided. For larger genotyping studies (e.g., GWAS, exome sequencing), the PI is to report to the WHI-CCC all duplicates identified. From this list, the WHI-CCC will confirm the correct/incorrect identification of the blind duplicates and any unexpected duplicates.
· Plasma, Serum, Urine, and non-genetic DNA assays Quality Control: WHI includes 10% blind duplicate QA samples (5% pairs) with all serum, plasma, red blood cell, and urine samples. For non-genetic DNA testing (e.g., telomere length, global DNA methylation), WHI includes 5% blind duplicate samples (2.5% pairs). The correlation coefficient and the average Coefficient of Variation % is computed based on the test results for these QA samples.