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​​​​​Specimens Available for Ancillary Studies

All biospecimens collected from WHI participants are available for use by Ancillary Studies (ASs) based on scientific merit. To access WHI biospecimens, investigators must have an approved and funded ancillary study. WHI Ancillary Studies Overview summarizes applying for an AS. 

Types of Specimen Available

Serum, Plasma, Red Blood Cells, and Urine

DNA 

​Buffy coat is stored frozen and DNA is extracted from stored buffy coat when it is requested for an ancillary study. DNA has been extracted for nearly all Hormone Trial, African American, and Hispanic participants, and all Long Life Study participants.

  • DNA Extraction methods: DNA was extracted using the methods below. The current ‘Five Prime’ extraction method was developed by 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 well in a variety of genotyping, telomere, and DNA methylation assays. An AS may receive a mix of DNA extracted by different methods, as well as DNA from samples that still need to be extracted. Extraction method is tracked in the WHI Specimen database. Please note that DNA is extracted on an "as needed" basis so the date of extraction does not correlate with the date of the blood draw.

    • 2000 – 2003 Qiagen/Bioserve

    • 2004 – 2005 Salt-precipitation

    • 2005 – 2007 Phenol Chloroform

    • 2007 to present Qiagen/Five Prime

  • DNA concentration assessment: Before July 2007, DNA concentration was assessed using spectrophotometry. Beginning in August 2007, DNA concentration was assessed using picogreen. Concentration method is tracked.

  • DNA plating: Plating of DNA is available thr​​ough the WHI CCC at an extra cost to investigators. It is preferred that investigators make arrangements for their labs to plate the DNA.

Note that NIH has limits on use of DNA for GWAS studies. See Specimen data available​, #5. Limitations on Use of Biospecimen Data in Public Datasets.​

RNA 

Refer to WHI Long Life Study – Synopsis of Blood Protocol


Number and volume of specimens available

To see the current number of samples available for specific outcomes and other criteria, use the WHI Query Builder, a website that lets users create ad-hoc queries that return the number of WHI participants with various criteria. It uses the same data used to create the dataset files and is designed to aid investigators researching ancillary study or paper proposals. 

Keep in mind that:

  • the number of participants with blood collections at each subsequent blood draw decreases due to drop out
  • not all participants reached their 9th year in the study so the number of samples at follow-up Year 9 is about half that at follow-up year 6
  • samples are not reserved for approved studies seeking funding
  • inventory decreases over time as funded Ancillary Studies use sample
See ​WHI Biorepository Usage/Inventory slides​, for an overview of biorepository use and remaining inventory for select outcomes and subgroups (last updated 4/24/17).

Limits on Samples Available

Without significant scientific justification, Ancillary Studies are limited to the following sample volumes (including any necessary "dead volume") from a given specimen collection time point:

  • 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 (only available on BMD center participants)

  • 2 ug DNA

  • 0.5 ug RNA (only available on 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.  Parsimonious use of sample will be an important factor in a study’s technical evaluation. 

As an example of amount of sample available to ASs, see the 2013 tables:  Blood and DNA Available to AS.  Investigators can get more current data by using the WHI Query Builder

Specimen 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 and reported to the PI.

    • NOTE: Blind duplicates are not split participant samples. Therefore, for example, the 5% serum blind duplicates increase the number of samples to be tested by 10%; similarly the 2.5% DNA blind duplicates increases the number of DNA samples to be tested by 5%. When preparing budgets, please include the costs for testing the blind duplicates. 

  • Sample Processing Quality Control
    The adequacy of serum and plasma aliquoting by the Specimen Processing Lab is evaluated by testing a subaliquot from each blind quality control sample for total cholesterol. Similarly, urine samples are tested for sodium. The correlation and average CV% between the members of each blind pair is computed and reviewed by the WHI Lab Working Group. 
 

Further information

See additional information from the WHI Biorepository page:

  

Contact the WHI Help Desk at helpdesk@whi.org if you need assistance or have questions.