Guidelines for AS Biospecimen Data Submission
It is a WHI and NHLBI requirement that all Ancillary Studies provide a biospecimen specimen assay results to the WHI Clinical Coordinating Center (WHI CCC) along with data documentation. Guidelines for preparing and documenting the data are provided below.
When to send specimen assay results to the WHI CCC
Submit specimen assay results to (CCC) after testing is completed for each sample Pull.
Note: A sample ‘Pull’ consists of 500-700 samples. So, if your study includes 2000 samples, the samples would be divided among four sample Pulls. Submitting assay results one Pull at a time allows the WHI CCC to provide you with the results of the blinded Quality Assurance (QA) samples that were included among the participant samples.
Where to send specimen assay results
· If the result file is not too large, send the Excel file as an email attachment to your WHI CCC Technical Coordinator (or to Megan Herndon mskinner@whi.org).
· If the result file is too large to send via email, contact your WHI CCC Technical Coordinator to make other arrangements for data submission
What to include with your specimen assay result submission
With the first result data submission, include a 1-page Word document with the information below. (This document will be posted to the WHI SharePoint site one year after the completion of your study at which time test results from your study will be shared.)
· Study Overview
· Synopsis of Participant Selection Criteria
· Synopsis of Laboratory Method(s)
How to format your specimen assay results
1. Use an Excel file if at all possible
2. Include the following data items in the Excel file:
· Pull number
· Draw ID number
· Assay name
- if there are abbreviations in the data file, provide the full assay name (append to the data file)
- ii. if an assay name has changed (i.e., there is a new name that is synonymous with the name used in the proposal), please provide this information
o Assay result
o Unit of measure
o Plate number, Run number, or Batch number
o Assay date
o Comments
(Note: The order of the data items does not matter as long as it is consistent)
3. Include a row in the Excel file for the Draw ID of every sample provided – even if there are no assay results to report. Note in the ‘Comment’ field the reason why a result is not available
4. Present the result data in the Excel file as it will be used in the study publications.
5. Report only one value per assay (i.e., if assay is run in duplicate, report the value to use).
6. Significant Digits: use the same number of significant digits for the same test result:
· If you plan to report 12.19 ng/ml, do not submit data as 12.19234 ng/ml
· If you plan to report values in decimals, do not drop a final ‘0’. For example, report 10.2 ng/ml as 10.20 ng/ml if you plan to report two digits to the right of the decimal point.
· Provide the data with the number of significant digits you plan to report in your publication. For example, do not report 10 digits if you plan to report data to the 3rd or 4th significant digit.
7. Units of Measure
· If you plan to report in ng/ml, do not submit data as ug/ml
8. Format the result data consistently across sample Pulls
· Do not change the order of columns, assay names, units, etc. after you have sent the first file.
Notes:
1. Following receipt of assay data on a sample Pull, the WHI CCC will review the file for errors and notify you if any errors are found. WHI will especially be looking to make sure that the following are true:
· Blood samples numbers match those that we sent
· The formatting guidelines, above, were followed
Once loaded, the WHI CCC will provide you with the results of the blind QA samples that were included among the participant samples.
· The WHI CCC must receive all assay result data before the CCC can grant the PI access to phenotype and/or covariate data.
2. GWAS data (and other large genotyping datasets):
· Blind duplicates: After your preliminary genotyping (“identifier/fingerprint” stage), send a list of duplicates (samples matching on >85% of called SNPs) to your WHI Study. WHI CCC will assess the list of duplicates to determine if the QA blind duplicates were correctly identified and check for any unexpected duplicates.
· Data cleaning: After genotyping is complete, contact your WHI Study Coordinator who will arrange to provide a limited data set of variables necessary for data cleaning (sample ID – Case/Control/QA status and possibly race).
3. Submission of genetic/phenotypic data to any public database (if applicable): You will be responsible for submitting your study data to dbGaP (or any other public database).
IMPORTANT: The WHI Draw ID or Common ID should, under no circumstances, be submitted to a public database. Data must only be submitted using the dbGaP sample ID (on specimen manifest) or your own study’s ID. You must communicate your plans for submission to your WHI Study Coordinator.