Frequently Asked Questions
Do you have an Epi25 consent form I can use to consent participants?
To date, Epi25 has aggregated DNA samples collected under previously approved IRB protocols at the sites’ home institutions. If you are unsure if your participants have provided sufficient informed consent in order to be included in Epi25 sequencing and data sharing, please reach out to Felecia and Cate.
What is the NIH Genomic Data Sharing Policy and why does it matter in Epi25?
The NIH GDS Policy applies to all NIH-funded research (e.g., grants, contracts, and intramural research) that generates large-scale human or non-human genomic data, regardless of the funding level, as well as the use of these data for subsequent research. Large-scale data include genome-wide association studies (GWAS), single nucleotide polymorphisms (SNP) arrays, and genome sequence, transcriptomic, epigenomic, and gene expression data. Because Epi25 is funded by a branch of the NIH (the NHGRI), the Epi25 genomic data will be deposited into dbGaP. Therefore, the NIH Genomic Data Sharing Policy applies to Epi25 genomic data.
In brief, the NIH Genomic Data Sharing Policy requires that - for participants consented after the policy effective date of January 25, 2015 - participants provided informed consent for broad sharing of samples/data, future use of samples/data, and deposition of data into a repository.
If your site has samples collected after January 25, 2015, and you would like to contribute them to Epi25, it is required that your consent forms used to collect these samples contain this language.
If your site has samples collected before January 25, 2015, the consent form must not be in consistent with broad sharing, future use, and deposition of data into a repository.
An FAQ about the NIH Genomic Data Sharing Policy can be found here: https://osp.od.nih.gov/scientific-sharing/genomic-data-sharing-faqs/
If I can provide an IRB approval letter that dbGaP data deposition is allowed, why do you require a Data Use Limitations letter?
Because the Broad is using Epi25 samples in a secondary use manner and did not approve the sample collection activities themselves, we require Data Use Limitations letters to indicate that A) sharing samples and data with the Broad is allowed B) sharing data in a controlled-access repository is allowed and C) if there are any use restrictions associated with the data. We use the Data Use Limitations letters to complete the Institutional Certification form that is required to register samples/data in dbGaP.
What if my ethics committee will not sign the Data Use Limitations letters?
Contact the Broad Project Manager to discuss options for signatories in the letter.
Will the Broad accept more or less DNA than the recommended 50 ul at 80 ng/ul?
The requested amount of DNA is 80 ng/ul at 50 ul. This amount of DNA assures that there will be enough material for any downstream analyses. If you have samples that cannot meet these requirements, we still may be able to accept the samples. Contact Felecia with any questions about the sample input requirements.
What about family samples? Can those be sequenced?
At this time, Epi25 is sequencing one affected case per family. Unaffected or affected family members are not eligible for Epi25.
What about data? Is there a process for applying for and using data?
The data access process for Epi25 is described on our "Joining Epi25" page, here.
What genomic data will I receive from the samples that my site contributes?
For samples that are whole exome sequenced, you will receive a variant called format (VCF) file for the samples that you contributed. By request, we can return the raw data (bam files) to you, but please be prepared for very large data files to be transferred and stored at your institution. At this time, these data are returned to you using an encrypted Aspera site.
As of Year 2 of the project, we are also genotyping Epi25 samples on a whole genome genotyping array. We are currently using the Illumina Infinium Global Screening Array with multi-disease content (GSA-MD). These data (VCF file, idats, gtcs) can be made available to you via a FireCloud Workspace (https://portal.firecloud.org). You will need FireCloud account associated with a Google ID in order to download your data. Please review this document for instructions on how to create an account and this document for options to download the data.
Please note that in the majority of cases, all samples that are selected by Epi25 for genomic data generation are both genotyped and whole exome sequenced. However, if samples have insufficient amounts of DNA, sometimes only one data type is generated.
When will I receive the WES and genotyping data for the samples I contribute?
Data are generated on a rolling basis but are released at the close of the funding cycle. Typically, that means that genomic data for a funding year are ready to be returned to sites at the start of the next calendar year.
Please note that it is a requirement of participation that your site contribute detailed phenotype data (using the Epi25 clinical data forms) before receiving genomic data.
Is Epi25 providing a summary of the results for the patients in my cohort? Can I return the genetic results back to participants?
No, Epi25 is not providing a high-level summary of the results from each participant. The genomic data generated as part of Epi25 are not meant to be used in a clinical setting. The lab protocols used to generate these data are for research purposes only; they are not CLIA-certified. Therefore, it is not recommended that these results are returned to participants.
I am an investigator from the EU. How can I send DNA samples and phenotype data to the US for Epi25 while complying with GDPR?
GDPR stands for the General Data Protection Regulation which and went into effect on May 25, 2018. GDPR is complex and each EU member state is still developing policies and procedures to comply with the new law. However, there are now stricter rules governing the transfer, use, and storage of “personal data” which includes DNA and health information. This means that you will likely need to enter in a specific agreement with the Broad and/or UCSF to transfer your sample and data. The contacts at each site will work with you to determine the type of agreement needed.
What are the Centers for Common Disease Genomics and how are they related to Epi25?
The Centers for Common Disease Genomics program is part of the NHGRI Genomic Sequencing Program. A CCDG grant at Broad funds the genomic data generation for Epi25. You can learn more about the CCDG and other funded sites here and here.
Epi25 genomic data is also made available to CCDG members very soon after it is generated. CCDG members have to apply to use the data, and after approval, the data will be shared in line with data use restrictions indicated on the Data Use Limitations letters.