NHGRI and NICHD dGTEx Applicant Webinar

Does the NIH think it likely that there will be subsequent Analysis R01 (or other grants) once these projects are established and generating data?

We do anticipate R01 additional analyses in the later years of the project.

Will the LDACC and BPC both be engaged together in designing the tissue/sample specific sampling SOP protocols?

Yes, the prioritization will be decided by the Steering Committee.

Is the Letter of Intent mandatory?

No, this is optional.

Is this an open competition?

Yes, anyone is welcome to apply.

Can applicants include investigators from abroad?

At this time, foreign institutions are not eligible to apply. Foreign components are not allowed.

Will there be an effort to specifically span genders and diversity of race/ethnic groups in the pediatric collections?

The NIH is interested in there being a representation of different genders and race/ethnic groups in the study, though NIH program staff recognizes that this may not be feasible. There should be an effort to do this.

What is the maximum post-mortem time that is planned for this RFA?

Ideally, 8 hours or less. Some tissues degrade more quickly, so the time may vary. Some pilot studies may need to be done though, since it may differ for pediatric populations, and this is based on adult GTEx.

Will the BPC plan to gather tissues from living donors?

No, dGTEx is focused on post-mortem samples, as this allows for the collection of many different types of organs and tissues.

Organ procurement organizations collect clinical data through Uniform DRAI (Uniform Donor Risk Assessment Interview) with the family. Is this good enough to collect clinical data, or does NIH program staff have a set of questions that should be asked?

The more information that is collected, the better. In the Research Strategy section of the RFA, applicants are asked to describe what clinical data will be collected. The Steering Committee will decide what set of questions should be asked.

Would a plan to add prenatal tissue collection be appropriate?

Not at this time.

Is an ELSI study required?

Yes, ELSI research is required.

Would the BPC need to advise on brain dissection strategies, or other tissue selection strategies?

NIH program staff envisions that the BPC and LDACC will work together on this in the Steering Committee in order to determine the best strategy. It depends on the number of brain sections that are dissected. It is expected that the BPC would have provisions to be able to do the expert brain dissections and be able to provide the tissues to the LDACC.

In addition to genomics, proteomics remains a viable option especially for such well curated samples. Is there a plan to integrate proteomics for characterizing these GTEx samples?

No, there is currently no plan to integrate proteomics, as the focus of the project is genomics.

What would the dGTEx and GTEx data integration look like? Would the coordinating center work with NIH to successfully generate integrated data?

Yes, the Coordinating Center and NIH program staff would work together to generate integrated data, but NIH program staff are encouraging applicants to propose ways to integrate the dGTEx and GTEx data.

Would the coordinating center need to store samples long term to release to research communities, or would the coordinating center need to send the tissues back to the BPC?

The former— applicants to the LDACC RFA should include a legacy plan for distributing samples to the research community.

“Coordinate with BPC to implement LIMS, including barcode-based identification received from BPC, tissue samples, and related material”—can you further clarify what is required?

All the information from the BPC regarding tissue samples will be deidentified. Also, all metadata about the tissues should be linked to the tissue samples. 

“Include self-sustaining legacy plan to provide sample aliquots to research community”- do you currently have a protocol for the GTEx? If so, will this be followed for dGTEx?

Yes, there is a protocol to distribute GTEx samples to the research community upon request. For dGTEx, applicants should include a plan for distributing samples to the research community. 

The adult GTEx samples are stored at the Broad Institute and are available for the community to use. Brain samples from GTEx are stored at the NeuroBioBank. NINDS and NIMH program staff would like to hear about applicants’ plans to store excess brain tissues.

How and when will it be decided to include other analyses (whole genome bisulfite sequencing, ChIP-Seq, etc.) with the study?

At this time, no decisions have been made about including other analyses, but applicants are welcome to propose additional analyses in their applications.

How will the LDACC work with AnVIL?

The LDACC will deposit data from gene expression and genotyping analyses in the AnVIL on a timely and regular basis.

As there is a plan to perform sequencing and make it available, is there a need for special authorization by the tissue donors’ families?

Under the Data Collection and Resource Sharing section of the LDACC RFA – “the informed consent document (obtained by the BPC) should include language that both the biospecimens and the derived data will be broadly shared without any identifying subject information with the biomedical community.” To recap, tissue donor’ families will be informed about the research that will be done with the tissue samples and consented for general research use.

Laboratory, Data Analysis, and Coordinating Center for the Developmental Genotype-Tissue Expression Project:

Jyoti Dayal, M.S.
National Human Genome Research Institute (NHGRI)
(301) 480-2307
jyotig@nih.gov

Pediatric Biospecimen Procurement Center (BPC) Supporting the Developmental Gene Expression (dGTEx) Project:

John Ilekis, Ph.D.
National Institute of Child Health and Human Development (NICHD)
(301) 435-6895
ilekisj@mail.nih.gov