Informatics Tools for the Pangenome Webinar FAQ

Intent of the NOFO and Responsiveness

 

Would a successful application to the Informatics Tools for the Pangenome NOFO propose developing a tool to analyze long-read sequencing data such as HiFi or ONT on the pangenome?

A successful application to the Informatics Tools for the Pangenome NOFO could develop a tool to analyze long-read sequencing data such as HiFi/ONT on the pangenome. Whatever is proposed, it is important that the application justifies the purpose of this tool, why it is important, and identifies which community/ies the tool would serve.

 

Will applying to the Informatics Tools for the Pangenome NOFO affect ESI status?

Yes. Receiving an award for the Informatics Tools for the Pangenome NOFO will affect ESI status.

 

Are applications required to include a component describing the UI of software tools?

Applicants will have to justify how the tool they develop will be used by the community they are aimed at. The HGRP wants some tools to serve communities that do not have extensive informatics expertise, and the UI would have to serve that community. Some tools may be built for a community with more computational/informatics resources, so the UI might be different for that tool. Applicants will still describe how their tool will be made available and how it will be made appropriate for the targeted community.

It is OK if the UI is being developed or has been developed under other funding, but the connection should be made clear in the proposal.

 

Are infrastructural tools acceptable applications for the Informatics Tools for the Pangenome NOFO?

No. Infrastructural tools are not acceptable applications for the Informatics Tools for the Pangenome NOFO, but if an applicant has an idea for an infrastructural tool, or has questions about how NHGRI is making the distinction between “infrastructure” and “user tools” please contact Adam Felsenfeld at adam_felsenfeld@nih.gov.

NHGRI is interested in the topic of developing infrastructure for the pangenome (eg reference representations), but applications on that topic are probably more appropriate for a regular R01.

 

Should an application for the Informatics Tools for the Pangenome NOFO include a plan for working with other centers (e.g. “Coordinating Center” and “Genomes Center”)?

Yes. An application for the Informatics Tools for the Pangenome should include a plan for working with the other centers. It is a requirement to work together with the other components. NHGRI wants the Coordinating Center to consolidate all of the tools so investigators can find them easily.

There will be changes in the reference representation over time, which will require contact with the other components to manage. There may also be other opportunities that arise that can make the science better or make the successful applicant’s product better. The expectation is that all award recipients attend HPRC Steering Committee meetings.

For more information about the interactions between Centers, please look at the Terms and Conditions in the NOFO. The NHGRI spells out its intent in this section, including that the Informatics Tools Centers will be a component of the Human Pangenome Reference Consortium.

 

How much emphasis should be placed on developing tools for HGRP data specifically compared to other data resources in the future (graph-based references in general) for applications submitted to the Informatics Tools for the Pangenome NOFO?

The tools developed for the Informatics Tools for the Pangenome NOFO should be mainly focused on HGRP data, but it is a strength if the tool can also be used with other similar data types or structures.

 

Can any of the funding from the Informatics Tools for the Pangenome NOFO be used to perform wet lab experiments to validate the informatics tools?

Up to 10% of the budget may be used for wet lab validations.

 

Is the HGRP involved in any collaborative efforts or partnerships to enhance human genome research and informatics tools?

Yes. The HGRP is involved in many collaborative efforts that are already ongoing. The HGRP is an open consortium that offers associate membership, so there are avenues for collaboration and information exchange even if someone is not a part of the consortium. The consortium as a whole is developing a resource that is intended to be used and adopted by the community, which requires working with many different groups within the community.

 

Would successful, funded applicants of the Informatics Tools for the Pangenome NOFO have early access to the next set of generated genomes to use in tool generation?

Successful applicants of the Informatics Tools for the Pangenome NOFO would have access to the data collected close to the time they are generated. The data are released very rapidly from the HPRC, so it is not anticipated that there would be a major lag before full public availability.

 

Will all data included in the pangenome reference be fully accessible?

Yes. The research participants for the NHGRI effort are consented for open, unrestricted release of sequence data. These data are, and will be, made available rapidly after generation through AnVIL and other means.

Note that the Human Pangenome Research Consortium (HPRC) also has a goal of working with international partners, which may raise data sovereignty and privacy challenges.

One example of a potential application is a tool that allows the analysis of large, restricted data sets together with the public HPRC data set.

Review, Award and Administration

 

What is the total budget for the Informatics Tools for the Pangenome NOFO?

The total budget for the Informatics Tools for the Pangenome NOFO is $2.0M in FY24 and $2.0M in FY26 to fund up to 6 awards. Each application should be less than or equal to $400,000/year Direct Cost.

 

Can applicants request more funds over $400k for the Informatics Tools for the Pangenome NOFO if they need more computational resources to develop tools?

No. Applicants cannot request more than $400k/year direct costs. If cloud compute is needed, an alternate route for cloud credits is available through STRIDES.

 

Do I need to submit a letter of intent (LOI)?

An LOI is not required. However, they are appreciated, and are helpful for planning the peer review.