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Administrative Supplement for IGVF Cost Extension

Award Number: U01HG012022
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2021
PERIOD OF PERFORMANCE END DATE: 05/31/2027

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Administrative Supplement for IGVF Cost Extension - PROJECT SUMMARY Over the first five years of the Radivojac Award, our team has delivered several foundational methodologies and resources to the IGVF consortium and the broader genomics community. These include ClinGen-adopted calibration framework that was applied to 13 missense and 8 in-frame indel variant effect predictors, the Ex- CALIBR method for calibrating high-throughput functional assays (the first of its kind), and a consortium-wide Pillar Project, where we had a key role, that reclassified 75% of VUS across 40 genes and preclassified over 60% of unobserved variants. We also produced multiple benchmarking studies, developed MutPred-PPI for predicting interaction-specific effects of missense variants and deposited more than 25TB of genome-scale predictions into the IGVF portal and catalog. With this administrative supplement, we are requesting a one-year extension to protect these investments, supplement community resources and finish what we have started. The additional year will allow us to com- plete six specific activities, which are mostly within Aims 1 and 3 of the original project: (1) extend ExCALIBR to handle multi-modal functional assay data (e.g., multiple phenotypes from LABEL-seq) using canonical fun- damental skew normal mixture models; (2) complete our mvHMM-based cold spot framework to automatically flag benign variants and help guide experimental design; (3) characterize how different lines of evidence, in- cluding computational, functional, and population, depend on each other, so we can refine ACMG/AMP combi- nation rules and avoid human judgement in evidence combination; (4) finish exTSP, our transcript- and tissue- aware missense interpretation tool, and validate it in PsychENCODE, CommonMind, and BrainGVEX cohorts for neuropsychiatric disorders; (5) substantially reduce in-frame indel variants of uncertain significance in Clin- Var using newly calibrated indel predictors and SGE data from the CAVA center; and (6) deposit all remaining data and metadata properly into the IGVF portal, IGVF catalog, MaveDB, and MaveMD. All of this work is squarely within the original scope, addresses immediate consortium needs, and ensures that community resources are fully integrated into public repositories. The extension will safeguard a substantial NIH investment, put usable tools directly into the hands of clinical geneticists, and meet our consortium com- mitments.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $564,812 )
2026	2026	NORTHEASTERN UNIVERSITY	360 HUNTINGTON AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	001	5	7/8/2026	SUPPLEMENT FOR EXPANSION	$564,812
2026	2025	NORTHEASTERN UNIVERSITY	360 HUNTINGTON AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	5	7/6/2026	NON-COMPETING CONTINUATION	$0
														Subtotal = $564,812

Issue Date FY: 2025 ( Subtotal = $622,328 )
2025	2025	NORTHEASTERN UNIVERSITY	360 HUNTINGTON AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	5	9/18/2025	NON-COMPETING CONTINUATION	$622,328
														Subtotal = $622,328

Issue Date FY: 2024 ( Subtotal = $622,326 )
2024	2024	NORTHEASTERN UNIVERSITY	360 HUNTINGTON AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	4	5/22/2024	NON-COMPETING CONTINUATION	$622,326
														Subtotal = $622,326

Issue Date FY: 2023 ( Subtotal = $635,027 )
2023	2023	NORTHEASTERN UNIVERSITY	360 HUNTINGTON AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	001	3	6/6/2023	NON-COMPETING CONTINUATION	$635,027
2023	2022	NORTHEASTERN UNIVERSITY	360 HUNTINGTON AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	2	5/2/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $635,027

Issue Date FY: 2022 ( Subtotal = $635,027 )
2022	2022	NORTHEASTERN UNIVERSITY	360 HUNTINGTON AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	2	5/27/2022	NON-COMPETING CONTINUATION	$635,027
														Subtotal = $635,027

Issue Date FY: 2021 ( Subtotal = $356,264 )
2021	2021	NORTHEASTERN UNIVERSITY	360 HUNTINGTON AVE	BOSTON	MA	02115	SUFFOLK	USA	Human Genome Research	000	1	9/3/2021	NEW	$356,264
														Subtotal = $356,264

Grand Total All Awards = $3,435,784

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Administrative Supplement for IGVF Cost Extension

Award Number: U01HG012022

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/01/2021

PERIOD OF PERFORMANCE END DATE: 05/31/2027

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