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A Modular Framework for Accurate, Interpretable, and Reproducible Analysis of Long Read RNA-Seq Data

Award Number: R01HG009937
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/18/2018
PERIOD OF PERFORMANCE END DATE: 01/31/2029

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A Modular Framework for Accurate, Interpretable, and Reproducible Analysis of Long Read RNA-Seq Data - PROJECT SUMMARY RNA sequencing is extensively used in biological and biomedical research to assess the expression of transcripts within and across biological samples. Recent technological advances allow sequencing of entire transcripts, enhancing isoform identification and allele expression analysis. As with short read RNA-seq, iterative algorithm development with design considerations towards the data and metadata infrastructure is key to support accurate scientific conclusions and facilitate computational reproducibility for users. Many specialized bioinformatic methods are available for long read data that are able to detect novel transcripts and to adapt algorithms for quantification of transcript abundance to the particular characteristics of long reads. However there is a need for easy-to-use pipelines for multi-sample analysis that can be run by biologists or other analysts without advanced bioinformatic training, covering read processing, feature discovery, quantification, feature aggregation, and inference/visualization. We aim to provide such a modular pipeline with enhanced accuracy, interpretability, and reproducibility for long read RNA-seq, easily deployable on cloud platforms such as AnVIL. The team of investigators has substantial experience developing efficient and easy-to-use tools for transcriptomics analysis, having designed ultra-fast algorithms for sequence read processing, modular pipelines leveraging best-in-class methods from abundance estimation to statistical analysis, and end-user workflows that are widely used in research labs in academic institutes and industry. The goal of the project is to develop and enhance RNA-seq analysis tools for new long read datasets, focusing on improving accuracy and interpretability, in particular for multi-sample datasets. In this proposal, we will 1) expand quantification tools for long read RNA-seq including novel models for quantification and correction for errors and technical bias; 2) simplify multi-sample analysis with high-level tools that augment processing steps, extend our automatic provenance detection framework to support new use cases in long read, and support data-driven feature aggregation; and 3) broaden user engagement by publishing workflows and tutorials, and hosting in-person and virtual workshops on AnVIL. The impact of this work will be to deliver software for long read RNA-seq that is user-friendly, integrates with existing pipelines, and is made accessible on cloud platforms like AnVIL.


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: 2025 ( Subtotal = $562,595 )
2025	2025	UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL	104 AIRPORT DR STE 2200	CHAPEL HILL	NC	27599	ORANGE	USA	Human Genome Research	001	7	2/1/2025	COMPETING CONTINUATION	$574,300
2025	2025	UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL	104 AIRPORT DR STE 2200	CHAPEL HILL	NC	27599	ORANGE	USA	Human Genome Research	002	7	4/23/2025	COMPETING CONTINUATION	$63,812
2025	2022	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BUILDING	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Human Genome Research	000	6	11/1/2024	NON-COMPETING CONTINUATION	-$75,517
														Subtotal = $562,595

Issue Date FY: 2022 ( Subtotal = $294,981 )
2022	2022	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Human Genome Research	000	6	7/7/2022	NON-COMPETING CONTINUATION	$294,981
														Subtotal = $294,981

Issue Date FY: 2021 ( Subtotal = $294,981 )
2021	2021	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Human Genome Research	003	5	6/29/2021	NON-COMPETING CONTINUATION	$294,981
2021	2019	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	WEST 5510 FRANKS MELVILLE MEMORIAL LIBRARY	STONY BROOK	NY	11794	SUFFOLK	USA	Human Genome Research	001	2	10/28/2020	NON-COMPETING CONTINUATION	-$1
2021	2019	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Human Genome Research	002	3	10/28/2020	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$157,266
2021	2018	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	WEST 5510 FRANKS MELVILLE MEMORIAL LIBRARY	STONY BROOK	NY	11794	SUFFOLK	USA	Human Genome Research	000	1	10/28/2020	NEW	-$157,265
														Subtotal = $294,981

Issue Date FY: 2020 ( Subtotal = $293,482 )
2020	2020	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Human Genome Research	002	4	8/14/2020	NON-COMPETING CONTINUATION	$293,841
2020	2019	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	WEST 5510 FRANKS MELVILLE MEMORIAL LIBRARY	STONY BROOK	NY	11794	SUFFOLK	USA	Human Genome Research	000	2	6/5/2020	NON-COMPETING CONTINUATION	-$304,951
2020	2019	UNIVERSITY OF MARYLAND, COLLEGE PARK	3112 LEE BLDG 7809 REGENTS DR	COLLEGE PARK	MD	20742	PRINCE GEORGES	USA	Human Genome Research	001	3	6/5/2020	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$304,592
														Subtotal = $293,482

Issue Date FY: 2019 ( Subtotal = $304,952 )
2019	2019	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	WEST 5510 FRANKS MELVILLE MEMORIAL LIBRARY	STONY BROOK	NY	11794	SUFFOLK	USA	Human Genome Research	000	2	6/13/2019	NON-COMPETING CONTINUATION	$304,952
														Subtotal = $304,952

Issue Date FY: 2018 ( Subtotal = $320,128 )
2018	2018	RESEARCH FOUNDATION FOR THE STATE UNIVERSITY OF NEW YORK, THE	WEST 5510 FRANKS MELVILLE MEMORIAL LIBRARY	STONY BROOK	NY	11794	SUFFOLK	USA	Human Genome Research	000	1	9/18/2018	NEW	$320,128
														Subtotal = $320,128

Grand Total All Awards = $2,071,119

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A Modular Framework for Accurate, Interpretable, and Reproducible Analysis of Long Read RNA-Seq Data

Award Number: R01HG009937

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/18/2018

PERIOD OF PERFORMANCE END DATE: 01/31/2029

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