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A molecular method to determine isoform frequencies in RNA-seq

Award Number: R21CA196438
ORGANIZATION: NATIONAL CANCER INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2015
PERIOD OF PERFORMANCE END DATE: 02/28/2019

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A molecular method to determine isoform frequencies in RNA-seq - ¿ DESCRIPTION (provided by applicant): Current methods for RNA-seq library preparation attempt to uniformly sample all sequences across every mRNA molecule, optimally with sufficient overlap to allow de novo reassembly of the mRNA sequences from which they derive, or alternatively, to allow inference of mRNA sequence by alignment with reference sequences. Genes that encode mRNAs in multiple isoforms present a challenge: given a complete set of short sequence reads that span every exon and splice junction, certain alternative underlying mRNA isoform models cannot be deconvoluted using data of this nature. This confounding situation occurs when more than one isoform model can explain the frequencies of exon and junction sequence reads, and it is mathematically unavoidable: ultimately, short sequence reads do not contain the information needed to unambiguously identify the correct isoform model for certain common splicing patterns. We propose to test a method to preserve the necessary information. In this method, the goal is to associate a single barcode with multiple sequence reads from the same mRNA molecule, and different barcodes with sequence reads from each other mRNA molecule transcribed from the same gene. This will be done by random primed synthesis of cDNA using barcoded random primers in such a manner that each mRNA molecule is exposed to one, and only one, barcode during random primed reverse transcription. In principle, this method produces molecule-specific collections of barcoded cDNAs, which, upon high throughput sequencing, can be aligned to reveal the specific structural details of mRNA isoforms on a molecule-by-molecule basis. This approach would solve the isoform model identifiability problem.


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: 2019 ( Subtotal = $0 )
2019	2017	VACCINE RESEARCH INSTITUTE OF SAN DIEGO	3030 BUNKER HILL ST # 203	SAN DIEGO	CA	92109	SAN DIEGO	USA	Cancer Biology Research	000	3	8/1/2019	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2017 ( Subtotal = $230,985 )
2017	2017	VACCINE RESEARCH INSTITUTE OF SAN DIEGO	3030 BUNKER HILL ST # 203	SAN DIEGO	CA	92109	SAN DIEGO	USA	Cancer Biology Research	000	3	8/9/2017	NON-COMPETING CONTINUATION	$230,985
														Subtotal = $230,985

Issue Date FY: 2016 ( Subtotal = $269,483 )
2016	2016	VACCINE RESEARCH INSTITUTE OF SAN DIEGO	3030 SCIENCE PARK ROAD	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	2	8/3/2016	NON-COMPETING CONTINUATION	$269,483
														Subtotal = $269,483

Issue Date FY: 2015 ( Subtotal = $269,483 )
2015	2015	VACCINE RESEARCH INSTITUTE OF SAN DIEGO	3030 SCIENCE PARK ROAD	SAN DIEGO	CA	92121	SAN DIEGO	USA	Cancer Biology Research	000	1	8/28/2015	NEW	$269,483
														Subtotal = $269,483

Grand Total All Awards = $769,951

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A molecular method to determine isoform frequencies in RNA-seq

Award Number: R21CA196438

ORGANIZATION: NATIONAL CANCER INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/01/2015

PERIOD OF PERFORMANCE END DATE: 02/28/2019

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