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Maximal resolution and full-length phasing for next-generation MHC-typing

Award Number: R43AI124837
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 07/12/2016
PERIOD OF PERFORMANCE END DATE: 06/30/2017

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Maximal resolution and full-length phasing for next-generation MHC-typing - Maximal resolution and full-length phasing for next-generation MHC-typing Arima Genomics 7. Project Summary/Abstract The Major Histocompatibility complex (MHC) locus is among the most polymorphic loci in the genome, and harbors genes that play critical roles in human immune health and disease. The polymorphic nature of the MHC locus allows for encoding every individual with a unique immune cell profile, hence, matching HLA genes among donors and recipients has been a critical step in mitigating immune rejections following organ transplants. Advances in next-generation sequencing technologies have increased the popularity of DNA sequencing as a means of typing the HLA locus for its clinical relevance. Yet current HLA typing technologies ignore potentially important DNA variants, type gene-by-gene at low resolution, and fail to haplotype phase non-HLA genes and other non-coding alleles in the MHC locus that are necessary for optimal donor-recipient matching. Arima Genomics has recently developed an innovative new approach to generate full-length haplotypes of the MHC locus at high-resolution, building on our proprietary HaploSeq technology for constructing chromosome-spanning haplotypes in the human genome. Our new technology, " HaploSeq-Mx" is capable of phasing the entire 3.5Mb HLA locus onto a single haplotype block at ~91% resolution and ~99% accuracy with just 2x sequencing depth. As a cost-effective, next-generation haplotyping technology, HaploSeq-Mx is poised to underpin a new standard in high-resolution locus-spanning MHC typing. The objectives of Arima Genomics' proposed R&D efforts involve improving HaploSeq-Mx's targeting efficiency to further reduce sequencing costs and advance the method to clinical utility, developing computational approaches to improve the accuracy of HaploSeq-Mx even further to >99.5%, and demonstrating feasibility of HaploSeq-Mx for MHC typing patient samples in a hematopoietic stem cell transplantation (HSCT) study with clinical collaborators at the Immunogenetics and Transplantation Laboratory (ITL) at the UCSD Center for Advanced Laboratory Medicine (CALM), while developing a new algorithm for donor-recipient matching. Successful completion of our research aims will contribute invaluable new knowledge to ongoing investigations of how human genetic variation influences patient outcomes in transplants, and will substantially advance the capabilities of our HLA typing technology toward commercial viability in clinical applications. HaploSeq-Mx promises to greatly enhance our understanding of human genetics in health and contribute to the realization of personalized medicine.


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: 2021 ( Subtotal = -$23,626 )
2021	2017	ARIMA GENOMICS LLC	7770 REGENTS RD #113390	SAN DIEGO	CA	92122	SAN DIEGO	USA	Allergy and Infectious Diseases Research	000	1	6/21/2021	SUPPLEMENT FOR EXPANSION	-$23,626
														Subtotal = -$23,626

Issue Date FY: 2018 ( Subtotal = $0 )
2018	2017	ARIMA GENOMICS LLC	7770 REGENTS RD #113390	SAN DIEGO	CA	92122	SAN DIEGO	USA	Allergy and Infectious Diseases Research	000	1	11/6/2017	SUPPLEMENT FOR EXPANSION	$0
														Subtotal = $0

Issue Date FY: 2017 ( Subtotal = $49,539 )
2017	2017	ARIMA GENOMICS LLC	7770 REGENTS RD #113390	SAN DIEGO	CA	92122	SAN DIEGO	USA	Allergy and Infectious Diseases Research	000	1	4/12/2017	SUPPLEMENT FOR EXPANSION	$49,539
														Subtotal = $49,539

Issue Date FY: 2016 ( Subtotal = $224,576 )
2016	2016	ARIMA GENOMICS LLC	7770 REGENTS RD #113390	SAN DIEGO	CA	92122	SAN DIEGO	USA	Allergy and Infectious Diseases Research	000	1	7/11/2016	NEW	$224,576
														Subtotal = $224,576

Grand Total All Awards = $250,489

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Maximal resolution and full-length phasing for next-generation MHC-typing

Award Number: R43AI124837

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 07/12/2016

PERIOD OF PERFORMANCE END DATE: 06/30/2017

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