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Improving genotype accuracy and haplotypic analysis for genome-wide studies

Award Number: R01HG004960
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/07/2009
PERIOD OF PERFORMANCE END DATE: 06/30/2012

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Improving genotype accuracy and haplotypic analysis for genome-wide studies - DESCRIPTION (provided by applicant): Genome-wide association studies (GWAS) are an effective tool for indentifying common genetic variants that contribute to disease and heritable traits. These studies use high-density oligoneculeotide arrays to assay hundreds of thousands of diallelic genetic markers in each individual. However, genome-wide association studies can also produce hundred of spurious disease-gene associations caused by genotyping error. This research will develop statistical and computational methods that use inter-marker correlation to substantially improve genotype accuracy. All existing methods for calling genotypes for large-scale data ignore the correlation between genetic markers. This correlation is highly informative, but exploiting inter-marker correlation is computationally difficult because it requires inference of the marker alleles inherited from a single parent (the haplotype phase). Recently, we have developed a novel method of haplotype phase inference for large-scale data sets of unrelated individuals that is orders of magnitude faster and more accurate than competing methods. The next step will be to improve haplotype phase inference and genotype calling by performing both tasks simultaneously. This will enable genotype uncertainty to be taken into account when inferring haplotype phase and inter-marker correlation to be taken into account when calling genotypes. Our methods will improve genotype accuracy, improve haplotype phase inference accuracy, decrease false positive associations due to genotyping error, and increase power to detect true genetic associations. We will extend these novel methods to call genotypes and phase haplotypes for parent-offspring trios where the additional relatedness information will lead to even larger gains in accuracy. The improved genotype accuracy and phased haplotypes from our methods will contribute to improved understanding of the genetic contribution to human disease. Our research will also address one of the main impediments to haplotypic analysis: the difficulty in interpreting analysis results. We will develop interactive methods for visualizing haplotype structure and haplotype-trait associations. These new data exploration methods will greatly simplify the task of identifying sequences of genetic variants that are associated with a trait. PUBLIC HEALTH RELEVANCE: Heritable genetic variants contribute to many common diseases, such as cardiovascular disease and diabetes. This research will develop new methods and tools that improve the accuracy of genetic data and that improve our ability to identify genetic variants that increase risk of disease. These methods and tools will contribute to the prevention, diagnosis, and treatment of heritable diseases in the United States and throughout the world.


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: 2018 ( Subtotal = $0 )
2018	2014	UNIVERSITY OF WASHINGTON	4333 BROOKLYN AVE NE	SEATTLE	WA	98195	KING	USA	Human Genome Research	000	6	10/27/2017	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2016 ( Subtotal = $0 )
2016	2014	UNIVERSITY OF WASHINGTON	3917 UNIVERSITY WAY NE	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	6	6/30/2016	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2014 ( Subtotal = $340,672 )
2014	2014	UNIVERSITY OF WASHINGTON	3917 UNIVERSITY WAY NE	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	6	5/28/2014	NON-COMPETING CONTINUATION	$340,672
														Subtotal = $340,672

Issue Date FY: 2013 ( Subtotal = $313,245 )
2013	2013	UNIVERSITY OF WASHINGTON	3917 UNIVERSITY WAY NE	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	5	7/26/2013	NON-COMPETING CONTINUATION	$313,245
														Subtotal = $313,245

Issue Date FY: 2012 ( Subtotal = $328,005 )
2012	2012	UNIVERSITY OF WASHINGTON	3917 UNIVERSITY WAY NE	SEATTLE	WA	98105	KING	USA	Human Genome Research	001	4	8/31/2012	COMPETING CONTINUATION	$328,005
2012	2011	UNIVERSITY OF WASHINGTON	3917 UNIVERSITY WAY NE	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	3	8/30/2012	NON-COMPETING CONTINUATION	$0
														Subtotal = $328,005

Issue Date FY: 2011 ( Subtotal = $202,776 )
2011	2011	UNIVERSITY OF WASHINGTON	3917 UNIVERSITY WAY NE	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	3	7/1/2011	NON-COMPETING CONTINUATION	$202,776
														Subtotal = $202,776

Issue Date FY: 2010 ( Subtotal = $110,570 )
2010	2010	UNIVERSITY OF WASHINGTON	3917 UNIVERSITY WAY NE	SEATTLE	WA	98105	KING	USA	Human Genome Research	000	2	9/23/2010	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$110,570
2010	2009	AUCKLAND UNISERVICES, LTD	20 SYMONDS STREET	AUCKLAND				NZL	Human Genome Research	001	1	9/23/2010	NEW	$0
														Subtotal = $110,570

Issue Date FY: 2009 ( Subtotal = $144,218 )
2009	2009	AUCKLAND UNISERVICES LIMITED	70 SYMONDS ST PRIVATE BAG 92019	AUCKLAND				NZL	Human Genome Research	000	1	8/3/2009	NEW	$144,218
														Subtotal = $144,218

Grand Total All Awards = $1,439,486

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Improving genotype accuracy and haplotypic analysis for genome-wide studies

Award Number: R01HG004960

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 08/07/2009

PERIOD OF PERFORMANCE END DATE: 06/30/2012

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