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Population dynamics and medical consequences of sex chromosome evolution

Award Number: R35GM124827
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/11/2017
PERIOD OF PERFORMANCE END DATE: 12/29/2024

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Population dynamics and medical consequences of sex chromosome evolution - PROJECT SUMMARY Sex-bias exists in the human genome in DNA content and gene expression. The human X and Y chromosomes are useful tools for inferring human demography, and crucial for our understanding of human health. However, despite the genomics era, X and Y chromosomes are still vastly underutilized, especially in a genome-wide context. Most established genomics methods and analyses fail to explicitly incorporate sex chromosomes, missing more than 5% of typical genomic variation, and ignoring regions known to contribute to disease. The study of sex chromosome evolution therefore addresses deficits in conventional approaches with critical implications for human health and biology. My research has focused on the integration of these chromosomes to build comprehensive analyses of human history and utilizing an evolutionary approach to characterize sex-bias in gene expression. This project will utilize multiple approaches for studying sex chromosome variation across human and non-human species. First, we will focus on development and extensive testing of novel methodology for accurately accounting for technical variation that affects alignment and variant calling on the sex chromosomes. Current alignment pipelines do not account for the shared homology between the X and Y chromosome, resulting in mis-mapping of reads between the sex chromosomes and reduced power for variant calling. We will incorporate sex chromosome biology to improve alignment and variant calling on the sex chromosomes. Second, we will study the evolution of sex chromosomes and X-inactivation in non-human animals, focused on our close evolutionary relative, the rhesus macaque. Third, we will study gene expression variation (with an emphasis on X-linked gene expression and X-inactivation) between the sexes, and between human populations in the human placenta. The placenta is the one organ routinely expelled from the body that also provides a crucial interface during development, and is not studied in current large-scale tissue expression projects. In collaboration with a long-term pregnancy outcome study we will generate and comprehensively analyze population-specific sex-bias in the human placenta. Fourth, we will study truly genome-wide patterns of variation (autosomes, X chromosome, Y chromosome, and mtDNA) in African populations. Populations in Africa are the most diverse in the world, and representation of that diversity is conspicuously absent from global population studies. In collaboration with anthropologists, who are studying, cultural variation, we will use patterns of variation across the sex chromosomes and autosomes to infer recent and ancient demography, informed by sex-biased migration and demography. Finally, we will contribute novel training materials for instructors and study student learning and self-efficacy as they learn genomics research skills. This work will improve methodology for studying sex-linked variation, provide estimates of sex-biased human demography, elucidate sex-biased expression in the human placenta, and utilize these research projects to improve training and inclusion of a diverse workforce.


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 = -$126,814 )
2025	2024	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	002	7	3/6/2025	NON-COMPETING CONTINUATION	$0
2025	2024	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	003	7	6/3/2025	NON-COMPETING CONTINUATION	-$126,814
2025	2024	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	000	7	11/14/2024	NON-COMPETING CONTINUATION	$0
2025	2021	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	001	5	1/15/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = -$126,814

Issue Date FY: 2024 ( Subtotal = $452,352 )
2024	2024	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	000	7	3/11/2024	NON-COMPETING CONTINUATION	$407,117
2024	2024	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	001	7	6/26/2024	NON-COMPETING CONTINUATION	$45,235
														Subtotal = $452,352

Issue Date FY: 2023 ( Subtotal = $453,734 )
2023	2023	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	001	6	5/31/2023	COMPETING CONTINUATION	$453,734
2023	2021	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	000	5	5/23/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $453,734

Issue Date FY: 2021 ( Subtotal = $323,010 )
2021	2021	ARIZONA STATE UNIVERSITY	660 S MILL AVE STE 312	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	000	5	7/19/2021	NON-COMPETING CONTINUATION	$323,010
														Subtotal = $323,010

Issue Date FY: 2020 ( Subtotal = $379,448 )
2020	2020	ARIZONA STATE UNIVERSITY	660 S MILL AVE STE 312	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	000	4	7/16/2020	NON-COMPETING CONTINUATION	$379,448
														Subtotal = $379,448

Issue Date FY: 2019 ( Subtotal = $380,415 )
2019	2019	ARIZONA STATE UNIVERSITY	660 S MILL AVE STE 312	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	000	3	7/18/2019	NON-COMPETING CONTINUATION	$380,415
														Subtotal = $380,415

Issue Date FY: 2018 ( Subtotal = $380,347 )
2018	2018	ARIZONA STATE UNIVERSITY	660 S MILL AVE STE 312	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	000	2	8/1/2018	NON-COMPETING CONTINUATION	$380,347
														Subtotal = $380,347

Issue Date FY: 2017 ( Subtotal = $380,460 )
2017	2017	ARIZONA STATE UNIVERSITY	660 S MILL AVE STE 312	TEMPE	AZ	85281	MARICOPA	USA	Biomedical Research and Research Training	000	1	9/11/2017	NEW	$380,460
														Subtotal = $380,460

Grand Total All Awards = $2,622,952

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Population dynamics and medical consequences of sex chromosome evolution

Award Number: R35GM124827

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/11/2017

PERIOD OF PERFORMANCE END DATE: 12/29/2024

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