A haplotype is a sequence of alleles on a chromosome. Two haplotypes are identical by descent if they are inherited from a common ancestor. Segments of identity by descent (IBD) are found at high frequency in population samples and can be detected with high accuracy in high density SNP array or sequence data. IBD segments can be used for computationally efficient and accurate estimation in many health-related applications including estimating population genetic parameters and performing genetic association testing. We propose to develop improved methodology for detecting IBD segments, with particular focus on quantifying uncertainty in IBD segment endpoints. We will also develop methods that use IBD segments to estimate mutation rates, migration rates, effective population sizes, and population split times.

Public Health Relevance

The genetic material (DNA) of all humans is highly similar due to common ancestry. In this project, we will develop methods for detecting recent common ancestry and utilizing it in analyses that shed light on population demography and mutation processes.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG005701-05
Application #
9330892
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Brooks, Lisa
Project Start
2010-08-11
Project End
2020-06-30
Budget Start
2017-07-01
Budget End
2018-06-30
Support Year
5
Fiscal Year
2017
Total Cost
Indirect Cost
Name
University of Washington
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
605799469
City
Seattle
State
WA
Country
United States
Zip Code
98195
Browning, Sharon R; Browning, Brian L (2015) Accurate Non-parametric Estimation of Recent Effective Population Size from Segments of Identity by Descent. Am J Hum Genet 97:404-18
1000 Genomes Project Consortium; Auton, Adam; Brooks, Lisa D et al. (2015) A global reference for human genetic variation. Nature 526:68-74
Zhang, Qian S; Browning, Brian L; Browning, Sharon R (2015) Genome-wide haplotypic testing in a Finnish cohort identifies a novel association with low-density lipoprotein cholesterol. Eur J Hum Genet 23:672-7
Qian, Yu; Browning, Brian L; Browning, Sharon R (2014) Efficient clustering of identity-by-descent between multiple individuals. Bioinformatics 30:915-22
Browning, Sharon R; Browning, Brian L (2013) Erratum to: Identity-by-descent-based heritability analysis in the Northern Finland Birth Cohort. Hum Genet 132:957-8
Browning, Sharon R; Browning, Brian L (2013) Identity-by-descent-based heritability analysis in the Northern Finland Birth Cohort. Hum Genet 132:129-38
de Candia, Teresa R; Lee, S Hong; Yang, Jian et al. (2013) Additive genetic variation in schizophrenia risk is shared by populations of African and European descent. Am J Hum Genet 93:463-70
Browning, Brian L; Browning, Sharon R (2013) Detecting identity by descent and estimating genotype error rates in sequence data. Am J Hum Genet 93:840-51
Browning, Brian L; Browning, Sharon R (2013) Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194:459-71
Kim, Jerry H; Jarvik, Gail P; Browning, Brian L et al. (2013) Exome sequencing reveals novel rare variants in the ryanodine receptor and calcium channel genes in malignant hyperthermia families. Anesthesiology 119:1054-65

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