Genomic Runs of Homozygosity Record

Population History and Consanguinity

Kirin et. al. 2010

Hadeel Abu JamousSeminar Spring 2016Virginia State University

Outline

Introduction Study Aims Methods Results Discussion

Introduction Runs of Homozygosity (ROH)

Segments from both parents are the same in the offspring

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Introduction Long ROH

Recent inbreeding (first cousin and second cousin marriages)

Short ROH Ancestral relatedness

Enough time for recombination during meiosis to occur

Study Aims Compare and characterize homozygosity between

populations With different degrees of isolation Consanguinity (first and second cousin

marriages)

Methods HGDP (Human Genome Diversity Project) dataset

Populations from all continents Bedouin, Druze, Palestinians, Mozabite Berbers,

Brahui, Baluchi, Makrani, Sindhi, and Pathan Analyzed data at the continental and population

level

Methods Continental groups

Europe Sub-Saharan Africa America (Native American) Oceania East Asia Central/South Asia West Asia

Methods Data: 660,918 single nucleotide polymorphism

markers from Illumina 650Y product 22 autosome-644,258 SNPS left SNPs with frequencies less than 1% in any of the 7

continental regions were removed= 415,130 SNPS

Methods PLINK used to determine ROH SPSS and R software used for calculations For each individual, FROH was calculated

Calculated by dividing the sum of ROH per individual by total length covered by SNPS, excluding the centromeres (2682.410 Mb)

Results-ROH Pattern across continental groups

Results-ROH Pattern across continental groups

Native Americans-longest ROHs for all ROH length categories.

Oceanians- the most number of ROHs measuring 0.5-1 Mb Reduced effective

population size and isolation

Results-ROH Pattern across continental groups South/Central Asians and West Asians

More ROHs lengths over 4 Mb compared to Africans and other Euroasians

19% of individuals – ROH over 16 Mb Consanguineous marriage

Results: Hunter-gatherers vs Farmers

Results: Hunter-gatherers vs Farmers Hunger-gatherers have higher numbers of total

ROH lengths for all ROH length categories compared to farmers

Discussion ROHs longer than 0.5 Mb

ROH provide a record of demographic history of populations and individuals

Discussion

South and West Asia (consanguineous) populations – more very long ROHs Short time for recombination in meiosis to occur

and break them up

Discussion

Oceanian population Large numbers of shorter ROH but few long ROH

Discussion

Native American population More short and long ROHs

Discussion

Across all populations Shorter ROH make up the majority of ROH

present The most inbred populations

ROH effects on disease risk

Reference Kirin, M., McQuillan R., Franklin, C.S., Campbell, H., McKeigue, P.M.,

Wilson, J.F. 2010. Genomic Runs of Homozygosity Record Population History and Consanguinity. Plos ONE; 5(11) : e13996

Questions