runs of homozygosity presentation
TRANSCRIPT
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