This document summarizes a study that analyzed genomic runs of homozygosity (ROH) in populations from the HGDP dataset to understand population history and consanguinity. The study found that Native American populations had the longest ROHs, Oceanian populations had the most short ROHs, and South/Central Asian and West Asian populations had more long ROHs, reflecting consanguineous marriages. Hunter-gatherer populations generally had more total ROH lengths than farmer populations. Overall, short ROHs made up most ROHs present across populations, but the most inbred populations had more long ROHs, providing information about demographic history and disease risk.

1. Genomic Runs of
Homozygosity Record
Population History and
Consanguinity
Kirin et. al. 2010
Hadeel Abu Jamous
Seminar Spring 2016
Virginia State University

2. Outline
Introduction
Study Aims
Methods
Results
Discussion

3. Introduction
Runs of Homozygosity (ROH)
Segments from both parents are the same in the offspring
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4. Introduction
Long ROH
Recent inbreeding (first cousin and second
cousin marriages)
Short ROH
Ancestral relatedness
Enough time for recombination during
meiosis to occur

5. Study Aims
Compare and characterize homozygosity between
populations
With different degrees of isolation
Consanguinity (first and second cousin
marriages)

6. 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

7. Methods
Continental groups
Europe
Sub-Saharan Africa
America (Native American)
Oceania
East Asia
Central/South Asia
West Asia

8. 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

9. 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)

10. Results-ROH Pattern across
continental groups

11. 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

12. 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

13. Results: Hunter-gatherers vs
Farmers

14. Results: Hunter-gatherers vs
Farmers
Hunger-gatherers have higher numbers of total
ROH lengths for all ROH length categories
compared to farmers

15. Discussion
ROHs longer than 0.5 Mb
ROH provide a record of demographic history of
populations and individuals

16. Discussion
South and West Asia (consanguineous)
populations – more very long ROHs
Short time for recombination in meiosis to
occur and break them up

17. Discussion
Oceanian population
Large numbers of shorter ROH but few long ROH

18. Discussion
Native American population
More short and long ROHs

19. Discussion
Across all populations
Shorter ROH make up the majority of ROH
present
The most inbred populations
ROH effects on disease risk

20. 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

21. Questions