Runs of homozygosity
Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that are present in an individual due to parents transmitting identical haplotypes to their offspring.[1]
The potential of predicting or estimating individual autozygosity for a subpopulation is the proportion of the autosomal genome above a specified length, termed Froh.[2]
A research study in UK Biobank, All of Us and Million Veteran Program found that FROH declines over time.[3]
Usage
This technique can be used to identify the genomic footprint of inbreeding in conservation programs, as organisms that have undergone recent inbreeding will exhibit long runs of homozygosity. For example, the step-wise reintroduction strategy of the Alpine Ibex in the Swiss Alps created several strong population bottlenecks that reduced the genetic diversity of the newly introduced individuals. The effect of inbreeding in the resulting sub-populations could be studied by measuring the runs of homozygosity in different individuals.[4]
In clinical laboratory testing, the detection of ROH in itself does not indicate a particular genetic disorder but indicates an increased risk of autosomal recessive inherited diseases.[5] As ROHs smaller than 3 Mb spread throughout the genome are common even in outbred populations,[6] these segments were usually thought to not be important enough to report.[5] Large ROH can be indicative of uniparental isodisomy[7] with follow-up testing to rule out false positives, there is currently no consistent reporting standards among different laboratories.[5]
ROH can be used to detect the possibility of incest in humans.[8][5]
References
- ^ Purfield DC, Berry DP, McParland S, Bradley DG (August 2012). "Runs of homozygosity and population history in cattle". BMC Genetics. 13: 70. doi:10.1186/1471-2156-13-70. PMC 3502433. PMID 22888858.
- ^ McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, et al. (September 2008). "Runs of homozygosity in European populations". American Journal of Human Genetics. 83 (3): 359–72. doi:10.1016/j.ajhg.2008.08.007. PMC 2556426. PMID 18760389.
- ^ Colbert, Sarah M.C.; Wendt, Frank R.; Pathak, Gita A.; Helmer, Drew A.; Hauser, Elizabeth R.; Keller, Matthew C.; Polimanti, Renato; Johnson, Emma C. (2023-06-01). "Declining autozygosity over time: An exploration in over 1 million individuals from three diverse cohorts". The American Journal of Human Genetics. 110 (6): 1008–1014. doi:10.1016/j.ajhg.2023.04.007. PMC 10257001. PMID 37178685 – via Elsevier Science Direct.
- ^ Grossen C, Biebach I, Angelone- Alasaad S, Keller LF, Croll D (2018). "Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations Evol Appl. 2018;11: 123–139". Evolutionary Applications. 11 (2): 123–139. doi:10.1111/eva.12490. PMC 5775499. PMID 29387150.
- ^ a b c d Gonzales, Patrick R.; Andersen, Erica F.; Brown, Teneille R.; Horner, Vanessa L.; Horwitz, Juli; Rehder, Catherine W.; Rudy, Natasha L.; Robin, Nathaniel H.; Thorland, Erik C.; on behalf of the ACMG Laboratory Quality Assurance Committee (2022-02-03). "Interpretation and reporting of large regions of homozygosity and suspected consanguinity/uniparental disomy, 2021 revision: A technical standard of the American College of Medical Genetics and Genomics (ACMG)". Genetics in Medicine. 24 (2): 255–261. doi:10.1016/j.gim.2021.10.004.
- ^ Ceballos, Francisco C.; Joshi, Peter K.; Clark, David W.; Ramsay, Michèle; Wilson, James F. (2018-04-15). "Runs of homozygosity: windows into population history and trait architecture". Nature Reviews Genetics. 19 (4): 220–234. doi:10.1038/nrg.2017.109. hdl:20.500.11820/1928cc4c-af43-489f-b743-52ae374412d7. ISSN 1471-0056.
- ^ Papenhausen, Peter; Schwartz, Stuart; Risheg, Hiba; Keitges, Elisabeth; Gadi, Inder; Burnside, Rachel D.; Jaswaney, Vikram; Pappas, John; Pasion, Romela; Friedman, Kenneth; Tepperberg, James (2011-04-15). "UPD detection using homozygosity profiling with a SNP genotyping microarray". American Journal of Medical Genetics Part A. 155 (4): 757–768. doi:10.1002/ajmg.a.33939.
- ^ Zhang, Sarah (18 March 2024). "DNA Tests Are Uncovering the True Prevalence of Incest". The Atlantic. Retrieved 12 May 2024.