Detecting autozygosity through runs of homozygosity: A comparison of three autozygosity detection algorithms

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Howrigan, Daniel P ^a   Simonson, Matthew A ^a   Keller, Matthew C ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; AUTOZYGOSITY; COMPUTER PROGRAM; CONTROLLED STUDY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC ASSOCIATION; GENOME; HOMOZYGOSITY; RUNS OF HOMOZYGOSITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; ZYGOSITY; BIOLOGY; CHROMOSOME MAP; COMPARATIVE STUDY; COMPUTER SIMULATION; DNA SEQUENCE; HOMOZYGOTE; HUMAN; HUMAN GENOME; METHODOLOGY; REGRESSION ANALYSIS;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GENOME, HUMAN; HOMOZYGOTE; HUMANS; LINKAGE DISEQUILIBRIUM; POLYMORPHISM, SINGLE NUCLEOTIDE; REGRESSION ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 80053176070     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-460     Document Type: Article

References (39)

1. Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet 2006, 15(5):789-795. 10.1093/hmg/ddi493, 16436455.
2. Charlesworth D, Willis JH. The genetics of inbreeding depression. Nat Rev Genet 2009, 10(11):783-796. 10.1038/nrg2664, 19834483.
3. Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF. Genomic runs of homozygosity record population history and consanguinity. PLoS One 2010, 5(11):e13996. 10.1371/journal.pone.0013996, 2981575, 21085596.
4. Li LH, Ho SF, Chen CH, Wei CY, Wong WC, Li LY, Hung SI, Chung WH, Pan WH, Lee MT, Tsai FJ, Chang CF, Wu JY, Chen YT. Long contiguous stretches of homozygosity in the human genome. Hum Mutat 2006, 27(11):1115-1121. 10.1002/humu.20399, 16955415.
5. McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF. Runs of homozygosity in European populations. Am J Hum Genet 2008, 83(3):359-372. 10.1016/j.ajhg.2008.08.007, 2556426, 18760389.
6. Nothnagel M, Lu TT, Kayser M, Krawczak M. Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans. Hum Mol Genet 2010, 19(15):2927-2935. 10.1093/hmg/ddq198, 20462934.
7. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie X, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, . International HapMap Consortium Genome-wide detection and characterization of positive selection in human populations. Nature 2007, 449(7164):913-918. 10.1038/nature06250, 2687721, 17943131, International HapMap Consortium.
8. Voight BF, Kudaravalli S, Wen X, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol 2006, 4(3):e72. 10.1371/journal.pbio.0040072, 1382018, 16494531.
9. Abu Safieh L, Aldahmesh MA, Shamseldin H, Hashem M, Shaheen R, Alkuraya H, Al Hazzaa SA, Al-Rajhi A, Alkuraya FS. Clinical and molecular characterisation of Bardet-Biedl syndrome in consanguineous populations: the power of homozygosity mapping. J Med Genet 2010, 47(4):236-241. 10.1136/jmg.2009.070755, 19858128.
10. Borck G, Ur Rehman A, Lee K, Pogoda HM, Kakar N, von Ameln S, Grillet N, Hildebrand MS, Ahmed ZM, Nurnberg G, Ansar M, Basit S, Javed Q, Morell RJ, Nasreen N, Shearer AE, Ahmad A, Kahrizi K, Shaikh RS, Ali RA, Khan SN, Goebel I, Meyer NC, Kimberling WJ, Webster JA, Stephan DA, Schiller MR, Bahlo M, Najmabadi H, Gillespie PG, Nurnberg P, Wollnik B, Riazuddin S, Smith RJ, Ahmad W, Muller U, Hammerschmidt M, Friedman TB, Riazuddin S, Leal SM, Ahmad J, Kubisch C. Loss-of-function mutations of ILDR1 cause autosomal-recessive hearing impairment DFNB42. Am J Hum Genet 2011, 88(2):127-137. 10.1016/j.ajhg.2010.12.011, 3035704, 21255762.
11. Collin RW, Safieh C, Littink KW, Shalev SA, Garzozi HJ, Rizel L, Abbasi AH, Cremers FP, den Hollander AI, Klevering BJ, Ben-Yosef T. Mutations in C2ORF71 cause autosomal-recessive retinitis pigmentosa. Am J Hum Genet 2010, 86(5):783-788. 10.1016/j.ajhg.2010.03.016, 2869006, 20398884.
12. Kalay E, Yigit G, Aslan Y, Brown KE, Pohl E, Bicknell LS, Kayserili H, Li Y, Tuysuz B, Nurnberg G, Kiess W, Koegl M, Baessmann I, Buruk K, Toraman B, Kayipmaz S, Kul S, Ikbal M, Turner DJ, Taylor MS, Aerts J, Scott C, Milstein K, Dollfus H, Wieczorek D, Brunner HG, Hurles M, Jackson AP, Rauch A, Nurnberg P, Wollnik B. CEP152 is a genome maintenance protein disrupted in Seckel syndrome. Nat Genet 2011, 43(1):23-26. 10.1038/ng.725, 21131973.
13. Walsh T, Shahin H, Elkan-Miller T, Lee MK, Thornton AM, Roeb W, Abu Rayyan A, Loulus S, Avraham KB, King MC, Kanaan M. Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82. Am J Hum Genet 2010, 87(1):90-94. 10.1016/j.ajhg.2010.05.010, 2896776, 20602914.
14. Zelinger L, Banin E, Obolensky A, Mizrahi-Meissonnier L, Beryozkin A, Bandah-Rozenfeld D, Frenkel S, Ben-Yosef T, Merin S, Schwartz SB, Cideciyan AV, Jacobson SG, Sharon D. A missense mutation in DHDDS, encoding dehydrodolichyl diphosphate synthase, is associated with autosomal-recessive retinitis pigmentosa in Ashkenazi Jews. Am J Hum Genet 2011, 88(2):207-215. 10.1016/j.ajhg.2011.01.002, 3035703, 21295282.
15. Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Kucherlapati R, Malhotra AK. Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci USA 2007, 104(50):19942-19947. 10.1073/pnas.0710021104, 2148402, 18077426.
16. Vine AE, McQuillin A, Bass NJ, Pereira A, Kandaswamy R, Robinson M, Lawrence J, Anjorin A, Sklar P, Gurling HM, Curtis D. No evidence for excess runs of homozygosity in bipolar disorder. Psychiatr Genet 2009, 19(4):165-170. 10.1097/YPG.0b013e32832a4faa, 19451863.
17. Wang S, Haynes C, Barany F, Ott J. Genome-wide autozygosity mapping in human populations. Genet Epidemiol 2009, 33(2):172-180. 10.1002/gepi.20344, 2802852, 18814273.
18. Nalls MA, Guerreiro RJ, Simon-Sanchez J, Bras JT, Traynor BJ, Gibbs JR, Launer L, Hardy J, Singleton AB. Extended tracts of homozygosity identify novel candidate genes associated with late-onset Alzheimer's disease. Neurogenetics 2009, 10(3):183-190. 10.1007/s10048-009-0182-4, 2908484, 19271249.
19. Spain SL, Cazier JB, Houlston R, Carvajal-Carmona L, Tomlinson I. Colorectal cancer risk is not associated with increased levels of homozygosity in a population from the United Kingdom. Cancer research 2009, 69(18):7422. 10.1158/0008-5472.CAN-09-0659, 19723657.
20. Hosking FJ, Papaemmanuil E, Sheridan E, Kinsey SE, Lightfoot T, Roman E, Irving JAE, Allan JM, Taylor M, Tomlinson IP. Genome-wide homozygosity signatures and childhood acute lymphoblastic leukemia risk. Blood 2010, 115(22):4472. 10.1182/blood-2009-09-244483, 20231427.
21. Enciso-Mora V, Hosking FJ, Houlston RS. Risk of breast and prostate cancer is not associated with increased homozygosity in outbred populations. European Journal of Human Genetics 2010, 18:909-914. 10.1038/ejhg.2010.53, 2987391, 20407466.
22. Yang TL, Guo Y, Zhang LS, Tian Q, Yan H, Papasian CJ, Recker RR, Deng HW. Runs of homozygosity identify a recessive locus 12q21.31 for human adult height. J Clin Endocrinol Metab 2010, 95(8):3777-3782. 10.1210/jc.2009-1715, 2913044, 20466785.
23. Ku CS, Naidoo N, Teo SM, Pawitan Y. Regions of homozygosity and their impact on complex diseases and traits. Hum Genet 2010, 129(1):1-15.
24. Ioannidis JP. Why most published research findings are false. PLoS Med 2005, 2(8):e124. 10.1371/journal.pmed.0020124, 1182327, 16060722.
25. Keller MC, Visscher PM, Goddard ME. Quantification of inbreeding due to distant ancestors and its detection using dense SNP data. Genetics 2011,
26. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81(3):559-575. 10.1086/519795, 1950838, 17701901.
27. Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I. Whole population, genome-wide mapping of hidden relatedness. Genome Res 2009, 19(2):318-326. 2652213, 18971310.
28. Browning SR, Browning BL. High-resolution detection of identity by descent in unrelated individuals. Am J Hum Genet 2010, 86(4):526-539. 10.1016/j.ajhg.2010.02.021, 2850444, 20303063.
29. Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from population-scale sequencing. Nature 2010, 467(7319):1061-1073. 10.1038/nature09534, 3042601, 20981092.
30. Chadeau-Hyam M, Hoggart CJ, O'Reilly PF, Whittaker JC, De Iorio M, Balding DJ. Fregene: simulation of realistic sequence-level data in populations and ascertained samples. BMC Bioinformatics 2008, 9:364. 10.1186/1471-2105-9-364, 2542380, 18778480.
31. Fisher RA. The genetical theory of natural selection 1930, Oxford, UK: Clarendon Press.
32. Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST. Genetic traces of ancient demography. Proc Natl Acad Sci USA 1998, 95(4):1961-1967. 10.1073/pnas.95.4.1961, 19224, 9465125.
33. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D. Calibrating a coalescent simulation of human genome sequence variation. Genome Res 2005, 15(11):1576-1583. 10.1101/gr.3709305, 1310645, 16251467.
34. Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, Crowe RR, Oksenberg JR, Mirel DB, Kendler KS, Freedman R, Gejman PV. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature 2009, 460(7256):753-757. 2775422, 19571809.
35. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R. Linkage disequilibrium in the human genome. Nature 2001, 411(6834):199-204. 10.1038/35075590, 11346797.
36. Fenner JN. Cross-cultural estimation of the human generation interval for use in genetics-based population divergence studies. Am J Phys Anthropol 2005, 128(2):415-423. 10.1002/ajpa.20188, 15795887.
37. Hedrick PW. Genetics of populations 2011, Sudbury, MA: Jones & Bartlett Publishers.
38. Rabbee N, Speed TP. A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics 2006, 22(1):7-12. 10.1093/bioinformatics/bti741, 16267090.
39. Sullivan PF, Purcell S. Analyzing genome-wide association study data: a tutorial using PLINK. Statistical genetics: gene mapping through linkage and association 2008, 355-391. New York: Taylor & Francis Group, Neale BM, Ferreira MA, Medland SE, Posthuma D.