Maximum-likelihood estimation of recent shared ancestry (ERSA)

Genome Research

Volumn 21, Issue 5, 2011, Pages 768-774

  Huff, Chad D ^a   Witherspoon, David J ^a   Simonson, Tatum S ^a   Xing, Jinchuan ^a   Watkins, W Scott ^a   Zhang, Yuhua ^a   Tuohy, Therese M ^b   Neklason, Deborah W ^b   Burt, Randall W ^b   Guthery, Stephen L ^c   Woodward, Scott R ^d   Jorde, Lynn B ^a  

^a UNIVERSITY OF UTAH HEALTH SCIENCES CENTER   (United States)

^b UNIVERSITY OF UTAH   (United States)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^d Sorenson Molecular Genealogy Foundation   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; GENOTYPE; HUMAN; HUMAN GENOME; LAST COMMON ANCESTOR; MAXIMUM LIKELIHOOD ESTIMATION OF RECENT SHARED ANCESTRY; MAXIMUM LIKELIHOOD METHOD; PEDIGREE; PRIORITY JOURNAL; RELATIVE; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME MAPPING; DNA; FAMILY; GENETIC LINKAGE; HUMANS; INHERITANCE PATTERNS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEDIGREE; POLYMORPHISM, SINGLE NUCLEOTIDE; PRINCIPAL COMPONENT ANALYSIS; SOFTWARE;

EID: 79955570035     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.115972.110     Document Type: Article

References (33)

1. Alonso A, Martin P, Albarran C, Garcia P, Fernandez de Simon L, Jesus Iturralde M, Fernandez-Rodriguez A, Atienza I, Capilla J, Garcia-Hirschfeld J, et al. 2005. Challenges of DNA profiling in mass disaster investigations. Croat Med J 46: 540-548. (Pubitemid 41248177)
2. Berkovic SF, Dibbens LM, Oshlack A, Silver JD, Katerelos M, Vears DF, Lullmann-Rauch R, Blanz J, Zhang KW, Stankovich J, et al. 2008. Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis. Am J Hum Genet 82: 673-684.
3. Bieber FR, Brenner CH, Lazer D. 2006. Finding criminals through DNA of their relatives. Science 312: 1315-1316. (Pubitemid 43839525)
4. Biesecker LG, Bailey-Wilson JE, Ballantyne J, Baum H, Bieber FR, Brenner C, Budowle B, Butler JM, Carmody G, Conneally PM, et al. 2005. Epidemiology. DNA identifications after the 9/11 World Trade Center attack. Science 310: 1122-1123.
5. Boehnke M, Cox NJ. 1997. Accurate inference of relationships in sib-pair linkage studies. Am J Hum Genet 61: 423-429. (Pubitemid 27382319)
6. Brenner CH. 2006. Some mathematical problems in the DNA identification of victims in the 2004 tsunami and similar mass fatalities. Forensic Sci Int 157: 172-180.
7. Browning SR, Browning BL. 2010. High-resolution detection of identity by descent in unrelated individuals. Am J Hum Genet 86: 526-539.
8. Budimlija ZM, Prinz MK, Zelson-Mundorff A, Wiersema J, Bartelink E, MacKinnon G, Nazzaruolo BL, Estacio SM, Hennessey MJ, Shaler RC. 2003. World Trade Center human identification project: Experiences with individual body identification cases. Croat Med J 44: 259-263. (Pubitemid 36828141)
9. Cash HD, Hoyle JW, Sutton AJ. 2003. Development under extreme conditions: Forensic bioinformatics in the wake of the World Trade Center disaster. Pac Symp Biocomput 2003: 638-653.
10. Cherny SS, Abecasis GR, Cookson WO, Sham PC, Cardon LR. 2001. The effect of genotype and pedigree error on linkage analysis: Analysis of three asthma genome scans. Genet Epidemiol (Suppl 1) 21: S117-S122. (Pubitemid 32958843)
11. DeWoody JA. 2005. Molecular approaches to the study of parentage, relatedness, and fitness: Practical applications for wild animals. J Wildl Manage 69: 1400-1418.
12. Donnelly KP. 1983. The probability that related individuals share some section of genome identical by descent. Theor Popul Biol 23: 34-63.
13. Epstein MP, Duren WL, Boehnke M. 2000. Improved inference of relationship for pairs of individuals. Am J Hum Genet 67: 1219-1231.
14. Genovese G, Leibon G, Pollak M, Rockmore D. 2010. Improved IBD detection using incomplete haplotype information. BMC Genet 11: 58. doi: 10.1186/1471-2156-11-58.
15. Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe'er I. 2009. Whole population, genome-wide mapping of hidden relatedness. Genome Res 19: 318-326.
16. International HapMap Consortium 2005. A haplotype map of the human genome. Nature 437: 1299-1320.
17. Leclair B. 2004. Large-scale comparative genotyping and kinship analysis: Evolution in its use for human identification in mass fatality incidents and missing persons databasing. Prog Forensic Genet 10: 42-44.
18. Leclair B, Shaler R, Carmody GR, Eliason K, Hendrickson BC, Judkins T, Norton MJ, Sears C, Scholl T. 2007. Bioinformatics and human identification in mass fatality incidents: The World Trade Center disaster. J Forensic Sci 52: 806-819.
19. McPeek MS, Sun L. 2000. Statistical tests for detection of misspecified relationships by use of genome-screen data. Am J Hum Genet 66: 1076-1094. (Pubitemid 30470506)
20. McVean GAT, Myers SR, Hunt S, Deloukas P, Bentley DR, Donnelly P. 2004. The fine-scale structure of recombination rate variation in the human genome. Science 304: 581-584. (Pubitemid 38541915)
21. Neklason DW, Stevens J, Boucher KM, Kerber RA, Matsunami N, Barlow J, Mineau G, Leppert MF, Burt RW. 2008. American founder mutation for attenuated familial adenomatous polyposis. Clin Gastroenterol Hepatol 6: 46-52. (Pubitemid 50008414)
22. Pemberton TJ,Wang C, Li JZ, Rosenberg NA. 2010. Inference of unexpected genetic relatedness among individuals in HapMap Phase III. Am J Hum Genet 87: 457-464.
23. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, et al. 2007. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575. (Pubitemid 47330214)
24. Simonson TS, Yang Y, Huff CD, Yun H, Qin G, Witherspoon DJ, Bai Z, Lorenzo FR, Xing J, Jorde LB, et al. 2010. Genetic evidence for high-altitude adaptation in Tibet. Science 329: 72-75.
25. Slate J, Santure AW, Feulner PGD, Brown EA, Ball AD, Johnston SE, Gratten J. 2010. Genome mapping in intensively studied wild vertebrate populations. Trends Genet 26: 275-284.
26. Stankovich J, Bahlo M, Rubio JP, Wilkinson CR, Thomson R, Banks A, Ring M, Foote SJ, Speed TP. 2005. Identifying nineteenth century genealogical links from genotypes. Hum Genet 117: 188-199.
27. Sun L,Wilder K, McPeek MS. 2002. Enhanced pedigree error detection. Hum Hered 54: 99-110. (Pubitemid 36091883)
28. Thomas A, Skolnick MH, Lewis CM. 1994. Genomic mismatch scanning in pedigrees. Math Med Biol 11: 1-16. (Pubitemid 2098868)
29. Thomas A, Camp NJ, Farnham JM, Allen-Brady K, Cannon-Albright LA. 2008. Shared genomic segment analysis. Mapping disease predisposition genes in extended pedigrees using SNP genotype assays. Ann Hum Genet 72: 279-287.
30. Voight BF, Pritchard JK. 2005. Confounding from cryptic relatedness in case-control association studies. PLoS Genet 1: e32. doi: 10.1371/journal.pgen. 0010032.
31. Weir BS, Anderson AD, Hepler AB. 2006. Genetic relatedness analysis: Modern data and new challenges. Nat Rev Genet 7: 771-780. (Pubitemid 44413221)
32. Xing J,Watkins WS, Shlien A,Walker E, Huff CD,Witherspoon DJ, Zhang Y, Simonson TS, Weiss RB, Schiffman JD, et al. 2010. Toward a more uniform sampling of human genetic diversity: A survey of worldwide populations by high-density genotyping. Genomics 96: 199-210.
33. Zupanic Pajnic I, Gornjak Pogorelc B, Balazic J. 2010. Molecular genetic identification of skeletal remains from the Second World War Konfin I mass grave in Slovenia. Int J Legal Med 124: 307-317.