Efficient haplotype block recognition of very long and dense genetic sequences

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Taliun, Daniel ^a,b   Gamper, Johann ^b   Pattaro, Cristian ^a  

^a INSTITUTE FOR RENEWABLE ENERGY   (Italy)

^b FREE UNIVERSITY OF BOZEN BOLZANO   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATED ESTIMATORS; COMPUTATIONAL REQUIREMENTS; GENOME-WIDE ASSOCIATION; INCREMENTAL OPTIMIZATION; LONG RANGE CORRELATIONS; ORIGINAL ALGORITHMS; RECOGNITION ALGORITHM; RHEUMATOID ARTHRITIS;

ALGORITHMS; DNA SEQUENCES;

GENES;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOME; HAPLOTYPE; HUMAN; METHODOLOGY; RHEUMATOID ARTHRITIS;

ALGORITHMS; ARTHRITIS, RHEUMATOID; COMPUTATIONAL BIOLOGY; GENE FREQUENCY; GENOME; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84892375712     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-10     Document Type: Article

References (35)

1. Reich DE, Cargill M, Bolk S, Ireland J, Sabeti PC, Richter DJ, Lavery T, Kouyoumjian R, Farhadian SF, Ward R, Lander ES. Linkage disequilibrium in the human genome. Nature 2001, 411(6834):199-204. 10.1038/35075590, 11346797.
2. Lewontin RC. The interaction of selection and linkage. I. general considerations; heterotic models. Genetics 1964, 49:49-67. 1210557, 17248194.
3. Hill W, Robertson A. Linkage disequilibrium in finite populations. Theo Appl Genet 1968, 38(6):226-231.
4. Gu S, Pakstis AJ, Kidd KK. HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations. Bioinformatics 2005, 21(20):3938-3939. 10.1093/bioinformatics/bti649, 16131520.
5. Pattaro C, Ruczinski I, Fallin D, Parmigiani G. Haplotype block partitioning as a tool for dimensionality reduction in SNP association studies. BMC Genomics 2008, 9:405. 10.1186/1471-2164-9-405, 2547855, 18759977.
6. Zapata C. On the uses and applications of the most commonly used measures of linkage disequilibrium from the comparative analysis of their statistical properties. Hum Hered 2011, 71(3):186-195. 10.1159/000327732, 21778738.
7. Zhang K, Qin Z, Chen T, Liu JS, Waterman MS, Sun F. HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics 2005, 21:131-134. 10.1093/bioinformatics/bth482, 15333454.
8. Gibson J, Tapper W, Ennis S, Collins A. Exome-based linkage disequilibrium maps of individual genes: functional clustering and relationship to disease. Hum Genet 2013, 132(2):233-243. 10.1007/s00439-012-1243-6, 23124193.
9. Tregouet DA, Konig IR, Erdmann J, Munteanu A, Braund PS, Hall AS, Groszhennig A, Linsel-Nitschke P, Perret C, DeSuremain M, Meitinger T, Wright BJ, Preuss M, Balmforth AJ, Ball SG, Meisinger C, Germain C, Evans A, Arveiler D, Luc G, Ruidavets JB, Morrison C, van der Harst P, Schreiber S, Neureuther K, Schafer A, Bugert P, El Mokhtari NE, Schrezenmeir J, Stark K, et al. Genome-wide haplotype association study identifies the, SLC22A3-LPAL2-LPA gene cluster as a risk locus for coronary artery disease. Nat Genet 2009, 41(3):283-285. 10.1038/ng.314, 19198611.
10. Lambert JC, Grenier-Boley B, Harold D, Zelenika D, Chouraki V, Kamatani Y, Sleegers K, Ikram MA, Hiltunen M, Reitz C, Mateo I, Feulner T, Bullido M, Galimberti D, Concari L, Alvarez V, Sims R, Gerrish A, Chapman J, Deniz-Naranjo C, Solfrizzi V, Sorbi S, Arosio B, Spalletta G, Siciliano G, Epelbaum J, Hannequin D, Dartigues JF, Tzourio C, Berr C, et al. Genome-wide haplotype association study identifies the, FRMD4A gene as a risk locus for Alzheimer's disease. Mol Psychiatry 2013, 18(4):461-470. 10.1038/mp.2012.14, 3606943, 22430674.
11. Song C, Chen GK, Millikan RC, Ambrosone CB, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming SL, Rodriguez-Gil JL, Chanock SJ, Wan P, Sheng X, Pooler LC, Van Den Berg DJ, Le Marchand L, Kolonel LN, Henderson BE, Haiman CA, Stram DO. A Genome-wide scan for breast cancer risk haplotypes among African American women. PLoS ONE 2013, 8(2):e57298. 10.1371/journal.pone.0057298, 3585353, 23468962.
12. Dering C, Hemmelmann C, Pugh E, Ziegler A. Statistical analysis of rare sequence variants: an overview of collapsing methods. Genet Epidemiol 2011, 35(S1):S12-S17. 10.1002/gepi.20643, 3277891, 22128052.
13. Wang K, Li M, Bucan M. Pathway-based approaches for analysis of genomewide association studies. Am J Hum Genet 2007, 81(6):1278-1283. 10.1086/522374, 2276352, 17966091.
14. Petersen A, Alvarez C, DeClaire S, Tintle NL. Assessing methods for assigning SNPs to genes in gene-based tests of association using common variants. PLoS ONE 2013, 8(5):e62161. 10.1371/journal.pone.0062161, 3669368, 23741293.
15. Christoforou A, Dondrup M, Mattingsdal M, Mattheisen M, Giddaluru S, Nöthen MM, Rietschel M, Cichon S, Djurovic S, Andreassen OA, Jonassen I, Steen VM, Puntervoll P, Hellard SL. Linkage-disequilibrium-based binning affects the interpretation of GWASs. Am J Hum Genet 2012, 90(4):727-733. 10.1016/j.ajhg.2012.02.025, 3322240, 22444669.
16. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, et al. Ensembl 2013. Nucl Acids Res 2013, 41(D1):D48-D55. 10.1093/nar/gks1236, 3531136, 23203987.
17. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res 2002, 12(6):996-1006. 186604, 12045153.
18. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet 2001, 29(2):229-232. 10.1038/ng1001-229, 11586305.
19. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BTN, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SPA, Cox DR. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001, 294(5547):1719-1723. 10.1126/science.1065573, 11721056.
20. Zhang K, Deng M, Chen T, Waterman MS, Sun F. A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci USA 2002, 99(11):7335-7339. 10.1073/pnas.102186799, 124231, 12032283.
21. Anderson EC, Novembre J. Finding haplotype block boundaries by using the minimum-description-length principle. Am J Human Genet 2003, 73(2):336-354.
22. Mourad R, Sinoquet C, Leray P. Probabilistic graphical models for genetic association studies. Brief Bioinformatics 2012, 13:20-33. 10.1093/bib/bbr015, 21450805.
23. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D. The structure of haplotype blocks in the human genome. Science 2002, 296(5576):2225-2229. 10.1126/science.1069424, 12029063.
24. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21(2):263-265. 10.1093/bioinformatics/bth457, 15297300.
25. 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 Human Genet 2007, 81(3):559-575.
26. Zapata C, Alvarez G, Carollo C. Approximate variance of the standardized measure of gametic disequilibrium D'. Am J Hum Genet 1997, 61(3):771-774. 10.1016/S0002-9297(07)64342-0, 1715938, 9326344.
27. Wall JD, Pritchard JK. Assessing the performance of the haplotype block model of linkage disequilibrium. Am J Hum Genet 2003, 73(3):502-515. 10.1086/378099, 1180676, 12916017.
28. The International HapMap Consortium The international HapMap project. Nature 2003, 426(6968):789-796. 10.1038/nature02168, 14685227, The International HapMap Consortium.
29. The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 2010, 467(7319):1061-1073. 10.1038/nature09534, 3042601, 20981092, The 1000 Genomes Project Consortium.
30. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006, 38:904-909. 10.1038/ng1847, 16862161.
31. Delaneau O, Marchini J, Zagury JF. A linear complexity phasing method for thousands of genomes. Nature Methods 2011, 9(2):179-181. 10.1038/nmeth.1785, 22138821.
32. Shim H, Chun H, Engelman C, Payseur B. Genome-wide association studies using single-nucleotide polymorphisms versus haplotypes: an empirical comparison with data from the North American Rheumatoid Arthritis consortium. BMC Proceedings 2009, 3(Suppl 7):S35. 10.1186/1753-6561-3-s7-s35, 2795933, 20018026.
33. Park J, Namkung J, Jhun M, Park T. Genome-wide analysis of haplotype interaction for the data from the North American Rheumatoid Arthritis Consortium. BMC Proceedings 2009, 3(Suppl 7):S34. 10.1186/1753-6561-3-s7-s34, 2795932, 20018025.
34. Lorenz AJ, Hamblin MT, Jannink JL. Performance of single nucleotide Polymorphisms versus Haplotypes for genome-wide association analysis in Barley. PLoS ONE 2010, 5(11):e14079. 10.1371/journal.pone.0014079, 2989918, 21124933.
35. Hindorff LA, MacArthur J, Morales J, Junkins HA, Hall PN, Klemm AK, Manolio TA. A catalog of published genome-wide association studies. http://www.genome.gov/gwastudies. [Accessed December 7,2013].