Maximum parsimony xor haplotyping by sparse dictionary selection

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Elmas, Abdulkadir ^a   Jajamovich, Guido H ^b   Wang, Xiaodong ^a  

^a Department of Earth and Environmental Sciences   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR;

ACCURACY; ARTICLE; CONTROLLED STUDY; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC DATABASE; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; PARSIMONY ANALYSIS; PURE PARSIMONY XOR HAPLOTYPING; SINGLE NUCLEOTIDE POLYMORPHISM; SPARSE DICTIONARY SELECTION; XOR HAPLOGEN;

ALGORITHMS; COMPUTATIONAL BIOLOGY; HAPLOTYPES; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84884407998     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-645     Document Type: Article

References (42)

1. Brookes A. The essence of SNPs. Gene 1999, 234:177-186. 10.1016/S0378-1119(99)00219-X, 10395891.
2. Risch N, Merikangas K. The future of genetic studies of complex human diseases. Science 1996, 273:1516-1517. 10.1126/science.273.5281.1516, 8801636.
3. Kwok PY, Gu Z. Single nucleotide polymorphism libraries: why and how are we building them?. Mol Med Today 1999, 5:538-543. 10.1016/S1357-4310(99)01601-9, 10562720.
4. Gray IC, Campbell DA, Spurr NK. Single nucleotide polymorphisms as tools in human genetics. Human Mol Genet 2000, 9:2403-2408.
5. Peters T, Sedlmeier R. Current methods for high-throughput detection of novel DNA polymorphisms. Drug Discov Today: Technol 2006, 3(2):123-129.
6. Xiao W, Oefner PJ. Denaturing high-performance liquid chromatography: a review. Human Mutat 2001, 17:439-474.
7. Bansal V, Bafna V. HapCUT: An efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 2008, 24(16):i153-i159. 10.1093/bioinformatics/btn298, 18689818.
8. He D, Choi A, Pipatsrisawat K, Darwiche A, Eskin E. Optimal algorithms for haplotype assembly from whole-genome sequence data. Bioinformatics 2010, 26(12):i183-i190. 10.1093/bioinformatics/btq215, 2881399, 20529904.
9. Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010, 34(8):816-834. 10.1002/gepi.20533, 3175618, 21058334.
10. Gupta A, Manuch J, Stacho L, Zhao X. Algorithm for haplotype inference via galled-tree networks with simple galls. J Comput Biol 2012, 19(4):439-454. 10.1089/cmb.2010.0145, 22468709.
11. Iliadis A, Anastassiou D, Wang X. A unified framework for haplotype inference in nuclear families. Ann Hum Genet 2012, 76(4):312-325. 10.1111/j.1469-1809.2012.00715.x, 22607042.
12. Lai E, Wang W, Jiang T, Wu K. A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree. BMC Bioinformatics 2012, 13(Suppl 17):S19. 10.1186/1471-2105-13-S17-S19, 3521470, 23281626.
13. He D, Han B, Eskin E. Hap-seq: An optimal algorithm for haplotype phasing with imputation using sequencing data. J Comput Biol 2013, 20(2):80-92. 10.1089/cmb.2012.0091, 23383995.
14. Kimura M, Crow JF. The number of alleles that can be maintained in a finite population. Genet 1964, 49:725-738.
15. Barzuza T, Beckmann JS, Shamir R, Pe'er I. Computational problems in perfect phylogeny haplotyping: Typing without calling the allele. IEEE/ACM Trans Comput Biol Bioinformatics 2008, 5:101-109.
16. Liberatore V. Matroid decomposition methods for the set maxima problem. Proceedings of the Ninth Annual ACM-SIAM Symposium on Discrete Algorithms 1998, 400-409. Philadelphia: Society for Industrial and Applied Mathematics.
17. Gusfield D. Haplotyping as perfect phylogeny: conceptual framework and efficient solutions. Proc. 6th Annual Conference on Research in Computational Molecular Biology (RECOMB 2002) 2002, 166-175. New York: ACM.
18. Barzuza T, Beckmann J, Shamir R, Pe'er I. Computational problems in perfect phylogeny haplotyping: Xor-Genotypes and tag SNPs. Combinatorial Pattern Matching, Volume 3109 2004, 14-31. Berlin, Heidelberg, New York: Springer-Verlag, Dogrusoz U, Muthukrishnan S, Sahinalp S.
19. Patil N, et al. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 2001, 294:1719-1723. 10.1126/science.1065573, 11721056.
20. Lancia G, Pinotti MC, Rizzi R. Haplotyping populations by pure parsimony: Complexity of exact and approximation algorithms. INFORMS J on Comput 2004, 16:348-359.
21. Gusfield D. Haplotype inference by pure parsimony. Comb Pattern Matching 2003, 144-155. Berlin, Heidelberg, New York: Springer-Verlag.
22. Wang L, Xu Y. Haplotype inference by maximum parsimony. Bioinformatics 2003, 19:1773-1780. 10.1093/bioinformatics/btg239, 14512348.
23. Sazonova N, Sazonov E, Harner EJ. Algorithm for haplotype resolution and block partitioning for partial XOR-genotype data. J of Biomed Inform 2010, 43:51-59.
24. Bonizzoni P, Della Vedova G, Dondi R, Pirola Y, Rizzi R. Pure parsimony xor haplotyping. IEEE/ACM Trans Comput Biol Bioinformatics 2010, 7:598-610.
25. Jajamovich GH, Wang X. Maximum-parsimony haplotype inference based on sparse representations of genotypes. IEEE Trans Signal Process 2012, 60:2013-2023.
26. Nemhauser GL, Wolsey LA, Fisher ML. An analysis of approximations for maximizing submodular set functions-I. Math Program 1978, 14:265-294.
27. Krause A, Cevher V. Submodular dictionary selection for sparse representation. Proceedings of 27th International Conference on Machine Learning (ICML 2010) 2010, 567-574. Madison: Omnipress.
28. Niu T, Qin Z, Xu X, Liu J. Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 2002, 70:157-169. 10.1086/338446, 448439, 11741196.
29. Liang K, Wang X. A deterministic sequential monte carlo method for haplotype inference. IEEE J Selected Topics Signal Process 2008, 2:322-331.
30. Hey J. What's so hot about recombination hotspots?. PLoS Biol 2004, 2:e190+. 423158, 15208734.
31. Bonin A, Bellemain E, Bronken Eidesen P, Pompanon F, Brochmann C, Taberlet P. How to track and assess genotyping errors in population genetics studies. Mol Ecol 2004, 13:3261-3273. 10.1111/j.1365-294X.2004.02346.x, 15487987.
32. Pompanon F, Bonin A, Bellemain E, Taberlet P. Genotyping errors: causes, consequences and solutions. Nat Rev Genet 2005, 6:847-846. 10.1038/nrg1707, 16304600.
33. Hackett CA, Broadfoot LB. Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps. Heredity 2003, 90:33-38. 10.1038/sj.hdy.6800173, 12522423.
34. Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nature Genet 2007, 39(7):906-913. 10.1038/ng2088, 17572673.
35. Tininini L, Bertolazzi P, Godi A, Lancia G. CollHaps: a heuristic approach to haplotype inference by parsimony. IEEE/ACM Trans Comput Biol Bioinformatics 2010, 7:511-523.
36. Hudson RR. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18:337-338. 10.1093/bioinformatics/18.2.337, 11847089.
37. Kerem B, Rommens J, Buchanan J, Markiewicz D, Cox T, Chakravarti A, Buchwald M, Tsui L. Identification of the cystic fibrosis gene: genetic analysis. Science 1989, 245:1073-1080. 10.1126/science.2570460, 2570460.
38. Halldorsson BV, Bafna V, Edwards N, Yooseph S, Istrail S. A survey of computational methods for determining haplotypes. Lecture Notes in Computer Science (2983): Computational Methods for SNPs and Haplotype Inference 2004, 26-47. Berlin, Heidelberg, New York: Springer-Verlag.
39. Stephens M, Scheet P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Human Genet 2005, 76(3):449-462.
40. Excoffier L, Laval G, Balding D. Gametic phase estimation over large genomic regions using an adaptive window approach. Human Genomics 2003, 1:7-19. 10.1186/1479-7364-1-1-7, 3525008, 15601529.
41. Iacobucci I, Sazzini M, Garagnani P, Ferrari A, Boattini A, Lonetti A, Papayannidis C, Mantovani V, Marasco E, Ottaviani E, Soverini S, Girelli D, Luiselli D, Vignetti M, Baccarani M, Martinelli G. A polymorphism in the chromosome 9p21 ANRIL locus is associated to Philadelphia positive acute lymphoblastic leukemia. Leukemia Res 2011, 35(8):1052-1059.
42. Pasmant E, Laurendeau I, Heron D, Vidaud M, Vidaud D, Bieche I. Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: Identification of ANRIL, an Antisense Noncoding RNA whose expression coclusters with ARF. Cancer Res 2007, 67(8):3963-3969. 10.1158/0008-5472.CAN-06-2004, 17440112.