Genome scanning by composite likelihood

American Journal of Human Genetics

Volumn 80, Issue 1, 2007, Pages 19-28

  Morton, Newton ^a   Maniatis, Nikolas ^a   Zhang, Weihua ^a   Ennis, Sarah ^a   Collins, Andrew ^a  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MARKER;

ACCURACY; ANALYTICAL ERROR; ARTICLE; CHROMOSOME MAP; COMPOSITE LIKELIHOOD; COMPUTER PROGRAM; DATA ANALYSIS; DISEASE ASSOCIATION; FALSE DISCOVERY RATE; GENE FREQUENCY; GENE LOCATION; GENE MAPPING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC LINKAGE; GENOME ANALYSIS; GENOME SCANNING; GENOTYPE PHENOTYPE CORRELATION; LINKAGE ANALYSIS; MALECOT MODEL; MATHEMATICAL ANALYSIS; MULTIFACTORIAL INHERITANCE; PRIORITY JOURNAL; STANDARD ERROR; STATISTICAL ANALYSIS; STATISTICAL MODEL;

EID: 33846019677     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/510401     Document Type: Article

References (33)

1. Kerem B, Rommens JM, Buchanan JA, Markiewicz D, Cox TK, Chakravarti A, Buchwald M, Tsui L-C (1989) Identification of the cystic fibrosis gene: genetic analysis. Science 245:1073-1080
2. Collins A, Morton NE (1998) Mapping a disease locus by allelic association. Proc Natl Acad Sci USA 95:1741-1745
3. Morton NE, Zhang W, Taillon-Miller P, Ennis S, Kwok P-Y, Collins A (2001) The optimal measure of allelic association. Proc Natl Acad Sci USA 98:5217-5221
4. Maniatis N, Collins A, Xu C-F, McCarthy LC, Hewett DR, Tapper W, Ennis S, Ke K, Morton NE (2002) The first linkage disequilibrium maps: delineation of hot and cold blocks by diplotype analysis. Proc Natl Acad Sci USA 99:2228-2233
5. Maniatis N, Morton NE, Gibson J, Xu C-F, Hosking LK, Collins A (2005) The optimal measure of linkage disequilibrium reduces error in association mapping of affection status. Hum Mol Genet 14:145-153
6. International HapMap Consortium (2003) The International HapMap Project. Nature 426:789-796
7. Morton NE (2006) Fifty years of genetic epidemiology, with special reference to Japan. J Hum Genet 51:269-277
8. Kaiser J (2006) NIH goes after whole genome in search of disease genes. Science 311:933
9. Morton NE (1955) Sequential tests for the detection of linkage. Am J Hum Genet 7:277-318
10. Storey JD, Tibshirani R (2003) Statistical significance for genome-wide studies. Proc Natl Acad Sci USA 100:9440-9445
11. Dalmasso C, Broet P, Moreau T (2004) A simple procedure for estimating the false discovery rate. Bioinformatics 21:660-668
12. Lindsay BG (1988) Composite likelihood methods. Contemp Math 80:221-239
13. Maniatis N, Collins A, Gibson J, Zhang W, Tapper W, Morton NE (2004) Positional cloning by linkage disequilibrium. Am J Hum Genet 74:846-855
14. Ioannidis JPA, Gwinn M, Little J, Higgins JPT, Bernstein JI, Boffetta P, Bondy M, Bray MS, Brenchley PE, Buffler PA, et al (2006) A road map for efficient and reliable human genome epidemiology. Nat Genet 38:3-5
15. Tukey JW (1962) The future of data analysis. Ann Math Stat 33:1-67
16. Lander E, Kruglyak L (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 11:241-247
17. International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437:1299-1320
18. Zeggini E, Raynor W, Morris AP, Hattersley AT, Walker M, Hitman GA, Deloukas P, Cardon LR, McCarthy MI (2005) An evaluation of HapMap sample size and tagging SNP performance in large-scale empirical and simulated datasets. Nat Genet 37:1320-1322
19. Tapper W, Collins A, Gibson J, Maniatis N, Ennis S, Morton NE (2005) A map of the human genome in linkage disequilibrium units. Proc Natl Acad Sci USA 102:11835-11839
20. Smith CAB (1953) The detection of linkage in human genetics. J Roy Stat Soc B 15:153-192
21. Lander ES, Botstein D (1987) Homozygosity mapping: a way to map human recessive traits with the DNA of inbred children. Science 236:1567-1570
22. Zhang W, Collins A, Morton NE (2004) Does haplotype diversity predict power for association mapping of disease genes? Hum Genet 115:157-164
23. Todd JA (2006) Statistical false positive or true disease pathway? Nat Genet 38:731-733
24. Iwamato K, Kato T (2006) Gene expression profiling in schizophrenia and related mental disorders. Neuroscientist 12:349-361
25. Risch N, Merikangas K (1996) The future of genetic studies of complex human disease. Science 273:1516-1517
26. Daly MJ, Rioux JV, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype structure in the human genome. Nat Genet 29:229-232
27. Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, et al (2004) Methods for high-density admixture mapping of disease genes. Am J Hum Genet 74:979-1000
28. Amundadottir LT, Sulem P, Gudmundsson J, Helgason A, Baker A, Agnarsson BA, Sigurdsson A, Benediktsdottir KR, Cazier JB, Sainz J, et al (2006) A common variant associated with prostate cancer in European and African populations. Nat Genet 38:652-658
29. Freedman ML, Haiman CA, Patterson N, McDonald GJ, Tandon A, Waliszewska A, Penney K, Steen RG, Ardie K, John EM, et al (2006) Admixture mapping identifies 8q24 as a prostate cancer risk locus in African-American men. Proc Nat Acad Sci USA 103:14068-14073
30. Browning SR (2006) Multilocus mapping using variable-length Markov chains. Am J Hum Genet 78:903-913
31. Dudbridge F, Koeleman BPC (2004) Efficient computation of significance levels from multiple association in large studies of correlated data, including genomewide association studies. Am J Hum Genet 75:424-435
32. Verzilli CJ, Stallard N, Whittaker JC (2006) Bayesian graphical models for genomewide association studies. Am J Hum Genet 79:100-112
33. Hosking LK, Boyd PR, Xu CF, Nissum M, Cantone K, Purvis IJ, Khakhar R, Barnes MR, Liberwirth U, Hagen-Mann K, et al (2002) Linkage disequilibrium mapping identifies a 390 kb region associated with CYP2D6 poor drug metabolising activity. Pharmacogenomics J 2:165-175