Measuring marker information content by the ambiguity of block boundaries observed in dense SNP data

Annals of Human Genetics

Volumn 71, Issue 1, 2007, Pages 127-140

  Gu, C Charles ^a   Yu, Kai ^a,b   Boerwinkle, Eric ^c  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c UNIVERSITY OF TEXAS   (United States)

Author keywords

Ethnic origin; Genome wide association; Haplotype block structure; Hapmap; Sample sizes; Tagging SNPs

Indexed keywords

ARTICLE; CAUCASIAN; CONTROLLED STUDY; ETHNIC DIFFERENCE; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE MAPPING; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC EPIDEMIOLOGY; GENETIC MARKER; GENOME ANALYSIS; GEOGRAPHIC ORIGIN; HAPLOTYPE; HUMAN; MAJOR CLINICAL STUDY; NEGRO; POPULATION GENETICS; PRIORITY JOURNAL; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTER SIMULATION; ETHNIC GROUPS; GENE FREQUENCY; GENETIC MARKERS; GENOME, HUMAN; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MONTE CARLO METHOD; POLYMORPHISM, SINGLE NUCLEOTIDE; SAMPLE SIZE;

EID: 33845260536     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2006.00315.x     Document Type: Article

References (41)

1. Abecasis, G. R., Noguchi, E., Heinzmann, A., Traherne, J. A., Bhattacharyya, S., Leaves, N. I., Anderson, G. G., Zhang, Y., Lench, N. J., Carey, A., Cardon, L. R., Moffatt, M. F. & Cookson, W. O. (2001) Extent and distribution of linkage disequilibrium in three genomic regions. Am J Hum Genet 68 (1), 191-7.
2. Bafna, V., Halldórsson, B. V., Schwartz, R. S., Clark, A. G. & Istrail, S. (2003) Haplotypes and informative SNP selection algorithms: Don't block out information. Proceedings of the Seventh Annual International Conference on Computational Molecular Biology (RECOMB 03).
3. Carlson, C. S., Eberle, M. A., Rieder, M. J., Yi, Q., Kruglyak, L. & Nickerson, D. A. (2004) Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet 74 (1), 106-20.
4. Clayton, D. (2001) Choosing a set of haplotype tagging SNPs from a larger set of diallelic loci, http://www.nature.com/ng/journal/v29/n2/ extref/ng1001-233-S10.pdf.
5. Daly, M. J., Rioux, J. D., Schaffner, S. F., Hudson, T. J. & Lander, E. S. (2001) High-resolution haplotype structure in the human genome. Nat Genet 29 (2), 229-32.
6. Dawson, E., Abecasis, G. R., Bumpstead, S., Chen, Y., Hunt, S., Beare, D. M., Pabial, J., Dibling, T., Tinsley, E., Kirby, S., Carter, D., Papaspyridonos, M., Livingstone, S., Ganske, R., Lohmussaar, E., Zernant, J., Tonisson, N., Remm, M., Magi, R., Puurand, T., Vilo, J., Kurg, A., Rice, K., Deloukas, P., Mott, R., Metspalu, A., Bentley, D. R., Cardon, L. R. & Dunham, I. (2002) A first-generation linkage disequilibrium map of human chromosome 22. Nature 418 (6897), 544-8.
7. Gabriel, S. B., Schaffner, S. F., Nguyen, H., Moore, J. M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S. N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E. S., Daly, M. J. & Altshuler, D. (2002) The structure of haplotype blocks in the human genome. Science 296 (5576), 2225-9.
8. Goldstein, D. B. (2001) Islands of linkage disequilibrium. Nat Genet 29 (2), 109-11.
9. Halldorsson, B. V., Bafna, V., Lippert, R., Schwartz, R., De La Vega, F. M., Clark, A. G. & Istrail, S. (2004) Optimal Haplotype Block-Free Selection of Tagging SNPs for Genome-Wide Association Studies. Genome Res. 14 (8), 1633-40.
10. Hinds, D. A., Stuve, L. L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D. G., Frazer, K. A. & Cox, D. R. (2005) Whole-genome patterns of common DNA variation in three human populations. Science 307 (5712), 1072-9.
11. Jeffreys, A. J., Kauppi, L. & Neumann, R. (2001) Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat Genet 29 (2), 217-22.
12. Johnson, G. C., Esposito, L., Barratt, B. J., Smith, A. N., Heward, J., Di Genova, G., Ueda, H., Cordell, H. J., Eaves, I. A., Dudbridge, F., Twells, R. C., Payne, F., Hughes, W., Nutland, S., Stevens, H., Carr, P., Tuomilehto-Wolf, E., Tuomilehto, J., Gough, S. C., Clayton, D. G. & Todd, J. A. (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29 (2), 233-7.
13. Ke, X., Hunt, S., Tapper, W., Lawrence, R., Stavrides, G., Ghori, J., Whittaker, P., Collins, A., Morris, A. P., Bentley, D., Cardon, L. R. & Deloukas, P. (2004) The impact of SNP density on fine-scale patterns of linkage disequilibrium. Hum. Mol. Genet. 13 (6), 577-88.
14. Kruglyak, L. & Nickerson, D. A. (2001) Variation is the spice of life. Nat Genet 27 (3), 234-6.
15. Lander, E. S. & Schork, N. J. (1994) Genetic dissection of complex traits. Science 265 (5181), 2037-48.
16. Lin, Z. & Altman, R. B. (2004) Finding haplotype tagging SNPs by use of principal components analysis. Am J Hum Genet 75 (5), 850-61.
17. Liu, N., Sawyer, S. L., Mukherjee, N., Pakstis, A. J., Kidd, J. R., Kidd, K. K., Brookes, A. J. & Zhao, H. (2004) Haplotype block structures show significant variation among populations. Genet Epidemiol 27 (4), 385-400.
18. Mannila, H., Koivisto, M., Perola, M., Varilo, T., Hennah, W., Ekelund, J., Lukk, M., Peltonen, L. & Ukkonen, E. (2003) Minimum Description Length Block Finder, a Method to Identify Haplotype Blocks and to Compare the Strength of Block Boundaries. Am J Hum Genet 73 (1).
19. McVean, G. A., Myers, S. R., Hunt, S., Deloukas, P., Bentley, D. R. & Donnelly, P. (2004) The fine-scale structure of recombination rate variation in the human genome. Science 304 (5670), 581-4.
20. Meng, Z., Zaykin, D. V., Xu, C. F., Wagner, M. & Ehm, M. G. (2003) Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am J Hum Genet 73 (1), 115-30.
21. Patil, N., Berno, A. J., Hinds, D. A., Barrett, W. A., Doshi, J. M., Hacker, C. R., Kautzer, C. R., Lee, D. H., Marjoribanks, C., McDonough, D. P., Nguyen, B. T., Norris, M. C., Sheehan, J. B., Shen, N., Stern, D., Stokowski, R. P., Thomas, D. J., Trulson, M. O., Vyas, K. R., Frazer, K. A., Fodor, S. P. & Cox, D. R. (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294 (5547), 1719-23.
22. Phillips, M. S., Lawrence, R., Sachidanandam, R., Morris, A. P., Balding, D. J., Donaldson, M. A., Studebaker, J. F., Ankener, W. M., Alfisi, S. V., Kuo, F. S., Camisa, A. L., Pazorov, V., Scott, K. E., Carey, B. J., Faith, J., Katari, G., Bhatti, H. A., Cyr, J. M., Derohannessian, V., Elosua, C., Forman, A. M., Grecco, N. M., Hock, C. R., Kuebler, J. M., Lathrop, J. A., Mockler, M. A., Nachtman, E. P., Restine, S. L., Varde, S. A., Hozza, M. J., Gelfand, C. A., Broxholme, J., Abecasis, G. R., Boyce-Jacino, M. T. & Cardon, L. R. (2003) Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat Genet 33 (3), 382-7.
23. Reich, D. E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P. C., Richter, D. J., Lavery, T., Kouyoumjian, R., Farhadian, S. F., Ward, R. & Lander, E. S. (2001) Linkage disequilibrium in the human genome. Nature 411 (6834), 199-204.
24. Rioux, J. D., Daly, M. J., Silverberg, M. S., Lindblad, K., Steinhart, H., Cohen, Z., Delmonte, T., Kocher, K., Miller, K., Guschwan, S., Kulbokas, E. J., O'Leary, S., Winchester, E., Dewar, K., Green, T., Stone, V., Chow, C., Cohen, A., Langelier, D., Lapointe, G., Gaudet, D., Faith, J., Branco, N., Bull, S. B., McLeod, R. S., Griffiths, A. M., Bitton, A., Greenberg, G. R., Lander, E. S., Siminovitch, K. A. & Hudson, T. J. (2001) Genetic variation in the 5q31 cytokine gene cluster confers susceptibility to Crohn disease. Nat Genet 29 (2), 223-8.
25. Risch, N. & Merikangas, K. (1996) The future of genetic studies of complex human diseases. Science 273 (5281), 1516-7.
26. Stram, D. O., Haiman, C. A., Hirschhorn, J. N., Altshuler, D., Kolonel, L. N., Henderson, B. E. & Pike, M. C. (2003) Choosing haplotype-tagging SNPS based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the Multiethnic Cohort Study. Hum Hered 55 (1), 27-36.
27. Sun, X., Stephens, J. C. & Zhao, H. (2004) The impact of sample size and marker selection on the study of haplotype structures. Hum Genomics 1 (3), 179-93.
28. Templeton, A. R., Weiss, K. M., Nickerson, D. A., Boerwinkle, E. & Sing, C. F. (2000) Cladistic structure within the human Lipoprotein lipase gene and its implications for phenotypic association studies. Genetics 156 (3), 1259-75.
29. The International HapMap Consortium (2003) The International HapMap Project. Nature 426 (6968), 789-96.
30. The International HapMap Consortium. http://www.hapmap.org/ whatishapmap.html.en.
31. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437 (7063), 1299-320.
32. Thomas, D. C. & Witte, J. S. (2002) Point: Population stratification: A problem for case-control studies of candidate-gene associations ? Cancer Epidemiol Biomarkers Prev 11 (6), 505-12.
33. Wacholder, S., Rothman, N. & Caporaso, N. (2002) Counterpoint: Bias from population stratification is not a major threat to the validity of conclusions from epidemiological studies of common polymorphisms and cancer. Cancer Epidemiol Biomarkers Prev 11 (6), 513-20.
34. Wang, N., Akey, J. M., Zhang, K., Chakraborty, R. & Jin, L. (2002) Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation. Am J Hum Genet 71 (5), 1227-34.
35. Weale, M. E., Depondt, C., Macdonald, S. J., Smith, A., Lai, P. S., Shorvon, S. D., Wood, N. W. & Goldstein, D. B. (2003) Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: implications for linkage-disequilibrium gene mapping. Am J Hum Genet 73 (3), 551-65.
36. Zerba, K. E., Kessling, A. M., Davignon, J. & Sing, C. F. (1991) Genetic structure and the search for genotype-phenotype relationships: an example from disequilibrium in the Apo B gene region. Genetics 129 (2), 525-33.
37. Zhang, K., Deng, M., Chen, T., Waterman, M. S. & Sun, F. (2002) A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci U S A 99 (11), 7335-9.
38. Zhang, K., Qin, Z. S., Liu, J. S., Chen, T., Waterman, M. S. & Sun, F. (2004a) Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res 14 (5), 908-16.
39. Zhang, K. & Jin, L. (2003) HaploBlockFinder: Haplotype block analyses. Bioinformatics 19 (10), 1300-1301.
40. Zhang, W., Collins, A., Gibson, J., Tapper, W. J., Hunt, S., Deloukas, P., Bentley, D. R. & Morton, N. E. (2004b) Impact of population structure, effective bottleneck time, and allele frequency on linkage disequilibrium maps. PNAS 101 (52), 18075-80.
41. Zhu, X., Fejerman, L., Luke, A., Adeyemo, A. & Cooper, R. S. (2005) Haplotypes produced from rare variants in the promoter and coding regions of angiotensinogen contribute to variation in angiotensinogen levels. Hum. Mol. Genet. 14 (5), 639-43.