Bayesian method for gene detection and mapping, using a case and control design and DNA pooling

Biostatistics

Volumn 8, Issue 3, 2007, Pages 546-565

  Johnson, Toby ^a,b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b ROTHAMSTED RESEARCH   (United Kingdom)

Author keywords

Association mapping; Case and control study; DNA pooling; Genetic association; LD mapping; QTL mapping

Indexed keywords

CYTOCHROME P450 2D6; DNA;

ALLELE; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; BIOMETRY; CASE CONTROL STUDY; CHROMOSOME MAP; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETIC MARKER; GENETIC PREDISPOSITION; GENETIC PROCEDURES; GENETICS; HUMAN; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICS;

ALLELES; BAYES THEOREM; BIOMETRY; CASE-CONTROL STUDIES; CHROMOSOME MAPPING; CYTOCHROME P-450 CYP2D6; DNA; GENE FREQUENCY; GENETIC MARKERS; GENETIC PREDISPOSITION TO DISEASE; GENETIC TECHNIQUES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 34648820399     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxl028     Document Type: Article

References (58)

1. ARNHEIM, N., STRANGE, C. AND ERLICH, H. (1985). Use of pooled DNA samples to detect linkage disequilibrium of polymorphic restriction fragments and human disease: studies of the HLA class II loci. Proceedings of the National Academy of Sciences of the United States of America 82, 6970-6974.
2. BADER, J. S., BANSAL, A. AND SHAM, P. (2001). Efficient SNP-based tests of association for quantitative phenotypes using pooled DNA. GeneScreen 1, 143-150.
3. BARCELLOS, L. F., KLITZ, W., FIELD, L. L., TOBIAS, R., BOWCOCK, A. M., WILSON, R., NELSON, M. P., NAGATOMI, J. AND THOMSON, G. (1997). Association mapping of disease loci, by use of a pooled DNA genomic screen. American Journal of Human Genetics 61, 734-747.
4. BROHEDE, J., DUNNE, R., MCKAY, J. D. AND HANNAN, G. N. (2005). PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays. Nucleic Acids Research 33, e142.
5. BUTCHER, L. M., MEABURN, E., KNIGHT, J., SHAM, P. C., SCHALKWYK, L. C., CRAIG, I. W. AND PLOMIN, R. (2005). SNPs, microarrays and pooled DNA: identification of four loci associated with mild mental impairment in a sample of 6000 children. Human Molecular Genetics 14, 1315-1325.
6. CARLSON, C. S., EBERLE, M. A., RIEDER, M. J., SMITH, J. D., KRUGLYAK, L. AND NICKERSON, D. A. (2003). Additional SNPs and linkage-disequilibrium analyses are necessary for whole-genome association studies in humans. Nature Genetics 33, 518-521.
7. CHURCHILL, G. A. AND DOERGE, R. W. (1994). Empirical threshold values for quantitative trait mapping. Genetics 138, 963-971.
8. CLAYTON, D. (2001). Population association. In: Balding, D. J., Bishop, M. and Cannings, C. (editors), Handbook of Statistical Genetics. Chichester, UK: Wiley, pp. 519-540.
9. COLLINS, A. AND MORTON, N. E. (1998). Mapping a disease locus by allelic association. Proceedings of the National Academy of Sciences of the United States of America 95, 1741-1745.
10. DARVASI, A. AND SOLLER, M. (1994). Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics 138, 1365-1373.
11. FREE SOFTWARE FOUNDATION (1991). GNU general public license. http://www.gnu.org/licenses/gpl.html. Accessed 3 May 2005.
12. GERMER, S., HOLLAND, M. J. AND HIGUCHI, R. (2000). High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Research 10, 258-266.
13. HINDS, D. A., SEYMOUR, A. B., DURHAM, L. K., BANERJEE, P., BALLINGER, D. G., MILOS, P. M., COX, D. R., THOMPSON, J. F. AND FRAZER, K. A. (2004). Application of pooled genotyping to scan candidate regions for association with HDL cholesterol levels. Human Genomics 1, 421-434.
14. HOSKING, L. K., BOYD, P. R., XU, C. F., NISSUM, M., CANTONE, K., PURVIS, I. J., KHAKHAR, R., BARNES, M. R., LIBERWIRTH, U., HAGEN-MANN, K. and others (2002). Linkage disequilibrium mapping identifies a 390 Kb region associated with CYP2D6 poor drug metabolising activity. The Pharmacogenomics Journal 2, 165-175.
15. HUDSON, R. R. (1983). Properties of a neutral allele model with intragenic recombination. Theoretical Population Biology 23, 183-201.
16. HUDSON, R. R. (2002). Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18, 337-338.
17. JEFFREYS, A. J., KAUPPI, L. AND NEUMANN, R. (2001). Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nature Genetics 29, 217-222.
18. JOHNSON, T. (2005a). Bayesian method for disease QTL detection and mapping, using a case and control design and DNA pooling. Preprint. http://www.arxiv.org/abs/q-bio.GN/0507018. Accessed 13 July 2005.
19. JOHNSON, T. (2005b). Multipoint linkage disequilibrium mapping using multilocus allele frequency data. Annals of Human Genetics 69, 474-498.
20. KAPLAN, N. AND MORRIS, R. (2001a). Issues concerning association studies for fine mapping a susceptibility gene for a complex disease. Genetic Epidemiology 20, 432-457.
21. KAPLAN, N. AND MORRIS, R. (2001b). Prospects for association-based fine mapping of a susceptibility gene for a complex disease. Theoretical Population Biology 60, 181-191.
22. LAW, G. R., ROLLINSON, S., FELTBOWER, R., ALLAN, J. M., MORGAN, G. J. AND ROMAN, E. (2004). Application of DNA pooling to large studies of disease. Statistics in Medicine 23, 3841-3850.
23. LE HELLARD, S., BALLEREAU, S. J., VISSCHER, P. M., TORRANCE, H. S., PINSON, J., MORRIS, S. W., THOMSON, M. L., SEMPLE, C. A. M., MUIR, W. J., BLACKWOOD, D. H. R. and others (2002). SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Research 30, e74.
24. LI, N. AND STEPHENS, M. (2003). Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165, 2213-2233.
25. LIU, J. S., SABATTI, C., TENG, J., KEATS, B. J. AND RISCH, N. (2001). Bayesian analysis of haplotypes for linkage disequilibrium mapping. Genome Research 11, 1716-1724.
26. MANIATIS, N., COLLINS, A., GIBSON, J., ZHANG, W., TAPPER, W. AND MORTON, N. E. (2004). Positional cloning by linkage disequilibrium. American Journal of Human Genetics 74, 846-855.
27. MANIATIS, N., MORTON, N. E., GIBSON, J., XU, C.-F., HOSKING, L. K. AND COLLINS, A. (2005). The optimal measure of linkage disequilibrium reduces error in association mapping of affection status. Human Molecular Genetics 14, 145-153.
28. MCPEEK, M. S. AND STRAHS, A. (1999). Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping. American Journal of Human Genetics 65, 858-875.
29. MCVEAN, G. A. T., MYERS, S. R., HUNT, S., DELOUKAS, P., BENTLEY, D. R. AND DONNELLY, P. (2004). The fine-scale structure of recombination rate variation in the human genome. Science 204, 581-584.
30. MEABURN, E., BUTCHER, L. M., LIU, L., FERNANDES, C., HANSEN, V., AL-CHALABI, A., PLOMIN, R., CRAIG, I. AND SCHALKWYK, L. C. (2005). Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs. BMC Genomics 6, 52.
31. MORRIS, A. P., WHITTAKER, J. C. AND BALDING, D. J. (2000). Bayesian fine-scale mapping of disease loci, by hidden Markov models. American Journal of Human Genetics 67, 155-169.
32. MORRIS, A. P., WHITTAKER, J. C. AND BALDING, D. J. (2002). Fine-scale mapping of disease loci via shattered coalescent modeling of genealogies. American Journal of Human Genetics 70, 686-707.
33. MORRIS, A. P., WHITTAKER, J. C. AND BALDING, D. J. (2004). Little loss of information due to unknown phase for fine-scale linkage-disequilibrium mapping with single-nucleotide- polymorphism genotype data. American Journal of Human Genetics 74, 945-953.
34. MORRIS, A. P., WHITTAKER, J. C., XU, C.-F., HOSKING, L. K. AND BALDING, D. J. (2003). Multipoint linkagedisequilibrium mapping narrows location interval and identifies mutation. Proceedings of the National Academy of Sciences of the United States of America 100, 13442-13446.
35. MOSKVINA, V., NORTON, N., WILLIAMS, N., HOLMANS, P., OWEN, M. AND O'DONOVAN, M. (2005). Stream-lined analysis of pooled genotype data in SNP-based association studies. Genetic Epidemiology 28, 273-282.
36. MOTT, R., TALBOT, C. J., TURRI, M. G., COLLINS, A. C. AND FLINT, J. (2000). A method for fine mapping quantitative trait loci in outbred animal stocks. Proceedings of the National Academy of Sciences of the United States of America 97, 12649-12654.
37. MYERS, S., BOTTOLO, L., FREEMAN, C., MCVEAN, G. AND DONNELLY, P. (2005). A fine-scale map of recombination rates and hotspots across the human genome. Science 310, 321-324.
38. NORTON, N., WILLIAMS, N. M., O'DONOVAN, M. C. AND OWEN, M. J. (2004). DNA pooling as a tool for large-scale association studies in complex traits. Annals of Medicine 36, 146-152.
39. O'HAGAN, A. AND FORSTER, J. (2004). Kendall's Advanced Theory of Statistics, Volume 2B: Bayesian Inference, 2nd edition. London: Arnold.
40. PATTERSON, N., HATTANGADI, N., LANE, B., LOHMUELLER, K. E., HAFLER, D. A., OKSENBERG, J. R., HAUSER, S. L., SMITH, M. M., O'BRIEN, S. J., ALTSHULER, D. and others (2004). Methods for high-density admixture mapping of disease genes. American Journal of Human Genetics 74, 979-1000.
41. PRENTICE, R. L. AND QI, L. (2006). Aspects of the design and analysis of high-dimensional SNP studies for disease risk estimation. Biostatistics 7, 339-354.
42. REEVE, J. P. AND RANNALA, B. (2002). DMLE+: Bayesian linkage disequilibrium gene mapping. Bioinformatics 18, 894-895.
43. RISCH, N. AND MERIKANGAS, K. (1996). The future of genetic studies of complex human diseases. Science 273, 1516-1517.
44. RISCH, N. AND TENG, J. (1998). The relative power of family-based and case-control designs for linkage disequilibrium studies of complex human diseases. I. DNA pooling. Genome Research 8, 1273-1288.
45. RISCH, N. J. (2000). Searching for genetic determinants in the new millennium. Nature 405, 847-856.
46. SAWCER, S. AND COMPSTON, A. (2003). The genetic analysis of multiple sclerosis in Europeans: concepts and design. Journal of Neuroimmunology 143, 13-16.
47. SHAM, P., BADER, J. S., CRAIG, I., O'DONOVAN, M. AND OWEN, M. (2002). DNA pooling: a tool for large-scale association studies. Nature Reviews Genetics 3, 862-871.
48. SHIFFMAN, D., LUKE, M. M., LAKOUBOVA, O. A., PULLINGER, C. R., AOUIZERAT, B. E., ZELLNER, C. A., PORTS, T. A., MICHAELS, A. D., DREW, D. W., CATANESE, J. J. and others (2004). Novel genetic markers associated with myocardial infarction: a genomic scale scan of putative functional polymorphisms. Poster from American College of Cardiology Meeting. http://www.celera.com/pdf/ACC04_poster_final_Page2.pdf. Accessed 7 September 2004.
49. SIMPSON, C. L., KNIGHT, J., BUTCHER, L. M., HANSEN, V. K., MEABURN, E., SCHALKWYK, L. C., CRAIG, I. W., POWELL, J. F., SHAM, P. C. AND AL-CHALABI, A. (2005). A central resource for accurate allele frequency estimation from pooled DNA genotyped on DNA microarrays. Nucleic Acids Research 33, e25.
50. TERWILLIGER, J. (1995). A powerful likelihood method for the analysis of linkage disequilibrium between trait loci and one or more polymorphic marker loci. American Journal of Human Genetics 56, 777-787.
51. THOMAS, D. C., HAILE, R. W. AND DUGGAN, D. (2005). Recent developments in genomewide association scans: a workshop summary and review. American Journal of Human Genetics 77, 337-345.
52. VISSCHER, P. M. AND LE HELLARD, S. (2003). Simple method to analyze SNP-based association studies using DNA pools. Genetic Epidemiology 24, 291-296.
53. WALDRON, E. R. B., WHITTAKER, J. C. AND BALDING, D. J. (2006). Fine mapping of disease genes via haplotype clustering. Genetic Epidemiology 30, 170-179.
54. XIONG, M. AND GUO, S.-W. (1997). Fine-scale genetic mapping based on linkage disequilibrium: theory and applications. American Journal of Human Genetics 60, 1513-1531.
55. ZHANG, S. AND ZHAO, H. (2000). Linkage disequilibrium mapping in populations of variable size using the decay of haplotype sharing and a stepwise-mutation model. Genetic Epidemiology 9, S99-S105.
56. ZHANG, S. AND ZHAO, H. (2002). Linkage disequilibrium mapping with genotype data. Genetic Epidemiology 22, 66-77.
57. ZOLLNER, S. AND PRITCHARD, J. K. (2005). Coalescent-based association mapping and fine mapping of complex trait loci. Genetics 169, 1071-1092.
58. ZUBENKO, G. S., HUGHES, H. B., STIFFLER, J. S., ZUBENKO, W. N. AND KAPLAN, B. B. (2002). Genome survey for susceptibility loci for recurrent, early-onset major depression: results at 10cM resolution. American Journal of Medical Genetics 114, 413-422.