References

Recombination

• McPeek MS (1996) An introduction to recombination and linkage analysis. In: Speed T, Waterman MS (eds) Genetic mapping and DNA sequencing: IMA volumes in mathematics and its applications, Vol 81. Springer-Verlag, New York, pp 1-14

Map functions

• Speed TP (1996) What is a genetic map function? In: Speed T, Waterman MS (eds) Genetic mapping and DNA sequencing: IMA volumes in mathematics and its applications, Vol 81. Springer-Verlag, New York, pp 65-88
• Zhao H, Speed TP (1996) On genetic map functions. Genetics 142:1369-1377

Interference

• McPeek MS, Speed TP (1995) Modeling interference in genetic recombination. Genetics 139:1031-1044
• Zhao H, Speed TP, McPeek MS (1995) Statistical analysis of crossover interference using the chi-square model. Genetics 139:1045-1056
• Zhao H, McPeek MS, Speed TP (1995) Statistical analysis of chromatid interference. Genetics 139:1057-1065

Applications

• Broman KW, Murray JC, Sheffield VC, White RL, Weber JL (1998) Comprehensive human genetic maps: individual and sex-specific variation in recombination. Am J Hum Genet 63:861-869 [pdf (534k)]
• Broman KW, Weber JL (2000) Characterization of human crossover interference. Am J Hum Genet 66:1911-1926 [pdf (291k)]
• Broman KW, Rowe LB, Churchill GA, Paigen K (2002) Crossover interference in the mouse. Genetics 160:1123-1131 [pdf (165k)]

• Baum LE, Petrie T, Soules G, Weiss N (1970) A maximization technique occurring in the statistical analysis of probabilistic functions of Markov chains. Ann Math Stat 41:164-171 [JSTOR]
• Rabiner LR (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE 77:257-286 [pdf (2.2M)]
• Lange K (1999) Numerical analysis for statisticians. Springer, New York, Sec 23.3
• Churchill GA (1989) Stochastic models for heterogeneous DNA sequences. Bulletin of Mathematical Biology. 51:79-94

• Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J Roy Stat Soc B 39:1-38 [JSTOR]
• Wu CFJ (1983) On the convergence properties of the EM algorithm. The Annals of Statistics 11:95-103 [JSTOR]
• Lander ES, Green P (1987) Construction of multilocus genetic linkage maps in humans. Proc Natl Acad Sci USA 84:2363-2367
• Lincoln SE, Lander ES (1992) Systematic detection of errors in genetic linkage data. Genomics 14:604-610

• Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185-199
• Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315-324
• Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963-971
• Broman KW (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Animal 30(7):44-52 [pdf]
• Broman KW, Speed TP (1999) A review of methods for identifying QTLs in experimental crosses. In: Seillier-Moiseiwitsch F (ed) Statistics in Molecular Biology and Genetics. IMS Lecture Notes-Monograph Series, Vol 33, pp 114-142 [pdf]
• Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3:43-52
• Doerge RW, Zeng Z-B, Weir BS (1997) Statistical issues in the search for genes affecting quantitative traits in experimental populations. Statistical Science 12:195-219

• Broman KW. QTL mapping in the case of a spike in the phenotype distribution. Genetics, to appear. [pdf]
• Kruglyak L, Lander ES (1995) A nonparametric approach for mapping quantitative trait loci. Genetics 139:1421-1428
• Xu S, Atchley WR (1996) Mapping quantitative trait loci for complex binary diseases using line crosses. Genetics 143:1417-1424
• Hackett CA, Weller JI (1995) Genetic mapping of quantitative trait loci for traits with ordinal distributions. Biometrics 51:1252-1263

• Silver LM (1995) Mouse Genetics: Concepts and Applications. Oxford University Press. Sec 9.2, pages 207-226
• Haldane JBS, Waddington CH (1931) Inbreeding and linkage. Genetics 16:357-374
• Williams RW, Gu J, Qi S, Lu L (2001) The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis. Genome Biol 2(11):research0046.1research0046.18 [pdf]
• Threadgill DW, Hunter KW, Williams RW (2002) Genetic dissection of complex and quantitative traits: from fantasy to reality via a community effort. Mamm Genome 13:175-8 [pdf]

• Murphy E. A., Mutalik G. S. (1969) Hum Hered 19:126-151 The application of Bayesian methods in genetic counselling.
• BRCAPRO homepage
• Parmigiani (2002) Modeling in Medical Decision Making. Wiley. [pdf of section 1.3]

• Berry et al BRCAPRO validation, sensitivity of genetic testing of BRCA1/BRCA2, and prevalence of other breast cancer susceptibility genes. J Clin Oncol 2002 Jun 1;20(11):2701-12
• Morris H. DeGroot, Stephen E. Fienberg The Comparison and Evaluation of Forecasters Statistician, Vol. 32, No. 1/2
• Edwin Iversen Jr., Giovanni Parmigiani and Donald Berry. Validating Bayesian Prediction Models: a Case Study in Genetic Susceptibility to Breast Cancer

• RA Fisher The effect of methods of ascertainment upon the estimation of frequencies. Ann Eugen 6:13-25
• Peter Kraft and Duncan C. Thomas Bias and Efficiency in Family-Based Gene-Characterization Studies: Conditional, Prospective, Retrospective, and Joint Likelihoods Am. J. Hum. Genet., 66:1119-1131, 2000
• Paul R. Burton, Lyle J. Palmer, Kevin Jacobs, Kevin J. Keen, Jane M. Olson, and Robert C. Elston Ascertainment Adjustment: Where Does It Take Us? Am. J. Hum. Genet., 67:1505-1514, 2001

• Edwin Iversen, Jr. and Sining Chen Population-Calibrated Gene Characterization: Cancer Penetrance Among BRCA1/2 Mutation Carriers ISDS Working Paper 01-09

• Struewing JP, Hartge P, Wacholder S, Baker SM, Berlin M, McAdams M, Timmerman MM, Brody LC, Tucker MA. The risk of cancer associated with specific mutations of BRCA1 and BRCA2 among Ashkenazi Jews. N Engl J Med 1997 May 15;336(20):1401-8
• Gail MH, Pee D, Benichou J, Carroll R.Designing studies to estimate the penetrance of an identified autosomal dominant mutation: cohort, case-control, and genotyped-proband designs. Genet Epidemiol 1999;16(1):15-39

• Broman KW, Speed TP (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses (with discussion). J Roy Stat Soc B 64:641-656, 731-775 [pdf | Discussion]
• Miller AJ (2002) Subset selection in regression, 2nd edition. Chapman & Hall/CRC.

• Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315-324
• Kao C-H, Zeng Z-B, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203-1216
• Sen S, Churchill GA (2001) A statistical framework for quantitative trait mapping. Genetics 159:371-387
• Yi N, Xu S (2002) Mapping quantitative trait loci with epistatic effects. Genetical Research 79:185-198
• Green PJ (1995) Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika 82:711-732 [JSTOR]

---

Course syllabus

Last modified: Wed Apr 15 23:09:46 2009