Statistical genetics seminar - Biostat 580B
topic and paper list chosen Oct. 1, 2002
(organized, somewhat, into related themes)

Topics suggested

• Trait models:
  • finding trait models for oligogenic traits,
  • finding trait models for multivariate traits
  • segregation analysis in the era of "complex trait genetics"
  • applications of other models (e.g., Cox model) in statistical genetics
  • environmental factors and inclusion in genetic epidemiology
• Understanding genetics of correlated/complex traits:
  • variance-component analysis
  • path analysis/SEM
  • extensions of H-E
• Population-based associations:
  • association tests
  • association studies with haplotypes: estimation and analysis
  • disequilibrium modelling
  • coalescent theory and methods
  • population stratification issues
  • defining ethnic (population) groups from genetic data
  • ratio models (e.g., haplotype relative risk)
• Error:
  • genotyping error
  • pedigree error
  • map estimation/misspecification
  • detection/dealing with error in pedigree data
• Mapping:
  • fine mapping for quantitative traits
  • linkage analyses for age at onset or a discrete trait
  • analysis using clustered SNP maps
• Experimental design for microarrays
• Multiple testing issues
• Use of data from multiple species (genome comparisons, etc.)

Some suggested papers (not a complete list of interesting papers!)

LD, haplotypes, allele frequency estimation, etc.

• B-Rao C. Sample size considerations in genetic polymorphism studies. HUMAN HEREDITY 52 (4): 191-200 2001
• Douglas JA, Boehnke M, Gillanders E, Trent JM, Gruber SB. Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nat Genet. 2001 Aug;28(4):361-4.
• Hollox EJ, Poulter M, Zvarik M, Ferak V, Krause A, Jenkins T, Saha N, Kozlov AI, Swallow DM. Lactase haplotype diversity in the Old World. Am J Hum Genet. 2001 Jan;68(1):160-172.
• Trikka D, Fang Z, Renwick A, Jones SH, Chakraborty R, Kimmel M, Nelson DL. Complex SNP-based haplotypes in three human helicases: Implications for cancer association studies GENOME RESEARCH 12 (4): 627-639 APR 2002
• Rohde K, Fuerst R. Haplotyping and estimation of haplotype frequencies for closely linked biallelic multilocus genetic phenotypes including nuclear family information. HUMAN MUTATION 17 (4): 289-295 2001
• EXCOFFIER L, SLATKIN M MAXIMUM-LIKELIHOOD-ESTIMATION OF MOLECULAR HAPLOTYPE FREQUENCIES IN A DIPLOID POPULATION. MOLECULAR BIOLOGY AND EVOLUTION 12 (5): 921-927 SEP 1995
• Kitamura Y, Moriguchi M, Kaneko H, Morisaki H, Morisaki T, Toyama K, Kamatani N. Determination of probability distribution of diplotype configuration (diplotype distribution) for each subject from genotypic data using the EM algorithm. ANNALS OF HUMAN GENETICS 66: 183-193 Part 3 MAY 2002
• HAWLEY ME, KIDD KK. HAPLO - A PROGRAM USING THE EM ALGORITHM TO ESTIMATE THE FREQUENCIES OF MULTISITE HAPLOTYPES. JOURNAL OF HEREDITY 86 (5): 409-411 SEP-OCT 1995
• Zhao JH, Sham PC Faster haplotype frequency estimation using unrelated subjects. HUMAN HEREDITY 53 (1): 36-41 2002

Haplotype blocks & structure

• Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BT, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SP, Cox DR. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science. 2001 Nov 23;294(5547):1719-23.
• Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES. High-resolution haplotype structure in the human genome. Nat Genet. 2001 Oct;29(2):229-32.
• Zhang K, Deng MH, Chen T, Waterman MS, Sun FZ. A dynamic programming algorithm for haplotype block partitioning. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 99 (11): 7335-7339 MAY 28 2002
• Dunning AM, Durocher F, Rennart G, Easton DF. Sampling distribution of summary linkage disequilibrium measures. Teare MD, ANNALS OF HUMAN GENETICS 66: 223-233 Part 3 MAY 2002

maps, gene identification & other stuff

• Reich DE, Schaffner SF, Daly MJ, McVean G, Mullikin JC, Higgins JM, Richter DJ, Lander ES, Altshuler D. Human genome sequence variation and the influence of gene history, mutation and recombination. Nat Genet. 2002 Sep;32(1):135-42.
• Chakraborty R, Kimmel M, Nelson DL. Complex SNP-based haplotypes in three human helicases: Implications for cancer association studies. Trikka D, Fang Z, Renwick A, Jones SH, GENOME RESEARCH 12 (4): 627-639 APR 2002
• Sabatti C, Teng J, Keats BJB, Risch N. Bayesian analysis of haplotypes for linkage disequilibrium mapping. Liu JS, GENOME RESEARCH 11 (10): 1716-1724 OCT 2001
• Li H. A permutation procedure for the haplotype method for identification of disease-predisposing variants ANNALS OF HUMAN GENETICS 65: 189-196 Part 2 MAR 2001
• Brem, Rachel B., Yvert, Gael, Clinton, Rebecca, Kruglyak, Leonid Genetic Dissection of Transcriptional Regulation in Budding Yeast Science 2002 296: 752-755
• Kong A, Gudbjartsson DF, Sainz J, Jonsdottir GM, Gudjonsson SA, Richardsson B, Sigurdardottir S, Barnard J, Hallbeck B, Masson G, Shlien A, Palsson ST, Frigge ML, Thorgeirsson TE, Gulcher JR, Stefansson K. A high-resolution recombination map of the human genome. Nat Genet. 2002 Jul;31(3):241-7.
• something controversial, although more 'political' than pure 'scientific": Waterston RH, Lander ES, Sulston JE. On the sequencing of the human genome. Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3712-6.