Statistical Genomics Course Reading & References

Course Reading

Required

1. ZB Zeng (2000) Unpublished Course Notes on QTLs. This will be central to the first half of the course. Available at DoIT Center by mon 15 jan 2001. [I have ordered 25 copies; 15 people are currently registered, and I expect auditors.]
2. Recent and key articles, both published and in preprint form.

   Recommended

3. M Lynch and B Walsh (1997) Fundamentals of Quantitative Genetics. Sinauer Associates. ISBN 0-87893-481-2. (see additional notes with updated material for Part II. Quantitative Trait Loci)

Statistical Genomics References

• Other Books on Statistical Genetics
• Journal Articles by Section
1. Genetic Linkage & Linkage Maps

2. Likelihood-Based Methodology
3. Complex Traits, QTLs & Polygenes
4. Data Resampling & Simulation

5. Combining Data Across Experiments
6. Linkage Disequilibrium

7. Microarray Expression Data Analysis
• UW Gene Expression Data Analysis (GEDA) List of Microarray Literature
• Other Linkage Information
• Statistical Problems in Genetics and Molecular Biology. Statistical Science 9: 307-381.

Other Books on Statistical Genetics

• NTJ Bailey (1961) Introduction to the Mathematical Theory of Genetic Linkage. Clarendon Press, Oxford.
• MG Bulmer (1985) The Mathematical Theory of Quantitative Genetics. Clarendon Press, Oxford.
• K Lange (1997) Mathematical and Statistical Methods for Genetic Analysis, Springer.
• B Liu (1998) Statistical Genomics. CRC Press.
• M Lynch and B Walsh (1997) Fundamentals of Quantitative Genetics. Sinauer Associates.
• J Ott (1991) Analysis of Human Genetic Linkage (rev). John Hopkins U Press.
• EA Thompson (2000) Statistical Inferences from Genetic Data on Pedigrees. IMS.
• BS Weir (1997) Genetic Data Analysis, 2nd. ed. Sinauer Associates.
• ZB Zeng (2000) Unpublished Course Notes on QTLs.
• Comparison of Book Tables of Contents

Journal Articles by Section

1. Genetic Linkage & Linkage Maps
2. Likelihood-Based Methodology
3. Complex Traits, QTLs & Polygenes
4. Data Resampling & Simulation
5. Combining Data Across Experiments
6. Microarray Expression Data Analysis

Genetic Linkage & Linkage Maps

• Lander and Green (1987) Construction of multilocus genetic linkage maps in humans'' PNAS 84: 2363-2367.
• NE Morton (1995) LODs past and present. Genetics 140: 7-12. [Abstract]

  Likelihood-Based Methodology

  Complex Traits, QTLs & Polygenes

• CJ Basten, BS Weir and Z-B Zeng (1995) A tutorial and reference manual for QTL Cartographer'', Center for Quantitative Genetics, NC St U. [Paper | Software | Data]
• Jansen and Stam (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447-1455. [Abstract]
• C Haley and S Knott (1992) A simple regression method for mapping quantitative trait loci of linked factors. J Genetics 8: 299-309.
• C Haley, S Knott and Elsen (1994) Mapping quantitative trait loci in crosses between outbred lines using least squares. Genetics 136: 1195-1207. [Abstract]
• Lander and Botstein (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185-199. [Abstract]
• J Liu, JM Mercer, LF Stam, GC Gibson, ZB Zeng, and CC Laurie (1996) Genetic analysis of a morphological shape difference in the male genitalia of Drosophila simulans and D. mauritiana. Genetics 142: 1129-1145. [Abstract]
• AH Paterson (1995) Molecular dissection of quantitative traits: progress and prospects. Genome Res 5: 321-333. [Abstract]
• Z-B Zeng (1993) Theoretical basis of separation of multiple linked gene effects on mapping quantitative trait loci. PNAS USA 90: 10972-10976. [Paper]
• Z-B Zeng (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457-1468. [Abstract]

  Multiple Interval Mapping

• J-L Janninka and R Jansen (2001) Mapping Epistatic Quantitative Trait Loci With One-Dimensional Genome Searches. Genetics 157: 445-454. [Paper]
• C Jansen (1990) A general Monte Carlo method for mapping multiple quantitative trait loci. Genetics 142: 305-311. [Abstract]
• True JR, Liu JJ, Stam LF, Zeng ZB, Laurie CC (1997) Quantitative genetic analysis of divergence in male secondary sexual traits between Drosophila simulans and Drosophila mauritiana. Evolution 51: 816-832. [NA]
• Zeng ZB, Liu JJ, Stam LF, Kao CH, Mercer JM, Laurie CC (2000) Genetic architecture of a morphological shape difference between two drosophila species. Genetics 154: 299-310. [Paper] [Data]
• Zeng ZB, Kao CH, Basten CJ (1999) Estimating the genetic architecture of quantitative traits. Genetical Res. 74 (3), 279-289, 1999. [NA]

  Data Resampling & Simulation

• GA Churchill and RW Doerge (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963-971. [Abstract]
• Doerge RW and Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142: 285-294. [Abstract]
• Jansen, R.C. (1993) Interval mapping of multiple quantitative trait loci. Genetics 1993 135: 205-211. [Abstract]
• L Kruglyak and ES Lander (1995) A nonparametric approach for mapping quantitative trait loci. Genetics 139: 1421-1428. [Abstract]
• JM Satagopan, BS Yandell, MA Newton and TC Osborn (1995) Markov chain Monte Carlo approach to detect polygene loci for complex traits. Genetics 144: 805-816. [Abstract]

  Combining Data Across Experiments

• Bernardo R (1995) Genetic models for predicting maize single-cross performance in unbalanced yield trial data. Crop Science 35: 141-147.
• Fisch RD, Ragot M and Gay G (1996) A generalization of the mixture model in the mapping of quantitative trait loci for progeny from a biparental cross of inbred lines. Genetics 143:571-577. [Abstract]
• C Jiang and Z-B Zeng (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140: 1111-1127. [Abstract]
• Liu YF and Zeng ZB (2000) A general mixture model approach for mapping quantitative trait loci from diverse cross designs involving multiple inbred lines. Genet Res 75: 345-355. [Paper]
• Zou F and Yandell BS (2000) QTL analysis for combined lines. (submitted).

  Linkage Disequilibrium

  (Again, we will probably not have lectures on this topic.)
• Devlin B, Risch N (1995) A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29: 311-322. [Paper]
• Devlin B, Risch N and Roeder K (1996) Disequilibrium mapping: Composite likelihood for pairwise disequilibrium. Genomics 36: 1-16. [Paper]
• Guo S-W, Xiong M (1997) Estimating the age of mutant disease alleles based on linkage disequilibrium. Hum Hered 47: 315-337.
• Hästbacka J, de la Chapelle A, Kaitila I, Sistonen P, Weaver W, Lander ES (1992) Linkage disequilibrium mapping in isolated founder populations: diastrophic dysplasia in Finland. Nat Genet 2: 204-211.
• Hästbacka J, de la Chapelle A, Mahtani MM, Clines G, Reeve-Daly MP, Daly M, Hamilton BA, et al (1994) The diastrophic dysplasia gene encodes a novel sulfate transporter: positional cloning by fine-structure linkage disequilibrium mapping. Cell 78: 1073-1087. [Abstract]
• Huang, J and Jiang Y, (2000) The score statistic of the LD-LOD analysis: Detecting linkage adaptive to linkage disequilibrium. Human Heredity 00: 000-000.
• Kaplan NL, Hill WG, Weir BS (1995) Likelihood methods for locating disease genes in nonequilibrium populations. Am J Hum Genet 56: 18-32.
• Kaplan NL, Weir BS (1995) Are moment bounds on the recombination fraction between a marker and disease locus too good to be true? allelic association mapping revisited for simple genetic diseases in the Finnish population. Am J Hum Genet 57: 1486-1498.
• Kingman JFC (1982) The coalescent. Stochastic Proc Appl 13: 235-248.
• Laitinen T, Kauppi P, Ignatius J, Ruotsalainen T, Daly MJ, Kääriäinen H, Kruglyak L, et al (1997) Genetic control of serum IgE levels and asthma: linkage and linkage disequilibrium studies in an isolated population. Hum Mol Genet 6: 2069-2076. [Paper]
• Rannala B, Slatkin M (1998) Likelihood analysis of disequilibrium mapping, and related problems. Am J Hum Genet 62: 459-473. [Paper]
• Slatkin, M (1999) Disequilibrium mapping of a quantitative trait locus in an expanding population. Am J Hum Gen 64: 1765-1773. [Paper]
• Thompson EA, Neel JV (1978)
• Thompson EA, Neel JV (1997) Allelic disequilibrium and allele frequency distribution as a function of social and demographic history. Am J Hum Genet 60: 197-204. [Abstract]
• Xiong M, Guo S-W (1997) Fine-scale genetic mapping based on linkage disequilibrium: theory and applications. Am J Hum Genet 60: 1513-1531. [Paper]

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  Microarray Expression Data Analysis

  • Microarray Data Overview
  • Biology Implications of Microarray Data Analysis
  • Clustering and Classification Methods
  • Principal Components/Singular Value Decomposition
  • Differential Expression: Anova and Experimental Design
  • Other Microarray Data Analysis References

  Microarray Data Overview

• Claverie, J. (1999) Computational methods for the identification of differential and coordinated gene expression. Human Molecular Genetics 8: 1821-1832. [Paper]

  Biology Implications of Microarray Data Analysis

• Hilsenbeck SG, Friedrichs WE, Schiff R, O'Connell P, Hansen RK, Osborne CK, and Fuqua SAW (1999) Statistical analysis of array expression data as applied to the problem of tamoxifen resistance. J.N.C.I. 91: 453-459. [Paper]
• Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, Armour CD, Bennett HA, Coffey E, Dai HY, He YDD, Kidd MJ, King AM, Meyer MR, Slade D, Lum PY, Stepaniants SB, Shoemaker DD, Gachotte D, Chakraburtty K, Simon J, Bard M, Friend SH (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126. [Paper] [Supplement] [Data (80Mb)]
• ST Nadler, JP Stoehr, KL Schueler, G Tanimoto, BS Yandell and AD Attie (2000) The expression of adipogenic genes is decreased in obesity and Diabetes mellitus. Proc. Nat. Acad. Sci. USA 97: 11371-11376. [Paper]
• Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YDD, Dai HY, Walker WL, Hughes TR, Tyers M, Boone C, Friend SH (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873-880. [Paper] [Supplement] [Data (7.5Mb)]
• Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D and Futcher B (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9: 3273-3297. [Paper]
• Wittes J, and Friedman HP (1999) Searching for evidence of altered gene expression: a comment on statistical analysis of microarray data. J.N.C.I. 91: 400-401. [Paper]

  Clustering and Classification Methods

• Dudoit, S., J. Fridlyand, and T.P. Speed (2000) Comparison of discrimination methods for the classification of tumors using gene expression data. Technical Report, Department of Statistics, UC-Berkeley. [Paper]
• Eisen MB, Spellman PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. PNAS 95: 14863-14868. [Paper]
• Getz G, Levine E, and Domany E (2000) Coupled two-way clustering analysis of gene microarray data. PNAS 97: 12079-12084. [Paper]
• Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES (1999) Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring. Science 286: 531-537. [Paper]
• Kerr, M.K., and G.A. Churchill (2000a) Bootstrapping cluster analysis: Assessing the reliability of conclusions from microarray experiments. Technical Report, Jackson Laboratory. [Paper]
• Lazzeroni, L. and Owen, A.B. (2000) Plaid models for gene expression data. TR, Department of Statistics, Stanford U, August 2000. [Paper]
• Hastie T, R Tibshirani, D Botstein and P Brown, (2000) Supervised harvesting of expression trees. TR, Department of Statistics, Stanford U, August 2000. [Paper]
• Tamayo P, Slonim D, Mesirov J, Zhu Q, Kitareewan S, Dmitrovsky E, Lander ES, Golub TR (1999) Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. PNAS 96: 2907-2912. [Paper]
• Tibshirani, R., T. Hastie, M. Eisen, D. Ross, D. Botstein, and P. Brown (1999) Clustering methods for the analysis of DNA microarray data. Technical Report, Department of Statistics, Stanford U. [Paper]
• Van der Laan, M.J. and J.F. Bryan 2000. Gene expression analysis with the parametric bootstrap. Technical Report, Biostatistics Program. UC Berkeley. [Paper]

  Principal Components/Singular Value Decomposition

• Alter O, Brown P, and Botstein D (2000) Singular value decomposition for genome-wide expression data processing and modeling. PNAS 97: 10101-10106. [Paper] [Supplement] [Data]
• West, M., J.R. Nevins, J.R. Marks, R. Spang, and H.Zuzan (2000). Bayesian regression analysis in the "large p, small n" paradigm with application in DNA microarray studies. Technical Report, Institute of Statistics and Decision Sciences, Duke University. [Paper]

  Differential Expression: Anova and Experimental Design

• Dudoit, S., Y.H. Yang, M.J. Callow, and T.P. Speed (2000) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Technical Report, Department of Statistics, UC-Berkeley. [Paper]
• Efron, B., R. Tibshirani, V. Goss, and G. Chu. Microarrays and their use in a comparative experiment. Technical Report, Department of Statistics, Stanford U. [Paper]
• Kerr, M.K., and G.A. Churchill (2000b) Experimental design for gene expression microarrays. Technical Report, Jackson Laboratory. [Paper]
• Kerr, M.K., Martin, M. and G.A. Churchill (2000c) Analysis of variance for gene expression microarray data. Technical Report, Jackson Laboratory. [Paper]
• Lee, M.L.T., F.C. Kuo, G.A. Whitmore, and J. Sklar (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. PNAS 97, 9834-9839. [Paper]
• Lin Y, Nadler ST, Attie AD and Yandell BS (2001) Mining for low-abundance transcripts in microarray data. TR 1031, Department of Statistics, U WI Madison.
• Newton, M.A., C.M. Kendziorski, C.S. Richmond, F.R. Blattner, and K.W. Tsui (2001) On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. J. Comp. Biol. 8 (1). To appear. [Paper]

  Other Microarray Data Analysis References

• Y.H. Yang, M. J. Buckley, S. Dudoit and T.P.Speed. Comparison of methods for image analysis on cDNA microarray data. November 2000. Technical Report, Department of Statistics, UC-Berkeley. [Paper]
• See also the UW Gene Expression Data Analysis (GEDA) List of Microarray Literature