STATISTICAL GENETICS Gene Mapping Through Linkage and Association

DF_refs

References from Statistical Genetics: Gene Mapping Through Linkage and Association

A-C D-F G-K L-N O-R S-T U-Z Online Material

Dalgaard, (2002). Introductory Statistics with R. New York, NY.: Springer Verlag.

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), 229-232 Abstract

Dardanoni, V., & Forcina, A. (1998). A unified approach to likelihood inference on stochastic orderings in a nonparametric context. Journal of the American Statistical Association, 93(443), 1112-1123

Davies, S., & Zadik, M. (1997). Comparison of methods for the isolation of methicillin resistant Staphylococcus aureus. J Clin Pathol, 50(3), 257-258 Abstract

Davies, W., Isles, A. R., & Wilkinson, L. S. (2005). Imprinted gene expression in the brain. Neurosci Biobehav Rev, 29(3), 421-430 Abstract

Daw, E. W., Thompson, E. A., & Wijsman, E. M. (2000). Bias in multipoint linkage analysis arising from map misspecification. Genet Epidemiol, 19(4), 366-380 Abstract

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), 544-548 Abstract

de Andrade, M., & Amos, C. I. (2000). Ascertainment issues in variance components models. Genet Epidemiol, 19(4), 333-344 Abstract

de Andrade, M., Fridley, B., Boerwinkle, E., & Turner, S. (2003). Diagnostic tools in linkage analysis for quantitative traits. Genet Epidemiol, 24(4), 302-308 Abstract

de Bakker, I., Yelensky, R., Pe’er, I., Gabriel, S. B., Daly, M. J., & Altshuler, D. (2005). Efficiency and power in genetic association studies. Nat Genet, 37(11), 1217-1223 Abstract

de Bakker, I., Burtt, N. P., Graham, R. R., Guiducci, C., Yelensky, R., Drake, J. A., Bersaglieri, T., Penney, K. L., Butler, J., Young, S., Onofrio, R. C., Lyon, H. N., Stram, D. O., Haiman, C. A., Freedman, M. L., Zhu, X., Cooper, R., Groop, L., Kolonel, L. N., Henderson, B. E., Daly, M. J., Hirschhorn, J. N., & Altshuler, D. (2006). Transferability of tag SNPs in genetic association studies in multiple populations. Nat Genet, 38(11), 1298-1303 Abstract

de Geus, E. J., Wright, M. J., Martin, N. G., & Boomsma, D. I. (2001). Genetics of brain function and cognition. Behav Genet, 31(6), 489-495 Abstract

de la Chapelle, A. (1993). Disease gene mapping in isolated human populations: the example of Finland. J Med Genet, 30(10), 857-865 Abstract

de la Chapelle, A., & Wright, F. A. (1998). Linkage disequilibrium mapping in isolated populations: the example of Finland revisited. Proc Natl Acad Sci U S A, 95(21), 12416-12423 Abstract

DeFries, J. C., & Fulker, D. W. (1986). Multivariate behavioral genetics and development: an overview. Behav Genet, 16(1), 1-10 Abstract

DeLisi, L. E., Shaw, S. H., Crow, T. J., Shields, G., Smith, A. B., Larach, V. W., Wellman, N., Loftus, J., Nanthakumar, B., Razi, K., Stewart, J., Comazzi, M., Vita, A., Heffner, T., & Sherrington, R. (2002). A genome-wide scan for linkage to chromosomal regions in 382 sibling pairs with schizophrenia or schizoaffective disorder. Am J Psychiatry, 159(5), 803-812 Abstract

Dempster, A. P., Laird, N. M., & Rubin, D. B. (1977). Maximum Likelihood from Incomplete Data Via Em Algorithm. Journal of the Royal Statistical Society Series B-Methodological, 39(1), 1-38

Deng, H. W., & Chen, W. M. (2001). The power of the transmission disequilibrium test (TDT) with both case-parent and control-parent trios. Genet Res, 78(3), 289-302 Abstract

Denison, D. G., & Holmes, C. C. (2001). Bayesian partitioning for estimating disease risk. Biometrics, 57(1), 143-149 Abstract

Derks, E. M., Dolan, C. V., & Boomsma, D. I. (2004). Effects of censoring on parameter estimates and power in genetic modeling. Twin Res, 7(6), 659-669 Abstract

Derks, E. M., Dolan, C. V., & Boomsma, D. I. (2007). Statistical power to detect genetic and environmental influences in the presence of data missing at random. Twin Res Hum Genet, 10(1), 159-167 Abstract

Devlin, B., & Risch, N. (1995). A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics, 29(2), 311-322 Abstract

Devlin, B., Daniels, M., & Roeder, K. (1997). The heritability of IQ. Nature, 388(6641), 468-471 Abstract

Devlin, B., & Roeder, K. (1999). Genomic control for association studies. Biometrics, 55(4), 997-1004 Abstract

Devlin, B., Roeder, K., & Wasserman, L. (2000). Genomic control for association studies: a semiparametric test to detect excess-haplotype sharing. Biostatistics, 1(4), 369-387 Abstract

Devlin, B., Roeder, K., & Wasserman, L. (2001). Genomic control, a new approach to genetic-based association studies. Theor Popul Biol, 60(3), 155-166 Abstract

Devlin, B., Bacanu, S. A., & Roeder, K. (2004). Genomic Control to the extreme. Nat Genet, 36(11), 1129-1130; author reply 1131 Abstract

Diao, G., & Lin, D. Y. (2006). Improving the power of association tests for quantitative traits in family studies. Genet Epidemiol, 30(4), 301-313 Abstract

Diego, V. P., Almasy, L., Dyer, T. D., Soler, J. M., & Blangero, J. (2003). Strategy and model building in the fourth dimension: a null model for genotype x age interaction as a Gaussian stationary stochastic process. BMC Genet, 4 Suppl 1, S34 Abstract

Ding, K., & Kullo, I. J. (2007). Methods for the selection of tagging SNPs: a comparison of tagging efficiency and performance. Eur J Hum Genet, 15(2), 228-236 Abstract

Dolan, C., van der Sluis, S., & Grasman, R. (2005). A note on normal theory power calculation in SEM with data missing completely at random. Structural Equation Modeling-a Multidisciplinary Journal, 12(2), 245-262

Dolan, C. V., & Boomsma, D. I. (1998). Optimal selection of sib pairs from random samples for linkage analysis of a QTL using the EDAC test. Behav Genet, 28(3), 197-206 Abstract

Dolan, C. V., Boomsma, D. I., & Neale, M. C. (1999a). A note on the power provided by sibships of sizes 2, 3, and 4 in genetic covariance modeling of a codominant QTL. Behav Genet, 29(3), 163-170 Abstract

Dolan, C. V., Boomsma, D. I., & Neale, M. C. (1999b). A simulation study of the effects of assignment of prior identity-by-descent probabilities to unselected sib pairs, in covariance-structure modeling of a quantitative-trait locus. Am J Hum Genet, 64(1), 268-280 Abstract

Dominicus, A., Skrondal, A., Gjessing, H. K., Pedersen, N. L., & Palmgren, J. (2006). Likelihood ratio tests in behavioral genetics: problems and solutions. Behav Genet, 36(2), 331-340 Abstract

Dong, C., Li, W. D., Geller, F., Lei, L., Li, D., Gorlova, O. Y., Hebebrand, J., Amos, C. I., Nicholls, R. D., & Price, R. A. (2005). Possible genomic imprinting of three human obesity-related genetic loci. Am J Hum Genet, 76(3), 427-437 Abstract

Douglas, J. A., Boehnke, M., & Lange, K. (2000). A multipoint method for detecting genotyping errors and mutations in sibling-pair linkage data. Am J Hum Genet, 66(4), 1287-1297 Abstract

Douglas, J. A., Boehnke, M., Gillanders, E., Trent, J. M., & Gruber, S. B. (2001). Experimentally-derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nat Genet, 28(4), 361-364 Abstract

Douglas, J. A., Skol, A. D., & Boehnke, M. (2002). Probability of detection of genotyping errors and mutations as inheritance inconsistencies in nuclear-family data. Am J Hum Genet, 70(2), 487-495 Abstract

Drigalenko, E. (1998). How sib pairs reveal linkage. Am J Hum Genet, 63(4), 1242-1245 Abstract

Dudbridge, F. (2003). Pedigree disequilibrium tests for multilocus haplotypes. Genet Epidemiol, 25(2), 115-121 Abstract

Dudbridge, F. (2006). UNPHASED User Guide. Technical Report 2006/5.. Cambridge: MRC

Biostatistics Unit.

Duerr, R. H., Taylor, K. D., Brant, S. R., Rioux, J. D., Silverberg, M. S., Daly, M. J., Steinhart, A. H., Abraham, C., Regueiro, M., Griffiths, A., Dassopoulos, T., Bitton, A., Yang, H., Targan, S., Datta, L. W., Kistner, E. O., Schumm, L. P., Lee, A. T., Gregersen, K., Barmada, M. M., Rotter, J. I., Nicolae, D. L., & Cho, J. H. (2006). A genome-wide association study identifies IL23R as an inflammatory bowel disease gene. Science, 314(5804), 1461-1463 Abstract

Duffy, D. L. (1997). BINNING 0.96: a program to call alleles based on approximate length data. (http://www.qimr.edu.au/davidD/binning.htm).

Duffy, D. L. (2006). An integrated genetic map for linkage analysis. Behav Genet, 36(1), 4-6 Abstract

Durner, M., Vieland, V. J., & Greenberg, D. A. (1999). Further evidence for the increased power of LOD scores compared with nonparametric methods. Am J Hum Genet, 64(1), 281-289 Abstract

Durrant, C., Zondervan, K. T., Cardon, L. R., Hunt, S., Deloukas, P., & Morris, A. (2004). Linkage disequilibrium mapping via cladistic analysis of single-nucleotide polymorphism haplotypes. Am J Hum Genet, 75(1), 35-43

Dutta, S., Sinha, S., Chattopadhyay, A., Gangopadhyay, K., Mukhopadhyay, J., Singh, M., & Mukhopadhyay, K. (2005). Cystathionine beta-synthase T833C/844INS68 polymorphism: a family-based study on mentally retarded children. Behav Brain Funct, 1, 25 Abstract

Eaves, L., & Meyer, J. (1994). Locating human quantitative trait loci: guidelines for the selection of sibling pairs for genotyping. Behav Genet, 24(5), 443-455 Abstract

Eaves, L., & Erkanli, A. (2003). Markov Chain Monte Carlo approaches to analysis of genetic and environmental components of human developmental change and G x E interaction. Behav Genet, 33(3), 279-299 Abstract

Eaves, L., Erkanli, A., Silberg, J., Angold, A., Maes, H. H., & Foley, D. (2005). Application of Bayesian inference using Gibbs sampling to item-response theory modeling of multi-symptom genetic data. Behav Genet, 35(6), 765-780 Abstract

Eaves, L. J., & Brumpton, R. J. (1972). Factors of Covariation in Nicotiana-Rustica. Heredity, 29(Oct), 151

Eaves, L. J. (1973). The structure of genotypic and environmental covariation for personality measurements: an analysis of the PEN. Br J Soc Clin Psychol, 12(3), 275-282 Abstract

Eaves, L. J., & Gale, J. S. (1974). A method for analyzing the genetic basis of covariation. Behav Genet, 4(3), 253-267 Abstract

Eaves, L. J., Martin, N. G., & Eysenck, S. B. G. (1977). A psychogenetical analysis of the covariance structure in four impulsiveness factors. Br. J. Math. Stat. Psychological Bulletin, 30, 185-197. Abstract

Eaves, L. J., Last, K. A., Young, A., & Martin, N. G. (1978). Model-fitting approaches to the analysis of human behaviour. Heredity, 41(3), 249-320 Abstract

Eaves, L. J., Neale, M. C., & Maes, H. (1996). Multivariate multipoint linkage analysis of quantitative trait loci. Behav Genet, 26(5), 519-525 Abstract

Edwards, A. L. (1976). An Introduction to Linear Regression and Correlation.. San Francisco, CA.: W.H. Freeman,.

Edwards, A. L. (1979). Multiple Regression and the Analysis of Variance and Covariance.. San Francisco, CA.: W.H. Freeman.

Edwards, B. J., Haynes, C., Levenstien, M. A., Finch, S. J., & Gordon, D. (2005). Power and sample size calculations in the presence of phenotype errors for case/control genetic association studies. BMC Genet, 6(1), 18 Abstract

Efron, B., & Tibshirani, R. (1993). An Introduction to the Bootstrap.. New York, NY.: Chapman and Hall.

Efron, B., & Tibshirani, R. (2002). Empirical bayes methods and false discovery rates for microarrays. Genet Epidemiol, 23(1), 70-86 Abstract

Ehm, M., & Wagner, M. (1998). A test statistic to detect errors in sib-pair relationships. Am J Hum Genet, 62(1), 181-188 Abstract

Ekstrom, C. T. (2004). Multipoint linkage analysis of quantitative traits on sex-chromosomes. Genet Epidemiol, 26(3), 218-230 Abstract

Elston, R. C., & Stewart, J. (1971). A general model for the genetic analysis of pedigree data. Hum Hered, 21(6), 523-542 Abstract

Elston, R. C., Buxbaum, S., Jacobs, K. B., & Olson, J. M. (2000). Haseman and Elston revisited. Genet Epidemiol, 19(1), 1-17 Abstract

Emigh, T. H. (1980). A comparison of tests for Hardy-Weinberg equilibrium. Biometrics, 36, 627-642

Epstein, M. P., Duren, W. L., & Boehnke, M. (2000). Improved inference of relationship for pairs of individuals. Am J Hum Genet, 67(5), 1219-1231 Abstract

Epstein, M. P., Lin, X., & Boehnke, M. (2003). A tobit variance-component method for linkage analysis of censored trait data. Am J Hum Genet, 72(3), 611-620 Abstract

Epstein, M. P., & Satten, G. A. (2003). Inference on haplotype effects in case-control studies using unphased genotype data. Am J Hum Genet, 73(6), 1316-1329 Abstract

Evans, D. M. (2002). The power of multivariate quantitative-trait loci linkage analysis is influenced by the correlation between variables. Am J Hum Genet, 70(6), 1599-1602 Abstract

Evans, D. M., & Medland, S. E. (2003). A note on including phenotypic information from monozygotic twins in variance components QTL linkage analysis. Ann Hum Genet, 67(Pt 6), 613-617 Abstract

Evans, D. M., & Cardon, L. R. (2005). A comparison of linkage disequilibrium patterns and estimated population recombination rates across multiple populations. Am J Hum Genet, 76(4), 681-687 Abstract

Evans, D. M., & Cardon, L. R. (2006). Genome-wide association: a promising start to a long race. Trends Genet, 22(7), 350-354 Abstract

Evans, M., Hastings, N., & Peacock, B. (2000). Statistical Distributions, (3rd ed.). New York, NY.: Wiley.

Everitt, B. S., & Hand, D. J. (1981). Finite mixture distributions.. London: Chapman and Hall.

Ewens, W. J., & Spielman, R. S. (1995). The transmission/disequilibrium test: history, subdivision, and admixture. Am J Hum Genet, 57(2), 455-464 Abstract

Ewens, W. J., & Grant, G. R. (2001). Statistical Methods in Bioinformatics.. New York, NY.: Springer.

Excoffier, L., & Slatkin, M. (1995). Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol, 12(5), 921-927 Abstract

Falconer, D. S. (1960). Quantitative Genetics. Edinburgh: Oliver and Boyd.

Falconer, D. S., & Mackay, T. F. C. (1996). Introduction to Quantitative Genetics,4th Edn.. Harlow: Longman.

Falk, C. T., & Rubinstein, (1987). Haplotype relative risks: an easy reliable way to construct a proper control sample for risk calculations. Ann Hum Genet, 51(Pt 3), 227-233 Abstract

Fallin, D., & Schork, N. J. (2000). Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet, 67(4), 947-959

Fan, J. B., Ma, J., Zhang, C. S., Tang, J. X., Gu, N. F., Feng, G. Y., St Clair, D., & He, L. (2003). A family-based association study of T1945C polymorphism in the proline dehydrogenase gene and schizophrenia in the Chinese population. Neurosci Lett, 338(3), 252-254 Abstract

Faraway, J. J. (1993). Improved sib-pair linkage test for disease susceptibility loci. Genet Epidemiol, 10(4), 225-233 Abstract

Farrer, L. A., Cupples, L. A., Haines, J. L., Hyman, B., Kukull, W. A., Mayeux, R., Myers, R. H., Pericak-Vance, M. A., Risch, N., & van Duijn, C. M. (1997). Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium. Jama, 278(16), 1349-1356 Abstract

Feingold, E., Brown, O., & Siegmund, D. (1993). Gaussian models for genetic linkage analysis using complete high-resolution maps of identity by descent. Am J Hum Genet, 53(1), 234-251 Abstract

Feingold, E. (2001). Methods for linkage analysis of quantitative trait loci in humans. Theor Popul Biol, 60(3), 167-180 Abstract

Feingold, E. (2002). Regression-based quantitative-trait-locus mapping in the 21st century. Am J Hum Genet, 71(2), 217-222 Abstract

Fernandez, J. R., Etzel, C., Beasley, T. M., Shete, S., Amos, C. I., & Allison, D. B. (2002). Improving the power of sib pair quantitative trait loci detection by phenotype winsorization. Hum Hered, 53(2), 59-67 Abstract

Ferreira, M. A. (2004). Linkage analysis: principles and methods for the analysis of human quantitative traits. Twin Res, 7(5), 513-530 Abstract

Ferreira, M. A., O’Gorman, L., Le Souef, P., Burton, R., Toelle, B. G., Robertson, C. F., Visscher, M., Martin, N. G., & Duffy, D. L. (2005). Robust estimation of experimentwise P values applied to a genome scan of multiple asthma traits identifies a new region of significant linkage on chromosome 20q13. Am J Hum Genet, 77(6), 1075-1085 Abstract

Fisher, R. A. (1918). The correlation between relatives on the supposition of Mendelian inheritance. . Trans. R. Soc, 52, 399-433 Abstract

Fisher, R. A. (1922). On the mathematical foundations of theoretical statistics. Phil. Trans. R. Soc. Lond. Ser. A, 222, 309-368

Fisher, R. A. (1934). The effect of methods of ascertainment upon the estimation of frequencies. 6, Ann. Eugen., 13-25

Fisher, R. A. (1954). Statistical Methods for Research Workers. New York, NY.: Hafner.

Flint-Garcia, S. A., Thornsberry, J. M., & Buckler, E. S. t. (2003). Structure of linkage disequilibrium in plants. Annu Rev Plant Biol, 54, 357-374 Abstract

Forrest, W. F., & Feingold, E. (2000). Composite statistics for QTL mapping with moderately discordant sibling pairs. Am J Hum Genet, 66(5), 1642-1660 Abstract

Forrest, W. F. (2001). Weighting improves the “new Haseman-Elston” method. Hum Hered, 52(1), 47-54 Abstract

Francks, C., DeLisi, L. E., Shaw, S. H., Fisher, S. E., Richardson, A. J., Stein, J. F., & Monaco, A. (2003). Parent-of-origin effects on handedness and schizophrenia susceptibility on chromosome 2p12-q11. Hum Mol Genet, 12(24), 3225-3230 Abstract

Frayling, T. M., Timpson, N. J., Weedon, M. N., Zeggini, E., Freathy, R. M., Lindgren, C. M., Perry, J. R., Elliott, K. S., Lango, H., Rayner, N. W., Shields, B., Harries, L. W., Barrett, J. C., Ellard, S., Groves, C. J., Knight, B., Patch, A. M., Ness, A. R., Ebrahim, S., Lawlor, D. A., Ring, S. M., Ben-Shlomo, Y., Jarvelin, M. R., Sovio, U., Bennett, A. J., Melzer, D., Ferrucci, L., Loos, R. J., Barroso, I., Wareham, N. J., Karpe, F., Owen, K. R., Cardon, L. R., Walker, M., Hitman, G. A., Palmer, C. N., Doney, A. S., Morris, A. D., Smith, G. D., Hattersley, A. T., & McCarthy, M. I. (2007). A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity. Science, 316(5826), 889-894 Abstract

Freedman, M. L., Reich, D., Penney, K. L., McDonald, G. J., Mignault, A. A., Patterson, N., Gabriel, S. B., Topol, E. J., Smoller, J. W., Pato, C. N., Pato, M. T., Petryshen, T. L., Kolonel, L. N., Lander, E. S., Sklar, P., Henderson, B., Hirschhorn, J. N., & Altshuler, D. (2004). Assessing the impact of population stratification on genetic association studies. Nat Genet, 36(4), 388-393 Abstract

Fulker, D. W. (1978). Multivariate extensions of a biometrical model of twin data. Prog Clin Biol Res, 24A, 217-236 Abstract

Fulker, D. W., Baker, L. A., & Bock, R. D. (1983). Estimating components of covariance using Lisrel. _ Data Analyst_, 1, 5-8

Fulker, D. W., & Cardon, L. R. (1994). A sib-pair approach to interval mapping of quantitative trait loci. Am J Hum Genet, 54(6), 1092-1103 Abstract

Fulker, D. W., Cherny, S. S., & Cardon, L. R. (1995). Multipoint interval mapping of quantitative trait loci, using sib pairs. Am J Hum Genet, 56(5), 1224-1233 Abstract

Fulker, D. W., & Cherny, S. S. (1996). An improved multipoint sib-pair analysis of quantitative traits. Behav Genet, 26(5), 527-532 Abstract

Fulker, D. W., Cherny, S. S., Sham, C., & Hewitt, J. K. (1999). Combined linkage and association sib-pair analysis for quantitative traits. Am J Hum Genet, 64(1), 259-267 Abstract

Fullerton, S. M., Clark, A. G., Weiss, K. M., Nickerson, D. A., Taylor, S. L., Stengard, J. H., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E., & Sing, C. F. (2000). Apolipoprotein E variation at the sequence haplotype level: implications for the origin and maintenance of a major human polymorphism. Am J Hum Genet, 67(4), 881-900 Abstract