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Selected articles
*Cargill,M, *Altshuler, D., Ireland,J, Sklar,P, Ardlie,K, Patil,N, Shaw,N, Lane,CR, Lim,EP, Kalyanaraman,N, Nemesh,J, Ziaugra,L, Friedland,L, Rolfe,A., Warrington,J, Lipshutz,R, Daley,GQ, and Lander,ES (1999) “Characterization of Single Nucleotide Polymorphisms in Coding Regions of Human Genes" Nature Genetics 22: 231-238.
*Altshuler, D., *Hirschhorn, J., Klannemark,M, Lindgren,CM, Vohl,MC, Nemesh,J, Lane,CR, Schaffner,SF, Bolk,S, Brewer,C, Tuomi,T, Gaudet,D, Hudson,TJ, Daly,M, Groop,L, and Lander,ES (2000) “The common PPAR gamma Pro12Ala polymorphism is associated with decreased risk of type II diabetes" Nature Genetics 26: 76-80.
Altshuler, D., Pollara,VJ, Cowles,CR, Van Etten,WJ, Baldwin,J, Linton,L, and Lander,ES (2000) “An SNP map of the human genome generated by reduced representation shotgun sequencing” Nature 407: 513-516.
The International SNP Map Working Group: Sachidanandam, R, Weissman, D, Schmidt, SC, Kakol, JK, Stein, LD, Marth G Sherry, D, Mullikin, JC, Mortimore, BJ, Willey, D, Hunt, SE, Cole, CG, Coggill, PC, Rice, CM, Ning, Z, Rogers, J, Bentley, DR, Kwok, P-Y, Mardis, ER, Yeh, RT, Schultz, B, Cook, L, Davenport, R, Dante, R, Fulton, L, Waterston, RH, McPherson, JD, Gilman, B, Schaffner, SF, Van Etten, WJ, Reich, DE, Higgins, J, Blumenstiel, B, Baldwin, J, Stange-Thomann, N, Zody, MC, Linton, LM, Lander, ES, and Altshuler, D., (2001) “A map of human genome sequence variation containing 1.4 million SNPs" Nature 409: 928-933.
Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel1 B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, and Altshuler, D. (2002) “The structure of haplotype blocks in the human genome” Science 296: 2225-2229
Reich, D.R., Schaffner, S.F., Daly, M.J., McVean, G., Mullikin, J.C., Higgins, J.M, Richter, D.J., Lander, E.S., Altshuler, D. (2002) “Human genome sequence variation and the influence of gene history, mutation and recombination” Nature Genetics 32(1): 135-42.
Cowles,C., Hirschhorn,J.N., Altshuler,D., and Lander,E.S. (2002) “Detection of regulatory polymorphism in mouse genes” Nature Genetics 32: 432–437.
Reich , DE , Gabriel, SB, and Altshuler, D., (2003) “Quality and Completeness of SNP Databases” Nature Genetics 33: 457-458.
Mootha*, VK, Lindgren*, CM, Eriksson, KF, Subramanian, A., Sihag, M, Lehar, J Puigserver, P., Carlsson, E, Ridderstråle, M, Laurila, E, Daly, MJ, Patterson, P, Mesirov, JP, Golub, TR, Tamayo, P., Spiegelman, B.,, Lander, ES, Hirschhorn, JN, Altshuler, D.,** and Groop, LC** (2003) “PGC-1α Responsive Genes Involved in Oxidative Phosphorylation are Coordinately Downregulated in Human Diabetes” Nature Genetics 34: 267-273.
Haiman CA, Stram DO, Pike MC, Kolonel LN, Burtt NP, Altshuler, D., Hirschhorn J, Henderson BE, “(2003) A comprehensive haplotype analysis of CYP19 and breast cancer risk: the Multiethnic Cohort” Human Molecular Genetics 12: 2679-92.
The International HapMap Consortium: (2003) "The International HapMap Project" Nature 426: 789-796.
Freedman ML, Reich DE, Penney K, MacDonald G, Patterson N, Gabriel S, Topol EJ, Smoller, JW, Pato CN, Pato MT, Petryshen T, Kolonel L, Sklar P, Lander ES, Henderson B, Hirschhorn JN, and Altshuler, D. (2004) “The impact of population stratification on genetic association studies” Nature Genetics 36:388-93.
Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, De The G, Essex M, Sankale JL, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, O'Brien SJ, Reich D. (2004) “A high-density admixture map for disease gene discovery in african Americans” American Journal of Human Genetics 74:1001-13.
Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O'Brien SJ, Altshuler D, Daly MJ, Reich D. (2004) “Methods for high-density admixture mapping of disease genes” American Journal of Human Genetics 74:979-1000.
Florez, JC, Burtt, N, de Bakker, PIW, Almgren, P, Tuomi, T, Holmkvist, J, Gaudet, D, Hudson, TJ, Schaffner, SF, Daly, MJ, Hirschhorn, JN, Groop, L and Altshuler, D. (2004) "Haplotype structure and genotype-phenotype correlations of the sulfonylurea receptor (SUR1) and the islet ATP-sensitive potassium channel (Kir6.2) gene region" Diabetes 53:1360-1368.
Florez JC, Sjogren M, Burtt N, Orho-Melander M, Schayer S, Sun M, Almgren P, Lindblad U, Tuomi T, Gaudet D, Hudson TJ, Daly MJ, Ardlie K, Hirschhorn JN, Altshuler, D. and Groop L (2004) “Association Testing in 9,000 People Fails to Confirm the Association of the Insulin Receptor Substrate-1 G972R” Diabetes 53:3313-8.
Freedman M, Pearce CL, Penney KL, Hirschhorn JN, Kolonel LN, Henderson BH and Altshuler, D. (2005) “Systematic evaluation of genetic variation at the androgen receptor locus and risk of prostate cancer in the Multiethnic Cohort Study” American Journal of Human Genetics 76:82-90.
Pearce CL, Hirschhorn JN, Wu AH, Burtt NP, Stram DO, Young S, Kolonel LN, Henderson BE, Altshuler, D. Pike MC. (2005) "Clarifying the PROGINS allele association in ovarian and breast cancer risk: a haplotype-based analysis." J National Cancer Institute 5;97:51-9.
Winckler W, Graham RR, de Bakker PIW, Sun M, Almgren P, Tuomi T, Gaudet D, Hudson TJ, Ardlie KG, Daly MJ, Hirschhorn JN, Groop L, and Altshuler, D. (2005) “Association Testing of Variants in the Hepatocyte Nuclear Factor 4a Gene With Risk of Type 2 Diabetes in 7,883 People.” Diabetes 54:886-92.
Winckler W, Myers SR, Richter DJ, Onofrio RC, McDonald GJ, Bontrop RE, McVean GAT, Gabriel SB, Reich D, Donnelly P, Altshuler, D. (2005) "Comparison of fine-scale recombination rates in human and chimpanzee" Science 308:107-11.
Florez JC, Agapakis CM, Burtt NP, Sun M, Almgren P, Rastam L, Tuomi T, Gaudet D, Hudson TJ, Daly MJ, Ardlie KG, Hirschhorn JN, Groop L, Altshuler D. (2005) Association “Testing of the Protein Tyrosine Phosphatase 1B Gene (PTPN1) With Type 2 Diabetes in 7,883 People.” Diabetes; 54:1884-91.
Freedman ML, Penney KL, Stram DO, Riley S, McKean-Cowdin R, Le Marchand L, Altshuler D, Haiman CA. (2005) “A haplotype-based case-control study of BRCA1 and sporadic breast cancer risk.” Cancer Research 65:7516-22.
Winckler W, Burtt NP, Holmkvist J, Cervin C, de Bakker PI, Sun M, Almgren P, Tuomi T, Gaudet D, Hudson TJ, Ardlie KG, Daly MJ, Hirschhorn JN, Altshuler D, Groop L. (2005) “Association of common variation in the HNF1α gene region with risk of type 2 diabetes” Diabetes 54:2336-42.
Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D (2005) “Calibrating a Coalescent Simulation of Human Genome Sequence Variation” Genome Research, 15(11):1576-83.
de Bakker PIW*, Yelensky R*, Pe’er I, Gabriel SB, Daly MJ and Altshuler D (2005) “Efficiency and power in genetic association studies” Nature Genetics, 37:1217-1223
The International HapMap Consortium (2005) “A haplotype map of the human genome” Nature, 437(7063):1299-320.
Plenge, RM, Padyukov,L Remmers,EF Purcell, S, Lee, AT, Karlson,EW Wolfe,F Daniel L. Kastner,Alfredsson,L Altshuler,D Gregersen,PK Klareskog,L and Rioux JD (2005) “Replication of Putative Candidate-Gene Associations with Rheumatoid Arthritis in >4,000 Samples from North America and Sweden: Association of Susceptibility with PTPN22, CTLA4, and PADI4” American Journal of Human Genetics, 77:1044–1060.
Kraft P, Pharoah P, Chanock SJ, Albanes D, Kolonel LN, Hayes RB, Altshuler D, Andriole G, Berg C, Boeing H, Burtt NP, Bueno-de-Mesquita B, Calle EE, Cann H, Canzian F, Chen YC, Crawford DE, Dunning AM, Feigelson HS, Freedman ML, Gaziano JM, Giovannucci E, Gonzalez CA, Haiman CA, Hallmans G, Henderson BE, Hirschhorn JN, Hunter DJ, Kaaks R, Key T, Le Marchand L, Ma J, Overvad K, Palli D, Pike MC, Riboli E, Rodriguez C, Setiawan WV, Stampfer MJ, Stram DO, Thomas G, Thun MJ, Travis R, Trichopoulou A, Virtamo J, Wacholder S (2005). “Genetic Variation in the HSD17B1 Gene and Risk of Prostate Cancer” PLoS Genetics, 1(5): e68, 0603-0613.
Florez JC, Wiltshire S, Agapakis CM, Burtt NP, de Bakker PIW, Almgren P, Bengtsson Boström K, Tuomi T, Gaudet D, Daly MJ, Hirschhorn JN, McCarthy MI, Altshuler D, Groop L. (2006) “High-density haplotype structure and association testing of the insulin-degrading enzyme (IDE) gene with type 2 diabetes in 4,206 people” Diabetes 55(1):128-35.
McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett J, Dallaire S, Gabriel SB, Lee C, Daly MJ and Altshuler D, for the International HapMap Consortium. “Common deletion polymorphisms in the human genome.” Published Online 12/5/05, Nature Genetics 38, 86-92.
Bonnen PE, Pe’er I, Plenge RM, Salit J, Lowe JK, Shepiro MH, Lifton RP, Breslow JL, Daly MJ, Reich DE, Jones KW, Stoffel M, Altshuler D, and Friedman JM. (2006) “Evaluating potential for whole genome scans in Kosrae – an isolated population in Micronesia” Nature Genetics 38, 214 – 217.
Selected reviews and chapters
Altshuler, D., Kruglyak, L., and Lander, E. (1998) "Genetic Polymorphisms and Disease" New England Journal of Medicine 338: 1626.
Altshuler, D., Daly, M and Kruglyak, L. (2000) “Guilt by Association" Nature Genetics 26: 135-137.
Hirschhorn, J.N. and Altshuler, D. (2002) “Editorial: Once and Again - Issues Surrounding Replication in Genetic Association Studies” Journal of Endocrinology & Metabolism 87(10): 4438-4441.
Florez, J, Hirschhorn, JN, and Altshuler, D. (2003) “The inherited basis of diabetes mellitus: general lessons for the genetic analysis of complex traits” Annual Reviews of Human Genetics and Genomics 4: 257-91.
Hirschhorn, J.N, Pearce, C.L., and Altshuler, D. (2003) "Genomic approaches to the genetics of hormone-responsive cancers" in Hormones and Cancer, Henderson, Ponder and Ross, eds, Oxford University Press, New York, NY.
The International HapMap Consortium* (2003) “Integrating ethics and science in the International HapMap Project “ Nature Reviews Genetics 5:467-75
Altshuler, D. (2004) “The Inherited Basis of Common Disease” Cecil’s Textbook of Medicine 22nd Edition, WB Saunders.
Altshuler JS and Altshuler D. (2004) “Organizational Challenges in Clinical Genomic Research”, Nature 429:478-81.
Kolonel LN, Altshuler D, Henderson BE (2004) The multiethnic cohort study: exploring genes, lifestyle and cancer risk” Nature Reviews Cancer 4:519-27.
Altshuler, D. and Clark AG (2005) "Harvesting Medical Information from the Human family tree" Science 307:1052-3.
Altshuler D, Hirschhorn JN (2005) “MEF2A sequence variants and coronary artery disease: a change of heart?” Journal of Clinical Investigation 115:831-3.
Daly MJ and Altshuler D (2005) “Partners in Crime” Nature Genetics 37:337-8.
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