Andrew Allen, PhD

Department:
Biostatistics and Bioinformatics

Email Address:
andrew.s.allen@duke.edu

Website:
www.duke.edu/~asallen

Address:
DUMC Box 2721

Durham, NC 27710

Telephone:
9196688043

Research Interests:
My research focuses on developing novel statistical methods for mapping complex disease genes. Recent work has focused on a number of topics, including: adjusting for population stratification in case-control studies; testing untyped markers in whole genome association studies; estimating copy-number polymorphisms from intensity data; and developing haplotype sharing approaches that can deal with computational requirements presented by whole genome data.

Publications:
2009 -- Allen AS, Epstein MP, Satten GA. Score-based adjustment for confounding by population stratification in genetic association studies. To appear in Genetic Epidemiology 2009.

2009 -- Pubmed # 19365859 -- Allen AS, Satten GA. A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease. Genet Epidemiol. 2009 Apr 13.

2009 -- Allen AS, Satten GA. Genome-wide association analysis of rheumatoid arthritis data via haplotype sharing. To appear in BMC Proceedings 2009.

2009 -- He M, Allen AS. Testing gene-treatment interactions in pharmacogenetic studies. To appear in Journal of Biopharmaceutical statistics 2009.

2009 -- Pubmed # 19724244 -- Laje G, Allen AS, Akula N, Manji H, John Rush A, McMahon FJ. Genome-wide association study of suicidal ideation emerging during citalopram treatment of depressed outpatients. Pharmacogenet Genomics. 2009 Sep;19(9):666-74.

2009 -- Laje G, Cannon DM, Allen AS, Klaver JM, Peck SA, Liu X, Manji HK, Drevets WC, McMahon FJ. Genetic variation in HTR2A influences serotonin transporter binding potential as measured using PET and [11C]DASB. To appear in the International Journal of Neuropsychopharmacology 2009.

2009 -- Pubmed # 19622101 -- Liu Y, Li YJ, Satten GA, Allen AS, Tzeng JY. A regression-based association test for case-control studies that uses inferred ancestral haplotype similarity. Ann Hum Genet. 2009 Sep;73(Pt 5):520-6.

2009 -- Sarasua SM, Collins JS, Williamson DM, Satten GA, Allen AS. Effect of population stratification on the identification of significant SNPs in genome wide association studies. To appear in BMC Proceedings 2009.

2008 -- Pubmed # 17948229 -- Allen AS, Satten GA. Robust estimation and testing of haplotype effects in case-control studies. Genet Epidemiol. 2008 Jan;32(1):29-40.

2008 -- Pubmed # 18252234 -- Epstein MP, Allen AS, Satten GA. Response to lee et Al. Am J Hum Genet. 2008 Feb;82(2):526-8.

2008 -- Pubmed # 18036642 -- Levesque MC, Hauswirth DW, Mervin-Blake S, Fernandez CA, Patch KB, Alexander KM, Allgood S, McNair PD, Allen AS, Sundy JS. Determinants of exhaled nitric oxide levels in healthy, nonsmoking African American adults. J Allergy Clin Immunol. 2008 Feb;121(2):396-402.e3.

2007 -- Pubmed # 18466465 -- Allen AS, Satten GA. Association mapping via a class of haplotype-sharing statistics. BMC Proc. 2007;1 Suppl 1:S123.

2007 -- Pubmed # 17266114 -- Allen AS, Satten GA. Inference on haplotype/disease association using parent-affected-child data: the projection conditional on parental haplotypes method.  Genet Epidemiol.  2007 Jan 31;31(3):211-223.

2007 -- Pubmed # 17483595 -- Allen AS, Satten GA. Statistical models for haplotype sharing in case-parent trio data. Hum Hered. 2007;64(1):35-44.

2007 -- Pubmed # 17436246 -- Epstein MP, Allen AS, Satten GA. A simple and improved correction for population stratification in case-control studies. Am J Hum Genet. 2007 May;80(5):921-30.

2007 -- Pubmed # 17123302 -- Kwee LC, Epstein MP, Manatunga AK, Duncan R, Allen AS, Satten GA. Simple methods for assessing haplotype-environment interactions in case-only and case-control studies. Genet Epidemiol. 2007 Jan;31(1):75-90.

2007 -- Pubmed # 18046754 -- de Andrade M, Allen AS, . Summary of contributions to GAW15 Group 13: candidate gene association studies. Genet Epidemiol. 2007 Nov 28;31(S1):S110-S117.

2006 -- Pubmed # 16496310 -- Allen AS, Martin ER, Qin X, Li YJ. Genetic association tests based on ranks (GATOR) for quantitative traits with and without censoring.  Genet Epidemiol.  2006 Apr;30(3):248-58.

2006 -- GA Satten,  AS Allen, MP Epstein. “Comment on ‘Likelihood-based inference on haplotype effects in genetic association studies’ by Lin and Zeng” Journal of the American Statistical Assocition 2006; 101:111-114.

2006 -- Pubmed # 16463349 -- Lyles RH, Allen AS, Dana Flanders W, Kupper LL, Christensen DL. Inference for case-control studies when exposure status is both informatively missing and misclassified. Stat Med. 2006 Feb 6.

2005 -- AS Allen, GA Satten, AA Tsiatis . Locally-efficient robust estimation of haplotype-disease association in family-based studies. Biometrika. 2005, 92(3): 559-571

2005 -- Pubmed # 16451682 -- Allen AS, Satten GA. Robust testing of haplotype/disease association.  BMC Genet.  2005 Dec 30;6 Suppl 1:S69.

2005 -- Pubmed # 15976776 -- Donahue MP, Allen AS. Genetic association studies in cardiology. Am Heart J. 2005 Jun;149(6):964-70.

2005 -- Pubmed # 16183419 -- Hedayati SS, Grambow SC, Szczech LA, Stechuchak KM, Allen AS, Bosworth HB. Physician-diagnosed depression as a correlate of hospitalizations in patients receiving long-term hemodialysis. Am J Kidney Dis. 2005 Oct;46(4):642-9.

2005 -- Pubmed # 16451665 -- Li YJ, Martin ER, Zhang L, Allen AS. Application of a rank-based genetic association test to age-at-onset data from the Collaborative Study on the Genetics of Alcoholism study. BMC Genet. 2005 Dec 30;6 Suppl 1:S53.

2004 -- Pubmed # 15493041 -- Anstrom KJ, Reed SD, Allen AS, Glendenning GA, Schulman KA. Long-term survival estimates for imatinib versus interferon-alpha plus low-dose cytarabine for patients with newly diagnosed chronic-phase chronic myeloid leukemia. Cancer. 2004 Dec 1;101(11):2584-92.

2003 -- Pubmed # 14975107 -- Allen AS, Collins JS, Rathouz PJ, Selander CL, Satten GA. Bootstrap calibration of TRANSMIT for informative missingness of parental genotype data. BMC Genet. 2003;4 Suppl 1:S39.

2003 -- Pubmed # 12592606 -- Allen AS, Rathouz PJ, Satten GA. Informative missingness in genetic association studies: case-parent designs.  Am J Hum Genet.  2003 Mar;72(3):671-80.

2003 -- Pubmed # 14655199 -- Griffith TF, Chua BS, Allen AS, Klassen PS, Reddan DN, Szczech LA. Characteristics of treated hypertension in incident hemodialysis and peritoneal dialysis patients. Am J Kidney Dis. 2003 Dec;42(6):1260-9.

2003 -- Pubmed # 12802814 -- Hasselblad V, Allen AS. Power calculations for large multi-arm placebo-controlled studies of dichotomous outcomes. Stat Med. 2003 Jun 30;22(12):1943-54.

2003 -- Pubmed # 14660978 -- Hauser ER, Allen AS. Where the rubber meets the road in pharmacogenetics: assessment of gene-environment interactions. Am Heart J. 2003 Dec;146(6):929-31.

2003 -- Pubmed # 12590411 -- Lyles RH, Allen AS. Missing data in the 2 x 2 table: patterns and likelihood-based analysis for cross-sectional studies with supplemental sampling. Stat Med. 2003 Feb 28;22(4):517-34.

2002 -- Pubmed # 12530786 -- Allen AS, Barnhart HX. Joint models for toxicology studies with dose-dependent number of implantations. Risk Anal. 2002 Dec;22(6):1165-73.

2002 -- Pubmed # 11821253 -- Lyles RH, Allen AS. Estimating crude or common odds ratios in case-control studies with informatively missing exposure data. Am J Epidemiol. 2002 Feb 1;155(3):274-81.

2001 -- Pubmed # 11430971 -- Dunlop AL, Allen AS, Frank E. Involving the male partner for interpreting the basal body temperature graph. Obstet Gynecol. 2001 Jul;98(1):133-8.

1999 -- Pubmed # 10203112 -- Lindeman RD, Romero LJ, Allen AS, Liang HC, Baumgartner RN, Koehler KM, Garry PJ. Alcohol consumption is negatively associated with the prevalence of coronary heart disease in the New Mexico Elder Health Survey. J Am Geriatr Soc. 1999 Apr;47(4):396-401.

1998 -- Pubmed # 9614614 -- Lindeman RD, Romero LJ, Hundley R, Allen AS, Liang HC, Baumgartner RN, Koehler KM, Schade DS, Garry PJ. Prevalences of type 2 diabetes, the insulin resistance syndrome, and coronary heart disease in an elderly, biethnic population. Diabetes Care. 1998 Jun;21(6):959-66.

1998 -- Pubmed # 9926905 -- Romero LJ, Lindeman RD, Hundley R, Koehler KM, Baumgartner RN, Allen AS, Schade DS, LaRue A, Ortiz IE, Garry PJ. Outcome of recruitment and report on participation rate in the New Mexico Elder Health Survey. Ethn Dis. 1998;8(3):350-9.