Skip Navigation

Your Environment. Your Health.

David M. Umbach, Ph.D.

Biostatistics Branch

David Umbach, Ph.D.
David M. Umbach, Ph.D.
Staff Scientist
Tel (919) 541-4939
Fax (919) 541-4311
umbach@niehs.nih.gov
P.O. Box 12233
Mail Drop A3-03
Research Triangle Park, North Carolina 27709
Delivery Instructions

Research Summary

David Umbach’s primary methodological interest is the development of new statistical tools for detecting and characterizing gene-environment interactions through epidemiologic studies. Currently, he is investigating extensions to a recently proposed hybrid design for studying genetic influences on risk. These extensions focus on utilizing exposure information, whether categorical or continuous, in the context of this design. He is also working on methods for use with a case-parents design when subjects are genotyped at multiple linked SNPs that allow discovery of potential risk-tagging haplotypes.

 

Umbach has recently developed an interest in the statistical design and analysis of studies involving gene expression microarrays and certain mass spectrometry techniques for proteomics, particularly SELDI-TOF. Data from these sources pose challenges for standard statistical techniques because there are typically many more observations on each sample than there are samples in a study.

 

He also actively collaborates with NIEHS researchers on a variety of studies. Topics include the following: aspects of genetic susceptibility to cancer, environmental and genetic influences on neurodegenerative diseases such as Parkinson’s disease and amyotrophic lateral sclerosis, effects of pesticides on respiratory diseases in the Agricultural Health Study cohort, and the hormonal effects of soy formula in infants.

Selected Publications

Statistical Methods for Genetic, Molecular and Environmental Epidemiology 

  1. Starling AP, Umbach DM, Kamel F, Long S, Sandler DP, Hoppin JA. Pesticide use and incident diabetes among wives of farmers in the Agricultural Health Study. Occupational and environmental medicine 2014 71(9):629-635.[Abstract ]
  2. Shi M, Umbach DM, Weinberg CR. Disentangling pooled triad genotypes for association studies. Annals of human genetics 2014 78(5):345-356.[Abstract ]
  3. Hoppin JA, Umbach DM, Long S, Rinsky JL, Henneberger PK, Salo PM, Zeldin DC, London SJ, Alavanja MC, Blair A, Beane Freeman LE, Sandler DP. Respiratory disease in United States farmers. Occupational and environmental medicine 71(7):484-491, 2014.[Abstract ]
  4. Weinberg CR, Shi M, DeRoo L, Taylor JA, Sandler DP, Umbach DM. Asymmetry in family history implicates nonstandard genetic mechanisms: application to the genetics of breast cancer. PLoS genetics 2014; 10(3):e1004174.[Abstract ]
  5. Li Y, Umbach DM, Li L. T-KDE: a method for genome-wide identification of constitutive protein binding sites from multiple ChIP-seq data sets. BMC genomics 2014 15:27[Abstract ]
  6. Adgent MA, Flake GP, Umbach DM, Stallings VA, Bernbaum JC, Rogan WJ. Urogenital epithelial cells as simple markers of estrogen response in infants: methods and applications. PloS one 8(10):e77061, 2013.[Abstract ]
  7. Waggoner JK, Henneberger PK, Kullman GJ, Umbach DM, Kamel F, Beane Freeman LE, Alavanja MC, Sandler DP, Hoppin JA. Pesticide use and fatal injury among farmers in the Agricultural Health Study. International archives of occupational and environmental health 86(2):177-187, 2013.[Abstract ]
  8. Shi M, Umbach DM, Weinberg CR. Case-sibling studies that acknowledge unstudied parents and enroll unmatched individuals. International journal of epidemiology 42(1):298-307, 2013.[Abstract ]
  9. Fang F, Umbach DM, Xu Z, Ye W, Sandler DP, Taylor JA, Kamel F. No association between DNA repair gene XRCC1 and amyotrophic lateral sclerosis. Neurobiology of aging 33(5):1015.e25-1015.e26, 2012. [Abstract ]
  10. Dinse GE, Umbach DM. Parameterizing dose-response models to estimate relative potency functions directly. Toxicological Sciences 2012 129(2):447-55.[Abstract ]
  11. Weinberg CR, Shi M, Umbach DM. Re.: "Genetic association and gene-environment interaction: a new method for overcoming the lack of exposure information in controls". American journal of epidemiology 2011; 173(11):1346-7.[Abstract ]
  12. Shaughnessy DT, Gangarosa LM, Schliebe B, Umbach DM, Xu Z, MacIntosh B, Knize MG, Matthews PP, Swank AE, Sandler RS, DeMarini DM, Taylor JA. Inhibition of fried meat-induced colorectal DNA damage and altered systemic genotoxicity in humans by crucifera, chlorophyllin, and yogurt. PLOS ONE 2011 6(4):e18707-.[Abstract ]
  13. Weinberg CR, Shi M, Umbach DM.  A sibling-augmented case-only approach for assessing multiplicative gene-environment interactions. American journal of epidemiology  2011;174(10):1183-1189.[Abstract ]  
  14. Saha-Chaudhuri P, Umbach DM, Weinberg CR. Pooled Exposure Assessment for Matched Case-Control Studies. Epidemiology 2011; 22(5):704-712.[Abstract ]
  15. Dinse GE, Umbach DM. Characterizing non-constant relative potency. Regulatory toxicology and pharmacology 2011; 60(3):342-352.[Abstract ]  
  16. Shi M, Umbach DM, Weinberg CR. Family based Gene-by-Environment Interaction Studies: Revelations and Remedies. Epidemiology (Cambridge, Mass.) 2011; 22(3):400-407.[Abstract ]
  17. Nguyen RHN, Umbach DM, Parad RB, Stroehla B, Rogan WJ, Estroff JA. US assessment of estrogen-responsive organ growth among healthy term infants: piloting methods for assessing estrogenic activity. Pediatric Radiology 2011; 41(5):633-642.[Abstract ]  
  18. Fang F, Kwee LC, Allen KD, Umbach DM, Ye W, Watson M, Keller J, Oddone EZ, Sandler DP, Schmidt S, Kamel F. Association between blood lead and the risk of amyotrophic lateral sclerosis. American journal of epidemiology 2010 171(10):1126-1133. [Abstract ]  
  19. Hoppin JA, Umbach DM, London SJ, Henneberger PK, Kullman GJ, Coble J, Alavanja MCR, Beane Freeman LE, Sandler DP. Pesticide use and adult-onset asthma among male farmers in the Agricultural Health Study. The European Respiratory Journal 2009; 34(6):1296-1303.[Abstract ]  
  20. Shi M, Umbach DM, Weinberg CR. Using case-parent triads to estimate relative risks associated with a candidate haplotype. Annals of Human Genetics 2009; 73(Pt 3):346-359.[Abstract ]
  21. Vermeulen SH, Shi M, Weinberg CR, Umbach DM. A hybrid design: case-parent triads supplemented by control-mother dyads. Genetic Epidemiology 2009; 33(2):136-144.[Abstract ]
  22. Weinberg CR, Umbach DM.  A hybrid design for studying genetic influences on risk of diseases with onset early in life. American Journal of Human Genetics 2005; 77:627-636.[Abstract ]
  23. Weinberg CR, Umbach DM. Choosing a retrospective design to assess joint genetic and environmental contributions to risk. American Journal of Epidemiology 2000; 152:197-203.[Abstract ]
  24. Umbach DM, Weinberg CR . The use of case-parent triads to study joint effects of genotype and exposure. American Journal of Human Genetics 2000; 66:251-261, 2000.[Abstract ]
  25. Umbach, D.M. Unit conversion as a source of misclassification in U.S. birthweight data. American Journal of Public Health 2000; 90:127-129.[Abstract ]  
  26. Weinberg, C.R., and D.M. Umbach. Using pooled exposure assessment to improve efficiency in case-control studies. Biometrics 1999; 55:718-726.[Abstract ]
  27. Umbach DM, Weinberg CR. Designing and analyzing case-control studies to exploit independence of genotype and exposure. Statistics in Medicine 1997; 16:1731-1743.[Abstract ]

 

Statistical Methods for Gene Expression Microarrays and Genomics

  1. Li Y, Huang W, Niu L, Umbach DM, Covo S, Li L. Characterization of constitutive CTCF/cohesin loci: a possible role in establishing topological domains in mammalian genomes, BMC Genomics 14:553, 2013.[Abstract ]
  2. Xu M, Weinberg CR, Umbach DM, Li L. coMOTIF: A method for Identifying Transcription Co-regulator Binding Sites in ChIP-seq Data. Bioinformatics (Oxford, England), 2011, 27(19):2625-2632.[Abstract ]
  3. Peddada SD, Umbach DM, Harris SF. A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. BMC bioinformatics 2009 Dec 2(10):438.[Abstract ]
  4. Watson A, Kent P, Alam M, Paller AS, Umbach DM, Yoon JW, Iannaccone PM, Walterhouse DO. GLI1 genotypes do not predict basal cell carcinoma risk: a case control study. Molecular cancer 2009 8:113-.[Abstract ]
  5. Huang W, Umbach DM, Ohler U, Li L.  Optimized mixed Markov models for motif identification. BMC Bioinformatics 2006; 2 June; 7:279 (electronic access).[Abstract ]  
  6. Huang W, Umbach DM, Li L.  Accurate anchoring alignment of divergent sequences. Bioinformatics 2006; 22:29-34.[Abstract ]  
  7. Liu D, Umbach DM, Peddada SD, Li L, Crockett P, Weinberg CR.  A random-periods model for expression of cell-cycle genes.  Proceedings of the National Academy of Sciences 2004; 101:7240-7245.[Abstract ]
  8. Peddada SD, Lobenhofer EK, Li L, Afshari CA, Weinberg CR, Umbach DM. Gene selection and clustering for time-course and dose-response microarray experiments using order restricted inference. Bioinformatics 2003; 19:834-841.[Abstract ]

 

Genetic Susceptibility to Cancer

  1. DeRoo LA, Bolick SCE, Xu Z, Umbach DM, Shore D, Weinberg CR, Sandler DP, Taylor JA. Global DNA methylation and one-carbon metabolism gene polymorphisms and the risk of breast cancer in the Sister Study. Carcinogenesis 35(2):333-338, 2014.[Abstract ]
  2. Han YY, Dinse GE, Umbach DM, Davis DL, Weissfeld JL. Age-period-cohort analysis of cancer not related to tobacco, screening, or HIV: Sex and race differences. Cancer Causes & Control 2010; 21(8):1227-1236.[Abstract ]  
  3. Swartz CD, King LC, Nesnow S, Umbach DM, Kumar S, DeMarini DM. Mutagenicity, stable DNA adducts, and abasic sites induced in salmonella by phenanthro[3,4-b]- and phenanthro[4,3-b]thiophenes, sulfur analogs of benzo[c]phenanthrene. Mutation Research 2009; 661(1-2):47-56.[Abstract ]  
  4. Swartz CD, Parks N, Umbach DM, Ward WO, Schaaper RM, DeMarini DM. Enhanced mutagenesis of Salmonella tester strains due to deletion of genes other than uvrB. Environmental and Molecular Mutagenesis 2007; 48(8):694-705[Abstract ]  
  5. Yim HW, Slebos RJC, Randell SH, Umbach DM, Rivera MP, Detterbeck FC, Taylor JA.  Smoking is associated with increased telomerase activity in short-term cultures of human bronchial epithelial cells.  Cancer Letters 2007; 246: 24-33.[Abstract ]  
  6. Terry P, Umbach DM, Taylor JA. APE1 genotype and risk of bladder cancer: evidence for effect modification by smoking.  International Journal of Cancer. 2006; 118:3170-3173.[Abstract ]  
  7. Terry P, Umbach DM, Taylor JA.  No association between SOD2 or NQO1 genotypes and risk of bladder cancer.  Cancer Epidemiology, Biomarkers and Prevention 2005; 14:753-754.[Abstract ]  
  8. Slebos RJC, Umbach DM, Sommer CA, Horner GA, Choi J, Taylor JA.  Analytical and statistical methods to evaluate microsatellite allelic imbalance in small amounts of DNA.  Laboratory Investigation 2004; 84:649-657.[Abstract ]

 

Neurodegenerative Diseases

  1. Kamel F, Goldman SM, Umbach DM, Chen H, Richardson G, Barber MR, Meng C, Marras C, Korell M, Kasten M, Hoppin JA, Comyns K, Chade A, Blair A, Bhudhikanok GS, Webster Ross G, William Langston J, Sandler DP, Tanner CM. Dietary fat intake, pesticide use, and Parkinson's disease. Parkinsonism & related disorders 20(1):82-87, 2014.[Abstract ]
  2. Goldman SM, Kamel F, Ross GW, Bhudhikanok GS, Hoppin JA, Korell M, Marras C, Meng C, Umbach DM, Kasten M, Chade AR, Comyns K, Richards MB, Sandler DP, Blair A, Langston JW, Tanner CM. Genetic modification of the association of paraquat and Parkinson's disease. Movement disorders 27(13):1652-8, 2012. [Abstract ]
  3. Goldman SM, Kamel F, Ross GW, Jelell SA, Bhudhikanok GS, Umbach D, Marras C, Hauser RA, Jankovic J, Factor SA, Bressman S, Lyons KE, Meng C, Korell M, Roucoux DF, Hoppin JA, Sandler DP, Langston JW, Tanner CM. Head injury, alpha-synuclein Rep1 and Parkinson's disease. Annals of neurology 2012 71(1):40-8.[Abstract ]
  4. Kamel F, Umbach DM, Bedlack RS, Richards M, Watson M, Alavanja MC, Blair A, Hoppin JA, Schmidt S, Sandler DP. Pesticide exposure and amyotrophic lateral sclerosis. Neurotoxicology 33(3):457-62, 2012.[Abstract ]
  5. McGuire V, Van Den Eeden SK, Tanner CM, Kamel F, Umbach DM, Marder K, Mayeux R, Ritz B, Ross GW, Petrovitch H, Topol B, Popat RA, Costello S, Manthripragada AD, Southwick A, Myers RM , Nelson LM, Nelson L. Association of DRD2 and DRD3 polymorphisms with Parkinson's disease in a multiethnic consortium. Journal of the neurological sciences 307(1-2):22-29, 2011.[Abstract ]
  6. Popat RA, Van Den Eeden SK, Tanner CM, Kamel F, Umbach DM, Marder K, Mayeux R, Ritz B, Ross GW, Petrovich H, Topol B, McGuire V, Costello S, Manthripragada AD, Southwick A, Myers RM, Nelson LM. Coffee, ADORA2A, and CYP1A2: the caffeine connection in Parkinson's disease. European journal of neurology 2011 18(5):756-65.[Abstract ]
  7. Fang F, Quinlan P, Ye WM, Barber MK, Umbach DM, Sandler DP, Kamel F. Workplace exposures and the risk of amyotrophic lateral sclerosis. Environmental health perspectives 117(9):1387-1392, 2009. [Abstract ]
  8. Kamel F, Umbach DM, Stallone L, Richards M, Hu H, Sandler DP, . Association of lead exposure with survival in Amyotrophic Lateral Sclerosis (ALS). Neurology; 2008; 116(7):943-947.[Abstract ]
  9. Chen H , Richards M , Sandler DP , Umbach DM , Kamel F. Head injury and amyotrophic lateral sclerosis. American Journal of Epidemiology 2007; 7:810-816.[Abstract ]  
  10. Kamel F, Tanner CM, Umbach DM, Hoppin JA, Alavanja MCR, Blair A, Comyns K, Goldman SM, Korell M, Langston JW, Ross GW, Sandler DP.  Pesticide exposure and self-reported Parkinson's Disease in the Agricultural Health Study. American Journal of Epidemiology 2006; 165:364-74.[Abstract ]  
  11. Kamel F,Umbach DM, Hu H, Munsat TL, Shefner JM, Taylor JA, Sander DP.  Lead Exposure as a Risk Factor for Amyotrophic Lateral Sclerosis (ALS).  Neurodegenerative Diseases 2005; 2 (3-4):195-201.[Abstract ]  
  12. Terry PD, Kamel F, Umbach DM, Lehman TA, Hu H, Sandler DP, Taylor JA. VEGF promoter haplotype and amyotrophic lateral sclerosis (ALS). Journal of Neurogenetics 2004; 18:429-434.[Abstract ]  
  13. Kamel F, Umbach DM, Hu H, Munsat TL, Shefner JM, Sandler DP. Lead exposure and amyotrophic lateral sclerosis (ALS). Epidemiology 2002; 13:311-319.[Abstract ]  

 

Respiratory Diseases in the Agricultural Health Study

  1. Hoppin JA, Long S, Umbach DM, Lubin JH, Starks SE, Gerr F, Thomas K, Hines CJ, Weichenthal S, Kamel F, Koutros S, Alavanja M, Beane Freeman LE, Sandler DP. Lifetime organophosphorous insecticide use among private pesticide applicators in the Agricultural Health Study. Journal of exposure science & environmental epidemiology 2012;  22(6):584-92.[Abstract ]
  2. Waggoner JK, Kullman GJ, Henneberger PK, Umbach DM, Blair A, Alavanja MCR, Kamel F, Lynch CF, Knott C, London SJ, Hines CJ, Thomas KW, Sandler DP, Lubin JH, Beane Freeman LE, Hoppin JA. Mortality in the agricultural health study: 1993-2007. American Journal of Epidemiology 2011; 173(1):71-83.[Abstract ]
  3. Hoppin JA, Valcin M, Henneberger PK, Kullman GJ, Umbach DM, London SJ, Alavanja MCR, Sandler DP. Pesticide use and chronic bronchitis among farmers in the Agricultural Health Study. American Journal of Industrial Medicine 2007; 50(12):969-979.[Abstract ]  
  4. Hoppin JA, Umbach DM, Kullman GJ, Henneberger PK, London SJ, Alavanja MCR, Sandler DP.  Pesticides and other agricultural factors associated with self-reported farmer’s lung among farm residents in the Agricultural Health Study.  Occupational and Environmental Medicine 2007; 65(5):334-341.[Abstract ]  
  5. Hoppin JA, Umbach DM, London SJ, Lynch CF, Alavanja MCR, Sandler DP.  Pesticides associated with wheeze among commercial pesticide applicators in the Agricultural Health Study. American Journal of Epidemiology 2006; 163:1129-1137.[Abstract ]  
  6. Hoppin JA, Umbach DM, London SJ, Alavanja MCR, Sandler DP. Diesel exhaust, solvents, and other occupational exposures as risk factors for wheeze among farmers. Am J Respir Crit Care Med 2004; 169:1308-1313.[Abstract ]  
  7. Hoppin JA, Umbach DM, London SJ, Alavanja MCR, Sandler DP. Chemical predictors of wheeze among farmer pesticide applicators in the Agricultural Health Study. American Journal of Respiratory and Clinical Care Medicine 2002; 165: 683-689.[Abstract ]  

Software

  • Case Control
    ("/Rhythmyx/assembler/render?sys_contentid=56407&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56407" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56407" sys_siteid="" sys_folderid="")This archive provides information for fitting log-linear models and carrying out statistical tests for a design that includes two samples from the same population: one sample of affected individuals and their mothers and a second sample of unaffected individuals and their mothers.
  • coMotif ("/Rhythmyx/assembler/render?sys_contentid=34836&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34836" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34836" sys_siteid="" sys_folderid="")
    A three-component mixture framework to model the joint distribution of two motifs as well as the situation where some sequences contain only one or none of the motifs.
  • Ctrl-mom-hybrid
    ("/Rhythmyx/assembler/render?sys_contentid=56408&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56408" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56408" sys_siteid="" sys_folderid="")This archive provides information for fitting log-linear models and carrying out statistical tests for a hybrid design that includes a sample of affected individuals and their parents and a sample of unaffected individuals and their mothers (case-parent triad/control-mother dyad design).
  • EpiCenter
    ("/Rhythmyx/assembler/render?sys_contentid=34838&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34838" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34838" sys_siteid="" sys_folderid="")EpiCenter is a powerful analysis tool of genome-wide mRNA-seq or ChIP-seq data for detecting differentially expressed genes or identifying changes in epigenetic modifications.
  • GEI-TRIMM
    ("/Rhythmyx/assembler/render?sys_contentid=56417&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56417" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56417" sys_siteid="" sys_folderid="")This package includes the program GEI-TRIMM, which implements the method described in the manuscript Shi M, Umbach DM, Weinberg CR 2010 "Testing Haplotype-Environment Interactions Using Case-parent Triads."
  • Hill Viewer
    ("/Rhythmyx/assembler/render?sys_contentid=34951&sys_revision=4&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34951" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34951" sys_siteid="" sys_folderid="")Used to visualize dose-response curves and relative potency functions based on two sets of Hill model parameters.
  • Hybrid Design
    ("/Rhythmyx/assembler/render?sys_contentid=34981&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="34981" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="34981" sys_siteid="" sys_folderid="")Provides information for fitting log-linear models and carrying out statistical tests.
  • Lem Scripts Case-Sibling (http://www.niehs.nih.govhttp://edit:9992/Rhythmyx/assembler/render?sys_authtype=0&sys_variantid=567&sys_revision=1&sys_contentid=75459&sys_context=0)
    This package contains R scripts for analyzing case-sibling data using missing-parents approach as described in the manuscript Shi M, Umbach DM, Weinberg CR 2012 "Case-sibling studies that acknowledge unstudied parents and enroll unmatched individuals".
  • R-SCRIPTS
    ("/Rhythmyx/assembler/render?sys_contentid=56430&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56430" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56430" sys_siteid="" sys_folderid="")This package contains two R scripts for generating scenarios 1-4 described in the manuscript Shi M, Weinberg CR 2011 "How much are we missing in SNP-by-SNP analyses of GWAS?"
  • TRIad Multi-Marker
    ("/Rhythmyx/assembler/render?sys_contentid=35906&sys_revision=3&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="35906" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="35906" sys_siteid="" sys_folderid="")Performs association tests for a child's or mother's genetic effects using multiple markers from triad families.
  • TRIMMEST
    ("/Rhythmyx/assembler/render?sys_contentid=56435&sys_revision=1&sys_variantid=639&sys_context=0&sys_authtype=0&sys_siteid=&sys_folderid=" sys_dependentvariantid="639" sys_dependentid="56435" inlinetype="rxhyperlink" rxinlineslot="103" sys_dependentid="56435" sys_siteid="" sys_folderid="")This package contains programs that fit log-linear models to estimate the relative risk associated with a candidate risk haplotype in a triad-based association study.

Back to Top