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Your Environment. Your Health.

David M. Umbach, Ph.D.

Biostatistics & Computational Biology Branch

David Umbach, Ph.D.
David M. Umbach, Ph.D.
Staff Scientist
Tel (919) 541-4939
P.O. Box 12233
Mail Drop A3-03
Research Triangle Park, NC 27709

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Research Summary

Statistical methods are indispensable tools used by scientists from many disciplines to draw valid inferences from data.  Statisticians then have two roles in advancing science: as developers of new and better statistical methods and as shepherds of the appropriate application of statistical tools and of the proper interpretation of their results.  Umbach’s research at the NIEHS encompasses both these roles.

Much of his work in method’s development has centered on improving study designs and analyses for genetic epidemiology, in particular, on designs that use affected individuals and their parents to understand genetic and environmental contributors to disease risk.  A second research interest, related to environmental epidemiology, is developing methods for using measurements on pooled specimens as predictors in regression models that assess relationships between risk factors and disease.  He has also contributed to methods in statistical genomics, for example, methods directed at identifying transcription-factor binding sites enriched in ChIP-seq or at assessing aspects of gene expression from RNA-seq data.  Recently, he has initiated some work related to toxicological studies of the effects of mixtures of chemical agents.

Umbach also serves as a statistical collaborator on several ongoing studies led by investigators in the NIEHS Epidemiology Branch.  With various collaborators, he is involved in the analysis of data from the Agricultural Health Study to investigate pesticides and other farming exposures as possible risk factors for respiratory diseases or other non-cancer endpoints.  In collaboration with Walter Rogan, he is studying the effects of a soy-formula diet on aspects of infant development.  With Freya Kamel and Honglei Chen, he works on environmental and genetic risk factors for such neurodegenerative diseases as Parkinson disease and amyotrophic lateral sclerosis (ALS).   He has also worked on studies of genetic susceptibility to cancer.

Selected Publications

Statistical Methods for Genetic and Environmental Epidemiology 

  1. Shi M, Umbach DM, Weinberg CR. Using parental phenotypes in case-parent studies. Frontiers in genetics 2015 6():221-.[Abstract]
  2. Li Y, Krahn JM, Flake GP, Umbach DM, Li L. Toward predicting metastatic progression of melanoma based on gene expression data. Pigment cell & melanoma research 2015 28(4):453-463.[Abstract]
  3. Eum KD, Seals RM, Taylor KM, Grespin M, Umbach DM, Hu H, Sandler DP, Kamel F, Weisskopf MG. Modification of the association between lead exposure and amyotrophic lateral sclerosis by iron and oxidative stress related gene polymorphisms. Amyotrophic lateral sclerosis & frontotemporal degeneration 2015 16(1-2):72-79.[Abstract]
  4. Shi M, Umbach DM, Weinberg CR. Disentangling pooled triad genotypes for association studies. Annals of human genetics 2014 78(5):345-356.[Abstract]
  5. 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]
  6. 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]
  7. 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]  
  8. Saha-Chaudhuri P, Umbach DM, Weinberg CR. Pooled Exposure Assessment for Matched Case-Control Studies. Epidemiology 2011; 22(5):704-712.[Abstract]
  9. 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]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. Weinberg, C.R., and D.M. Umbach. Using pooled exposure assessment to improve efficiency in case-control studies. Biometrics 1999; 55:718-726.[Abstract]
  15. 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 Genomics

  1. Niu L, Huang W, Umbach DM, Li L. IUTA: a tool for effectively detecting differential isoform usage from RNA-Seq data. BMC genomics 2014 15(October):862-.[Abstract]
  2. 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]
  3. 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]
  4. 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]
  5. Li L, Umbach DM, Terry P, Taylor JA.  Application of the GA/KNN method to SELDI proteomics data analysis.  Bioinformatics 2004; 20:1638-1640.[Abstract]
  6. 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]
  7. 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]


Statistical Methods related to Chemical Mixtures

  1. Dinse GE, Umbach DM. Parameterizing dose-response models to estimate relative potency functions directly. Toxicological Sciences 2012 129(2):447-55.[Abstract]
  2. Dinse GE, Umbach DM. Characterizing non-constant relative potency. Regulatory toxicology and pharmacology 2011; 60(3):342-352.[Abstract]  


The Agricultural Health Study

  1. Beard JD, Umbach DM, Hoppin JA, Richards M, Alavanja MC, Blair A, Sandler DP, Kamel F. Pesticide Exposure and Depression among Male Private Pesticide Applicators in the Agricultural Health Study. Environmental health perspectives 2014 122(9):984-991.[Abstract]
  2. 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]
  3. Henneberger PK, Liang X, London SJ, Umbach DM, Sandler DP, Hoppin JA. Exacerbation of symptoms in agricultural pesticide applicators with asthma. International archives of occupational and environmental health 2014 87(4):423-432. [Abstract]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]  
  9. Hoppin JA, Umbach DM, London SJ, Henneberger PK, Kullman GJ, Alavanja MCR, Sandler DP.  Pesticide exposure and atopic and non-atopic asthma among farm women in the Agricultural Health Study.  American Journal of Respiratory and Clinical Care Medicine. 2008; 177:11-18.[Abstract]
  10. 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]  
  11. 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]  


Soy-Formula and Infant Development

  1. 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]
  2. Cao Y, Calafat AM, Doerge DR, Umbach DM, Bernbaum JC, Twaddle NC, Ye X, Rogan WJ.  Isoflavones in urine, saliva, and blood of infants – data from a pilot study on the estrogenic activity of soy formula.  Journal of Exposure Science and Environmental Epidemiology 2009; 19:223-234.[Abstract]
  3. Bernbaum JC, Umbach DM, Ragan NB, Ballard JL, Archer J, Schmidt-Davis H, Rogan WJ.  Pilot studies of sex estrogen-related physical findings in infants.  Environmental Health Perspectives 2008; 116:416-420.[Abstract]


Neurodegenerative Diseases

  1. Furlong M, Tanner CM, Goldman SM, Bhudhikanok GS, Blair A, Chade A, Comyns K, Hoppin JA, Kasten M, Korell M, Langston JW, Marras C, Meng C, Richards M, Ross GW, Umbach DM, Sandler DP, Kamel F. Protective glove use and hygiene habits modify the associations of specific pesticides with Parkinson's disease. Environment international 2015 75():144-150.[Abstract]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. Tanner CM, Kamel F, Ross GW, Hoppin JA, Goldman SM, Korell M, Marras C, Bhudhikanok GS, Kasten M, Chade A, Comyns K, Meng C, Priestley B, Fernandez H, Cambi F, Umbach DM, Blair A, Sandler DP, Langston JW. Rotenone, paraquat and Parkinson’s disease. Environmental Health Perspectives 2011; 119(6):866-872.[Abstract]
  8. 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]
  9. Chen H, Huang X, Guo X, Mailman RB, Park Y, Kamel F, Umbach DM, Xu Q, Hollenbeck A,  Schatzkin A, Blair A. Smoking duration, intensity, and the risk of Parkinson’s disease.  Neurology 2010; 74:878-884.[Abstract]
  10. 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]
  11. 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]  
  12. 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]  
  13. 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]  
  14. 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]  


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. 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]
  3. 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]
  4. Stern MC, Umbach DM, van Gils C, Lunn RM, Taylor JA. DNA repair gene XRCC1 polymorphisms, smoking, and bladder cancer risk. Cancer Epidemiology Biomarkers and Prevention 2001; 10:125-131.[Abstract]
  5. Lunn RM, Helzlsouer KJ, Parshad R, Umbach DM, Harris E, Sanford KK, Bell DA. XPD polymorphisms: effects on DNA repair proficiency. Carcinogenesis 2000; 21:551-555.[Abstract]
  6. Taylor JA, Umbach DM, Stephens E, Castranio T, Paulson D, Robertson C, Mohler J, Bell DA. The role of N-acetylation polymorphisms in smoking-associated bladder cancer: evidence of a gene-gene-exposure 3-way interaction. Cancer Research 1998; 58: 3603-3610.[Abstract]


  • 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.
    ("/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".
    ("/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.
    ("/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.

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