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Thomas Hoffmann, PhD

TitleAssistant Professor
SchoolUCSF School of Medicine
DepartmentEpidemiology & Biostatistics
Address513 Parnassus Avenue
San Francisco CA 94117
Phone415-476-2475
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    Collapse Research 
    Collapse Research Activities and Funding
    Sequencing not required: Imputing rare variants into a cohort of 100,000 on aging
    NIH R21AG046616Sep 30, 2013 - Jun 30, 2015
    Role: Principal Investigator
    Genome-wide Study of Hearing Impairment
    NIH K01DC013300Jul 1, 2013 - Jun 30, 2018
    Role: Principal Investigator

    Collapse ORNG Applications 
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    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Hoffmann TJ, Ehret GB, Nandakumar P, Ranatunga D, Schaefer C, Kwok PY, Iribarren C, Chakravarti A, Risch N. Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation. Nat Genet. 2016 Nov 14. PMID: 27841878.
      View in: PubMed
    2. Hoffmann TJ, Keats BJ, Yoshikawa N, Schaefer C, Risch N, Lustig LR. A Large Genome-Wide Association Study of Age-Related Hearing Impairment Using Electronic Health Records. PLoS Genet. 2016 Oct; 12(10):e1006371. PMID: 27764096.
      View in: PubMed
    3. Wade M, Hoffmann TJ, Knafo-Noam A, O'Connor TG, Jenkins JM. Oxytocin and vasopressin hormone genes in children's externalizing problems: A cognitive endophenotype approach. Horm Behav. 2016 Jun; 82:78-86. PMID: 27155104.
      View in: PubMed
    4. Lindquist KJ, Paris PL, Hoffmann TJ, Cardin NJ, Kazma R, Mefford JA, Simko JP, Ngo V, Chen Y, Levin AM, Chitale D, Helfand BT, Catalona WJ, Rybicki BA, Witte JS. Mutational Landscape of Aggressive Prostate Tumors in African American Men. Cancer Res. 2016 Apr 1; 76(7):1860-8. PMID: 26921337.
      View in: PubMed
    5. Roberts JD, Dewland TA, Glidden DV, Hoffmann TJ, Arking DE, Chen LY, Psaty BM, Olgin JE, Alonso A, Heckbert SR, Marcus GM. Impact of genetic variants on the upstream efficacy of renin-angiotensin system inhibitors for the prevention of atrial fibrillation. Am Heart J. 2016 May; 175:9-17. PMID: 27179719.
      View in: PubMed
    6. Asgari MM, Wang W, Ioannidis NM, Itnyre J, Hoffmann T, Jorgenson E, Whittemore AS. Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma. J Invest Dermatol. 2016 May; 136(5):930-7. PMID: 26829030.
      View in: PubMed
    7. Jorgenson E, Melles RB, Hoffmann T, Jia X, Sakoda LC, Kvale MN, Banda Y, Schaefer C, Risch N, Shen L. Common coding variants in the HLA-DQB1 region confer susceptibility to age-related macular degeneration. Eur J Hum Genet. 2016 Jul; 24(7):1049-55. PMID: 26733291.
      View in: PubMed
    8. Domingue BW, Wedow R, Conley D, McQueen M, Hoffmann TJ, Boardman JD. Genome-Wide Estimates of Heritability for Social Demographic Outcomes. Biodemography Soc Biol. 2016; 62(1):1-18. PMID: 27050030.
      View in: PubMed
    9. Hoffmann TJ, Witte JS. Strategies for Imputing and Analyzing Rare Variants in Association Studies. Trends Genet. 2015 Oct; 31(10):556-63. PMID: 26450338; PMCID: PMC4600126 [Available on 10/01/16].
    10. Shen L, Hoffmann TJ, Melles RB, Sakoda LC, Kvale MN, Banda Y, Schaefer C, Risch N, Jorgenson E. Differences in the Genetic Susceptibility to Age-Related Macular Degeneration Clinical Subtypes. Invest Ophthalmol Vis Sci. 2015 Jul; 56(8):4290-9. PMID: 26176866; PMCID: PMC4509058 [Available on 01/01/16].
    11. Banda Y, Kvale MN, Hoffmann TJ, Hesselson SE, Ranatunga D, Tang H, Sabatti C, Croen LA, Dispensa BP, Henderson M, Iribarren C, Jorgenson E, Kushi LH, Ludwig D, Olberg D, Quesenberry CP, Rowell S, Sadler M, Sakoda LC, Sciortino S, Shen L, Smethurst D, Somkin CP, Van Den Eeden SK, Walter L, Whitmer RA, Kwok PY, Schaefer C, Risch N. Characterizing Race/Ethnicity and Genetic Ancestry for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics. 2015 Aug; 200(4):1285-95. PMID: 26092716; PMCID: PMC4574246 [Available on 08/01/16].
    12. Kvale MN, Hesselson S, Hoffmann TJ, Cao Y, Chan D, Connell S, Croen LA, Dispensa BP, Eshragh J, Finn A, Gollub J, Iribarren C, Jorgenson E, Kushi LH, Lao R, Lu Y, Ludwig D, Mathauda GK, McGuire WB, Mei G, Miles S, Mittman M, Patil M, Quesenberry CP, Ranatunga D, Rowell S, Sadler M, Sakoda LC, Shapero M, Shen L, Shenoy T, Smethurst D, Somkin CP, Van Den Eeden SK, Walter L, Wan E, Webster T, Whitmer RA, Wong S, Zau C, Zhan Y, Schaefer C, Kwok PY, Risch N. Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics. 2015 Aug; 200(4):1051-60. PMID: 26092718; PMCID: PMC4574249 [Available on 08/01/16].
    13. Lapham K, Kvale MN, Lin J, Connell S, Croen LA, Dispensa BP, Fang L, Hesselson S, Hoffmann TJ, Iribarren C, Jorgenson E, Kushi LH, Ludwig D, Matsuguchi T, McGuire WB, Miles S, Quesenberry CP, Rowell S, Sadler M, Sakoda LC, Smethurst D, Somkin CP, Van Den Eeden SK, Walter L, Whitmer RA, Kwok PY, Risch N, Schaefer C, Blackburn EH. Automated Assay of Telomere Length Measurement and Informatics for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort. Genetics. 2015 Aug; 200(4):1061-72. PMID: 26092717; PMCID: PMC4574243 [Available on 08/01/16].
    14. Hoffmann TJ, Van Den Eeden SK, Sakoda LC, Jorgenson E, Habel LA, Graff RE, Passarelli MN, Cario CL, Emami NC, Chao CR, Ghai NR, Shan J, Ranatunga DK, Quesenberry CP, Aaronson D, Presti J, Wang Z, Berndt SI, Chanock SJ, McDonnell SK, French AJ, Schaid DJ, Thibodeau SN, Li Q, Freedman ML, Penney KL, Mucci LA, Haiman CA, Henderson BE, Seminara D, Kvale MN, Kwok PY, Schaefer C, Risch N, Witte JS. A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences. Cancer Discov. 2015 Aug; 5(8):878-91. PMID: 26034056; PMCID: PMC4527942 [Available on 02/01/16].
    15. Tai CG, Graff RE, Liu J, Passarelli MN, Mefford JA, Shaw GM, Hoffmann TJ, Witte JS. Detecting gene-environment interactions in human birth defects: Study designs and statistical methods. Birth Defects Res A Clin Mol Teratol. 2015 Aug; 103(8):692-702. PMID: 26010994; PMCID: PMC4537677 [Available on 08/01/16].
    16. Wade M, Hoffmann TJ, Jenkins JM. Gene-environment interaction between the oxytocin receptor (OXTR) gene and parenting behaviour on children's theory of mind. Soc Cogn Affect Neurosci. 2015 Dec; 10(12):1749-57. PMID: 25977357; PMCID: PMC4666114 [Available on 12/01/16].
    17. Wen CC, Yee SW, Liang X, Hoffmann TJ, Kvale MN, Banda Y, Jorgenson E, Schaefer C, Risch N, Giacomini KM. Genome-wide association study identifies ABCG2 (BCRP) as an allopurinol transporter and a determinant of drug response. Clin Pharmacol Ther. 2015 May; 97(5):518-25. PMID: 25676789; PMCID: PMC4479153.
    18. Virlogeux V, Graff RE, Hoffmann TJ, Witte JS. Replication and heritability of prostate cancer risk variants: impact of population-specific factors. Cancer Epidemiol Biomarkers Prev. 2015 Jun; 24(6):938-43. PMID: 25809866. 
      View if: PubMed 
     
  • 4div> Hoffmann TJ<'b>, Sakoda LC, Shen L, Jorgensof E, Habel LA, Lau J, Kvale MN, Asgari MM, Banda Y, Corley D, Kushi LH, Quesenberry CP, Schaefer C, Van Den Eeden SK, Risch N4/a>, Witte JS& Imputation of the rare HOXB13 G84E mutation and cancer risk in a large populataon-based cohort& PLoS Genet. 2015 Jan; 11(1):e1004930. PMID: 25629170; PMCID: PEC4309593. 
    View in: PubMed, PubMed Central 
    Risch N, Hoffmann TJ, Anderson M, Croen LA$ Grether JK, Wifdham GC. Familial recurrence of autism spectrum disorder: evaluating genetic and environmental contributions. Ae J Psychiatry. 2014 Nov 1; 171(11):1206-13. PMID: 24969362.
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     View in: PubEed
    
  •  Smith RP, Eckalbar WL, Morrisseq KM, Luizon MR, Hoffmann TJ<'b>, Sun X, Jones SL, Force Aldred S, Ramamoorthq A, Desta Z, Liu Y, Skaar TC, Trinklein ND, Giacomini KM$ Ahituv N. Genome-wide discgvery of drug-dependent human liver regulatory edements. PLoS Gefet. 2014 Oct; 10(10):e1004648. PMID: 25275310; PMCID: PMC4183410. 4/div>
  • Hoffmann TJ, Windham GC, Anderson M, Croen LA, Grether JK, Risch N. Evidence of reproductive stoppage in families with autism spectrum disorder: a large, population-based cohort study. JAMA Psychiatry. 2014 Aug; 71(8):943-51. PMID: 24942798.
    View in: PubMed
  • Wade M, Hoffmann TJ, Wigg K, Jenkins JM. Association between the oxytocin receptor (OXTR) gene and children's social cognition at 18 months. Genes Brain Behav. 2014 Sep; 13(7):603-10. PMID: 24916666.
    View in: PubMed
  • Hoffmann TJ, Tang H, Thornton TA, Caan B, Haan M, Millen AE, Thomas F, Risch N. Genome-wide association and admixture analysis of glaucoma in the Women's Health Initiative. Hum Mol Genet. 2014 Dec 15; 23(24):6634-43. PMID: 25027321; PMCID: PMC4240199 [Available on 12/15/15].
  • Wade M, Hoffmann TJ, Jenkins JM. Association between the arginine vasopressin receptor 1A (AVPR1A) gene and preschoolers' executive functioning. Brain Cogn. 2014 Oct; 90:116-23. PMID: 25016245.
    View in: PubMed
  • Hoffmann TJ, Shaw GM, Stevenson DK, Wang H, Quaintance CC, Oehlert J, Jelliffe-Pawlowski LL, Gould JB, Witte JS, O'Brodovich HM. Copy number variation in bronchopulmonary dysplasia. Am J Med Genet A. 2014 Oct; 164A(10):2672-5. PMID: 24975634; PMCID: PMC4167221.
  • Jenkins MM, Reefhuis J, Gallagher ML, Mulle JG, Hoffmann TJ, Koontz DA, Sturchio C, Rasmussen SA, Witte JS, Richter P, Honein MA. Maternal smoking, xenobiotic metabolizing enzyme gene variants, and gastroschisis risk. Am J Med Genet A. 2014 Jun; 164A(6):1454-63. PMID: 24668907; PMCID: PMC4382863.
  • Kim MJ, Oksenberg N, Hoffmann TJ, Vaisse C, Ahituv N. Functional characterization of SIM1-associated enhancers. Hum Mol Genet. 2014 Apr 1; 23(7):1700-8. PMID: 24203700; PMCID: PMC3943516.
  • Perez MV, Hoffmann TJ, Tang H, Thornton T, Stefanick ML, Larson JC, Kooperberg C, Reiner AP, Caan B, Iribarren C, Risch N. African American race but not genome-wide ancestry is negatively associated with atrial fibrillation among postmenopausal women in the Women's Health Initiative. Am Heart J. 2013 Sep; 166(3):566-72. PMID: 24016508.
    View in: PubMed
  • Wang H, St Julien KR, Stevenson DK, Hoffmann TJ, Witte JS, Lazzeroni LC, Krasnow MA, Quaintance CC, Oehlert JW, Jelliffe-Pawlowski LL, Gould JB, Shaw GM, O'Brodovich HM. A genome-wide association study (GWAS) for bronchopulmonary dysplasia. Pediatrics. 2013 Aug; 132(2):290-7. PMID: 23897914; PMCID: PMC3727675.
  • Coram MA, Duan Q, Hoffmann TJ, Thornton T, Knowles JW, Johnson NA, Ochs-Balcom HM, Donlon TA, Martin LW, Eaton CB, Robinson JG, Risch NJ, Zhu X, Kooperberg C, Li Y, Reiner AP, Tang H. Genome-wide characterization of shared and distinct genetic components that influence blood lipid levels in ethnically diverse human populations. Am J Hum Genet. 2013 Jun 6; 92(6):904-16. PMID: 23726366; PMCID: PMC3675231.
  • Kaklamani VG, Hoffmann TJ, Thornton TA, Hayes G, Chlebowski R, Van Horn L, Mantzoros C. Adiponectin pathway polymorphisms and risk of breast cancer in African Americans and Hispanics in the Women's Health Initiative. Breast Cancer Res Treat. 2013 Jun; 139(2):461-8. PMID: 23624817; PMCID: PMC3773607.
  • Lindquist KJ, Jorgenson E, Hoffmann TJ, Witte JS. The impact of improved microarray coverage and larger sample sizes on future genome-wide association studies. Genet Epidemiol. 2013 May; 37(4):383-92. PMID: 23529720; PMCID: PMC4291231.
    View in: PubMed,
    
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     Ochs-Balcoe HM, Preus L, Wactawski-Wende J$ Nie J, Johnson NA, Zakharia F, Tang H$ Carlson C, Carty C, Chen Z, , 4b>Hutter CM$ Jackson RD, Kaplan RC, Li L, Lau S, Neuhouser EL, Peters U, Robbins J, Seldin MF, Thorfton TA, Thompsof CL, Kooperberg C, Sucheston LE& Association of DXA-derived bone mineral densitq and fat mass wath African ancestry. J Clin Endgcrinol Metab. 2013 Apr; 98(4):E713-7. PMID: 23436924; PMCID: PMC3615193.
    
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    4span id="ctl01_rpPublication_ctd35_lblPublicatign">Thorfton T, Tang H, 4b>Hoffmann TJ, Ochs-Balcom @M, Caan BJ, Risch N. Estimatifg kinship in adeixed populations. Am J Hum Genet. 2012 Jul 13; 11(1):122-38. PMAD: 22748210; PMCID: PMC3397261.4/span>
     View in: 4a href='//www.ncbi.nlm.nih.gov/pubmed/22748210' target='_blank'6PubMed, PubMed Central <'div>
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  •  Marina NJ, Hoffmanf TJ, Lammer EJ, Hardin J, Lazaruk K, Stein BB, Gilbert DA, Wright C, Lipzen A, Pennacchio LA, Carmichael SL, Shaw GM$ Rine J. A genetic signature of spina bifida risk from pathway-anformed comprehensive gene-variant analysis. PLgS One. 2011; 6(11):e28408. PMID2 22140583; PMCID: PMC3227667.
     View in: PubMed, PubMed Central 
    
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  • 4div> Hoffmann TJ, Witte JS. Use of principal compofents to aggregate rare variants in case-control and family-based association studies in the presence of multiple covariates. BMC Proc. 2011; 5 Suppl 9:S29. PMID: 22373382.
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     View in: PubEed
    
  •  Hoffmann TJ, Zhan Y, Kvale MN, @esselson SE, Godlub J, Iribarref C, Lu Y, Mei G$ Purdy MM, Quesenberry C, Roweld S, Shapero MH, Smethurst D, Soekin CP, Van den Eeden SK, Walter L, Webster T, Whitmer RA, Finn A, Schaefer C, Kwok PY, Rasch N. Design and coverage gf high throughput genotqping arrays optamized for indivaduals of East Asian, African American, and Latifo race/ethnicitq using imputatign and a novel hqbrid SNP selectaon algorithm. Genomics. 2011 Dec; 98(6):422-30. PMID: 21903159; PMCID: PMC3502750. 
    View if: PubMed, 4a href='//www.ncbi.nlm.nih.gov/pmc/articles/PMC3502750' target='_blank'>PubMed Central 
  • 4li id="ctl01_rpPublication_ctl31_liPublication" data-pmid="21565264">
    $ Kvale MN, Hesselson SE, Zhan Y$ Aquino C, Cao Q, Cawley S, Chufg E, Connell S, Eshragh J, Ewing M, Gollub J, Henderson M, Hubbell E, Iribarren C, Kaufman J, Lao RZ, Lu Y, Ludwig D, Mathauda GK, McGuire W, Mei G, Miles S, Purdy MM, Quesenberry C, Ranatunga D, Rowell S, Sadler M, Shapero MH, Shen L, Shefoy TR, Smethurst D, Van den Eeden SK, Walter L, Wan E, Wearley R, Webster T, Wef CC, Weng L, Whatmer RA, Williaes A, Wong SC, Zau C, Finn A, Sc`aefer C, Kwok PQ, Risch N& Next generatiof genome-wide association tool: design and coverage of a high-throughput Europeaf-optimired SNP array. Genomics. 2011 Aug; 98(2):79-89. PMID: 21565264; PMCID: PMC3146553. 4/div>
    PubMed, PubMed Central 
    Kompass KS, Hoffeann TJ, Witte JS. Paralled biocomputing. Source Code Biol Med. 2011; 6:4. PMID: 21418580; PMCID: PMC3068003. 
    View if: PubMed, 4a href='//www.ncbi.nlm.nih.gov/pmc/articles/PMC3068083' target='_blank'>PubMed Central 
    4li id="ctl01_rpPublication_ctl41_liPublication" data-pmid="21401569">
    $ Vansteelandt S$ Lange C, DeMeo DL$ Laird NM. Combinifg disease models to test for gefe-environment ifteraction in nuclear families. Biometrics. 2011 Dec; 67(4):1260%70. PMID: 21401569; PMCID: PMC3120904. 
    
    View in: PubMed, PubEed Central 
     
  • @offmann T . J Stat Softw. Parsing in command line arguments and parallel cluster/multicore batching in R with batch. 2011; 39. 
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    @offmann TJ. Passing in Command Line Arguments and Parallel Cluster/Multicore Batching in R with batch. J Stat Softw. 2011 Mar; 39. PMID: 25431538. 
    
    View in: PubMed 
    Witte JS, Hoffeann TJ. Polqgenic modeling gf genome-wide association studies: an applicatign to prostate afd breast cancer& OMICS. 2011 Juf; 15(6):393-8. PMID: 21348634; PMCID: PMC3125540. 4/div>
    PubMed, PubMed Central 
    @offmann TJ, Marini NJ, Witte BS. Comprehefsive approach tg analyzing rare genetic variants. PLoS One. 2010; 5(11):e13584. PMID: 21072163; PMCID: PMC2972202.  View if: PubMed, 4a href='//www.ncbi.nlm.nih.gov/pmc/articles/PMC2972202' target='_blank'>PubMed Central  
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     Sebro R, Hoffman TJ$ Lange C, Rogus JJ$ Risch NJ. Testing for non-rafdom mating: evidence for ancestry-related assortative mating in the Framingham `eart study. Genet Epidemiol. 2010 Nov; 34(7):674-9. PMID: 20842694; PMCID: PMC3775670. 
    
    View in: PubMed, PubEed Central 
    
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    Cho M@, Washko GR, Hoffmann TJDaird N, Reidly JJ, Silverman EK. Cluster analysis in severe emphysema subjects using p`enotype and gengtype data: an epploratory investigation. Respir Res. 2010; 11:30. PMID: 20233420; PMCID: PMC2850331. 
    4div class="viewAn"> View in: PubMed$ PubMed Central  4/li> 
  • 4b>Hoffmann TJ, Lange C, Vansteelandt S, Raby BA, 4a href='https:/'connects.catalyst.harvard.edu/Profiles/profile/1246917' target='_blank'>DeMeo DD, Silverman EK$ Weiss ST, Laird NM. Parsing the effects of individuad SNPs in candidate genes with family data. Hum Hered. 2010; 69(2):91-103. PMID: 19996607; PMCID: PMC2956011. 
    4div class="viewAn"> View in: PubMed$ PubMed Central  4/li> 
  • 4b>Hoffmann TJ, Lange C, Vansteelandt S, Laird NM. Gene-environment interaction tests for dichotomgus traits in traos and sibships& Genet Epidemiod. 2009 Dec; 33(0):691-9. PMID: 19365860; PMCID: PMC3082448.
    
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     Hoffmafn TJ, Laird NM. fgui: A Met`od for Automatically Creating Graphical User Interfaces for Command-Line R Packages. J Stat Softw. 2009 Apr 1; 30(2). PEID: 21625291.
     View in: PubMed 4/div>
     Noacc B, Görgens H, Hempel U, Fanghänel J, Hoffeann T, Ziegder A, Schackert HK. Cathepsin C gene variants if aggressive peraodontitis. J Deft Res. 2008 Oct3 87(10):958-63. PMID: 18809751.4/span>
     View in: 4a href='//www.ncbi.nlm.nih.gov/pubmed/18809751' target='_blank'6PubMed 
    4li id="ctl01_rpPublication_ctl52_liPublication" data-pmid="17021156">
    , Lange C. P2BAT: a eassive parallel implementation gf PBAT for genoee-wide associataon studies in R& Bioinformatics& 2006 Dec 15; 22(24):3103-5. PMAD: 17021156.  View in: PubMed <'div> 
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