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John Witte, PhD, MS

TitleProfessor
InstitutionUniversity of California San Francisco
DepartmentEpidemiology & Biostatistics
Address1450 Third St
San Francisco CA 94158
Phone415-502-6882
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    Collapse Biography 
    Collapse Education and Training
    UC Santa BarbaraBS6/1986Mathematical Sciences
    UC BerkeleyMS5/1988Engineering
    UC Los AngelesPhD6/1994Epidemiology
    Univ. Southern California, Los AngelesPost-doc10/1995Biostatistics

    Collapse Overview 
    Collapse Overview
    I have extensive experience in the design and statistical analysis of genetic epidemiologic projects. My research program encompasses a synthesis of methodological and applied genetic epidemiology, with the overall aim of deciphering the mechanisms underlying complex diseases and traits. I have developed widely used methods and software for studying rare genetic variants, pathways, interactions, and genome-wide association studies. I am applying these methods to studies of cancer, birth defects, and pharmacogenomics. Current projects in my lab include developing methods for effectively evaluating pleiotropy, determining the germline and somatic basis of prostate cancer risk and aggressiveness, and detecting genes that impact drug / treatment response. We have also recently been evaluating the use of cell free DNA (liquid biopsies) for prediction of prostate cancer risk and progression. In addition, I direct an NIH-Funded post-Doctoral training grant in Genetic Cancer Epidemiology, and have mentored over 40 pre- and post-doctoral fellows.


    Collapse Research 
    Collapse Research Activities and Funding
    Genome-wide Pleiotropy Scan across Multiple Cancers
    NIH/NCI R01CA201358Aug 1, 2016 - Jul 31, 2020
    Role: Principal Investigator
    Genomewide Association Study of Prostate Cancer
    NIH/NCI U01CA127298Sep 18, 2008 - Aug 31, 2014
    Role: Principal Investigator
    Training in Molecular& Genetic Epidemiology of Cancer
    NIH/NCI R25CA112355Dec 1, 2004 - Aug 31, 2019
    Role: Principal Investigator
    Androgen Pathway Factors and Prostate Cancer
    NIH/NCI R01CA094211Jul 15, 2002 - Jun 30, 2007
    Role: Principal Investigator
    Computational Genomic Epidemiology of Cancer (CoGEC) Training Program
    NIH/NCI R25CA094186Dec 1, 2001 - Jul 31, 2017
    Role: Co-Principal Investigator
    Genetic Epidemiology of Prostate Cancer Risk and Progression
    NIH/NCI R01CA088164Sep 1, 2000 - Jun 30, 2016
    Role: Principal Investigator
    Pharmacogenomics of Membrane Transporters
    NIH U19GM061390Apr 1, 2000 - Jun 30, 2015
    Role: Co-Investigator
    Cancer Center Support Grant
    NIH/NCI P30CA082103Aug 5, 1999 - May 31, 2018
    Role: Co-Investigator
    HIERARCHICAL MODELING IN CANCER RESEARCH
    NIH/NCI R29CA073270Jul 1, 1996 - Jun 30, 2001
    Role: Principal Investigator
    Human Genetic Analysis Resource
    NIH P41RR003655Sep 30, 1987 - Jul 31, 2012
    Role: Co-Investigator

    Collapse ORNG Applications 
    Collapse Websites
    Collapse In The News
    Collapse Twitter

    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.
    List All   |   Timeline
    1. Cario CL, Witte JS. Samasy: an automated system for sample selection and robotic transfer. Biotechniques. 2018 Dec; 65(6):357-360. PMID: 30477330.
      View in: PubMed
    2. McCarthy ME, Oltman SP, Baer RJ, Ryckman KK, Rogers EE, Steurer-Muller MA, Witte JS, Jelliffe-Pawlowski LL. Newborn Metabolic Profile Associated with Hyperbilirubinemia With and Without Kernicterus. Clin Transl Sci. 2018 Oct 28. PMID: 30369069.
      View in: PubMed
    3. Rashkin SR, Chua KC, Ho C, Mulkey F, Jiang C, Mushiroda T, Kubo M, Friedman PN, Rugo HS, McLeod HL, Ratain MJ, Castillos F, Naughton M, Overmoyer B, Toppmeyer D, Witte JS, Owzar K, Kroetz DL. A Pharmacogenetic Prediction Model of Progression-Free Survival in Breast Cancer using Genome-Wide Genotyping Data from CALGB 40502 (Alliance). Clin Pharmacol Ther. 2018 Sep 27. PMID: 30260474.
      View in: PubMed
    4. Graff RE, Kachuri L, Witte JS. Personalized Prostate Cancer Screening Based on a Single Midlife Prostate-specific Antigen Measurement. Eur Urol. 2018 Sep 26. PMID: 30268658.
      View in: PubMed
    5. Li M, He Z, Tong X, Witte JS, Lu Q. Detecting Rare Mutations with Heterogeneous Effects Using a Family-Based Genetic Random Field Method. Genetics. 2018 Aug 13. PMID: 30104420.
      View in: PubMed
    6. Zhang C, Wiemels JL, Hansen HM, Gonzalez-Maya J, Endicott AA, de Smith AJ, Smirnov IV, Witte JS, Morimoto LM, Metayer C, Walsh KM. Two HLA class II gene variants are independently associated with pediatric osteosarcoma risk. Cancer Epidemiol Biomarkers Prev. 2018 Jul 23. PMID: 30038050.
      View in: PubMed
    7. Johnson DB, Bordeaux JM, Kim JY, Vaupel CA, Rimm DL, Ho TH, Joseph RW, Daud AI, Conry RM, Gaughan EM, Hernandez-Aya LF, Dimou A, Funchain P, Smithy JW, Witte JS, McKee SB, Ko J, Wrangle J, Dabbas B, Tangri S, Lameh J, Hall JM, Markowitz J, Balko JM, Dakappagari NK. Quantitative Spatial Profiling of PD-1/PD-L1 Interaction and HLA-DR/IDO-1 Predicts Improved Outcomes of anti-PD-1 Therapies in Metastatic Melanoma. Clin Cancer Res. 2018 Jul 18. PMID: 30021908.
      View in: PubMed
    8. Cario CL, Witte JS. Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations. Bioinformatics. 2018 Mar 15; 34(6):936-942. PMID: 29106441.
      View in: PubMed
    9. Majumdar A, Haldar T, Bhattacharya S, Witte JS. An efficient Bayesian meta-analysis approach for studying cross-phenotype genetic associations. PLoS Genet. 2018 Feb; 14(2):e1007139. PMID: 29432419.
      View in: PubMed
    10. Asai Y, Eslami A, van Ginkel CD, Akhabir L, Wan M, Yin D, Ellis G, Ben-Shoshan M, Marenholz I, Martino D, Ferreira MA, Allen K, Mazer B, de Groot H, de Jong NW, Gerth van Wijk R, Dubois AEJ, Grosche S, Ashley S, Rüschendorf F, Kalb B, Beyer K, Nöthen MM, Lee YA, Chin R, Cheuk S, Hoffman J, Jorgensen E, Witte JS, Melles RB, Hong X, Wang X, Hui J, Musk AWB, Hunter M, James AL, Koppelman GH, Sandford AJ, Clarke AE, Daley D. A Canadian genome-wide association study and meta-analysis confirm HLA as a risk factor for peanut allergy independent of asthma. J Allergy Clin Immunol. 2018 Apr; 141(4):1513-1516. PMID: 29325868.
      View in: PubMed
    11. Wu YH, Graff RE, Passarelli MN, Hoffman JD, Ziv E, Hoffmann TJ, Witte JS. Identification of Pleiotropic Cancer Susceptibility Variants from Genome-Wide Association Studies Reveals Functional Characteristics. Cancer Epidemiol Biomarkers Prev. 2018 Jan; 27(1):75-85. PMID: 29150481.
      View in: PubMed
    12. Ferreira MA, Vonk JM, Baurecht H, Marenholz I, Tian C, Hoffman JD, Helmer Q, Tillander A, Ullemar V, van Dongen J, Lu Y, Rüschendorf F, Esparza-Gordillo J, Medway CW, Mountjoy E, Burrows K, Hummel O, Grosche S, Brumpton BM, Witte JS, Hottenga JJ, Willemsen G, Zheng J, Rodríguez E, Hotze M, Franke A, Revez JA, Beesley J, Matheson MC, Dharmage SC, Bain LM, Fritsche LG, Gabrielsen ME, Balliu B. Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology. Nat Genet. 2017 Dec; 49(12):1752-1757. PMID: 29083406.
      View in: PubMed
    13. Asai Y, Eslami A, van Ginkel CD, Akhabir L, Wan M, Ellis G, Ben-Shoshan M, Martino D, Ferreira MA, Allen K, Mazer B, de Groot H, de Jong NW, Gerth van Wijk RN, Dubois AEJ, Chin R, Cheuk S, Hoffman J, Jorgensen E, Witte JS, Melles RB, Hong X, Wang X, Hui J, Musk AWB, Hunter M, James AL, Koppelman GH, Sandford AJ, Clarke AE, Daley D. Genome-wide association study and meta-analysis in multiple populations identifies new loci for peanut allergy and establishes C11orf30/EMSY as a genetic risk factor for food allergy. J Allergy Clin Immunol. 2018 Mar; 141(3):991-1001. PMID: 29030101.
      View in: PubMed
    14. McAllister K, Mechanic LE, Amos C, Aschard H, Blair IA, Chatterjee N, Conti D, Gauderman WJ, Hsu L, Hutter CM, Jankowska MM, Kerr J, Kraft P, Montgomery SB, Mukherjee B, Papanicolaou GJ, Patel CJ, Ritchie MD, Ritz BR, Thomas DC, Wei P, Witte JS. Current Challenges and New Opportunities for Gene-Environment Interaction Studies of Complex Diseases. Am J Epidemiol. 2017 Oct 01; 186(7):753-761. PMID: 28978193.
      View in: PubMed
    15. Gauderman WJ, Mukherjee B, Aschard H, Hsu L, Lewinger JP, Patel CJ, Witte JS, Amos C, Tai CG, Conti D, Torgerson DG, Lee S, Chatterjee N. Update on the State of the Science for Analytical Methods for Gene-Environment Interactions. Am J Epidemiol. 2017 Oct 01; 186(7):762-770. PMID: 28978192.
      View in: PubMed
    16. Mechanic LE, Lindström S, Daily KM, Sieberts SK, Amos CI, Chen HS, Cox NJ, Dathe M, Feuer EJ, Guertin MJ, Hoffman J, Liu Y, Moore JH, Myers CL, Ritchie MD, Schildkraut J, Schumacher F, Witte JS, Wang W, Williams SM. Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology. PLoS Genet. 2017 09; 13(9):e1006945. PMID: 28957327.
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    17. Conti DV, Wang K, Sheng X, Bensen JT, Hazelett DJ, Cook MB, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Sanderson M, John EM, Park JY, Xu J, Stevens VL, Berndt SI, Huff CD, Wang Z, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Sellers TA, Yamoah K, Murphy AB, Crawford DC, Gapstur SM, Bush WS, Aldrich MC, Cussenot O, Petrovics G, Cullen J, Neslund-Dudas C, Stern MC, Jarai ZK, Govindasami K, Chokkalingam AP, Hsing AW, Goodman PJ, Hoffmann T, Drake BF, Hu JJ, Clark PE, Van Den Eeden SK, Blanchet P, Fowke JH, Casey G, Hennis AJM, Han Y, Lubwama A, Thompson IM, Leach R, Easton DF, Schumacher F, Van den Berg DJ, Gundell SM, Stram A, Wan P, Xia L, Pooler LC, Mohler JL, Fontham ETH, Smith GJ, Taylor JA, Srivastava S, Eeles RA, Carpten J, Kibel AS, Multigner L, Parent ME, Menegaux F, Cancel-Tassin G, Klein EA, Brureau L, Stram DO, Watya S, Chanock SJ, Witte JS, Blot WJ, Henderson BE, Haiman CA. Two Novel Susceptibility Loci for Prostate Cancer in Men of African Ancestry. J Natl Cancer Inst. 2017 Aug 01; 109(8). PMID: 29117387.
      View in: PubMed
    18. Zhang C, de Smith AJ, Smirnov IV, Wiencke JK, Wiemels JL, Witte JS, Walsh KM. Non-additive and epistatic effects of HLA polymorphisms contributing to risk of adult glioma. J Neurooncol. 2017 Nov; 135(2):237-244. PMID: 28721485.
      View in: PubMed
    19. Ng MCY, Graff M, Lu Y, Justice AE, Mudgal P, Liu CT, Young K, Yanek LR, Feitosa MF, Wojczynski MK, Rand K, Brody JA, Cade BE, Dimitrov L, Duan Q, Guo X, Lange LA, Nalls MA, Okut H, Tajuddin SM, Tayo BO, Vedantam S, Bradfield JP, Chen G, Chen WM, Chesi A, Irvin MR, Padhukasahasram B, Smith JA, Zheng W, Allison MA, Ambrosone CB, Bandera EV, Bartz TM, Berndt SI, Bernstein L, Blot WJ, Bottinger EP, Carpten J, Chanock SJ, Chen YI, Conti DV, Cooper RS, Fornage M, Freedman BI, Garcia M, Goodman PJ, Hsu YH, Hu J, Huff CD, Ingles SA, John EM, Kittles R, Klein E, Li J, McKnight B, Nayak U, Nemesure B, Ogunniyi A, Olshan A, Press MF, Rohde R, Rybicki BA, Salako B, Sanderson M, Shao Y, Siscovick DS, Stanford JL, Stevens VL, Stram A, Strom SS, Vaidya D, Witte JS, Yao J, Zhu X, Ziegler RG, Zonderman AB, Adeyemo A, Ambs S, Cushman M, Faul JD, Hakonarson H, Levin AM, Nathanson KL, Ware EB, Weir DR, Zhao W, Zhi D. Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium. PLoS Genet. 2017 Apr; 13(4):e1006719. PMID: 28430825.
      View in: PubMed
    20. Mosley JD, Shoemaker MB, Wells QS, Darbar D, Shaffer CM, Edwards TL, Bastarache L, McCarty CA, Thompson W, Chute CG, Jarvik GP, Crosslin DR, Larson EB, Kullo IJ, Pacheco JA, Peissig PL, Brilliant MH, Linneman JG, Witte JS, Denny JC, Roden DM. Investigating the Genetic Architecture of the PR Interval Using Clinical Phenotypes. Circ Cardiovasc Genet. 2017 Apr; 10(2). PMID: 28416512.
      View in: PubMed
    21. Hoffman JD, Graff RE, Emami NC, Tai CG, Passarelli MN, Hu D, Huntsman S, Hadley D, Leong L, Majumdar A, Zaitlen N, Ziv E, Witte JS. Cis-eQTL-based trans-ethnic meta-analysis reveals novel genes associated with breast cancer risk. PLoS Genet. 2017 Mar; 13(3):e1006690. PMID: 28362817.
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    22. Hoffmann TJ, Passarelli MN, Graff RE, Emami NC, Sakoda LC, Jorgenson E, Habel LA, Shan J, Ranatunga DK, Quesenberry CP, Chao CR, Ghai NR, Aaronson D, Presti J, Nordström T, Wang Z, Berndt SI, Chanock SJ, Mosley JD, Klein RJ, Middha M, Lilja H, Melander O, Kvale MN, Kwok PY, Schaefer C, Risch N, Van Den Eeden SK, Witte JS. Genome-wide association study of prostate-specific antigen levels identifies novel loci independent of prostate cancer. Nat Commun. 2017 Jan 31; 8:14248. PMID: 28139693.
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    23. Graff RE, Möller S, Passarelli MN, Witte JS, Skytthe A, Christensen K, Tan Q, Adami HO, Czene K, Harris JR, Pukkala E, Kaprio J, Giovannucci EL, Mucci LA, Hjelmborg JB. Familial Risk and Heritability of Colorectal Cancer in the Nordic Twin Study of Cancer. Clin Gastroenterol Hepatol. 2017 Aug; 15(8):1256-1264. PMID: 28130150.
      View in: PubMed
    24. Emami NC, Leong L, Wan E, Van Blarigan EL, Cooperberg MR, Tenggara I, Carroll PR, Chan JM, Witte JS, Simko JP. Tissue Sources for Accurate Measurement of Germline DNA Genotypes in Prostate Cancer Patients Treated With Radical Prostatectomy. Prostate. 2017 Mar; 77(4):425-434. PMID: 27900799.
      View in: PubMed
    25. Karami S, Han Y, Pande M, Cheng I, Rudd J, Pierce BL, Nutter EL, Schumacher FR, Kote-Jarai Z, Lindstrom S, Witte JS, Fang S, Han J, Kraft P, Hunter DJ, Song F, Hung RJ, McKay J, Gruber SB, Chanock SJ, Risch A, Shen H, Haiman CA, Boardman L, Ulrich CM, Casey G, Peters U, Amin Al Olama A, Berchuck A, Berndt SI, Bezieau S, Brennan P, Brenner H, Brinton L, Caporaso N, Chan AT, Chang-Claude J, Christiani DC, Cunningham JM, Easton D, Eeles RA, Eisen T, Gala M, Gallinger SJ, Gayther SA, Goode EL, Grönberg H, Henderson BE, Houlston R, Joshi AD, Küry S, Landi MT, Le Marchand L, Muir K, Newcomb PA, Permuth-Wey J, Pharoah P, Phelan C, Potter JD, Ramus SJ, Risch H, Schildkraut J, Slattery ML, Song H, Wentzensen N, White E, Wiklund F, Zanke BW, Sellers TA, Zheng W, Chatterjee N, Amos CI, Doherty JA. Telomere structure and maintenance gene variants and risk of five cancer types. Int J Cancer. 2016 Dec 15; 139(12):2655-2670. PMID: 27459707.
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    26. Marini NJ, Yang W, Asrani K, Witte JS, Rine J, Lammer EJ, Shaw GM. Sequence variation in folate pathway genes and risks of human cleft lip with or without cleft palate. Am J Med Genet A. 2016 Nov; 170(11):2777-2787. PMID: 27604992.
      View in: PubMed
    27. Rand KA, Song C, Dean E, Serie DJ, Curtin K, Sheng X, Hu D, Huff CA, Bernal-Mizrachi L, Tomasson MH, Ailawadhi S, Singhal S, Pawlish K, Peters ES, Bock CH, Stram A, Van Den Berg DJ, Edlund CK, Conti DV, Zimmerman T, Hwang AE, Huntsman S, Graff J, Nooka A, Kong Y, Pregja SL, Berndt SI, Blot WJ, Carpten J, Casey G, Chu L, Diver WR, Stevens VL, Lieber MR, Goodman PJ, Hennis AJ, Hsing AW, Mehta J, Kittles RA, Kolb S, Klein EA, Leske C, Murphy AB, Nemesure B, Neslund-Dudas C, Strom SS, Vij R, Rybicki BA, Stanford JL, Signorello LB, Witte JS, Ambrosone CB, Bhatti P, John EM, Bernstein L, Zheng W, Olshan AF, Hu JJ, Ziegler RG, Nyante SJ, Bandera EV, Birmann BM, Ingles SA, Press MF, Atanackovic D, Glenn MJ, Cannon-Albright LA, Jones B, Tricot G, Martin TG, Kumar SK, Wolf JL, Deming Halverson SL, Rothman N, Brooks-Wilson AR, Rajkumar SV, Kolonel LN, Chanock SJ, Slager SL, Severson RK, Janakiraman N, Terebelo HR, Brown EE, De Roos AJ, Mohrbacher AF, Colditz GA, Giles GG, Spinelli JJ, Chiu BC, Munshi NC, Anderson KC, Levy J, Zonder JA, Orlowski RZ, Lonial S, Camp NJ, Vachon CM, Ziv E, Stram DO, Hazelett DJ, Haiman CA, Cozen W. A Meta-analysis of Multiple Myeloma Risk Regions in African and European Ancestry Populations Identifies Putatively Functional Loci. Cancer Epidemiol Biomarkers Prev. 2016 12; 25(12):1609-1618. PMID: 27587788.
      View in: PubMed
    28. Zhou K, Yee SW, Seiser EL, van Leeuwen N, Tavendale R, Bennett AJ, Groves CJ, Coleman RL, van der Heijden AA, Beulens JW, de Keyser CE, Zaharenko L, Rotroff DM, Out M, Jablonski KA, Chen L, Javorský M, Židzik J, Levin AM, Williams LK, Dujic T, Semiz S, Kubo M, Chien HC, Maeda S, Witte JS, Wu L, Tkác I, Kooy A, van Schaik RHN, Stehouwer CDA, Logie L. Variation in the glucose transporter gene SLC2A2 is associated with glycemic response to metformin. Nat Genet. 2016 09; 48(9):1055-1059. PMID: 27500523.
      View in: PubMed
    29. Brenner DR, Brennan P, Boffetta P, Amos CI, Spitz MR, Chen C, Goodman G, Heinrich J, Bickeböller H, Rosenberger A, Risch A, Muley T, McLaughlin JR, Benhamou S, Bouchardy C, Lewinger JP, Witte JS, Chen G, Bull S, Hung RJ. Erratum to: Hierarchical modeling identifies novel lung cancer susceptibility variants in inflammation pathways among 10,140 cases and 11,012 controls. Hum Genet. 2016 08; 135(8):963. PMID: 27264937.
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    30. Lee SA, Mefford JA, Huang Y, Witte JS, Martin JN, Haas DW, Mclaren PJ, Mushiroda T, Kubo M, Byakwaga H, Hunt PW, Kroetz DL. Host genetic predictors of the kynurenine pathway of tryptophan catabolism among treated HIV-infected Ugandans. AIDS. 2016 Jul 17; 30(11):1807-15. PMID: 27088321; PMCID: PMC4925250 [Available on 07/17/17].
    31. Majumdar A, Haldar T, Witte JS. Determining Which Phenotypes Underlie a Pleiotropic Signal. Genet Epidemiol. 2016 07; 40(5):366-81. PMID: 27238845; PMCID: PMC4929010.
    32. Sapru A, Liu KD, Wiemels J, Hansen H, Pawlikowska L, Poon A, Jorgenson E, Witte JS, Calfee CS, Ware LB, Matthay MA. Association of common genetic variation in the protein C pathway genes with clinical outcomes in acute respiratory distress syndrome. Crit Care. 2016 May 23; 20(1):151. PMID: 27215212; PMCID: PMC4876559.
    33. Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res. 2016 07; 26(7):863-73. PMID: 27197206; PMCID: PMC4937562.
    34. Mosley JD, Witte JS, Larkin EK, Bastarache L, Shaffer CM, Karnes JH, Stein CM, Phillips E, Hebbring SJ, Brilliant MH, Mayer J, Ye Z, Roden DM, Denny JC. Identifying genetically driven clinical phenotypes using linear mixed models. Nat Commun. 2016 Apr 25; 7:11433. PMID: 27109359; PMCID: PMC4848547.
    35. Carmichael SL, Yang W, Ma C, Roberts E, Kegley S, English P, Lammer EJ, Witte JS, Shaw GM. Joint effects of genetic variants and residential proximity to pesticide applications on hypospadias risk. Birth Defects Res A Clin Mol Teratol. 2016 Aug; 106(8):653-8. PMID: 27098078; PMCID: PMC4983249 [Available on 08/01/17].
    36. Li M, Li J, He Z, Lu Q, Witte JS, Macleod SL, Hobbs CA, Cleves MA. Testing Allele Transmission of an SNP Set Using a Family-Based Generalized Genetic Random Field Method. Genet Epidemiol. 2016 May; 40(4):341-51. PMID: 27061818.
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    37. Gusev A, Shi H, Kichaev G, Pomerantz M, Li F, Long HW, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Zheng W, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJ, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Witte JS, Casey G, Kaggwa S, Cook MB, Stram DO, Blot WJ, Eeles RA, Easton D, Kote-Jarai Z, Al Olama AA, Benlloch S, Muir K, Giles GG, Southey MC, Fitzgerald LM, Gronberg H, Wiklund F, Aly M, Henderson BE, Schleutker J, Wahlfors T, Tammela TL, Nordestgaard BG, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Stanford JL, Thibodeau SN, McDonnell SK, Schaid DJ, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Teerlink C, Brenner H, Dieffenbach AK, Arndt V, Park JY, Sellers TA, Lin HY, Slavov C, Kaneva R, Mitev V, Batra J, Spurdle A, Clements JA, Teixeira MR, Pandha H, Michael A, Paulo P, Maia S, Kierzek A. Atlas of prostate cancer heritability in European and African-American men pinpoints tissue-specific regulation. Nat Commun. 2016 Apr 07; 7:10979. PMID: 27052111.
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    38. 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 04 01; 76(7):1860-8. PMID: 26921337; PMCID: PMC4772140 [Available on 04/01/17].
    39. Han Y, Rand KA, Hazelett DJ, Ingles SA, Kittles RA, Strom SS, Rybicki BA, Nemesure B, Isaacs WB, Stanford JL, Zheng W, Schumacher FR, Berndt SI, Wang Z, Xu J, Rohland N, Reich D, Tandon A, Pasaniuc B, Allen A, Quinque D, Mallick S, Notani D, Rosenfeld MG, Jayani RS, Kolb S, Gapstur SM, Stevens VL, Pettaway CA, Yeboah ED, Tettey Y, Biritwum RB, Adjei AA, Tay E, Truelove A, Niwa S, Chokkalingam AP, John EM, Murphy AB, Signorello LB, Carpten J, Leske MC, Wu SY, Hennis AJM, Neslund-Dudas C, Hsing AW, Chu L, Goodman PJ, Klein EA, Zheng SL, Witte JS, Casey G, Lubwama A, Pooler LC, Sheng X, Coetzee GA, Cook MB, Chanock SJ, Stram DO, Watya S, Blot WJ, Conti DV, Henderson BE, Haiman CA. Prostate Cancer Susceptibility in Men of African Ancestry at 8q24. J Natl Cancer Inst. 2016 Jul; 108(7). PMID: 26823525; PMCID: PMC4948565 [Available on 07/01/17].
    40. Scarbrough PM, Weber RP, Iversen ES, Brhane Y, Amos CI, Kraft P, Hung RJ, Sellers TA, Witte JS, Pharoah P, Henderson BE, Gruber SB, Hunter DJ, Garber JE, Joshi AD, McDonnell K, Easton DF, Eeles R, Kote-Jarai Z, Muir K, Doherty JA, Schildkraut JM. A Cross-Cancer Genetic Association Analysis of the DNA Repair and DNA Damage Signaling Pathways for Lung, Ovary, Prostate, Breast, and Colorectal Cancer. Cancer Epidemiol Biomarkers Prev. 2016 Jan; 25(1):193-200. PMID: 26637267; PMCID: PMC4713268.
    41. Majumdar A, Witte JS, Ghosh S. Semiparametric Allelic Tests for Mapping Multiple Phenotypes: Binomial Regression and Mahalanobis Distance. Genet Epidemiol. 2015 Dec; 39(8):635-50. PMID: 26493781; PMCID: PMC4958458.
    42. Kwok B, Hall JM, Witte JS, Xu Y, Reddy P, Lin K, Flamholz R, Dabbas B, Yung A, Al-Hafidh J, Balmert E, Vaupel C, El Hader C, McGinniss MJ, Nahas SA, Kines J, Bejar R. MDS-associated somatic mutations and clonal hematopoiesis are common in idiopathic cytopenias of undetermined significance. Blood. 2015 Nov 19; 126(21):2355-61. PMID: 26429975; PMCID: PMC4653764.
    43. Hoffmann TJ, Witte JS. Strategies for Imputing and Analyzing Rare Variants in Association Studies. Trends Genet. 2015 Oct; 31(10):556-563. PMID: 26450338.
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    44. Hung RJ, Ulrich CM, Goode EL, Brhane Y, Muir K, Chan AT, Marchand LL, Schildkraut J, Witte JS, Eeles R, Boffetta P, Spitz MR, Poirier JG, Rider DN, Fridley BL, Chen Z, Haiman C, Schumacher F, Easton DF, Landi MT, Brennan P, Houlston R, Christiani DC, Field JK, Bickeböller H, Risch A, Kote-Jarai Z, Wiklund F, Grönberg H, Chanock S, Berndt SI, Kraft P, Lindström S, Al Olama AA, Song H, Phelan C, Wentzensen N, Peters U, Slattery ML. Cross Cancer Genomic Investigation of Inflammation Pathway for Five Common Cancers: Lung, Ovary, Prostate, Breast, and Colorectal Cancer. J Natl Cancer Inst. 2015 Nov; 107(11). PMID: 26319099; PMCID: PMC4675100 [Available on 11/01/16].
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    95. N'Diaye A, Chen GK, Palmer CD, Ge B, Tayo B, Mathias RA, Ding J, Nalls MA, Adeyemo A, Adoue V, Ambrosone CB, Atwood L, Bandera EV, Becker LC, Berndt SI, Bernstein L, Blot WJ, Boerwinkle E, Britton A, Casey G, Chanock SJ, Demerath E, Deming SL, Diver WR, Fox C, Harris TB, Hernandez DG, Hu JJ, Ingles SA, John EM, Johnson C, Keating B, Kittles RA, Kolonel LN, Kritchevsky SB, Le Marchand L, Lohman K, Liu J, Millikan RC, Murphy A, Musani S, Neslund-Dudas C, North KE, Nyante S, Ogunniyi A, Ostrander EA, Papanicolaou G, Patel S, Pettaway CA, Press MF, Redline S, Rodriguez-Gil JL, Rotimi C, Rybicki BA, Salako B, Schreiner PJ, Signorello LB, Singleton AB, Stanford JL, Stram AH, Stram DO, Strom SS, Suktitipat B, Thun MJ, Witte JS, Yanek LR, Ziegler RG, Zheng W, Zhu X, Zmuda JM, Zonderman AB, Evans MK, Liu Y, Becker DM, Cooper RS, Pastinen T, Henderson BE, Hirschhorn JN, Lettre G, Haiman CA. Identification, replication, and fine-mapping of Loci associated with adult height in individuals of african ancestry. PLoS Genet. 2011 Oct; 7(10):e1002298. PMID: 21998595; PMCID: PMC3188544.
    96. Cheng I, Levin AM, Tai YC, Plummer S, Chen GK, Neslund-Dudas C, Casey G, Rybicki BA, Witte JS. Copy number alterations in prostate tumors and disease aggressiveness. Genes Chromosomes Cancer. 2012 Jan; 51(1):66-76. PMID: 21965145; PMCID: PMC3209417.
    97. DuBois SG, Goldsby R, Segal M, Woo J, Copren K, Kane JP, Pullinger CR, Matthay KK, Witte J, Lessnick SL, Robison LL, Bhatia S, Strong LC. Evaluation of polymorphisms in EWSR1 and risk of Ewing sarcoma: a report from the Childhood Cancer Survivor Study. Pediatr Blood Cancer. 2012 Jul 15; 59(1):52-6. PMID: 21793187; PMCID: PMC3204324.
    98. Hinch AG, Tandon A, Patterson N, Song Y, Rohland N, Palmer CD, Chen GK, Wang K, Buxbaum SG, Akylbekova EL, Aldrich MC, Ambrosone CB, Amos C, Bandera EV, Berndt SI, Bernstein L, Blot WJ, Bock CH, Boerwinkle E, Cai Q, Caporaso N, Casey G, Cupples LA, Deming SL, Diver WR, Divers J, Fornage M, Gillanders EM, Glessner J, Harris CC, Hu JJ, Ingles SA, Isaacs W, John EM, Kao WH, Keating B, Kittles RA, Kolonel LN, Larkin E, Le Marchand L, McNeill LH, Millikan RC, Murphy A, Musani S, Neslund-Dudas C, Nyante S, Papanicolaou GJ, Press MF, Psaty BM, Reiner AP, Rich SS, Rodriguez-Gil JL, Rotter JI, Rybicki BA, Schwartz AG, Signorello LB, Spitz M, Strom SS, Thun MJ, Tucker MA, Wang Z, Wiencke JK, Witte JS, Wrensch M, Wu X, Yamamura Y, Zanetti KA, Zheng W, Ziegler RG, Zhu X, Redline S, Hirschhorn JN, Henderson BE, Taylor HA, Price AL, Hakonarson H, Chanock SJ, Haiman CA, Wilson JG, Reich D, Myers SR. The landscape of recombination in African Americans. Nature. 2011 Jul 20; 476(7359):170-5. PMID: 21775986.
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    100. Witte JS. Of models and methods. Cancer Epidemiol Biomarkers Prev. 2011 Jun; 20(6):1059-60. PMID: 21652535.
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    101. Haiman CA, Chen GK, Blot WJ, Strom SS, Berndt SI, Kittles RA, Rybicki BA, Isaacs WB, Ingles SA, Stanford JL, Diver WR, Witte JS, Chanock SJ, Kolb S, Signorello LB, Yamamura Y, Neslund-Dudas C, Thun MJ, Murphy A, Casey G, Sheng X, Wan P, Pooler LC, Monroe KR, Waters KM, Le Marchand L, Kolonel LN, Stram DO, Henderson BE. Characterizing genetic risk at known prostate cancer susceptibility loci in African Americans. PLoS Genet. 2011 May; 7(5):e1001387. PMID: 21637779; PMCID: PMC3102736.
    102. Haiman CA, Chen GK, Blot WJ, Strom SS, Berndt SI, Kittles RA, Rybicki BA, Isaacs WB, Ingles SA, Stanford JL, Diver WR, Witte JS, Hsing AW, Nemesure B, Rebbeck TR, Cooney KA, Xu J, Kibel AS, Hu JJ, John EM, Gueye SM, Watya S, Signorello LB, Hayes RB, Wang Z, Yeboah E, Tettey Y, Cai Q, Kolb S, Ostrander EA, Zeigler-Johnson C, Yamamura Y, Neslund-Dudas C, Haslag-Minoff J, Wu W, Thomas V, Allen GO, Murphy A, Chang BL, Zheng SL, Leske MC, Wu SY, Ray AM, Hennis AJ, Thun MJ, Carpten J, Casey G, Carter EN, Duarte ER, Xia LY, Sheng X, Wan P, Pooler LC, Cheng I, Monroe KR, Schumacher F, Le Marchand L, Kolonel LN, Chanock SJ, Van Den Berg D, Stram DO, Henderson BE. Genome-wide association study of prostate cancer in men of African ancestry identifies a susceptibility locus at 17q21. Nat Genet. 2011 Jun; 43(6):570-3. PMID: 21602798.
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    103. Catalona WJ, Bailey-Wilson JE, Camp NJ, Chanock SJ, Cooney KA, Easton DF, Eeles RA, FitzGerald LM, Freedman ML, Gudmundsson J, Kittles RA, Margulies EH, McGuire BB, Ostrander EA, Rebbeck TR, Stanford JL, Thibodeau SN, Witte JS, Isaacs WB. National Cancer Institute Prostate Cancer Genetics Workshop. Cancer Res. 2011 May 15; 71(10):3442-6. PMID: 21558387.
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    104. Kompass KS, Hoffmann TJ, Witte JS. Parallel biocomputing. Source Code Biol Med. 2011 Mar 18; 6:4. PMID: 21418580; PMCID: PMC3068083.
    105. Witte JS, Hoffmann TJ. Polygenic modeling of genome-wide association studies: an application to prostate and breast cancer. OMICS. 2011 Jun; 15(6):393-8. PMID: 21348634; PMCID: PMC3125548.
    106. Kompass KS, Witte JS. Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer. BMC Med Genomics. 2011 Jan 12; 4:6. PMID: 21226949; PMCID: PMC3032645.
    107. Witte JS. Personalized prostate cancer screening: improving PSA tests with genomic information. Sci Transl Med. 2010 Dec 15; 2(62):62ps55. PMID: 21160075.
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    108. Chang BL, Spangler E, Gallagher S, Haiman CA, Henderson B, Isaacs W, Benford ML, Kidd LR, Cooney K, Strom S, Ingles SA, Stern MC, Corral R, Joshi AD, Xu J, Giri VN, Rybicki B, Neslund-Dudas C, Kibel AS, Thompson IM, Leach RJ, Ostrander EA, Stanford JL, Witte J, Casey G, Eeles R, Hsing AW, Chanock S, Hu JJ, John EM, Park J, Stefflova K, Zeigler-Johnson C, Rebbeck TR. Validation of genome-wide prostate cancer associations in men of African descent. Cancer Epidemiol Biomarkers Prev. 2011 Jan; 20(1):23-32. PMID: 21071540; PMCID: PMC3110616.
    109. Hoffmann TJ, Marini NJ, Witte JS. Comprehensive approach to analyzing rare genetic variants. PLoS One. 2010 Nov 03; 5(11):e13584. PMID: 21072163; PMCID: PMC2972202.
    110. Liu X, Cheng I, Plummer SJ, Suarez BK, Casey G, Catalona WJ, Witte JS. Fine-mapping of prostate cancer aggressiveness loci on chromosome 7q22-35. Prostate. 2011 May 15; 71(7):682-9. PMID: 20945404; PMCID: PMC3027848.
    111. Reese AC, Hardin J, Cheng I, Casey G, Witte JS. Non-Steroidal Anti-Inflammatory Drugs, Variation in Inflammatory Genes, and Aggressive Prostate Cancer. Pharmaceuticals (Basel). 2010 Oct 08; 3(10):3127-3142. PMID: 24023525.
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    112. Tai YC, Kvale MN, Witte JS. Segmentation and estimation for SNP microarrays: a Bayesian multiple change-point approach. Biometrics. 2010 Sep; 66(3):675-83. PMID: 19764955; PMCID: PMC3766751.
    113. Cheng I, Plummer SJ, Neslund-Dudas C, Klein EA, Casey G, Rybicki BA, Witte JS. Prostate cancer susceptibility variants confer increased risk of disease progression. Cancer Epidemiol Biomarkers Prev. 2010 Sep; 19(9):2124-32. PMID: 20651075; PMCID: PMC2950095.
    114. Atkinson EJ, McDonnell SK, Witte JS, Crawford DC, Fan Y, Fridley B, Li D, Li L, Rodin A, Sadee W, Speed T, Weiss ST, Yang J, Yerges L, Schaid DJ. Conference Scene: Lessons learned from the 5th Statistical Analysis Workshop of the Pharmacogenetics Research Network. Pharmacogenomics. 2010 Mar; 11(3):297-303. PMID: 20235785.
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    115. Cheng I, Witte JS, Jacobsen SJ, Haque R, Quinn VP, Quesenberry CP, Caan BJ, Van Den Eeden SK. Prostatitis, sexually transmitted diseases, and prostate cancer: the California Men's Health Study. PLoS One. 2010 Jan 15; 5(1):e8736. PMID: 20090948; PMCID: PMC2806913.
    116. Witte JS. Genome-wide association studies and beyond. Annu Rev Public Health. 2010; 31:9-20 4 p following 20. PMID: 20235850; PMCID: PMC3997166.
    117. Jorgenson E, Kvale M, Witte JS. VALID: visualization of association study results and linkage disequilibrium. Genet Epidemiol. 2009 Nov; 33(7):599-603. PMID: 19197947; PMCID: PMC3258024.
    118. Reese AC, Fradet V, Witte JS. Omega-3 fatty acids, genetic variants in COX-2 and prostate cancer. J Nutrigenet Nutrigenomics. 2009; 2(3):149-58. PMID: 19776642; PMCID: PMC2820568.
    119. Khoury MJ, McBride CM, Schully SD, Ioannidis JP, Feero WG, Janssens AC, Gwinn M, Simons-Morton DG, Bernhardt JM, Cargill M, Chanock SJ, Church GM, Coates RJ, Collins FS, Croyle RT, Davis BR, Downing GJ, Duross A, Friedman S, Gail MH, Ginsburg GS, Green RC, Greene MH, Greenland P, Gulcher JR, Hsu A, Hudson KL, Kardia SL, Kimmel PL, Lauer MS, Miller AM, Offit K, Ransohoff DF, Roberts JS, Rasooly RS, Stefansson K, Terry SF, Teutsch SM, Trepanier A, Wanke KL, Witte JS, Xu J. The Scientific Foundation for personal genomics: recommendations from a National Institutes of Health-Centers for Disease Control and Prevention multidisciplinary workshop. Genet Med. 2009 Aug; 11(8):559-67. PMID: 19617843; PMCID: PMC2936269.
    120. Cheng I, Witte JS, McClure LA, Shema SJ, Cockburn MG, John EM, Clarke CA. Socioeconomic status and prostate cancer incidence and mortality rates among the diverse population of California. Cancer Causes Control. 2009 Oct; 20(8):1431-40. PMID: 19526319.
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    121. Fradet V, Cheng I, Casey G, Witte JS. Dietary omega-3 fatty acids, cyclooxygenase-2 genetic variation, and aggressive prostate cancer risk. Clin Cancer Res. 2009 Apr 01; 15(7):2559-66. PMID: 19318492; PMCID: PMC2749066.
    122. Ross PL, Cheng I, Liu X, Cicek MS, Carroll PR, Casey G, Witte JS. Carboxypeptidase 4 gene variants and early-onset intermediate-to-high risk prostate cancer. BMC Cancer. 2009 Feb 26; 9:69. PMID: 19245716; PMCID: PMC2657151.
    123. Carmichael SL, Witte JS, Shaw GM. Nutrient pathways and neural tube defects: a semi-Bayesian hierarchical analysis. Epidemiology. 2009 Jan; 20(1):67-73. PMID: 19234400.
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    124. Witte JS. Prostate cancer genomics: towards a new understanding. Nat Rev Genet. 2009 Feb; 10(2):77-82. PMID: 19104501; PMCID: PMC2721916.
    125. Cheng I, Witte JS. The role of genetic variation in Toll-like receptor 4 in prostate cancer susceptibility: a review. Expert Opin Med Diagn. 2008 Feb; 2(2):143-9. PMID: 23485134.
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    126. Cheng I, Plummer SJ, Jorgenson E, Liu X, Rybicki BA, Casey G, Witte JS. 8q24 and prostate cancer: association with advanced disease and meta-analysis. Eur J Hum Genet. 2008 Apr; 16(4):496-505. PMID: 18231127; PMCID: PMC2819154.
    127. Cordell HJ, de Andrade M, Babron MC, Bartlett CW, Beyene J, Bickeböller H, Culverhouse R, Cupples LA, Daw EW, Dupuis J, Falk CT, Ghosh S, Goddard KA, Goode EL, Hauser ER, Martin LJ, Martinez M, North KE, Saccone NL, Schmidt S, Tapper W, Thomas D, Tritchler D, Vieland VJ, Wijsman EM, Wilcox MA, Witte JS, Yang Q, Ziegler A, Almasy L, Maccluer JW. Genetic Analysis Workshop 15: gene expression analysis and approaches to detecting multiple functional loci. BMC Proc. 2007; 1 Suppl 1:S1. PMID: 18466438; PMCID: PMC2367529.
    128. Chen GK, Jorgenson E, Witte JS. An empirical evaluation of the common disease-common variant hypothesis. BMC Proc. 2007; 1 Suppl 1:S5. PMID: 18466549; PMCID: PMC2367531.
    129. Jorgenson E, Witte JS. Genome-wide association studies of cancer. Future Oncol. 2007 Aug; 3(4):419-27. PMID: 17661717.
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    130. Chen GK, Witte JS. Enriching the analysis of genomewide association studies with hierarchical modeling. Am J Hum Genet. 2007 Aug; 81(2):397-404. PMID: 17668389; PMCID: PMC1950795.
    131. Cheng I, Krumroy LM, Plummer SJ, Casey G, Witte JS. MIC1 and IL1RN genetic variation and advanced prostate cancer risk. Cancer Epidemiol Biomarkers Prev. 2007 Jun; 16(6):1309-11. PMID: 17548705.
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    132. Witte JS. Multiple prostate cancer risk variants on 8q24. Nat Genet. 2007 May; 39(5):579-80. PMID: 17460686.
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    133. Thomas DC, Witte JS, Greenland S. Dissecting effects of complex mixtures: who's afraid of informative priors? Epidemiology. 2007 Mar; 18(2):186-90. PMID: 17301703.
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    134. Liu X, Cicek MS, Plummer SJ, Jorgenson E, Casey G, Witte JS. Association of testis derived transcript gene variants and prostate cancer risk. J Urol. 2007 Mar; 177(3):894-8. PMID: 17296370.
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    135. Cheng I, Plummer SJ, Casey G, Witte JS. Toll-like receptor 4 genetic variation and advanced prostate cancer risk. Cancer Epidemiol Biomarkers Prev. 2007 Feb; 16(2):352-5. PMID: 17301271.
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    136. Jorgenson E, Deitcher SR, Cicek M, Liu X, Plummer S, Casey G, Witte JS. Plasminogen activator inhibitor type-1 (PAI-1) polymorphism 4G/5G is associated with prostate cancer among men with a positive family history. Prostate. 2007 Feb 01; 67(2):172-7. PMID: 17044080.
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    137. Liu X, Schumacher FR, Plummer SJ, Jorgenson E, Casey G, Witte JS. Trans-fatty acid intake and increased risk of advanced prostate cancer: modification by RNASEL R462Q variant. Carcinogenesis. 2007 Jun; 28(6):1232-6. PMID: 17234723.
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    138. Witte JS, Schnell AH, Cordell HJ, Spielman RS, Amos CI, Miller MB, Almasy L, MacCluer JW. Introduction to Genetic Analysis Workshop 15 summaries. Genet Epidemiol. 2007; 31 Suppl 1:S1-6. PMID: 18046756.
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    139. Chen GK, Zheng T, Witte JS, Goode EL, Gao L, Hu P, Suh YJ, Suktitipat B, Szymczak S, Woo JH, Zhang W. Genome-wide association analyses of expression phenotypes. Genet Epidemiol. 2007; 31 Suppl 1:S7-S11. PMID: 18046762.
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    140. Cicek MS, Liu X, Schumacher FR, Casey G, Witte JS. Vitamin D receptor genotypes/haplotypes and prostate cancer risk. Cancer Epidemiol Biomarkers Prev. 2006 Dec; 15(12):2549-52. PMID: 17164384.
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    141. Jorgenson E, Witte JS. A gene-centric approach to genome-wide association studies. Nat Rev Genet. 2006 Nov; 7(11):885-91. PMID: 17047687.
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    142. Liu X, Plummer SJ, Nock NL, Casey G, Witte JS. Nonsteroidal antiinflammatory drugs and decreased risk of advanced prostate cancer: modification by lymphotoxin alpha. Am J Epidemiol. 2006 Nov 15; 164(10):984-9. PMID: 16931544.
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    143. Tung JY, Rosen MP, Nelson LM, Turek PJ, Witte JS, Cramer DW, Cedars MI, Reijo-Pera RA. Novel missense mutations of the Deleted-in-AZoospermia-Like (DAZL) gene in infertile women and men. Reprod Biol Endocrinol. 2006 Aug 02; 4:40. PMID: 16884537; PMCID: PMC1557510.
    144. Sapru A, Wiemels JL, Witte JS, Ware LB, Matthay MA. Acute lung injury and the coagulation pathway: Potential role of gene polymorphisms in the protein C and fibrinolytic pathways. Intensive Care Med. 2006 Sep; 32(9):1293-303. PMID: 16770611.
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    145. Nock NL, Liu X, Cicek MS, Li L, Macarie F, Rybicki BA, Plummer SJ, Maclennan GT, Casey G, Witte JS. Polymorphisms in polycyclic aromatic hydrocarbon metabolism and conjugation genes, interactions with smoking and prostate cancer risk. Cancer Epidemiol Biomarkers Prev. 2006 Apr; 15(4):756-61. PMID: 16614120.
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    146. Nock NL, Cicek MS, Li L, Liu X, Rybicki BA, Moreira A, Plummer SJ, Casey G, Witte JS. Polymorphisms in estrogen bioactivation, detoxification and oxidative DNA base excision repair genes and prostate cancer risk. Carcinogenesis. 2006 Sep; 27(9):1842-8. PMID: 16569655.
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    147. Jorgenson E, Witte JS. Coverage and power in genomewide association studies. Am J Hum Genet. 2006 May; 78(5):884-8. PMID: 16642443; PMCID: PMC1474045.
    148. Casey G, Neville PJ, Liu X, Plummer SJ, Cicek MS, Krumroy LM, Curran AP, McGreevy MR, Catalona WJ, Klein EA, Witte JS. Podocalyxin variants and risk of prostate cancer and tumor aggressiveness. Hum Mol Genet. 2006 Mar 01; 15(5):735-41. PMID: 16434482.
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    149. Liu X, Jorgenson E, Witte JS. Hierarchical modeling in association studies of multiple phenotypes. BMC Genet. 2005 Dec 30; 6 Suppl 1:S104. PMID: 16451560; PMCID: PMC1866835.
    150. Liu X, Rybicki BA, Casey G, Witte JS. Relationship between body size and prostate cancer in a sibling based case-control study. J Urol. 2005 Dec; 174(6):2169-73. PMID: 16280757.
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    151. Tung JY, Rosen MP, Nelson LM, Turek PJ, Witte JS, Cramer DW, Cedars MI, Pera RA. Variants in Deleted in AZoospermia-Like (DAZL) are correlated with reproductive parameters in men and women. Hum Genet. 2006 Feb; 118(6):730-40. PMID: 16328470.
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    152. Li L, Cicek MS, Casey G, Witte JS. No association between genetic polymorphisms in insulin and insulin receptor substrate-1 and prostate cancer. Cancer Epidemiol Biomarkers Prev. 2005 Oct; 14(10):2462-3. PMID: 16214935.
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    153. Cicek MS, Liu X, Casey G, Witte JS. Role of androgen metabolism genes CYP1B1, PSA/KLK3, and CYP11alpha in prostate cancer risk and aggressiveness. Cancer Epidemiol Biomarkers Prev. 2005 Sep; 14(9):2173-7. PMID: 16172228.
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    154. Jorgenson E, Liu X, Witte JS. Case-control analyses: Geneopardy! Genet Epidemiol. 2005; 29 Suppl 1:S86-90. PMID: 16342187.
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    155. Li L, Cicek MS, Casey G, Witte JS. No association between a tetranucleotide repeat polymorphism of CYP19 and prostate cancer. Cancer Epidemiol Biomarkers Prev. 2004 Dec; 13(12):2280-1. PMID: 15598794.
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    156. Thompson D, Witte JS, Slattery M, Goldgar D. Increased power for case-control studies of single nucleotide polymorphisms through incorporation of family history and genetic constraints. Genet Epidemiol. 2004 Nov; 27(3):215-24. PMID: 15389928.
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    157. Cicek MS, Nock NL, Li L, Conti DV, Casey G, Witte JS. Relationship between methylenetetrahydrofolate reductase C677T and A1298C genotypes and haplotypes and prostate cancer risk and aggressiveness. Cancer Epidemiol Biomarkers Prev. 2004 Aug; 13(8):1331-6. PMID: 15298954.
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    158. Hung RJ, Brennan P, Malaveille C, Porru S, Donato F, Boffetta P, Witte JS. Using hierarchical modeling in genetic association studies with multiple markers: application to a case-control study of bladder cancer. Cancer Epidemiol Biomarkers Prev. 2004 Jun; 13(6):1013-21. PMID: 15184258.
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    159. Cicek MS, Conti DV, Curran A, Neville PJ, Paris PL, Casey G, Witte JS. Association of prostate cancer risk and aggressiveness to androgen pathway genes: SRD5A2, CYP17, and the AR. Prostate. 2004 Apr 01; 59(1):69-76. PMID: 14991867.
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    160. Loukola A, Chadha M, Penn SG, Rank D, Conti DV, Thompson D, Cicek M, Love B, Bivolarevic V, Yang Q, Jiang Y, Hanzel DK, Dains K, Paris PL, Casey G, Witte JS. Comprehensive evaluation of the association between prostate cancer and genotypes/haplotypes in CYP17A1, CYP3A4, and SRD5A2. Eur J Hum Genet. 2004 Apr; 12(4):321-32. PMID: 14560315.
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    161. Singer JB, Hill AE, Burrage LC, Olszens KR, Song J, Justice M, O'Brien WE, Conti DV, Witte JS, Lander ES, Nadeau JH. Genetic dissection of complex traits with chromosome substitution strains of mice. Science. 2004 Apr 16; 304(5669):445-8. PMID: 15031436.
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    162. Li L, Cicek MS, Casey G, Witte JS. No association between genetic polymorphisms in IGF-I and IGFBP-3 and prostate cancer. Cancer Epidemiol Biomarkers Prev. 2004 Mar; 13(3):497-8. PMID: 15006930.
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    163. Rybicki BA, Conti DV, Moreira A, Cicek M, Casey G, Witte JS. DNA repair gene XRCC1 and XPD polymorphisms and risk of prostate cancer. Cancer Epidemiol Biomarkers Prev. 2004 Jan; 13(1):23-9. PMID: 14744728.
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    164. Xing C, Schumacher FR, Conti DV, Witte JS. Comparison of missing data approaches in linkage analysis. BMC Genet. 2003 Dec 31; 4 Suppl 1:S44. PMID: 14975112; PMCID: PMC1866480.
    165. Witte JS, Suarez BK, Thiel B, Lin J, Yu A, Banerjee TK, Burmester JK, Casey G, Catalona WJ. Genome-wide scan of brothers: replication and fine mapping of prostate cancer susceptibility and aggressiveness loci. Prostate. 2003 Dec 01; 57(4):298-308. PMID: 14601026.
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    166. Li L, Yu H, Schumacher F, Casey G, Witte JS. Relation of serum insulin-like growth factor-I (IGF-I) and IGF binding protein-3 to risk of prostate cancer (United States). Cancer Causes Control. 2003 Oct; 14(8):721-6. PMID: 14674736.
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    167. Plummer SJ, Conti DV, Paris PL, Curran AP, Casey G, Witte JS. CYP3A4 and CYP3A5 genotypes, haplotypes, and risk of prostate cancer. Cancer Epidemiol Biomarkers Prev. 2003 Sep; 12(9):928-32. PMID: 14504207.
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    168. Neville PJ, Conti DV, Krumroy LM, Catalona WJ, Suarez BK, Witte JS, Casey G. Prostate cancer aggressiveness locus on chromosome segment 19q12-q13.1 identified by linkage and allelic imbalance studies. Genes Chromosomes Cancer. 2003 Apr; 36(4):332-9. PMID: 12619157.
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    169. Conti DV, Witte JS. Hierarchical modeling of linkage disequilibrium: genetic structure and spatial relations. Am J Hum Genet. 2003 Feb; 72(2):351-63. PMID: 12525994; PMCID: PMC379228.
    170. Thompson D, Stram D, Goldgar D, Witte JS. Haplotype tagging single nucleotide polymorphisms and association studies. Hum Hered. 2003; 56(1-3):48-55. PMID: 14614238.
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    171. Casey G, Neville PJ, Plummer SJ, Xiang Y, Krumroy LM, Klein EA, Catalona WJ, Nupponen N, Carpten JD, Trent JM, Silverman RH, Witte JS. RNASEL Arg462Gln variant is implicated in up to 13% of prostate cancer cases. Nat Genet. 2002 Dec; 32(4):581-3. PMID: 12415269.
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    172. Neville PJ, Conti DV, Paris PL, Levin H, Catalona WJ, Suarez BK, Witte JS, Casey G. Prostate cancer aggressiveness locus on chromosome 7q32-q33 identified by linkage and allelic imbalance studies. Neoplasia. 2002 Sep-Oct; 4(5):424-31. PMID: 12192601; PMCID: PMC1564121.
    173. Fijal BA, Idury RM, Witte JS. Analysis of mutational spectra: locating hotspots and clusters of mutations using recursive segmentation. Stat Med. 2002 Jul 15; 21(13):1867-85. PMID: 12111894.
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    174. Thomas DC, Witte JS. Point: population stratification: a problem for case-control studies of candidate-gene associations? Cancer Epidemiol Biomarkers Prev. 2002 Jun; 11(6):505-12. PMID: 12050090.
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    175. Nelson KA, Witte JS. Androgen receptor CAG repeats and prostate cancer. Am J Epidemiol. 2002 May 15; 155(10):883-90. PMID: 11994226.
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    176. Palmer LJ, Schnell AH, Witte JS, Elston RC. Parametric linkage analysis. Methods Mol Biol. 2002; 195:13-35. PMID: 12070879.
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    177. Witte JS, Palmer LJ, O'Connor RD, Hopkins PJ, Hall JM. Relation between tumour necrosis factor polymorphism TNFalpha-308 and risk of asthma. Eur J Hum Genet. 2002 Jan; 10(1):82-5. PMID: 11896460.
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