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Pamela Paris, PhD

TitleProfessor
SchoolUCSF School of Medicine
DepartmentUrology
Address1450 3rd Street
San Francisco CA 94158
Phone415-514-2559
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    Research Interests

    Our laboratory conducts translational cancer genomics research. The overarching goal is to identify drug targets with associated prognostic biomarkers. To date, their primary focus has been primary and metastatic prostate cancer.


    Collapse Research 
    Collapse Research Activities and Funding
    External validation of GEMCaP, a prognostic DNA biomarker set for CaP recurrence
    NIH/NCI R01CA158200Apr 5, 2011 - Mar 31, 2016
    Role: Principal Investigator
    CaP Metastasis Biomarkers: Validation/Genomics/Biology
    NIH/NCI R01CA115484Sep 1, 2005 - Jun 30, 2011
    Role: Principal Investigator

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    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. Lindquist KJ, Sanford T, Friedlander TW, Paris P, Porten SP. Copy number gains at chr3p25 and chr11p11 are associated with lymph node involvement and survival in muscle-invasive bladder tumors. PLoS One. 2017; 12(11):e0187975. PMID: 29140994.
      View in: PubMed
    2. Nguyen HG, Welty C, Lindquist K, Ngo V, Gilbert E, Bengtsson H, Magi-Galluzzi C, Jean-Gilles J, Yao J, Cooperberg M, Messing E, Klein EA, Carroll PR, Paris PL. Validation of GEMCaP as a DNA based biomarker to predict prostate cancer recurrence after radical prostatectomy. J Urol. 2017 Sep 20. PMID: 28941923.
      View in: PubMed
    3. Aggarwal R, Behr S, Paris P, Truillet C, Parker MFL, Huynh LT, Wei J, Hann B, Youngren J, Premasekharan G, Huang J, Ranatunga N, Chang E, Gao KT, Ryan CJ, Small EJ, Evans MJ. Real-Time Transferrin-Based PET Detects MYC-Positive Prostate Cancer. Mol Cancer Res. 2017 Sep; 15(9):1221-1229. PMID: 28592703.
      View in: PubMed
    4. Friedlander TW, Graff JN, Zejnullahu K, Anantharaman A, Zhang L, Paz R, Premasekharan G, Russell C, Huang Y, Kim W, Aggarwal RR, Lin AM, Fong L, Alumkal JJ, Beer TM, Sharifi N, Alyamani M, Dittamore R, Small EJ, Paris PL, Ryan CJ. High-Dose Abiraterone Acetate in Men With Castration Resistant Prostate Cancer. Clin Genitourin Cancer. 2017 Jun 03. PMID: 28655452.
      View in: PubMed
    5. Anantharaman A, Friedlander T, Lu D, Krupa R, Premasekharan G, Hough J, Edwards M, Paz R, Lindquist K, Graf R, Jendrisak A, Louw J, Dugan L, Baird S, Wang Y, Dittamore R, Paris PL. Programmed death-ligand 1 (PD-L1) characterization of circulating tumor cells (CTCs) in muscle invasive and metastatic bladder cancer patients. BMC Cancer. 2016 Sep 22; 16(1):744. PMID: 27658492.
      View in: PubMed
    6. Premasekharan G, Gilbert E, Okimoto RA, Hamirani A, Lindquist KJ, Ngo VT, Roy R, Hough J, Edwards M, Paz R, Foye A, Sood R, Copren KA, Gubens M, Small EJ, Bivona TG, Collisson EA, Friedlander TW, Paris PL. An improved CTC isolation scheme for pairing with downstream genomics: Demonstrating clinical utility in metastatic prostate, lung and pancreatic cancer. Cancer Lett. 2016 Sep 28; 380(1):144-52. PMID: 27343980.
      View in: PubMed
    7. 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].
    8. Nordström T, Van Blarigan EL, Ngo V, Roy R, Weinberg V, Song X, Simko J, Carroll PR, Chan JM, Paris PL. Associations between circulating carotenoids, genomic instability and the risk of high-grade prostate cancer. Prostate. 2016 Mar; 76(4):339-48. PMID: 26585352.
      View in: PubMed
    9. Alva A, Friedlander T, Clark M, Huebner T, Daignault S, Hussain M, Lee C, Hafez K, Hollenbeck B, Weizer A, Premasekharan G, Tran T, Fu C, Ionescu-Zanetti C, Schwartz M, Fan A, Paris P. Circulating Tumor Cells as Potential Biomarkers in Bladder Cancer. J Urol. 2015 Sep; 194(3):790-8. PMID: 25912492.
      View in: PubMed
    10. Azad AA, Volik SV, Wyatt AW, Haegert A, Le Bihan S, Bell RH, Anderson SA, McConeghy B, Shukin R, Bazov J, Youngren J, Paris P, Thomas G, Small EJ, Wang Y, Gleave ME, Collins CC, Chi KN. Androgen Receptor Gene Aberrations in Circulating Cell-Free DNA: Biomarkers of Therapeutic Resistance in Castration-Resistant Prostate Cancer. Clin Cancer Res. 2015 May 15; 21(10):2315-24. PMID: 25712683.
      View in: PubMed
    11. Hashizume R, Andor N, Ihara Y, Lerner R, Gan H, Chen X, Fang D, Huang X, Tom MW, Ngo V, Solomon D, Mueller S, Paris PL, Zhang Z, Petritsch C, Gupta N, Waldman TA, James CD. Pharmacologic inhibition of histone demethylation as a therapy for pediatric brainstem glioma. Nat Med. 2014 Dec; 20(12):1394-6. PMID: 25401693; PMCID: PMC4257862.
    12. Wang J, Paris PL, Chen J, Ngo V, Yao H, Frazier ML, Killary AM, Liu CG, Liang H, Mathy C, Bondada S, Kirkwood K, Sen S. Next generation sequencing of pancreatic cyst fluid microRNAs from low grade-benign and high grade-invasive lesions. Cancer Lett. 2015 Jan 28; 356(2 Pt B):404-9. PMID: 25304377.
      View in: PubMed
    13. Heselmeyer-Haddad KM, Berroa Garcia LY, Bradley A, Hernandez L, Hu Y, Habermann JK, Dumke C, Thorns C, Perner S, Pestova E, Burke C, Chowdhury SA, Schwartz R, Schäffer AA, Paris PL, Ried T. Single-cell genetic analysis reveals insights into clonal development of prostate cancers and indicates loss of PTEN as a marker of poor prognosis. Am J Pathol. 2014 Oct; 184(10):2671-86. PMID: 25131421; PMCID: PMC4188868.
    14. Levin AM, Lindquist KJ, Avila A, Witte JS, Paris PL, Rybicki BA. Performance of the Genomic Evaluators of Metastatic Prostate Cancer (GEMCaP) tumor biomarker for identifying recurrent disease in African American patients. Cancer Epidemiol Biomarkers Prev. 2014 Aug; 23(8):1677-82. PMID: 24891551; PMCID: PMC4119547.
    15. Nagarajan RP, Zhang B, Bell RJ, Johnson BE, Olshen AB, Sundaram V, Li D, Graham AE, Diaz A, Fouse SD, Smirnov I, Song J, Paris PL, Wang T, Costello JF. Recurrent epimutations activate gene body promoters in primary glioblastoma. Genome Res. 2014 May; 24(5):761-74. PMID: 24709822; PMCID: PMC4009606.
    16. Friedlander TW, Ngo VT, Dong H, Premasekharan G, Weinberg V, Doty S, Zhao Q, Gilbert EG, Ryan CJ, Chen WT, Paris PL. Detection and characterization of invasive circulating tumor cells derived from men with metastatic castration-resistant prostate cancer. Int J Cancer. 2014 May 15; 134(10):2284-93. PMID: 24166007.
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    17. Friedlander TW, Premasekharan G, Paris PL. Looking back, to the future of circulating tumor cells. Pharmacol Ther. 2014 Jun; 142(3):271-80. PMID: 24362084.
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    18. Friedlander TW, Roy R, Tomlins SA, Ngo VT, Kobayashi Y, Azameera A, Rubin MA, Pienta KJ, Chinnaiyan A, Ittmann MM, Ryan CJ, Paris PL. Common structural and epigenetic changes in the genome of castration-resistant prostate cancer. Cancer Res. 2012 Feb 01; 72(3):616-25. PMID: 22158653.
      View in: PubMed
    19. Ritz A, Paris PL, Ittmann MM, Collins C, Raphael BJ. Detection of recurrent rearrangement breakpoints from copy number data. BMC Bioinformatics. 2011 Apr 21; 12:114. PMID: 21510904; PMCID: PMC3112242.
    20. Paris PL, Weinberg V, Albo G, Roy R, Burke C, Simko J, Carroll P, Collins C. A group of genome-based biomarkers that add to a Kattan nomogram for predicting progression in men with high-risk prostate cancer. Clin Cancer Res. 2010 Jan 01; 16(1):195-202. PMID: 20028763; PMCID: PMC2854027.
    21. Paris PL, Kobayashi Y, Zhao Q, Zeng W, Sridharan S, Fan T, Adler HL, Yera ER, Zarrabi MH, Zucker S, Simko J, Chen WT, Rosenberg J. Functional phenotyping and genotyping of circulating tumor cells from patients with castration resistant prostate cancer. Cancer Lett. 2009 May 18; 277(2):164-73. PMID: 19162393.
      View in: PubMed
    22. Paris PL. A whole-genome amplification protocol for a wide variety of DNAs, including those from formalin-fixed and paraffin-embedded tissue. Methods Mol Biol. 2009; 556:89-98. PMID: 19488873.
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    23. Paris PL, Sridharan S, Hittelman AB, Kobayashi Y, Perner S, Huang G, Simko J, Carroll P, Rubin MA, Collins C. An oncogenic role for the multiple endocrine neoplasia type 1 gene in prostate cancer. Prostate Cancer Prostatic Dis. 2009; 12(2):184-91. PMID: 18779856; PMCID: PMC2844124.
    24. Mosquera JM, Perner S, Genega EM, Sanda M, Hofer MD, Mertz KD, Paris PL, Simko J, Bismar TA, Ayala G, Shah RB, Loda M, Rubin MA. Characterization of TMPRSS2-ERG fusion high-grade prostatic intraepithelial neoplasia and potential clinical implications. Clin Cancer Res. 2008 Jun 01; 14(11):3380-5. PMID: 18519767; PMCID: PMC3717517.
    25. Raphael BJ, Volik S, Yu P, Wu C, Huang G, Linardopoulou EV, Trask BJ, Waldman F, Costello J, Pienta KJ, Mills GB, Bajsarowicz K, Kobayashi Y, Sridharan S, Paris PL, Tao Q, Aerni SJ, Brown RP, Bashir A, Gray JW, Cheng JF, de Jong P, Nefedov M, Ried T, Padilla-Nash HM, Collins CC. A sequence-based survey of the complex structural organization of tumor genomes. Genome Biol. 2008; 9(3):R59. PMID: 18364049; PMCID: PMC2397511.
    26. Hittelman A, Sridharan S, Roy R, Fridlyand J, Loda M, Collins C, Paris PL. Evaluation of whole genome amplification protocols for array and oligonucleotide CGH. Diagn Mol Pathol. 2007 Dec; 16(4):198-206. PMID: 18043282.
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    27. Paris PL, Sridharan S, Scheffer A, Tsalenko A, Bruhn L, Collins C. High resolution oligonucleotide CGH using DNA from archived prostate tissue. Prostate. 2007 Sep 15; 67(13):1447-55. PMID: 17654530; PMCID: PMC2844769.
    28. Perner S, Mosquera JM, Demichelis F, Hofer MD, Paris PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, De Marzo AM, Rubin MA. TMPRSS2-ERG fusion prostate cancer: an early molecular event associated with invasion. Am J Surg Pathol. 2007 Jun; 31(6):882-8. PMID: 17527075.
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    29. Mosquera JM, Perner S, Demichelis F, Kim R, Hofer MD, Mertz KD, Paris PL, Simko J, Collins C, Bismar TA, Chinnaiyan AM, Rubin MA. Morphological features of TMPRSS2-ERG gene fusion prostate cancer. J Pathol. 2007 May; 212(1):91-101. PMID: 17385188.
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    30. Paris PL, Hofer MD, Albo G, Kuefer R, Gschwend JE, Hautmann RE, Fridyland J, Simko J, Carroll PR, Rubin MA, Collins C. Genomic profiling of hormone-naïve lymph node metastases in patients with prostate cancer. Neoplasia. 2006 Dec; 8(12):1083-9. PMID: 17217626; PMCID: PMC1783716.
    31. Volik S, Raphael BJ, Huang G, Stratton MR, Bignel G, Murnane J, Brebner JH, Bajsarowicz K, Paris PL, Tao Q, Kowbel D, Lapuk A, Shagin DA, Shagina IA, Gray JW, Cheng JF, de Jong PJ, Pevzner P, Collins C. Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res. 2006 Mar; 16(3):394-404. PMID: 16461635; PMCID: PMC1415204.
    32. Paris PL, Weinberg V, Simko J, Andaya A, Albo G, Rubin MA, Carroll PR, Collins C. Preliminary evaluation of prostate cancer metastatic risk biomarkers. Int J Biol Markers. 2005 Jul-Sep; 20(3):141-5. PMID: 16247872.
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    33. van Duin M, van Marion R, Watson JE, Paris PL, Lapuk A, Brown N, Oseroff VV, Albertson DG, Pinkel D, de Jong P, Nacheva EP, Dinjens W, van Dekken H, Collins C. Construction and application of a full-coverage, high-resolution, human chromosome 8q genomic microarray for comparative genomic hybridization. Cytometry A. 2005; 63(1):10-9. PMID: 15619731.
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    34. Macoska JA, Paris P, Collins C, Andaya A, Beheshti B, Chaib H, Kant R, Begley L, MacDonald JW, Squire JA. Evolution of 8p loss in transformed human prostate epithelial cells. Cancer Genet Cytogenet. 2004 Oct 01; 154(1):36-43. PMID: 15381370.
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    35. Watson JE, Kamkar S, James K, Kowbel D, Andaya A, Paris PL, Simko J, Carroll P, McAlhany S, Rowley D, Collins C. Molecular analysis of WFDC1/ps20 gene in prostate cancer. Prostate. 2004 Oct 01; 61(2):192-9. PMID: 15305342.
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    36. Zhou Y, Huang D, Paris PL, Sauter CS, Prock KA, Hoffman GS. An analysis of CTLA-4 and proinflammatory cytokine genes in Wegener's granulomatosis. Arthritis Rheum. 2004 Aug; 50(8):2645-50. PMID: 15334480.
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    37. Rubin MA, Varambally S, Beroukhim R, Tomlins SA, Rhodes DR, Paris PL, Hofer MD, Storz-Schweizer M, Kuefer R, Fletcher JA, Hsi BL, Byrne JA, Pienta KJ, Collins C, Sellers WR, Chinnaiyan AM. Overexpression, amplification, and androgen regulation of TPD52 in prostate cancer. Cancer Res. 2004 Jun 01; 64(11):3814-22. PMID: 15172988.
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    38. Paris PL, Andaya A, Fridlyand J, Jain AN, Weinberg V, Kowbel D, Brebner JH, Simko J, Watson JE, Volik S, Albertson DG, Pinkel D, Alers JC, van der Kwast TH, Vissers KJ, Schroder FH, Wildhagen MF, Febbo PG, Chinnaiyan AM, Pienta KJ, Carroll PR, Rubin MA, Collins C, van Dekken H. Whole genome scanning identifies genotypes associated with recurrence and metastasis in prostate tumors. Hum Mol Genet. 2004 Jul 01; 13(13):1303-13. PMID: 15138198.
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    39. Watson JE, Doggett NA, Albertson DG, Andaya A, Chinnaiyan A, van Dekken H, Ginzinger D, Haqq C, James K, Kamkar S, Kowbel D, Pinkel D, Schmitt L, Simko JP, Volik S, Weinberg VK, Paris PL, Collins C. Integration of high-resolution array comparative genomic hybridization analysis of chromosome 16q with expression array data refines common regions of loss at 16q23-qter and identifies underlying candidate tumor suppressor genes in prostate cancer. Oncogene. 2004 Apr 22; 23(19):3487-94. PMID: 15007382.
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    40. 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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    41. 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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    42. van Dekken H, Paris PL, Albertson DG, Alers JC, Andaya A, Kowbel D, van der Kwast TH, Pinkel D, Schröder FH, Vissers KJ, Wildhagen MF, Collins C. Evaluation of genetic patterns in different tumor areas of intermediate-grade prostatic adenocarcinomas by high-resolution genomic array analysis. Genes Chromosomes Cancer. 2004 Mar; 39(3):249-56. PMID: 14732926.
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    43. 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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    44. Paris PL, Albertson DG, Alers JC, Andaya A, Carroll P, Fridlyand J, Jain AN, Kamkar S, Kowbel D, Krijtenburg PJ, Pinkel D, Schröder FH, Vissers KJ, Watson VJ, Wildhagen MF, Collins C, Van Dekken H. High-resolution analysis of paraffin-embedded and formalin-fixed prostate tumors using comparative genomic hybridization to genomic microarrays. Am J Pathol. 2003 Mar; 162(3):763-70. PMID: 12598311; PMCID: PMC1868117.
    45. 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.
    46. Skacel M, Paris PL, Pettay JD, Tsiftsakis EK, Tubbs RR, Casey G, Hsi ED. Diffuse large B-cell lymphoma of the stomach: assessment of microsatellite instability, allelic imbalance, and trisomy of chromosomes 3, 12, and 18. Diagn Mol Pathol. 2002 Jun; 11(2):75-82. PMID: 12045710.
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    47. Paris PL, Witte JS, Kupelian PA, Levin H, Klein EA, Catalona WJ, Casey G. Identification and fine mapping of a region showing a high frequency of allelic imbalance on chromosome 16q23.2 that corresponds to a prostate cancer susceptibility locus. Cancer Res. 2000 Jul 01; 60(13):3645-9. PMID: 10910080.
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    48. Paris PL, Kupelian PA, Hall JM, Williams TL, Levin H, Klein EA, Casey G, Witte JS. Association between a CYP3A4 genetic variant and clinical presentation in African-American prostate cancer patients. Cancer Epidemiol Biomarkers Prev. 1999 Oct; 8(10):901-5. PMID: 10548319.
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    49. Paris PL, Langenhan JM, Kool ET. Probing DNA sequences in solution with a monomer-excimer fluorescence color change. Nucleic Acids Res. 1998 Aug 15; 26(16):3789-93. PMID: 9685497; PMCID: PMC147755.
    50. Guckian KM, Schweitzer BA, Ren RX, Sheils CJ, Paris PL, Tahmassebi DC, Kool ET. Experimental Measurement of Aromatic Stacking Affinities in the Context of Duplex DNA. J Am Chem Soc. 1996 Aug 28; 118(34):8182-8183. PMID: 20882117.
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    51. Ren RX, Chaudhuri NC, Paris PL, Rumney S, Kool ET. Naphthalene, Phenanthrene, and Pyrene as DNA Base Analogues: Synthesis, Structure, and Fluorescence in DNA. J Am Chem Soc. 1996 Aug 21; 118(33):7671-7678. PMID: 20865136.
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