Photo of Giovanni Parmigiani,  PhD

Giovanni Parmigiani, PhD

Dana-Farber Cancer Institute

Dana-Farber Cancer Institute
Phone: (617) 632-3012
Fax: (617) 632-2444

Giovanni Parmigiani, PhD

Dana-Farber Cancer Institute


  • Professor, Biostatistics, Harvard T.H. Chan School Of Public Health
  • Chair and Professor, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute



  • Member, Center Scientific Council
  • Associate Director, Population Science, Executive Committee

Research Abstract

Models and software for predicting who is at risk of carrying genetic variants that confer susceptibility to cancer. Application to breast, ovarian, colorectal, pancreatic and skin cancer.

Statistical methods for the analysis of high throughput genomic data: analysis of cancer genome sequencing projects; integration of genomic information across technologies; cross-study validation of genomics results.

Statistical methods for complex medical decisions: comprehensive models for lifetime history of chronic disease outcomes; decision trees and dynamic programming.

Bayesian modeling and computation: multilevel models; decision theoretic approaches to inference; sequential experimental design, Markov chain Monte Carlo methods.


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  • Tyekucheva S, Martin NE, Stack EC, Wei W, Vathipadiekal V, Waldron L, Fiorentino M, Lis RT, Stampfer MJ, Loda M, Parmigiani G, Mucci LA, Birrer M. Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues. J Mol Diagn 2015; 17:374-81. PubMed
  • Hatchi E, Skourti-Stathaki K, Ventz S, Pinello L, Yen A, Kamieniarz-Gdula K, Dimitrov S, Pathania S, McKinney KM, Eaton ML, Kellis M, Hill SJ, Parmigiani G, Proudfoot NJ, Livingston DM. BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair. Mol Cell 2015; 57:636-47. PubMed
  • Trippa L, Wen PY, Parmigiani G, Berry DA, Alexander BM. Combining progression-free survival and overall survival as a novel composite endpoint for glioblastoma trials. 2015. PubMed
  • Tomasetti C, Marchionni L, Nowak MA, Parmigiani G, Vogelstein B. Only three driver gene mutations are required for the development of lung and colorectal cancers. Proc Natl Acad Sci U S A 2015; 112:118-23. PubMed
  • Mazzola E, Blackford A, Parmigiani G, Biswas S. Recent Enhancements to the Genetic Risk Prediction Model BRCAPRO. Cancer Inform 2015; 14:147-57. PubMed
  • Rashid NU, Sperling AS, Bolli N, Wedge DC, Van Loo P, Tai YT, Shammas MA, Fulciniti M, Samur MK, Richardson PG, Magrangeas F, Minvielle S, Futreal PA, Anderson KC, Avet-Loiseau H, Campbell PJ, Parmigiani G, Munshi NC. Differential and limited expression of mutant alleles in multiple myeloma. Blood 2014. PubMed
  • Braun D, Gorfine M, Parmigiani G. Misreported Family Histories and Underestimation of Risk. J Clin Oncol 2014. PubMed
  • Bernau C, Riester M, Boulesteix AL, Parmigiani G, Huttenhower C, Waldron L, Trippa L. Cross-study validation for the assessment of prediction algorithms. Bioinformatics 2014; 30:i105-12. PubMed
  • Mazzola E, Chipman J, Cheng SC, Parmigiani G. Recent BRCAPRO upgrades significantly improve calibration. Cancer Epidemiol Biomarkers Prev 2014. PubMed
  • Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G. Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. Journal of the National Cancer Institute 2014. PubMed
  • Riester M, Wei W, Waldron L, Culhane AC, Trippa L, Oliva E, Kim SH, Michor F, Huttenhower C, Parmigiani G, Birrer MJ. Risk prediction for late-stage ovarian cancer by meta-analysis of 1525 patient samples. Journal of the National Cancer Institute 2014. PubMed
  • Bolli N, Avet-Loiseau H, Wedge DC, Van Loo P, Alexandrov LB, Martincorena I, Dawson KJ, Iorio F, Nik-Zainal S, Bignell GR, Hinton JW, Li Y, Tubio JM, McLaren S, O' Meara S, Butler AP, Teague JW, Mudie L, Anderson E, Rashid N, Tai YT, Shammas MA, Sperling AS, Fulciniti M, Richardson PG, Parmigiani G, Magrangeas F, Minvielle S, Moreau P, Attal M, Facon T, Futreal PA, Anderson KC, Campbell PJ, Munshi NC. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun 2014; 5:2997. PubMed
  • Ho YY, Cope LM, Parmigiani G. Modular network construction using eQTL data: an analysis of computational costs and benefits. Front Genet 2014; 5:40. PubMed
  • Parmigiani G, Boca S, Ding J, Trippa L. Statistical tools and R software for cancer driver probabilities. Methods Mol Biol 2013; 1101:113-34. PubMed
  • Biswas S, Arun B, Parmigiani G. Reclassification of predictions for uncovering subgroup specific improvement. Stat Med 2013. PubMed
  • Gorfine M, Hsu L, Parmigiani G. Frailty Models for Familial Risk with Application to Breast Cancer. Journal of the American Statistical Association 2014; 108:1205-1215. PubMed
  • Boca SM, Bravo HC, Caffo B, Leek JT, Parmigiani G. A decision-theory approach to interpretable set analysis for high-dimensional data. Biometrics 2013; 69:614-23. PubMed
  • Gartner JJ, Parker SC, Prickett TD, Dutton-Regester K, Stitzel ML, Lin JC, Davis S, Simhadri VL, Jha S, Katagiri N, Gotea V, Teer JK, Wei X, Morken MA, Bhanot UK, , Chen G, Elnitski LL, Davies MA, Gershenwald JE, Carter H, Karchin R, Robinson W, Robinson S, Rosenberg SA, Collins FS, Parmigiani G, Komar AA, Kimchi-Sarfaty C, Hayward NK, Margulies EH, Samuels Y. Whole-genome sequencing identifies a recurrent functional synonymous mutation in melanoma. Proc Natl Acad Sci U S A 2013; 110:13481-6. PubMed
  • Ahn J, Yuan Y, Parmigiani G, Suraokar MB, Diao L, Wistuba II, Wang W. DeMix: deconvolution for mixed cancer transcriptomes using raw measured data. Bioinformatics 2013; 29:1865-71. PubMed
  • Chipman J, Drohan B, Blackford A, Parmigiani G, Hughes K, Bosinoff P. Providing access to risk prediction tools via the HL7 XML-formatted risk web service. Breast Cancer Res Treat 2013; 140:187-93. PubMed
  • Biswas S, Atienza P, Chipman J, Hughes K, Barrera AM, Amos CI, Arun B, Parmigiani G. Simplifying clinical use of the genetic risk prediction model BRCAPRO. Breast Cancer Res Treat 2013; 139:571-9. PubMed
  • Gorfine M, Hsu L, Zucker DM, Parmigiani G. Calibrated predictions for multivariate competing risks models. Lifetime Data Analysis 2013. PubMed
  • Trippa L, Lee EQ, Wen PY, Batchelor TT, Cloughesy T, Parmigiani G, Alexander BM. Reply to B. Freidlin et al. J Clin Oncol 2013; 31:970-1. PubMed
  • Tomasetti C, Vogelstein B, Parmigiani G. Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation. Proc Natl Acad Sci U S A 2013; 110:1999-2004. PubMed
  • Tomasetti C, Demetri GD, Parmigiani G. Why tyrosine kinase inhibitor resistance is common in advanced gastrointestinal stromal tumors. F1000Res 2014; 2:152. PubMed
  • Mazzola E, Cheng SC, Parmigiani G. The penetrance of ductal carcinoma in situ among BRCA1 and BRCA2 mutation carriers. Breast Cancer Res Treat 2012; 137:315-8. PubMed
  • Sausen M, Leary RJ, Jones S, Wu J, Reynolds CP, Liu X, Blackford A, Parmigiani G, Diaz LA, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE, Hogarty MD. Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma. Nat Genet 2012; 45:12-7. PubMed
  • Ganzfried BF, Riester M, Haibe-Kains B, Risch T, Tyekucheva S, Jazic I, Wang XV, Ahmadifar M, Birrer MJ, Parmigiani G, Huttenhower C, Waldron L. curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. Database (Oxford) 2013; 2013:bat013. PubMed
  • Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, O'Shaughnessy J, Kinzler KW, Parmigiani G, Vogelstein B, Diaz LA, Velculescu VE. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med 2012; 4:162ra154. PubMed
  • Waldron L, Ogino S, Hoshida Y, Shima K, McCart Reed AE, Simpson PT, Baba Y, Nosho K, Segata N, Vargas AC, Cummings MC, Lakhani SR, Kirkner GJ, Giovannucci E, Quackenbush J, Golub TR, Fuchs CS, Parmigiani G, Huttenhower C. Expression Profiling of Archival Tumors for Long-term Health Studies. Clin Cancer Res 2012; 18:6136-6146. PubMed
  • Coopey SB, Mazzola E, Buckley JM, Sharko J, Belli AK, Kim EM, Polubriaginof F, Parmigiani G, Garber JE, Smith BL, Gadd MA, Specht MC, Guidi AJ, Roche CA, Hughes KS. The role of chemoprevention in modifying the risk of breast cancer in women with atypical breast lesions. Breast Cancer Res Treat 2012. PubMed
  • Trippa L, Lee EQ, Wen PY, Batchelor TT, Cloughesy T, Parmigiani G, Alexander BM. Bayesian adaptive randomized trial design for patients with recurrent glioblastoma. J Clin Oncol 2012; 30:3258-63. PubMed
  • Victoria X, Blades N, Ding J, Sultana R, Parmigiani G. Estimation of sequencing error rates in short reads. BMC Bioinformatics 2012; 13:185. PubMed
  • Parsons DW, Li M, Zhang X, Jones S, Leary RJ, Lin JC, Boca SM, Carter H, Samayoa J, Bettegowda C, Gallia GL, Jallo GI, Binder ZA, Nikolsky Y, Hartigan J, Smith DR, Gerhard DS, Fults DW, VandenBerg S, Berger MS, Marie SK, Shinjo SM, Clara C, Phillips PC, Minturn JE, Biegel JA, Judkins AR, Resnick AC, Storm PB, Curran T, He Y, Rasheed BA, Friedman HS, Keir ST, McLendon R, Northcott PA, Taylor MD, Burger PC, Riggins GJ, Karchin R, Parmigiani G, Bigner DD, Yan H, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The genetic landscape of the childhood cancer medulloblastoma. Science 2011; 331:435-9. PubMed
  • Boca SM, Kinzler K, Velculescu VE, Vogelstein B, Parmigiani G. Patient-oriented gene set analysis for cancer mutation data. Genome Biol 2010; 11:R112. PubMed
  • Fertig EJ, Ding J, Favorov AV, Parmigiani G, Ochs MF. CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data. Bioinformatics 2010; 26:2792-3. PubMed
  • Ho YY, Parmigiani G, Louis TA, Cope LM. Modeling Liquid Association. Biometrics 2010. PubMed
  • Wang W, Niendorf KB, Patel D, Blackford A, Marroni F, Sober AJ, Parmigiani G, Tsao H. Estimating CDKN2A carrier probability and personalizing cancer risk assessments in hereditary melanoma using MelaPRO. Cancer Res 2010; 70:552-9. PubMed
  • Scharpf RB, Iacobuzio-Donahue CA, Cope L, Ruczinski I, Garrett-Mayer E, Lakkur S, Campagna D, Parmigiani G. Cross-platform Comparison of Two Pancreatic Cancer Phenotypes. Cancer Inform 2010; 9:257-64. PubMed
  • Guda K, Moinova H, He J, Jamison O, Ravi L, Natale L, Lutterbaugh J, Lawrence E, Lewis S, Willson JK, Lowe JB, Wiesner GL, Parmigiani G, Barnholtz-Sloan J, Dawson DW, Velculescu VE, Kinzler KW, Papadopoulos N, Vogelstein B, Willis J, Gerken TA, Markowitz SD. Inactivating germ-line and somatic mutations in polypeptide N-acetylgalactosaminyltransferase 12 in human colon cancers. Proc Natl Acad Sci U S A 2009; 106:12921-5. PubMed
  • Blackford A, Serrano OK, Wolfgang CL, Parmigiani G, Jones S, Zhang X, Parsons DW, Lin JC, Leary RJ, Eshleman JR, Goggins M, Jaffee EM, Iacobuzio-Donahue CA, Maitra A, Cameron JL, Olino K, Schulick R, Winter J, Herman JM, Laheru D, Klein AP, Vogelstein B, Kinzler KW, Velculescu VE, Hruban RH. SMAD4 gene mutations are associated with poor prognosis in pancreatic cancer. Clin Cancer Res 2009; 15:4674-9. PubMed
  • He X, Marchionni L, Hansel DE, Yu W, Sood A, Yang J, Parmigiani G, Matsui W, Berman DM. Differentiation of a highly tumorigenic basal cell compartment in urothelial carcinoma. Stem Cells 2009; 27:1487-95. PubMed
  • Lin X, Afsari B, Marchionni L, Cope L, Parmigiani G, Naiman D, Geman D. The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. BMC Bioinformatics 2009; 10:256. PubMed
  • Parmigiani G, Boca S, Lin J, Kinzler KW, Velculescu V, Vogelstein B. Design and analysis issues in genome-wide somatic mutation studies of cancer. Genomics 2008; 93:17-21. PubMed
  • Tai YC, Chen S, Parmigiani G, Klein AP. Incorporating tumor immunohistochemical markers in BRCA1 and BRCA2 carrier prediction. Breast Cancer Res 2008; 10:401. PubMed
  • Marchionni L, Wilson RF, Wolff AC, Marinopoulos S, Parmigiani G, Bass EB, Goodman SN. Systematic review: gene expression profiling assays in early-stage breast cancer. Ann Intern Med 2008; 148:358-69. PubMed
  • Tai YC, Domchek S, Parmigiani G, Chen S. Breast cancer risk among male BRCA1 and BRCA2 mutation carriers. Journal of the National Cancer Institute 2007; 99:1811-4. PubMed
  • Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JK, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PV, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science 2007; 318:1108-13. PubMed
  • Parmigiani G, Chen S, Iversen ES Jr, Friebel TM, Finkelstein DM, Anton-Culver H, Ziogas A, Weber BL, Eisen A, Malone KE, Daling JR, Hsu L, Ostrander EA, Peterson LE, Schildkraut JM, Isaacs C, Corio C, Leondaridis L, Tomlinson G, Amos CI, Strong LC, Berry DA, Weitzel JN, Sand S, Dutson D, Kerber R, Peshkin BN, Euhus DM. Validity of models for predicting BRCA1 and BRCA2 mutations. Ann Intern Med 2007; 147:441-50. PubMed
  • Lin J, Gan CM, Zhang X, Jones S, Sjöblom T, Wood LD, Parsons DW, Papadopoulos N, Kinzler KW, Vogelstein B, Parmigiani G, Velculescu VE. A multidimensional analysis of genes mutated in breast and colorectal cancers. Genome Res 2007; 17:1304-18. PubMed
  • Wang W, Chen S, Brune KA, Hruban RH, Parmigiani G, Klein AP. PancPRO: risk assessment for individuals with a family history of pancreatic cancer. J Clin Oncol 2007; 25:1417-22. PubMed
  • Chen S, Parmigiani G. Meta-analysis of BRCA1 and BRCA2 penetrance. J Clin Oncol 2007; 25:1329-33. PubMed
  • Sjöblom T, Jones S, Wood LD, Parsons DW, Lin J, Barber TD, Mandelker D, Leary RJ, Ptak J, Silliman N, Szabo S, Buckhaults P, Farrell C, Meeh P, Markowitz SD, Willis J, Dawson D, Willson JK, Gazdar AF, Hartigan J, Wu L, Liu C, Parmigiani G, Park BH, Bachman KE, Papadopoulos N, Vogelstein B, Kinzler KW, Velculescu VE. The consensus coding sequences of human breast and colorectal cancers. Science 2006; 314:268-74. PubMed
  • Chen S, Wang W, Lee S, Nafa K, Lee J, Romans K, Watson P, Gruber SB, Euhus D, Kinzler KW, Jass J, Gallinger S, Lindor NM, Casey G, Ellis N, Giardiello FM, Offit K, Parmigiani G, . Prediction of germline mutations and cancer risk in the Lynch syndrome. JAMA 2006; 296:1479-87. PubMed