Zoltan Szallasi, MD

Boston Children's Hospital

Boston Children's Hospital
Phone: (617) 355-2179


zszallasi@chip.org

Zoltan Szallasi, MD

Boston Children's Hospital

EDUCATIONAL TITLES

  • Assistant Professor, Pediatrics, Harvard Medical School
  • Assistant Professor, Pediatrics, Boston Children's Hospital

DF/HCC PROGRAM AFFILIATION

Research Abstract

High throughput measurements, such as microarray based gene expression profiling, offers a more complete view of the biochemical changes associated with cancer. However, more data means more noise, more uncertainty and an explosion of the hypothesis space, all impeding association based learning often applied both in basic and clinical cancer research. Our group is interested in the meaningful and responsible application of high throughput measurements for cancer research. We implemented several methods that increased the reliability of microarray measurements. We are also interested in approaches that combine high throughput measurements in a manner that describe essential biology in a robust fashion, such as developing a gene expression signature of chromosomal instability.

Publications

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  • Josa V, Krzystanek M, Eklund AC, Salamon F, Zarand A, Szallasi Z, Baranyai Z. Relationship of postoperative thrombocytosis and survival of patients with colorectal cancer. Int J Surg 2015. PubMed
  • Jósa V, Krzystanek M, Vass T, Lang T, Juhász V, Szilágyi K, Tihanyi B, Harsányi L, Szállási Z, Salamon F, Baranyai Z. Thrombocytosis of Liver Metastasis from Colorectal Cancer as Predictive Factor. Pathol Oncol Res 2015. PubMed
  • Dewhurst SM, McGranahan N, Burrell RA, Rowan AJ, Grönroos E, Endesfelder D, Joshi T, Mouradov D, Gibbs P, Ward RL, Hawkins NJ, Szallasi Z, Sieber OM, Swanton C. Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. 2014; 4:175-85. PubMed
  • Martinez P, Birkbak NJ, Gerlinger M, McGranahan N, Burrell RA, Rowan AJ, Joshi T, Fisher R, Larkin J, Szallasi Z, Swanton C. Parallel evolution of tumour subclones mimics diversity between tumours. J Pathol 2013; 230:356-64. PubMed
  • Seo JH, Li Q, Fatima A, Eklund A, Szallasi Z, Polyak K, Richardson AL, Freedman ML. Deconvoluting complex tissues for expression quantitative trait locus-based analyses. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120363. PubMed
  • Birkbak NJ, Kochupurakkal B, Izarzugaza JM, Eklund AC, Li Y, Liu J, Szallasi Z, Matulonis UA, Richardson AL, Iglehart JD, Wang ZC. Tumor mutation burden forecasts outcome in ovarian cancer with BRCA1 or BRCA2 mutations. PLoS ONE 2013; 8:e80023. PubMed
  • Baranyai Z, Mersich T, Dede K, Besznyák I, Zaránd A, Teknős D, Nagy P, Salamon F, Nagy P, Nagy Z, Kótai Z, Szász M, Lukács L, Szállási Z, Jósa V, Jakab F. [From project based sample collection to a biobank.] 2011; 152:606-609. PubMed
  • Lee AJ, Endesfelder D, Rowan AJ, Walther A, Birkbak NJ, Futreal PA, Downward J, Szallasi Z, Tomlinson IP, Howell M, Kschischo M, Swanton C. Chromosomal Instability Confers Intrinsic Multidrug Resistance. Cancer Res 2011; 71:1858-1870. PubMed
  • Birkbak NJ, Eklund AC, Li Q, McClelland SE, Endesfelder D, Tan P, Tan IB, Richardson AL, Szallasi Z, Swanton C. Paradoxical relationship between chromosomal instability and survival outcome in cancer. Cancer Res 2011. PubMed
  • Burrell RA, Juul N, Johnston SR, Reis-Filho JS, Szallasi Z, Swanton C. Targeting chromosomal instability and tumour heterogeneity in HER2-positive breast cancer. J Cell Biochem 2010; 111:782-90. PubMed
  • Györffy B, Lanczky A, Eklund AC, Denkert C, Budczies J, Li Q, Szallasi Z. An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients. Breast Cancer Res Treat 2010; 123:725-31. PubMed
  • Juul N, Szallasi Z, Eklund AC, Li Q, Burrell RA, Gerlinger M, Valero V, Andreopoulou E, Esteva FJ, Symmans WF, Desmedt C, Haibe-Kains B, Sotiriou C, Pusztai L, Swanton C. Assessment of an RNA interference screen-derived mitotic and ceramide pathway metagene as a predictor of response to neoadjuvant paclitaxel for primary triple-negative breast cancer: a retrospective analysis of five clinical trials. Lancet Oncol 2010; 11:358-65. PubMed
  • Silver DP, Richardson AL, Eklund AC, Wang ZC, Szallasi Z, Li Q, Juul N, Leong CO, Calogrias D, Buraimoh A, Fatima A, Gelman RS, Ryan PD, Tung NM, De Nicolo A, Ganesan S, Miron A, Colin C, Sgroi DC, Ellisen LW, Winer EP, Garber JE. Efficacy of neoadjuvant Cisplatin in triple-negative breast cancer. J Clin Oncol 2010; 28:1145-53. PubMed
  • Eklund AC, Friis P, Wernersson R, Szallasi Z. Optimization of the BLASTN substitution matrix for prediction of non-specific DNA microarray hybridization. Nucleic Acids Res 2010; 38:e27. PubMed
  • Li Y, Zou L, Li Q, Haibe-Kains B, Tian R, Li Y, Desmedt C, Sotiriou C, Szallasi Z, Iglehart JD, Richardson AL, Wang ZC. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. Nat Med 2010; 16:214-8. PubMed
  • Li Q, Eklund AC, Juul N, Haibe-Kains B, Workman CT, Richardson AL, Szallasi Z, Swanton C. Minimising immunohistochemical false negative ER classification using a complementary 23 gene expression signature of ER status. PLoS ONE 2010; 5:e15031. PubMed
  • Swanton C, Larkin JM, Gerlinger M, Eklund AC, Howell M, Stamp G, Downward J, Gore M, Futreal PA, Escudier B, Andre F, Albiges L, Beuselinck B, Oudard S, Hoffmann J, Gyorffy B, Torrance CJ, Boehme KA, Volkmer H, Toschi L, Nicke B, Beck M, Szallasi Z. Predictive biomarker discovery through the parallel integration of clinical trial and functional genomics datasets. Genome Med 2010; 2:53. PubMed
  • Swanton C,Nicke B,Schuett M,Eklund AC,Ng C,Li Q,Hardcastle T,Lee A,Roy R,East P,Kschischo M,Endesfelder D,Wylie P,Kim SN,Chen JG,Howell M,Ried T,Habermann JK,Auer G,Brenton JD,Szallasi Z,Downward J. Chromosomal instability determines taxane response. Proc Natl Acad Sci U S A 2009; 106:8671-6. PubMed
  • Lage K,Hansen NT,Karlberg EO,Eklund AC,Roque FS,Donahoe PK,Szallasi Z,Jensen TS,Brunak S. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc Natl Acad Sci U S A 2008; 105:20870-5. PubMed
  • Lee AJ,East P,Pepper S,Nicke B,Szallasi Z,Eklund AC,Downward J,Swanton C. Concordance of exon array and real-time PCR assessment of gene expression following cancer cell cytotoxic drug exposure. Cell Cycle 2008; 7:3947-8. PubMed
  • Swanton C,Szallasi Z,Brenton JD,Downward J. Functional genomic analysis of drug sensitivity pathways to guide adjuvant strategies in breast cancer. Breast Cancer Res 2008; 10:214. PubMed
  • Eklund AC, Szallasi Z. Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biol 2008; 9:R26. PubMed
  • Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet 2006; 38:1043-8. PubMed
  • Carter SL, Eklund AC, Mecham BH, Kohane IS, Szallasi Z. Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements. BMC Bioinformatics 2005; 6:107. PubMed
  • Stelling J, Sauer U, Szallasi Z, Doyle FJ, Doyle J. Robustness of cellular functions. Cell 2004; 118:675-85. PubMed
  • Mecham BH, Klus GT, Strovel J, Augustus M, Byrne D, Bozso P, Wetmore DZ, Mariani TJ, Kohane IS, Szallasi Z. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements. Nucleic Acids Res 2004; 32:e74. PubMed
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