Irina Ostrovnaya

Summary

Affiliation: Memorial Sloan-Kettering Cancer Center
Country: USA

Publications

  1. pmc Comparison of properties of tests for assessing tumor clonality
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Biometrics 64:1018-22. 2008
  2. pmc A classification model for distinguishing copy number variants from cancer-related alterations
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Bioinformatics 11:297. 2010
  3. pmc Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Bioinformatics 27:1698-9. 2011
  4. pmc Radiogenomics of clear cell renal cell carcinoma: associations between CT imaging features and mutations
    Christoph A Karlo
    From the Genitourinary Imaging Group, Department of Radiology C A K, P L D P, J C, H H, O A, Urology Service, Department of Surgery A A H, P R, Human Oncology and Pathogenesis Program A A H, J J H, Department of Epidemiology and Biostatistics I O, and Department of Medicine, Genitourinary Oncology Service R M, J J H, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Radiology Academic Offices, Room C278, New York, NY 10065
    Radiology 270:464-71. 2014
  5. pmc Lack of survival advantage with autologous stem-cell transplantation in high-risk neuroblastoma consolidated by anti-GD2 immunotherapy and isotretinoin
    Brian H Kushner
    Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Oncotarget 7:4155-66. 2016
  6. pmc Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer
    Gopa Iyer
    Memorial Sloan Kettering Cancer Center, Cornell University, New York, NY, USA
    J Clin Oncol 31:3133-40. 2013
  7. pmc Phase II study of everolimus in metastatic urothelial cancer
    Matthew I Milowsky
    Genitourinary Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BJU Int 112:462-70. 2013
  8. pmc A metastasis or a second independent cancer? Evaluating the clonal origin of tumors using array copy number data
    Irina Ostrovnaya
    Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Stat Med 29:1608-21. 2010
  9. pmc Phase I Study of Everolimus in Combination with Gemcitabine and Split-Dose Cisplatin in Advanced Urothelial Carcinoma
    Wassim Abida
    Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Bladder Cancer 2:111-117. 2016
  10. pmc Genomic Characterization of Upper Tract Urothelial Carcinoma
    John P Sfakianos
    Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
    Eur Urol 68:970-7. 2015

Detail Information

Publications38

  1. pmc Comparison of properties of tests for assessing tumor clonality
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Biometrics 64:1018-22. 2008
    ..Much of the efficiency deficit can be recovered, however, by restricting the allelic imbalance parameter estimate to a prespecified range, assuming that this parameter is in the prespecified range...
  2. pmc A classification model for distinguishing copy number variants from cancer-related alterations
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Bioinformatics 11:297. 2010
    ..In order to identify important cancer genes CNAs and CNVs must be distinguished. Although the Database of Genomic Variants (DGV) contains a list of all known CNVs, there is no standard methodology to use the database effectively...
  3. pmc Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic profiles
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Bioinformatics 27:1698-9. 2011
    ..For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results...
  4. pmc Radiogenomics of clear cell renal cell carcinoma: associations between CT imaging features and mutations
    Christoph A Karlo
    From the Genitourinary Imaging Group, Department of Radiology C A K, P L D P, J C, H H, O A, Urology Service, Department of Surgery A A H, P R, Human Oncology and Pathogenesis Program A A H, J J H, Department of Epidemiology and Biostatistics I O, and Department of Medicine, Genitourinary Oncology Service R M, J J H, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Radiology Academic Offices, Room C278, New York, NY 10065
    Radiology 270:464-71. 2014
    ..To investigate associations between computed tomographic (CT) features of clear cell renal cell carcinoma (RCC) and mutations in VHL, PBRM1, SETD2, KDM5C, or BAP1 genes...
  5. pmc Lack of survival advantage with autologous stem-cell transplantation in high-risk neuroblastoma consolidated by anti-GD2 immunotherapy and isotretinoin
    Brian H Kushner
    Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Oncotarget 7:4155-66. 2016
    ..ASCT may not be needed to improve outcome when anti-GD2 immunotherapy is used for consolidation after dose-intensive conventional chemotherapy...
  6. pmc Prevalence and co-occurrence of actionable genomic alterations in high-grade bladder cancer
    Gopa Iyer
    Memorial Sloan Kettering Cancer Center, Cornell University, New York, NY, USA
    J Clin Oncol 31:3133-40. 2013
    ..We sought to define the prevalence and co-occurrence of actionable genomic alterations in patients with high-grade bladder cancer to serve as a platform for therapeutic drug discovery...
  7. pmc Phase II study of everolimus in metastatic urothelial cancer
    Matthew I Milowsky
    Genitourinary Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BJU Int 112:462-70. 2013
    ..To maximize benefit from targeted agents such as everolimus, the preselection of patients based on molecular phenotype is required...
  8. pmc A metastasis or a second independent cancer? Evaluating the clonal origin of tumors using array copy number data
    Irina Ostrovnaya
    Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Stat Med 29:1608-21. 2010
    ..Our data analyses show that in many cases a strong clonal signal emerges. Sensitivity analyses show that most of the diagnoses are robust when the data are of high quality...
  9. pmc Phase I Study of Everolimus in Combination with Gemcitabine and Split-Dose Cisplatin in Advanced Urothelial Carcinoma
    Wassim Abida
    Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Bladder Cancer 2:111-117. 2016
    ..Cisplatin-based combination chemotherapy is standard first-line treatment for patients with advanced urothelial carcinoma (UC). Molecular profiling studies reveal that the PI3K/AKT/mTOR pathway is altered in a significant percentage of UCs...
  10. pmc Genomic Characterization of Upper Tract Urothelial Carcinoma
    John P Sfakianos
    Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
    Eur Urol 68:970-7. 2015
    ..Despite a similar histologic appearance, upper tract urothelial carcinoma (UTUC) and urothelial carcinoma of the bladder (UCB) tumors have distinct epidemiologic and clinicopathologic differences...
  11. pmc Prognostic model for predicting survival of patients with metastatic urothelial cancer treated with cisplatin-based chemotherapy
    Andrea B Apolo
    Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA
    J Natl Cancer Inst 105:499-503. 2013
    ..69) and 0.58 (95% CI = 0.52 to 0.65), respectively, with superiority of the four-variable model compared with the MSKCC risk-score model for OS (the U statistic and its standard deviation were used to calculate the two-sided P = .02)...
  12. ncbi request reprint Alterations in the PI3K/Akt signaling pathway and association with outcome in invasive high-grade urothelial cancer (UC)
    Arjun Vasant Balar
    Memorial Sloan Kettering Cancer Center, New York, NY
    J Clin Oncol 30:277. 2012
    ..Molecular profiling of invasive high-grade UC demonstrates that PI3K/Akt pathway alterations occur in up to 15% of cases. The prognostic value of PI3K/Akt pathway alterations in invasive UC is unknown...
  13. pmc The high incidence of vascular thromboembolic events in patients with metastatic or unresectable urothelial cancer treated with platinum chemotherapy agents
    Christopher M Tully
    Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
    Cancer 122:712-21. 2016
    ....
  14. pmc Osteochondroma in long-term survivors of high-risk neuroblastoma
    Brian H Kushner
    Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
    Cancer 121:2090-6. 2015
    ..Current treatment of high-risk neuroblastoma includes dose-intensive chemotherapy, local RT, an anti-GD2 monoclonal antibody (MoAb), and isotretinoin. Late effects are emerging...
  15. pmc Frequent somatic CDH1 loss-of-function mutations in plasmacytoid variant bladder cancer
    Hikmat A Al-Ahmadie
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    Nat Genet 48:356-8. 2016
    ..Consistent with the aggressive clinical behavior of plasmacytoid carcinomas, which frequently recur locally, CRISPR/Cas9-mediated knockout of CDH1 in bladder cancer cells enhanced cell migration. ..
  16. pmc Validation and genomic interrogation of the MET variant rs11762213 as a predictor of adverse outcomes in clear cell renal cell carcinoma
    A Ari Hakimi
    Memorial Sloan Kettering Cancer Center, New York, New York
    Cancer 122:402-10. 2016
    ..This finding was validated with The Cancer Genome Atlas (TCGA) cohort, and the biologic implications were explored...
  17. pmc Genomic predictors of survival in patients with high-grade urothelial carcinoma of the bladder
    Philip H Kim
    Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Eur Urol 67:198-201. 2015
    ..Genomic profiling may aid in the identification of UCB patients at highest risk following RC...
  18. pmc Synthetic lethality in ATM-deficient RAD50-mutant tumors underlies outlier response to cancer therapy
    Hikmat Al-Ahmadie
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
    Cancer Discov 4:1014-21. 2014
    ....
  19. pmc The safety and efficacy of single-agent pemetrexed in platinum-resistant advanced urothelial carcinoma: a large single-institution experience
    Richard M Bambury
    Memorial Sloan Kettering Cancer Center, New York, New York, USA Tulane University School of Medicine, New Orleans, Louisiana, USA
    Oncologist 20:508-15. 2015
    ..We also investigated candidate prognostic factors for overall survival in this setting to explore whether the neutrophil-lymphocyte ratio (NLR) had independent prognostic significance...
  20. pmc Impact of recurrent copy number alterations and cancer gene mutations on the predictive accuracy of prognostic models in clear cell renal cell carcinoma
    A Ari Hakimi
    Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York Electronic address
    J Urol 192:24-9. 2014
    ....
  21. pmc The impact of genetic heterogeneity on biomarker development in kidney cancer assessed by multiregional sampling
    Alexander Sankin
    Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York City, New York
    Cancer Med 3:1485-92. 2014
    ..The mutational burden of renal tumors varies by region sampled. Single site assessment of key tumor suppressor mutations in primary ccRCC may not adequately capture the genetic predictors of tumor behavior...
  22. pmc Bone marrow minimal residual disease was an early response marker and a consistent independent predictor of survival after anti-GD2 immunotherapy
    Nai Kong V Cheung
    All authors Memorial Sloan Kettering Cancer Center, New York, NY
    J Clin Oncol 33:755-63. 2015
    ..Early response markers of minimal residual disease (MRD) in the BM that are also predictive of survival could help individualize patient therapies...
  23. pmc Combining integrated genomics and functional genomics to dissect the biology of a cancer-associated, aberrant transcription factor, the ASPSCR1-TFE3 fusion oncoprotein
    Rachel Kobos
    Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, USA
    J Pathol 229:743-54. 2013
    ..More generally, this work establishes a combined integrated genomics/functional genomics strategy to dissect the biology of oncogenic, chimeric transcription factors...
  24. pmc Phase II study of gemcitabine, carboplatin, and bevacizumab in patients with advanced unresectable or metastatic urothelial cancer
    Arjun V Balar
    Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    J Clin Oncol 31:724-30. 2013
    ..This trial evaluated the efficacy and safety of bevacizumab with GCa in advanced UC...
  25. pmc Oncotargets GD2 and GD3 are highly expressed in sarcomas of children, adolescents, and young adults
    Konstantin Dobrenkov
    Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York
    Pediatr Blood Cancer 63:1780-5. 2016
    ..In this study, the pattern of GD2 and GD3 expression among pediatric/adolescent or young adult tumors was determined, providing companion diagnostics for targeted therapy...
  26. ncbi request reprint Association of single-nucleotide polymorphisms in BCL2L1 and TACC3 with response to bacillus Calmette-Guérin intravesical therapy in non-muscle-invasive bladder cancer
    Shaheen Alanee
    Memorial Sloan Kettering Cancer Center, New York, NY American Cancer Society, Atlanta, GA
    J Clin Oncol 30:260. 2012
    ..This study examines the association between germline single nucleotide polymorphisms (SNPs) and response to BCG therapy...
  27. doi request reprint Deep MicroRNA sequencing reveals downregulation of miR-29a in neuroblastoma central nervous system metastasis
    Irene Y Cheung
    Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
    Genes Chromosomes Cancer 53:803-14. 2014
    ..These findings raised the hypothesis that miR-29a could be a biomarker for neuroblastoma CNS metastasis, and its downregulation may play a pivotal role in CNS progression...
  28. pmc Key role for myeloid cells: phase II results of anti-G(D2) antibody 3F8 plus granulocyte-macrophage colony-stimulating factor for chemoresistant osteomedullary neuroblastoma
    Nai Kong V Cheung
    Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY
    Int J Cancer 135:2199-205. 2014
    ..MRD response may be an indicator of tumor sensitivity to anti-G(D2) immunotherapy. Correlative studies highlight the antineoplastic potency of myeloid effectors...
  29. pmc Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network
    A Ari Hakimi
    Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Clin Cancer Res 19:3259-67. 2013
    ..To investigate the impact of newly identified chromosome 3p21 epigenetic tumor suppressors PBRM1, SETD2, and BAP1 on cancer-specific survival (CSS) of 609 patients with clear cell renal cell carcinoma (ccRCC) from 2 distinct cohorts...
  30. pmc Estimating the dose-toxicity curve in completed phase I studies
    Alexia Iasonos
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Stat Med 30:2117-29. 2011
    ..Confidence intervals around the toxicity probabilities at each dose level are estimated using the cumulative toxicity data. A programming code is included...
  31. pmc Testing clonal relatedness of tumors using array comparative genomic hybridization: a statistical challenge
    Irina Ostrovnaya
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Clin Cancer Res 16:1358-67. 2010
    ....
  32. pmc Boomerang: A method for recursive reclassification
    Sean M Devlin
    Memorial Sloan Kettering Cancer Center, New York, New York 10065, U S A
    Biometrics 72:995-1002. 2016
    ..Lastly, the method is illustrated on an acute myeloid leukemia data set where a new refined classifier incorporates four new mutations into the existing three category classifier and is validated on an independent data set. ..
  33. pmc Clonal relationships between lobular carcinoma in situ and other breast malignancies
    Colin B Begg
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
    Breast Cancer Res 18:66. 2016
    ..We sought to confirm these findings with an extensive study of fresh frozen breast specimens from women undergoing mastectomy...
  34. pmc Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures
    Yasin Senbabaoglu
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Genome Biol 17:231. 2016
    ..Here, we employ a gene expression-based computational method to profile the infiltration levels of 24 immune cell populations in 19 cancer types...
  35. doi request reprint Recurrent pre-existing and acquired DNA copy number alterations, including focal TERT gains, in neuroblastoma central nervous system metastases
    David Cobrinik
    Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065
    Genes Chromosomes Cancer 52:1150-66. 2013
    ..Among the acquired lesions, increased TERT copy number and expression appears likely to function in lieu of MYCNA to promote CNS metastasis...
  36. pmc Genome sequencing identifies a basis for everolimus sensitivity
    Gopa Iyer
    Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Science 338:221. 2012
    ....
  37. pmc Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers
    Nicolas Girard
    Pao Lab, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Clin Cancer Res 15:5184-90. 2009
    ..Decisions are currently made using the Martini and Melamed criteria, which are mostly based on tumor location and histologic type. New genomic tools could improve the ability to assess tumor clonality...
  38. pmc Evaluation of the clonal origin of multiple primary melanomas using molecular profiling
    Irene Orlow
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    J Invest Dermatol 129:1972-82. 2009
    ....