Adam B Olshen

Summary

Affiliation: Memorial Sloan-Kettering Cancer Center
Country: USA

Publications

  1. pmc Breast tumor copy number aberration phenotypes and genomic instability
    Jane Fridlyand
    Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94143, USA
    BMC Cancer 6:96. 2006
  2. pmc Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping
    Adam B Olshen
    Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Genet 9:14. 2008
  3. ncbi request reprint Circular binary segmentation for the analysis of array-based DNA copy number data
    Adam B Olshen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Biostatistics 5:557-72. 2004
  4. ncbi request reprint Coactivation of receptor tyrosine kinases in malignant mesothelioma as a rationale for combination targeted therapy
    Marie Brevet
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, USA
    J Thorac Oncol 6:864-74. 2011
  5. ncbi request reprint Constitutive gene expression predisposes morphogen-mediated cell fate responses of NT2/D1 and 27X-1 human embryonal carcinoma cells
    Rajendrakumar S V Chadalavada
    Cell Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Stem Cells 25:771-8. 2007
  6. pmc Pattern discovery and cancer gene identification in integrated cancer genomic data
    Qianxing Mo
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 110:4245-50. 2013
  7. pmc Integrative subtype discovery in glioblastoma using iCluster
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS ONE 7:e35236. 2012
  8. pmc Identification and validation of a gene expression signature that predicts outcome in adult men with germ cell tumors
    James E Korkola
    Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, USA
    J Clin Oncol 27:5240-7. 2009
  9. 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
  10. 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

Detail Information

Publications40

  1. pmc Breast tumor copy number aberration phenotypes and genomic instability
    Jane Fridlyand
    Department of Epidemiology and Biostatistics, University of California San Francisco, CA 94143, USA
    BMC Cancer 6:96. 2006
    ..g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes...
  2. pmc Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping
    Adam B Olshen
    Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    BMC Genet 9:14. 2008
    ..435,632 SNPs overlapped and met annotation criteria in the two groups...
  3. ncbi request reprint Circular binary segmentation for the analysis of array-based DNA copy number data
    Adam B Olshen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Biostatistics 5:557-72. 2004
    ..The method is evaluated by simulation and is demonstrated on cell line data with known copy number alterations and on a breast cancer cell line data set...
  4. ncbi request reprint Coactivation of receptor tyrosine kinases in malignant mesothelioma as a rationale for combination targeted therapy
    Marie Brevet
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York 10065, USA
    J Thorac Oncol 6:864-74. 2011
    ....
  5. ncbi request reprint Constitutive gene expression predisposes morphogen-mediated cell fate responses of NT2/D1 and 27X-1 human embryonal carcinoma cells
    Rajendrakumar S V Chadalavada
    Cell Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Stem Cells 25:771-8. 2007
    ..This study also demonstrates that EC cells can serve as robust models to investigate early lineage choices during both embryonic and extra-embryonic human development...
  6. pmc Pattern discovery and cancer gene identification in integrated cancer genomic data
    Qianxing Mo
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 110:4245-50. 2013
    ..Application of the cancer genome atlas colorectal cancer data reveals distinct integrated tumor subtypes, suggesting different genetic pathways in colon cancer progression...
  7. pmc Integrative subtype discovery in glioblastoma using iCluster
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
    PLoS ONE 7:e35236. 2012
    ..The data analysis workflow we propose provides a unified and computationally scalable framework to harness the full potential of large-scale integrated cancer genomic data for integrative subtype discovery...
  8. pmc Identification and validation of a gene expression signature that predicts outcome in adult men with germ cell tumors
    James E Korkola
    Cell Biology Program, Sloan Kettering Institute for Cancer Research, New York, USA
    J Clin Oncol 27:5240-7. 2009
    ..Currently, patients are risk-stratified on the basis of clinical presentation and serum tumor markers. The introduction of molecular markers could improve outcome prediction...
  9. 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...
  10. 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...
  11. pmc Parent-specific copy number in paired tumor-normal studies using circular binary segmentation
    Adam B Olshen
    Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
    Bioinformatics 27:2038-46. 2011
    ..The raw data from such experiments are two-dimensional, but are unphased. Consequently, inference based on them necessitates development of new analytic methods...
  12. pmc Assessing gene-level translational control from ribosome profiling
    Adam B Olshen
    Department of Epidemiology and Biostatistics, Helen Diller Family Comprehensive Cancer Center, Department of Medicine and Department of Urology, University of California, San Francisco, CA 94158, USA and Department of Health Research and Policy, Stanford University School of Medicine, Stanford, CA 94305, USA
    Bioinformatics 29:2995-3002. 2013
    ..Despite its promise for deeply characterizing mammalian proteomes, few analytical methods exist for the comprehensive analysis of this paired RNA and ribosome data...
  13. pmc Copy number and gene expression differences between African American and Caucasian American prostate cancer
    Amy E Rose
    Department of Urology, New York University School of Medicine, New York, New York 10016, USA
    J Transl Med 8:70. 2010
    ....
  14. 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...
  15. doi request reprint Pathway activation in large B-cell non-Hodgkin lymphoma cell lines by doxorubicin reveals prognostic markers of in vivo response
    Jane Houldsworth
    Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Leuk Lymphoma 49:2170-80. 2008
    ..Thus, the response of DLBCL in vivo and in vitro is defined by several distinct molecular and genetic pathways which is, perhaps, not surprising given the heterogeneous clinical, morphologic and genetic nature of DLBCL...
  16. pmc Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis
    Ronglai Shen
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
    Bioinformatics 25:2906-12. 2009
    ..A more statistically powerful approach would incorporate all data types simultaneously and generate a single integrated cluster assignment...
  17. pmc Antitumor activity of SNX-2112, a synthetic heat shock protein-90 inhibitor, in MET-amplified tumor cells with or without resistance to selective MET Inhibition
    Thomas Bachleitner-Hofmann
    Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Clin Cancer Res 17:122-33. 2011
    ..MET, a tyrosine kinase that is constitutively active in tumor cells with MET oncogene amplification, has recently been identified as another HSP-90 client...
  18. ncbi request reprint A faster circular binary segmentation algorithm for the analysis of array CGH data
    E S Venkatraman
    Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Bioinformatics 23:657-63. 2007
    ..This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm...
  19. ncbi request reprint Down-regulation of stem cell genes, including those in a 200-kb gene cluster at 12p13.31, is associated with in vivo differentiation of human male germ cell tumors
    James E Korkola
    Cell Biology Program and Departments of Medicine, Epidemiology and Biostatistics, and Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Cancer Res 66:820-7. 2006
    ..Furthermore, the differential expression of core stem cell genes may explain the differences in pluripotency between embryonal carcinomas and seminomas...
  20. ncbi request reprint Transcriptional program of bone morphogenetic protein-2-induced epithelial and smooth muscle differentiation of pluripotent human embryonal carcinoma cells
    Rajendrakumar S V Chadalavada
    Cell Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 391, New York, NY 10021, USA
    Funct Integr Genomics 5:59-69. 2005
    ..This study suggests that BMP-2-induced differentiation of NT2/D1 cells provides a powerful assay to study early human epithelial and smooth muscle development...
  21. pmc CD32B is highly expressed on clonal plasma cells from patients with systemic light-chain amyloidosis and provides a target for monoclonal antibody-based therapy
    Ping Zhou
    Sloan Kettering Institute, Department of Medicine, New York, NY 10021, USA
    Blood 111:3403-6. 2008
    ..These data provide a rationale for the novel therapeutic targeting of CD32B using the humanized 2B6 MoAb in patients with systemic AL-amyloidosis...
  22. ncbi request reprint Molecular profiling of endometrial cancers from African-American and Caucasian women
    Sarah E Ferguson
    Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Gynecol Oncol 101:209-13. 2006
    ..The purpose of this study was to test the hypothesis that African-American women with EC have a distinct gene expression profile compared to Caucasian women with EC...
  23. pmc Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice
    Shixia Huang
    Program in Cancer Biology and Genetics, Sloan Kettering Institute, New York, NY 10021, USA
    Genome Biol 6:R84. 2005
    ..These mice might therefore be useful models for discovering changes in gene expression during cancer development...
  24. pmc Genetic analysis of the early natural history of epithelial ovarian carcinoma
    Bhavana Pothuri
    Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS ONE 5:e10358. 2010
    ....
  25. pmc The Eph-receptor A7 is a soluble tumor suppressor for follicular lymphoma
    Elisa Oricchio
    Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Cell 147:554-64. 2011
    ..Our study attests to the power of combining descriptive tumor genomics with functional screens and reveals EPHA7(TR) as tumor suppressor with immediate therapeutic potential...
  26. ncbi request reprint Insights into extramedullary tumour cell growth revealed by expression profiling of human plasmacytomas and multiple myeloma
    Cyrus V Hedvat
    Laboratory of Molecular Aspects of Hematopoiesis, Sloan Kettering Institute, New York, NY, USA
    Br J Haematol 122:728-44. 2003
    ..Defining how malignant plasma cell growth is regulated in the bone marrow versus at extramedullary sites will help to delineate the mechanisms underlying the dependence of tumour cell growth on angiogenesis and cell adhesion...
  27. ncbi request reprint Global gene expression profiling of pleural mesotheliomas: overexpression of aurora kinases and P16/CDKN2A deletion as prognostic factors and critical evaluation of microarray-based prognostic prediction
    Fernando Lopez-Rios
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Cancer Res 66:2970-9. 2006
    ..Gene expression profiling of mesotheliomas is an important discovery tool, but its power in clinical prognostication has been overestimated...
  28. pmc Genes that mediate breast cancer metastasis to lung
    Andy J Minn
    Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 436:518-24. 2005
    ..Others contribute to aggressive growth selectively in the lung. Many encode extracellular proteins and are of previously unknown relevance to cancer metastasis...
  29. pmc Array comparative genomic hybridization reveals genomic copy number changes associated with outcome in diffuse large B-cell lymphomas
    Weiyi Chen
    Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Blood 107:2477-85. 2006
    ..Overall, array-CGH identified relatively small genomic regions associated with outcome, which, along with follow-up expression studies, may reveal target genes important in DLBCL clinical behavior...
  30. pmc Differential exoprotease activities confer tumor-specific serum peptidome patterns
    Josep Villanueva
    Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    J Clin Invest 116:271-84. 2006
    ..Our findings also have important implications for future peptide biomarker discovery efforts...
  31. ncbi request reprint Gene expression-based classification of nonseminomatous male germ cell tumors
    James E Korkola
    Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Oncogene 24:5101-7. 2005
    ..Thus, the expression-based classifier accurately assigned a single predominant histology to mixed NSGCTs, and identified transcripts differentially expressed between histologic components with relevance to NSGCT differentiation...
  32. ncbi request reprint Stratification of intermediate-risk endometrial cancer patients into groups at high risk or low risk for recurrence based on tumor gene expression profiles
    Sarah E Ferguson
    Departments of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Clin Cancer Res 11:2252-7. 2005
    ..Here, we test whether global gene expression profiling can distinguish intermediate-risk tumors into high-risk and low-risk subgroups...
  33. ncbi request reprint Gene expression profiling of tamoxifen-associated uterine cancers: evidence for two molecular classes of endometrial carcinoma
    Sarah E Ferguson
    Gynecology and Breast Research Laboratory, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Gynecol Oncol 92:719-25. 2004
    ..The purpose of this study was to test the hypothesis that tamoxifen-associated endometrial carcinomas have a distinct gene expression profile compared to matched cases not associated with this exposure...
  34. ncbi request reprint Inhibition of heat shock protein 90 function down-regulates Akt kinase and sensitizes tumors to Taxol
    David B Solit
    Department of Medicine, Program in Cell Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Cancer Res 63:2139-44. 2003
    ..These results suggest that Hsp90 inhibitors can effectively suppress Akt activity in animal models of human cancer at nontoxic doses, thus sensitizing tumor cells to proapoptotic stimuli...
  35. ncbi request reprint Deriving quantitative conclusions from microarray expression data
    Adam B Olshen
    Comprehensive Cancer Center, Cancer Research Institute, and Department of Laboratory Medicine, University of California, San Francisco, CA 94143 0128, USA
    Bioinformatics 18:961-70. 2002
    ..While many methods have been developed to analyze such data, most have been visualization-based. Methods that yield quantitative conclusions have been diverse and complex...
  36. ncbi request reprint Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors
    Joris A Veltman
    Cancer Center, University of California San Francisco, California 94143 0808, USA
    Cancer Res 63:2872-80. 2003
    ....
  37. pmc Genome-wide association study provides evidence for a breast cancer risk locus at 6q22.33
    Bert Gold
    Laboratory of Genomic Diversity, Human Genetics Section, National Cancer Institute Frederick, Frederick, MD 21702, USA
    Proc Natl Acad Sci U S A 105:4340-5. 2008
    ..Candidate genes in the 6q22.33 region include ECHDC1, which encodes a protein involved in mitochondrial fatty acid oxidation, and also RNF146, which encodes a ubiquitin protein ligase, both known pathways in breast cancer pathogenesis...
  38. doi request reprint Associations among multiple markers and complex disease: models, algorithms, and applications
    Themistocles L Assimes
    Department of Medicine, Division of Cardiovascular Medicine, Stanford University, Stanford, CA 94305 5406, USA
    Adv Genet 60:437-64. 2008
    ..To summarize, the ultimate goals of approaches we provide is to predict phenotype, typically untoward or not, within a specific window of time. Our approach is neither through linkage nor from finding haplotype frequencies per se...
  39. ncbi request reprint Genomic copy number analysis of non-small cell lung cancer using array comparative genomic hybridization: implications of the phosphatidylinositol 3-kinase pathway
    Pierre P Massion
    UCSF Comprehensive Cancer Center, University of California, San Francisco, California 94143 0808, USA
    Cancer Res 62:3636-40. 2002
    ..75), suggesting that these copy number increases contribute to activation of PI3K signaling in SqCas of the lung...
  40. ncbi request reprint Array-based comparative genomic hybridization for the differential diagnosis of renal cell cancer
    Monica Wilhelm
    Cancer Center and Departments of Laboratory Medicine and Urology, University of California San Francisco, San Francisco, California 94143 0808, USA
    Cancer Res 62:957-60. 2002
    ..These results indicate that array-based CGH is capable of diagnosing the vast majority of renal cell carcinomas based on their genetic profiles...