Gene expression-based diagnostics for molecular cancer classification of difficult to diagnose tumors

Bibliography

• Bild AH, Potti A, Nevins JR. Linking oncogenic pathways with therapeutic opportunities. Nat Rev Cancer 2006;6(9):735-41
   PubMed Web of Science ®Google Scholar
• Swanton C, Caldas C. From genomic landscapes to personalized cancer management-is there a roadmap? Ann NY Acad Sci 2010;1210:34-44
   PubMed Web of Science ®Google Scholar
• Yap TA, Gerlinger M, Futreal PA, Intratumor heterogeneity: seeing the wood for the trees. Sci Transl Med 2012;4(127):127ps10
   PubMed Web of Science ®Google Scholar
• Englert CR, Petricoin EF, Krizman DB, Emmert-Buck MR. Molecular profiling of human cancer: new opportunities. Curr Opin Mol Ther 1999;1(6):712-19
   PubMed Web of Science ®Google Scholar
• Greco FA, Erlander MG. Molecular classification of cancers of unknown primary site. Mol Diagn Ther 2009;13(6):367-73
   PubMed Web of Science ®Google Scholar
• Bender RA, Erlander MG. Molecular classification of unknown primary cancer. Semin Oncol 2009;36(1):38-43
   PubMed Web of Science ®Google Scholar
• Monzon FA, Koen TJ. Diagnosis of metastatic neoplasms: molecular approaches for identification of tissue of origin. Arch Pathol Lab Med 2010;134(2):216-24
   PubMed Web of Science ®Google Scholar
• Sorlie T, Perou CM, Tibshirani R, Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci USA 2001;98(19):10869-74
   PubMed Web of Science ®Google Scholar
• Schilsky RL. Personalized medicine in oncology: the future is now. Nat Rev Drug Discov 2010;9(5):363-6
   PubMed Web of Science ®Google Scholar
• Dennis JL, Oien KA. Hunting the primary: novel strategies for defining the origin of tumours. J Pathol 2005;205(2):236-47
   PubMed Web of Science ®Google Scholar
• Oien KA. Pathologic evaluation of unknown primary cancer. Semin Oncol 2009;36(1):8-37
   PubMed Web of Science ®Google Scholar
• Marchevsky AM, Gupta R, Balzer B. Diagnosis of metastatic neoplasms: a clinicopathologic and morphologic approach. Arch Pathol Lab Med 2010;134(2):194-206
   PubMed Web of Science ®Google Scholar
• Greco FA, Hainsworth JD. In: DeVita VTJ, Hellman S, Rosenberg SA, editors. Cancer: principles and practice of oncology. 9th edition. Lippincott Willinams & Wilkins; Philadelphia, PA: 2011. p. 2033-51
   Google Scholar
• Varadhachary GR, Abbruzzese JL, Lenzi R. Diagnostic strategies for unknown primary cancer. Cancer 2004;100(9):1776-85
   PubMed Web of Science ®Google Scholar
• Massard C, Loriot Y, Fizazi K. Carcinomas of an unknown primary origin-diagnosis and treatment. Nat Rev Clin Oncol 2011;8(12):701-10
   PubMed Web of Science ®Google Scholar
• Pavlidis N, Fizazi K. Cancer of unknown primary (CUP). Crit Rev Oncol Hematol 2005;54(3):243-50
   PubMed Web of Science ®Google Scholar
• Anderson GG, Weiss LM. Determining tissue of origin for metastatic cancers: meta-analysis and literature review of immunohistochemistry performance. Appl Immunohistochem Mol Morphol 2010;18(1):3-8
   PubMedGoogle Scholar
• Comperat E, Zhang F, Perrotin C, Variable sensitivity and specificity of TTF-1 antibodies in lung metastatic adenocarcinoma of colorectal origin. Mod Pathol 2005;18(10):1371-6
   PubMed Web of Science ®Google Scholar
• Taylor CR, Levenson RM. Quantification of immunohistochemistry–issues concerning methods, utility and semiquantitative assessment II. Histopathology 2006;49(4):411-24
   PubMed Web of Science ®Google Scholar
• Park SY, Kim BH, Kim JH, Panels of immunohistochemical markers help determine primary sites of metastatic adenocarcinoma. Arch Pathol Lab Med 2007;131(10):1561-7
   PubMed Web of Science ®Google Scholar
• Pavlidis N, Pentheroudakis G. Cancer of unknown primary site. Lancet 2012;379(9824):1428-35
   PubMed Web of Science ®Google Scholar
• Abbruzzese JL, Abbruzzese MC, Lenzi R, Analysis of a diagnostic strategy for patients with suspected tumors of unknown origin. J Clin Oncol 1995;13(8):2094-103
   PubMed Web of Science ®Google Scholar
• Varadhachary GR, Raber MN, Matamoros A, Abbruzzese JL. Carcinoma of unknown primary with a colon-cancer profile-changing paradigm and emerging definitions. Lancet Oncol 2008;9(6):596-9
   PubMed Web of Science ®Google Scholar
• Golub TR, Slonim DK, Tamayo P, Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999;286(5439):531-7
   PubMed Web of Science ®Google Scholar
• Ramaswamy S, Tamayo P, Rifkin R, Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 2001;98(26):15149-54
   PubMed Web of Science ®Google Scholar
• Su AI, Welsh JB, Sapinoso LM, Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res 2001;61(20):7388-93
   PubMed Web of Science ®Google Scholar
• Perou CM, Sorlie T, Eisen MB, Molecular portraits of human breast tumours. Nature 2000;406(6797):747-52
   PubMed Web of Science ®Google Scholar
• Weigelt B, Glas AM, Wessels LF, Gene expression profiles of primary breast tumors maintained in distant metastases. Proc Natl Acad Sci USA 2003;100(26):15901-5
   PubMed Web of Science ®Google Scholar
• Ma XJ, Patel R, Wang X, Molecular classification of human cancers using a 92-gene real-time quantitative polymerase chain reaction assay. Arch Pathol Lab Med 2006;130(4):465-73
   PubMed Web of Science ®Google Scholar
• Xie HL, Li ZY, Gan RL, Differential gene and protein expression in primary gastric carcinomas and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis. J Dig Dis 2010;11(3):167-75
   PubMed Web of Science ®Google Scholar
• Koh SS, Wei JP, Li X, Differential gene expression profiling of primary cutaneous melanoma and sentinel lymph node metastases. Mod Pathol 2012;25(6):828-37
   PubMed Web of Science ®Google Scholar
• Bloom G, Yang IV, Boulware D, Multi-platform, multi-site, microarray-based human tumor classification. Am J Pathol 2004;164(1):9-16
   PubMed Web of Science ®Google Scholar
• Tothill RW, Kowalczyk A, Rischin D, An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. Cancer Res 2005;65(10):4031-40
   PubMed Web of Science ®Google Scholar
• Talantov D, Baden J, Jatkoe T, A quantitative reverse transcriptase-polymerase chain reaction assay to identify metastatic carcinoma tissue of origin. J Mol Diagn 2006;8(3):320-9
   PubMed Web of Science ®Google Scholar
• Bridgewater J, van Laar R, Floore A, Van TVL. Gene expression profiling may improve diagnosis in patients with carcinoma of unknown primary. Br J Cancer 2008;98(8):1425-30
   PubMed Web of Science ®Google Scholar
• Rosenfeld N, Aharonov R, Meiri E, MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol 2008;26(4):462-9
   PubMed Web of Science ®Google Scholar
• Monzon FA, Lyons-Weiler M, Buturovic LJ, Multicenter validation of a 1,550-gene expression profile for identification of tumor tissue of origin. J Clin Oncol 2009;27(15):2503-8
   PubMed Web of Science ®Google Scholar
• Rosenwald S, Gilad S, Benjamin S, Validation of a microRNA-based qRT-PCR test for accurate identification of tumor tissue origin. Mod Pathol 2010;23(6):814-23
   PubMed Web of Science ®Google Scholar
• Erlander MG, Ma XJ, Kesty NC, Performance and clinical evaluation of the 92-gene real-time PCR assay for tumor classification. J Mol Diagn 2011;13(5):493-503
   PubMed Web of Science ®Google Scholar
• Pillai R, Deeter R, Rigl CT, Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimens. J Mol Diagn 2011;13(1):48-56
   PubMed Web of Science ®Google Scholar
• Emmert-Buck MR, Bonner RF, Smith PD, Laser capture microdissection. Science 1996;274(5289):998-1001
   PubMed Web of Science ®Google Scholar
• Foye A, Febbo PG. Cancer gene profiling in prostate cancer. Methods Mol Biol 2010;576:293-326
   PubMedGoogle Scholar
• Joseph A, Gnanapragasam VJ. Laser-capture microdissection and transcriptional profiling in archival FFPE tissue in prostate cancer. Methods Mol Biol 2011;755:291-300
   PubMedGoogle Scholar
• Funel N, Giovannetti E, Pollina LE, Critical role of laser microdissection for genetic, epigenetic and proteomic analyses in pancreatic cancer. Expert Rev Mol Diagn 2011;11(7):695-701
   PubMed Web of Science ®Google Scholar
• Stany MP, Vathipadiekal V, Ozbun L, Identification of novel therapeutic targets in microdissected clear cell ovarian cancers. PLoS One 2011;6(7):e21121
   PubMedGoogle Scholar
• Harrell JC, Dye WW, Harvell DM, Contaminating cells alter gene signatures in whole organ versus laser capture microdissected tumors: a comparison of experimental breast cancers and their lymph node metastases. Clin Exp Metastasis 2008;25(1):81-8
   PubMed Web of Science ®Google Scholar
• Farragher SM, Tanney A, Kennedy RD, Paul Harkin D. RNA expression analysis from formalin fixed paraffin embedded tissues. Histochem Cell Biol 2008;130(3):435-45
   PubMed Web of Science ®Google Scholar
• Ludyga N, Grunwald B, Azimzadeh O, Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses. Virchows Arch 2012;460(2):131-40
   PubMed Web of Science ®Google Scholar
• Bonin S, Hlubek F, Benhattar J, Multicentre validation study of nucleic acids extraction from FFPE tissues. Virchows Arch 2010;457(3):309-17
   PubMed Web of Science ®Google Scholar
• Fodor SP, Rava RP, Huang XC, Multiplexed biochemical assays with biological chips. Nature 1993;364(6437):555-6
   PubMed Web of Science ®Google Scholar
• Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995;270(5235):467-70
   PubMed Web of Science ®Google Scholar
• Sharov V, Kwong KY, Frank B, The limits of log-ratios. BMC Biotechnol 2004;4:3
   PubMedGoogle Scholar
• Abdueva D, Wing M, Schaub B, Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays. J Mol Diagn 2010;12(4):409-17
   PubMed Web of Science ®Google Scholar
• Cronin M, Sangli C, Liu ML, Analytical validation of the Oncotype DX genomic diagnostic test for recurrence prognosis and therapeutic response prediction in node-negative, estrogen receptor-positive breast cancer. Clin Chem 2007;53(6):1084-91
   PubMed Web of Science ®Google Scholar
• Lyon E, Wittwer CT. LightCycler technology in molecular diagnostics. J Mol Diagn 2009;11(2):93-101
   PubMed Web of Science ®Google Scholar
• Higuchi R, Fockler C, Dollinger G, Watson R. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology (NY) 1993;11(9):1026-30
   PubMedGoogle Scholar
• Cronin M, Pho M, Dutta D, Measurement of gene expression in archival paraffin-embedded tissues: development and performance of a 92-gene reverse transcriptase-polymerase chain reaction assay. Am J Pathol 2004;164(1):35-42
   PubMed Web of Science ®Google Scholar
• Li J, Smyth P, Cahill S, Improved RNA quality and TaqMan Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials. BMC Biotechnol 2008;8:10
   PubMed Web of Science ®Google Scholar
• Antonov J, Popovici V, Delorenzi M, Molecular risk assessment of BIG 1-98 participants by expression profiling using RNA from archival tissue. BMC Cancer 2010;10:37
   PubMedGoogle Scholar
• Varadhachary GR, Talantov D, Raber MN, Molecular profiling of carcinoma of unknown primary and correlation with clinical evaluation. J Clin Oncol 2008;26(27):4442-8
   PubMed Web of Science ®Google Scholar
• American Cancer Society. Cancer Facts & Figures 2010. 2010. Available from: http://www.cancer.org/acs/groups/content/@epidemiologysurveilance/documents/document/acspc-026238.pdf [Cited 29 September 2010]
   Google Scholar
• Simon R. Roadmap for developing and validating therapeutically relevant genomic classifiers. J Clin Oncol 2005;23(29):7332-41
   PubMed Web of Science ®Google Scholar
• Leeflang MM, Deeks JJ, Gatsonis C, Bossuyt PM. Systematic reviews of diagnostic test accuracy. Ann Intern Med 2008;149(12):889-97
   PubMed Web of Science ®Google Scholar
• Jennings L, Van Deerlin VM, Gulley ML. Recommended principles and practices for validating clinical molecular pathology tests. Arch Pathol Lab Med 2009;133(5):743-55
   PubMed Web of Science ®Google Scholar
• Moraleda J, Grove N, Tran Q, Gene expression data analytics with interlaboratory validation for identifying anatomical sites of origin of metastatic carcinomas. J Clin Oncol 2004;22(14S):9625
   Google Scholar
• Monzon FA, Dumur CI. Diagnosis of uncertain primary tumors with the pathwork tissue-of-origin test. Expert Rev Mol Diagn 2010;10(1):17-25
   PubMed Web of Science ®Google Scholar
• Dumur CI, Lyons-Weiler M, Sciulli C, Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancers. J Mol Diagn 2008;10(1):67-77
   PubMed Web of Science ®Google Scholar
• Beck AH, Rodriguez-Paris J, Zehnder J, Schrijver I. Evaluation of a gene expression microarray-based assay to determine tissue type of origin on a diverse set of 49 malignancies. Am J Surg Pathol 2011;35(7):1030-7
   PubMed Web of Science ®Google Scholar
• Dumur CI, Fuller CE, Blevins TL, Clinical verification of the performance of the pathwork tissue of origin test: utility and limitations. Am J Clin Pathol 2011;136(6):924-33
   PubMed Web of Science ®Google Scholar
• Hornberger J, Varadhachary G, Gutierrez H, Changes in management and survival outcomes for patients receiving gene-expression-based tissue-of-origin test results for difficult-to-diagnose primary cancers. J Clin Oncol 2012;30(Suppl 4):abstract 397
   Google Scholar
• Lu J, Getz G, Miska EA, MicroRNA expression profiles classify human cancers. Nature 2005;435(7043):834-8
   PubMed Web of Science ®Google Scholar
• de Planell-Saguer M, Rodicio MC. Analytical aspects of microRNA in diagnostics: a review. Anal Chim Acta 2011;699(2):134-52
   PubMed Web of Science ®Google Scholar
• Varadhachary GR, Spector Y, Abbruzzese JL, Prospective gene signature study using microRNA to identify the tissue of origin in patients with carcinoma of unknown primary. Clin Cancer Res 2011;17(12):4063-70
   PubMed Web of Science ®Google Scholar
• Aharonov RT, Rosenwald S, Edmonston TB, A second-generation microRNA-based assay for diagnosing tumor tissue origin. J Clin Oncol 2011;29(Suppl):abstract 10575
   Google Scholar
• Kerr SE, Schnabel CA, Sullivan PS, Zhang Y, Multisite validation study to determine performance characteristics of a 92-gene molecular cancer classifier. Clin Cancer Res 2012. [Epub ahead of print]
   PubMed Web of Science ®Google Scholar
• Hainsworth JD, Spigel DR, Rubin MS, Treatment of carcinoma of unknown primary site (CUP) directed by molecular profiling diagnosis: a prospective, phase II trial. J Clin Oncol 2010;28(Suppl 15s):abstract 10540
   Google Scholar
• Hainsworth JD, Schnabel CA, Erlander MG, A retrospective study of treatment outcomes in patients with carcinoma of unknown primary site and a colorectal cancer molecular profile. Clin Colorectal Cancer 2012;11(2):112-8
   PubMed Web of Science ®Google Scholar
• Scagliotti GV, Parikh P, von Pawel J, Phase III study comparing cisplatin plus gemcitabine with cisplatin plus pemetrexed in chemotherapy-naive patients with advanced-stage non-small-cell lung cancer. J Clin Oncol 2008;26(21):3543-51
   PubMed Web of Science ®Google Scholar
• Sandler A, Yi J, Dahlberg S, Treatment outcomes by tumor histology in Eastern Cooperative Group Study E4599 of bevacizumab with paclitaxel/carboplatin for advanced non-small cell lung cancer. J Thorac Oncol 2010;5(9):1416-23
   PubMed Web of Science ®Google Scholar
• Chapman PB, Hauschild A, Robert C, Improved survival with vemurafenib in melanoma with BRAF V600E mutation. N Engl J Med 2011;364(26):2507-16
   PubMed Web of Science ®Google Scholar
• Kopetz S, Desai J, Chan E, PLX4032 in metastatic colorectal cancer patients with mutant BRAF tumors. J Clin Oncol 2010;28(15s Suppl):abstract 3534
   Google Scholar
• Cappuzzo F, Cho YG, Sacconi A, p95HER2 truncated form in resected non-small cell lung cancer. J Thorac Oncol 2012;7(3):520-7
   PubMed Web of Science ®Google Scholar
• La Thangue NB, Kerr DJ. Predictive biomarkers: a paradigm shift towards personalized cancer medicine. Nat Rev Clin Oncol 2011;8(10):587-96
   PubMed Web of Science ®Google Scholar
• Kerr SE, Schnabel CA, Sullivan PS, Multisite analytical validation of a 92-gene molecular classifier for cancers of uncertain primary. Mod Pathol 2012;25(Suppl 2):abstract 1888
   Google Scholar
• Davies H, Bignell GR, Cox C, Mutations of the BRAF gene in human cancer. Nature 2002;417(6892):949-54
   PubMed Web of Science ®Google Scholar
• Curtin JA, Fridlyand J, Kageshita T, Distinct sets of genetic alterations in melanoma. N Engl J Med 2005;353(20):2135-47
   PubMed Web of Science ®Google Scholar
• Ogino S, Shima K, Meyerhardt JA, Predictive and prognostic roles of BRAF mutation in stage III colon cancer: results from intergroup trial CALGB 89803. Clin Cancer Res 2012;18(3):890-900
   PubMed Web of Science ®Google Scholar
• Di Fiore F, Blanchard F, Charbonnier F, Clinical relevance of KRAS mutation detection in metastatic colorectal cancer treated by cetuximab plus chemotherapy. Br J Cancer 2007;96(8):1166-9
   PubMed Web of Science ®Google Scholar
• Lievre A, Bachet JB, Le Corre D, KRAS mutation status is predictive of response to cetuximab therapy in colorectal cancer. Cancer Res 2006;66(8):3992-5
   PubMed Web of Science ®Google Scholar
• Amado RG, Wolf M, Peeters M, Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer. J Clin Oncol 2008;26(10):1626-34
   PubMed Web of Science ®Google Scholar
• Sequist LV, Heist RS, Shaw AT, Implementing multiplexed genotyping of non-small-cell lung cancers into routine clinical practice. Ann Oncol 2011;22(12):2616-24
   PubMed Web of Science ®Google Scholar
• Roberts PJ, Stinchcombe TE, Der CJ, Socinski MA. Personalized medicine in non-small-cell lung cancer: is KRAS a useful marker in selecting patients for epidermal growth factor receptor-targeted therapy? J Clin Oncol 2010;28(31):4769-77
   PubMed Web of Science ®Google Scholar
• Slamon DJ, Godolphin W, Jones LA, Studies of the HER-2/neu proto-oncogene in human breast and ovarian cancer. Science 1989;244(4905):707-12
   PubMed Web of Science ®Google Scholar
• Kunz PL, Mojtahed A, Fisher GA, HER2 expression in gastric and gastroesophageal junction adenocarcinoma in a US population: clinicopathologic analysis with proposed approach to HER2 assessment. Appl Immunohistochem Mol Morphol 2012;20(1):13-24
   PubMedGoogle Scholar
• Bang YJ, Van Cutsem E, Feyereislova A, Trastuzumab in combination with chemotherapy versus chemotherapy alone for treatment of HER2-positive advanced gastric or gastro-oesophageal junction cancer (ToGA): a phase 3, open-label, randomised controlled trial. Lancet 2010;376(9742):687-97
   PubMed Web of Science ®Google Scholar
• Krug LM, Miller VA, Patel J, Randomized phase II study of weekly docetaxel plus trastuzumab versus weekly paclitaxel plus trastuzumab in patients with previously untreated advanced nonsmall cell lung carcinoma. Cancer 2005;104(10):2149-55
   PubMed Web of Science ®Google Scholar
• Chen X, Yuan Y, Gu Z, Shen K. Accuracy of estrogen receptor, progesterone receptor, and HER2 status between core needle and open excision biopsy in breast cancer: a meta-analysis. Breast Cancer Res Treat 2012. [Epub ahead of print]
   Google Scholar
• Fisher B, Costantino J, Redmond C, A randomized clinical trial evaluating tamoxifen in the treatment of patients with node-negative breast cancer who have estrogen-receptor-positive tumors. N Engl J Med 1989;320(8):479-84
   PubMed Web of Science ®Google Scholar
• Walker MJ, Beattie CW, Patel MK, Estrogen receptor in malignant melanoma. J Clin Oncol 1987;5(8):1256-61
   PubMed Web of Science ®Google Scholar
• Falkson CI, Ibrahim J, Kirkwood JM, Phase III trial of dacarbazine versus dacarbazine with interferon alpha-2b versus dacarbazine with tamoxifen versus dacarbazine with interferon alpha-2b and tamoxifen in patients with metastatic malignant melanoma: an Eastern Cooperative Oncology Group study. J Clin Oncol 1998;16(5):1743-51
   PubMed Web of Science ®Google Scholar
• Rusthoven JJ, Quirt IC, Iscoe NA, Randomized, double-blind, placebo-controlled trial comparing the response rates of carmustine, dacarbazine, and cisplatin with and without tamoxifen in patients with metastatic melanoma. National Cancer Institute of Canada Clinical Trials Group. J Clin Oncol 1996;14(7):2083-90
   PubMed Web of Science ®Google Scholar