Categorization of cancer through genomic complexity could guide research and management strategies

Journal of Pathology

Volumn 236, Issue 4, 2015, Pages 397-402

  Horlings, Hugo M ^a   Flanagan, Adrienne M ^b   Huntsman, David G ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

bone tumours; cancer; classification; high throughput nucleotide sequencing; ovarian cancer

Indexed keywords

BRG1 PROTEIN; COLLAGEN TYPE 2; DNA; FIBROBLAST GROWTH FACTOR RECEPTOR; FIBROBLAST GROWTH FACTOR RECEPTOR 1; ISOCITRATE DEHYDROGENASE 1; ISOCITRATE DEHYDROGENASE 2; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; TUMOR MARKER;

ARTICLE; BONE CANCER; BREAST CANCER; CANCER CLASSIFICATION; CANCER GENETICS; CANCER IMMUNOTHERAPY; CANCER RESEARCH; CANCER THERAPY; CHONDROSARCOMA; CLEAR CELL CARCINOMA; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DIAGNOSTIC VALUE; DNA DAMAGE; DNA REPAIR; GENETIC HETEROGENEITY; GENOMIC COMPLEXITY; GENOMICS; HISTOPATHOLOGY; HUMAN; MOLECULARLY TARGETED THERAPY; OSTEOCLASTOMA; OSTEOSARCOMA; OVARY CANCER; OVARY CARCINOMA; PRIORITY JOURNAL; ANIMAL; BIOPSY; BONE NEOPLASMS; FEMALE; GENETIC PREDISPOSITION; GENETIC SCREENING; GENETICS; MALE; OVARIAN NEOPLASMS; PATHOLOGY; PATIENT SELECTION; PERSONALIZED MEDICINE; PHENOTYPE; PREDICTIVE VALUE; PROCEDURES; PROGNOSIS;

ANIMALS; BIOPSY; BONE NEOPLASMS; FEMALE; GENETIC PREDISPOSITION TO DISEASE; GENETIC TESTING; GENOMICS; HUMANS; INDIVIDUALIZED MEDICINE; MALE; MOLECULAR TARGETED THERAPY; OVARIAN NEOPLASMS; PATIENT SELECTION; PHENOTYPE; PREDICTIVE VALUE OF TESTS; PROGNOSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 84937519148     PISSN: 00223417     EISSN: 10969896     Source Type: Journal    
DOI: 10.1002/path.4542     Document Type: Article

References (43)

1. Hanahan D, Weinberg RA,. The hallmarks of cancer. Cell 2000; 100: 57-70.
2. Roychowdhury S, Iyer MK, Robinson DR, et al., Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci Transl Med 2011; 3: 111ra121.
3. Perou CM, Sørlie T, Eisen MB, et al., Molecular portraits of human breast tumours. Nature 2000; 406: 747-752.
4. Alizadeh AA, Eisen MB, Davis RE, et al., Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000; 403: 503-511.
5. The Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, et al., The Cancer Genome Atlas Pan-Cancer analysis project. Nature Genet 2013; 45: 1113-1120.
6. Akbani R, Ng PKS, Werner HMJ, et al., A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nature Commun 2014; 5: 3887.
7. Lawrence MS, Stojanov P, Garraway LA, et al., Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014; 505: 495-501.
8. Kandoth C, McLellan MD, Ye K, et al., Mutational landscape and significance across 12 major cancer types. Nature 2013; 502: 333-339.
9. Ciriello G, Schultz N, Sander C,. Emerging landscape of oncogenic signatures across human cancers. Nature Genet 2013; 45: 1127-1133.
10. Horlings HM, Shah SP, Huntsman DG,. Using somatic mutations to guide treatment decisions. JAMA Oncol 2015; DOI: 10.1001/jamaoncol.2015.35.
11. Prahallad A, Sun C, Huang S, et al., Unresponsiveness of colon cancer to BRAF(V600E) inhibition through feedback activation of EGFR. Nature 2012; 483: 100-103.
12. Hicks J, Krasnitz A, Lakshmi B, et al., Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res 2006; 16: 1465-1479.
13. Russnes HG, Vollan HKM, Lingjaerde OC, et al., Genomic architecture characterizes tumor progression paths and fate in breast cancer patients. Sci Transl Med 2010; 2: 38ra47.
14. Vollan HKM, Rueda OM, Chin S-F, et al., A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Mol Oncol 2015; 9: 115-127.
15. Curtis C, Shah SP, Chin S-F, et al., The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature 2013; 486: 346-352.
16. Young RH, Oliva E, Scully RE,. Small cell carcinoma of the ovary, hypercalcemic type. A clinicopathological analysis of 150 cases. Am J Surg Pathol 1994; 18: 1102-1116.
17. Ramos P, Karnezis AN, Hendricks WPD, et al., Loss of the tumor suppressor SMARCA4 in small cell carcinoma of the ovary, hypercalcemic type (SCCOHT). Rare Diseases 2014; 2: e967148.
18. Ramos P, Karnezis AN, Craig DW, et al., Small cell carcinoma of the ovary, hypercalcemic type, displays frequent inactivating germline and somatic mutations in SMARCA4. Nature Genet 2014; 46: 427-429.
19. Jelinic P, Mueller JJ, Olvera N, et al., Recurrent SMARCA4 mutations in small cell carcinoma of the ovary. Nature Genet 2014; 46: 424-426.
20. Witkowski L, Carrot-Zhang J, Albrecht S, et al., Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type. Nature Genet 2014; 46: 438-443.
21. Kupryjańczyk J, Dansonka-Mieszkowska A, Moes-Sosnowska J, et al., Ovarian small cell carcinoma of hypercalcemic type-evidence of germline origin and smarca4 gene inactivation. A pilot study. Pol J Pathol 2013; 4: 238-246.
22. Behjati S, Tarpey PS, Presneau N, et al., Distinct H3F3A and H3F3B driver mutations define chondroblastoma and giant cell tumor of bone. Nature Genet 2013; 45: 1479-1482.
23. Presneau N, Baumhoer D, Behjati S, et al., Diagnostic value of H3F3A mutations in giant cell tumour of bone compared to osteoclast-rich mimics. J Pathol Clin Res 2015; 1: 113-123.
24. Anglesio MS, Carey MS, Köbel M,. Clear cell carcinoma of the ovary: a report from the first Ovarian Clear Cell Symposium, June 24th, 2010. Gynecol Oncol 2011; 121: 407-415.
25. Sheppard KE, Cullinane C, Hannan KM, et al., Synergistic inhibition of ovarian cancer cell growth by combining selective PI3K/mTOR and RAS/ERK pathway inhibitors. Eur J Cancer 2013; 49: 3936-3944.
26. Amary MF, Bacsi K, Maggiani F, et al., IDH1 and IDH2 mutations are frequent events in central chondrosarcoma and central and periosteal chondromas but not in other mesenchymal tumours. J Pathol 2011; 224: 334-343.
27. Tarpey PS, Behjati S, Cooke SL, et al., Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma. Nature Genet 2013; 45: 923-926.
28. Lee Y, Miron A, Drapkin R, et al., A candidate precursor to serous carcinoma that originates in the distal fallopian tube. J Pathol 2006; 211: 26-35.
29. Bell D, Berchuck A, Birrer M, et al., Integrated genomic analyses of ovarian carcinoma. Nature 2011; 474: 609-615.
30. Bashashati A, Ha G, Tone A, et al., Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling. J Pathol 2013; 231: 21-34.
31. Hartwell LH,. Integrating genetic approaches into the discovery of anticancer drugs. Science 1997; 278: 1064-1068.
32. Ledermann J, Harter P, Gourley C, et al., Olaparib maintenance therapy in platinum-sensitive relapsed ovarian cancer. N Engl J Med 2012; 366: 1382-1392.
33. Tse BW, Collins A, Oehler MK,. Antibody-based immunotherapy for ovarian cancer: where are we at? Ann Oncol 2014; 25: 322-331.
34. Bauzon M, Hermiston T,. Armed therapeutic viruses-a disruptive therapy on the horizon of cancer immunotherapy. Front Immunol 2014; 5: 74.
35. Kirn DH, Thorne SH,. Targeted and armed oncolytic poxviruses: a novel multi-mechanistic therapeutic class for cancer. Nature Rev Cancer 2009; 9: 64-71.
36. Sadikovic B, Yoshimoto M, Chilton-MacNeill S, et al., Identification of interactive networks of gene expression associated with osteosarcoma oncogenesis by integrated molecular profiling. Hum Mol Genet 2009; 18: 1962-1975.
37. Selvarajah S, Yoshimoto M, Ludkovski O, et al., Genomic signatures of chromosomal instability and osteosarcoma progression detected by high resolution array CGH and interphase FISH. Cytogenet Genome Res 2008; 122: 5-15.
38. Chen X, Bahrami A, Pappo A, et al., Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. Cell Rep 2014; 7: 104-112.
39. Nik-Zainal S, Alexandrov LB, Wedge DC, et al., Mutational processes molding the genomes of 21 breast cancers. Cell 2012; 149: 979-993.
40. Roberts SA, Sterling J, Thompson C, et al., Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Mol Cell 2012; 46: 424-435.
41. Stephens PJ, Greenman CD, Fu B, et al., Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 2011; 144: 27-40.
42. Perry JA, Kiezun A, Tonzi P, et al., Complementary genomic approaches highlight the PI3K/mTOR pathway as a common vulnerability in osteosarcoma. Proc Natl Acad Sci U S A 2014; 111: E5564-E5573.
43. Amary MF, Ye H, Berisha F, et al., Fibroblastic growth factor receptor 1 amplification in osteosarcoma is associated with poor response to neo-adjuvant chemotherapy. Cancer Med 2014; 3: 980-987.