Comparative sequencing analysis reveals high genomic concordance between matched primary and metastatic colorectal cancer lesions

Genome Biology

Volumn 15, Issue 8, 2014, Pages

  Brannon, A Rose ^a   Vakiani, Efsevia ^a   Sylvester, Brooke E ^a   Scott, Sasinya N ^a   McDermott, Gregory ^a,c   Shah, Ronak H ^a   Kania, Krishan ^a   Viale, Agnes ^a   Oschwald, Dayna M ^b   Vacic, Vladimir ^b   Emde, Anne Katrin ^b   Cercek, Andrea ^a   Yaeger, Rona ^a   Kemeny, Nancy E ^a   Saltz, Leonard B ^a   Shia, Jinru ^a   D'Angelica, Michael I ^a   Weiser, Martin R ^a   Solit, David B ^a,c   Berger, Michael F ^a,c  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b Memorial Sloan Kettering Cancer Center Human Oncology and Pathogenesis Program ^*  (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B RAF KINASE; ALCOHOL DEHYDROGENASE; BRAF PROTEIN, HUMAN; GUANOSINE TRIPHOSPHATASE; KRAS PROTEIN, HUMAN; LACTATE-MALATE TRANSHYDROGENASE; MEMBRANE PROTEIN; NRAS PROTEIN, HUMAN; ONCOPROTEIN; RAS PROTEIN;

ADULT; AGED; ARTICLE; BRAF GENE; CANCER GENETICS; CANCER STAGING; CANCER TISSUE; COLORECTAL CANCER; COMPARATIVE STUDY; CONTROLLED STUDY; FEMALE; GENETIC HETEROGENEITY; HISTOPATHOLOGY; HUMAN; HUMAN CELL; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; METASTATIC COLORECTAL CANCER; MICROSATELLITE INSTABILITY; MULTIPLEX POLYMERASE CHAIN REACTION; MUTATIONAL ANALYSIS; NEXT GENERATION SEQUENCING; NRAS GENE; ONCOGENE; ONCOGENE K RAS; PHENOTYPIC VARIATION; SEQUENCE ANALYSIS; COLORECTAL TUMOR; DNA SEQUENCE; GENETICS; HEK293 CELL LINE; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; METASTASIS; MIDDLE AGED; PATHOLOGY; PROCEDURES; VERY ELDERLY;

ADULT; AGED; AGED, 80 AND OVER; ALCOHOL OXIDOREDUCTASES; COLORECTAL NEOPLASMS; FEMALE; GENOME, HUMAN; GTP PHOSPHOHYDROLASES; HEK293 CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MEMBRANE PROTEINS; MIDDLE AGED; NEOPLASM METASTASIS; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS B-RAF; RAS PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 84920285505     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-014-0454-7     Document Type: Article

References (31)

1. Bedard PL, Hansen AR, Ratain MJ, Siu LL: Tumour heterogeneity in the clinic. Nature 2013, 501:355-364.
2. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, Raine K, Latimer C, Santos CR, Nohadani M, Eklund AC, Spencer-Dene B, Clark G, Pickering L, Stamp G, Gore M, Szallasi Z, Downward J, Futreal A, Swanton C: Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012, 366:883-892.
3. Yachida S, Jones S, Bozic I, Antal T, Leary R, Fu B, Kamiyama M, Hruban RH, Eshleman JR, Nowak MA, Velculescu VE, Kinzler KW, Vogelstein B, Iacobuzio-Donahue CA: Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 2010, 467:1114-1117.
4. Jones S, Chen WD, Parmigiani G, Diehl F, Beerenwinkel N, Antal T, Traulsen A, Nowak MA, Siegel C, Velculescu VE, Kinzler KW, Vogelstein B, Willis J, Markowitz SD: Comparative lesion sequencing provides insights into tumor evolution. Proc Natl Acad Sci U S A 2008, 105:4283-4288.
5. Vermaat JS, Nijman IJ, Koudijs MJ, Gerritse FL, Scherer SJ, Mokry M, Roessingh WM, Lansu N, de Bruijn E, van Hillegersberg R, van Diest PJ, Cuppen E, Voest EE: Primary colorectal cancers and their subsequent hepatic metastases are genetically different: implications for selection of patients for targeted treatment. Clin Cancer Res 2012, 18:688-699.
6. Vakiani E, Janakiraman M, Shen R, Sinha R, Zeng Z, Shia J, Cercek A, Kemeny N, D'Angelica M, Viale A, Heguy A, Paty P, Chan TA, Saltz LB, Weiser M, Solit DB: Comparative genomic analysis of primary versus metastatic colorectal carcinomas. J Clin Oncol 2012, 30:2956-2962.
7. Cancer Genome Atlas Network: Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012, 487:330-337.
8. Fearon ER, Vogelstein B: A genetic model for colorectal tumorigenesis. Cell 1990, 61:759-767.
9. Domingo E, Church DN, Sieber O, Ramamoorthy R, Yanagisawa Y, Johnstone E, Davidson B, Kerr DJ, Tomlinson IP, Midgley R: Evaluation of PIK3CA mutation as a predictor of benefit from nonsteroidal anti-inflammatory drug therapy in colorectal cancer. J Clin Oncol 2013, 31:4297-4305.
10. Lavi O, Greene JM, Levy D, Gottesman MM: The role of cell density and intratumoral heterogeneity in multidrug resistance. Cancer Res 2013, 73:7168-7175.
11. Peradziryi H, Kaplan NA, Podleschny M, Liu X, Wehner P, Borchers A, Tolwinski NS: PTK7/Otk interacts with Wnts and inhibits canonical Wnt signalling. EMBO J 2011, 30:3729-3740.
12. Firestein R, Bass AJ, Kim SY, Dunn IF, Silver SJ, Guney I, Freed E, Ligon AH, Vena N, Ogino S, Chheda MG, Tamayo P, Finn S, Shrestha Y, Boehm JS, Jain S, Bojarski E, Mermel C, Barretina J, Chan JA: CDK8 is a colorectal cancer oncogene that regulates beta-catenin activity. Nature 2008, 455:547-551.
13. Voss MH, Hakimi AA, Pham CG, Brannon AR, Chen YB, Cunha LF, Akin O, Liu H, Takeda S, Scott SN, Socci ND, Viale A, Schultz N, Sander C, Reuter VE, Russo P, Cheng EH, Motzer RJ, Berger MF, Hsieh JJ: Tumor Genetic Analyses of Patients with Metastatic Renal Cell Carcinoma and Extended Benefit from mTOR Inhibitor Therapy. Clin Cancer Res 2014, 20:1955-1964.
14. Italiano A, Hostein I, Soubeyran I, Fabas T, Benchimol D, Evrard S, Gugenheim J, Becouarn Y, Brunet R, Fonck M, Francois E, Saint-Pual MC, Pedeutour F: KRAS and BRAF mutational status in primary colorectal tumors and related metastatic sites: biological and clinical implications. Ann Surg Oncol 2010, 17:1429-1434.
15. Knijn N, Mekenkamp LJ, Klomp M, Vink-Borger ME, Tol J, Teerenstra S, Meijer JW, Tebar M, Riemersma S, van Krieken JH, Punt CJ, Nagtegaal ID: KRAS mutation analysis: a comparison between primary tumours and matched liver metastases in 305 colorectal cancer patients. Br J Cancer 2011, 104:1020-1026.
16. Santini D, Loupakis F, Vincenzi B, Floriani I, Stasi I, Canestrari E, Rulli E, Maltese PE, Andreoni F, Masi G, Graziano F, Baldi GG, Salvatore L, Russo A, Perrone G, Tommasino MR, Magnani M, Falcone A, Tonini G, Ruzzo A: High concordance of KRAS status between primary colorectal tumors and related metastatic sites: implications for clinical practice. Oncologist 2008, 13:1270-1275.
17. Diaz LA Jr, Williams RT, Wu J, Kinde I, Hecht JR, Berlin J, Allen B, Bozic I, Reiter JG, Nowak MA, Kinzler KW, Oliner KS, Vogelstein B: The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 2012, 486:537-540.
18. Misale S, Yaeger R, Hobor S, Scala E, Janakiraman M, Liska D, Valtorta E, Schiavo R, Buscarino M, Siravegna G, Bencardino K, Cercek A, Chen CT, Veronese S, Zanon C, Sartore-Bianchi A, Gambacorta M, Gallicchio M, Vakiani E, Boscaro V: Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature 2012, 486:532-536.
19. Boland CR, Thibodeau SN, Hamilton SR, Sidransky D, Eshleman JR, Burt RW, Meltzer SJ, Rodriguez-Bigas MA, Fodde R, Ranzani GN, Srivastava S: A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res 1998, 58:5248-5257.
20. Won HH, Scott SN, Brannon AR, Shah RH, Berger MF: Detecting somatic genetic alterations in tumor specimens by exon capture and massively parallel sequencing. J Vis Exp 2013, 80:e50710.
21. Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
22. Picard. [ http://broadinstitute.github.io/picard/ ]
23. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing Subgroup: The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
24. Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G: Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 2013, 31:213-219.
25. Oncotator. [ http://www.broadinstitute.org/oncotator ]
26. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, Butler AP, Teague JW, Campbell PJ, Stratton MR, Futreal PA: COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 2011, 39:D945-D950.
27. Pratilas CA, Hanrahan AJ, Halilovic E, Persaud Y, Soh J, Chitale D, Shigematsu H, Yamamoto H, Sawai A, Janakiraman M, Taylor BS, Pao W, Toyooka S, Ladanyi M, Gazdar A, Rosen N, Solit DB: Genetic predictors of MEK dependence in non-small cell lung cancer. Cancer Res 2008, 68:9375-9383.
28. Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK: Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 2012, 28:1811-1817.
29. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010, 20:1297-1303.
30. BioPortal for Cancer Genomics. [ http://cbioportal.org ]
31. Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, Jacobsen A, Byrne CJ, Heuer ML, Larsson E, Antipin Y, Reva B, Goldberg AP, Sander C, Schultz N: The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2012, 2:401-404.