Intra-tumor genetic heterogeneity in rectal cancer

Laboratory Investigation

Volumn 96, Issue 1, 2016, Pages 4-15

  Hardiman, Karin M ^a   Ulintz, Peter J ^b   Kuick, Rork D ^b   Hovelson, Daniel H ^b   Gates, Christopher M ^b   Bhasi, Ashwini ^b   Rodrigues Grant, Ana ^b   Liu, Jianhua ^a   Cani, Andi K ^a   Greenson, Joel K ^b   Tomlins, Scott A ^a   Fearon, Eric R ^a,b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; CLINICAL ARTICLE; CLINICAL FEATURE; COLORECTAL CANCER; CONTROLLED STUDY; COPY NUMBER VARIATION; FEMALE; GENE FREQUENCY; GENETIC HETEROGENEITY; GENETIC VARIABILITY; HUMAN; MALE; MIDDLE AGED; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; BIOLOGY; CHEMISTRY; DNA MICROARRAY; GENE DOSAGE; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; RECTUM; RECTUM TUMOR;

AGED; COMPUTATIONAL BIOLOGY; FEMALE; GENE DOSAGE; GENE FREQUENCY; GENETIC HETEROGENEITY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MIDDLE AGED; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; RECTAL NEOPLASMS; RECTUM;

EID: 84951987155     PISSN: 00236837     EISSN: 15300307     Source Type: Journal    
DOI: 10.1038/labinvest.2015.131     Document Type: Article

References (37)

1. Siegel R, Naishadham D, Jemal A. Cancer statistics, 2012. CA Cancer J Clin 2012; 62: 10-29
2. van Gijn W, Marijnen CA, Nagtegaal ID, et al. Preoperative radiotherapy combined with total mesorectal excision for resectable rectal cancer: 12-year follow-up of the multicentre, randomised controlled TME trial. Lancet Oncol 2011; 12: 575-582
3. Habr-Gama A, de Souza PM, Ribeiro Jr. U, et al. Low rectal cancer: impact of radiation and chemotherapy on surgical treatment. Dis Colon Rectum 1998; 41: 1087-1096
4. Garcia-Aguilar J, Hernandez de Anda E, Sirivongs P, et al. A pathologic complete response to preoperative chemoradiation is associated with lower local recurrence and improved survival in rectal cancer patients treated by mesorectal excision. Dis Colon Rectum 2003; 46: 298-304
5. Garcia-Aguilar J, Chen Z, Smith DD, et al. Identification of a biomarker profile associated with resistance to neoadjuvant chemoradiation therapy in rectal cancer. Ann Surg 2011; 254: 486-492
6. Zhang J, Fujimoto J, Wedge DC, et al. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science 2014; 346: 256-259
7. de Bruin EC, McGranahan N, Mitter R, et al. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 2014; 346: 251-256
8. Gerlinger M, Rowan AJ, Horswell S, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012; 366: 883-892
9. Landau DA, Carter SL, Stojanov P, et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell 2013; 152: 714-726
10. Nik-Zainal S, Alexandrov LB, Wedge DC, et al. Mutational processes molding the genomes of 21 breast cancers. Cell 2012; 149: 979-993
11. Nik-Zainal S, Van Loo P, Wedge DC, et al. The life history of 21 breast cancers. Cell 2012; 149: 994-1007
12. Ding L, Ley TJ, Larson DE, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 2012; 481: 506-510
13. Torres L, Ribeiro FR, Pandis N, et al. Intratumor genomic heterogeneity in breast cancer with clonal divergence between primary carcinomas and lymph node metastases. Breast Cancer Res Treat 2007; 102: 143-155
14. Miller CA, White BS, Dees ND, et al. SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput Biol 2014; 10: e1003665
15. Sottoriva A, Kang H, Ma Z, et al. A Big Bang model of human colorectal tumor growth. Nat Genet 2015; 47: 209-216
16. Baldus SE, Schaefer KL, Engers R, et al. Prevalence and heterogeneity of KRAS, BRAF, and PIK3CA mutations in primary colorectal adenocarcinomas and their corresponding metastases. Clin Cancer Res 2010; 16: 790-799
17. Losi L, Baisse B, Bouzourene H, et al. Evolution of intratumoral genetic heterogeneity during colorectal cancer progression. Carcinogenesis 2005; 26: 916-922
18. Billich A Thymosin alpha SciClone Pharmaceuticals. Curr Opin Investig Drugs 2002; 3: 698-707
19. Frank DN. BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. BMC Bioinformatics 2009; 10: 362
20. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25: 1754-1760
21. Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25: 2078-2079
22. Li H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 2011; 27: 2987-2993
23. Cingolani P, Platts A, Wang le L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012; 6: 80-92
24. McDaniel AS, Zhai Y, Cho KR, et al. HRAS mutations are frequent in inverted urothelial neoplasms. Hum Pathol 2014; 45: 1957-1965
25. Chang X, Wang K. wANNOVAR: annotating genetic variants for personal genomes via the web. J Med Genet 2012; 49: 433-436
26. Cani AK, Hovelson DH, McDaniel AS, et al. Next-Gen Sequencing Exposes Frequent MED12 Mutations and Actionable Therapeutic Targets in Phyllodes Tumors. Molecular Cancer Res 2015; 13: 613-619
27. Hovelson DH, McDaniel AS, Cani AK, et al. Development and validation of a scalable next-generation sequencing system for assessing relevant somatic variants in solid tumors. Neoplasia 2015; 17: 385-399
28. Warrick JI, Hovelson DH, Amin A, et al. Tumor evolution and progression in multifocal and paired non-invasive/invasive urothelial carcinoma. Virchows Arch 2015; 466: 297-311
29. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002; 30: 207-210
30. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012; 487: 330-337
31. Xie T, Dario G, Lamb JR, et al. A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations. PLoS One 2012; 7: e42001
32. Diaz Jr. LA, Williams RT, Wu J, et al. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 2012; 486: 537-540
33. Crockford A, Jamal-Hanjani M, Hicks J, et al. Implications of intratumour heterogeneity for treatment stratification. J Pathol 2014; 232: 264-273
34. Commo F, Ferte C, Soria JC, et al. Impact of centralization on aCGHbased genomic profiles for precision medicine in oncology. Ann Oncol 2015; 26: 582-588
35. Cosentino F, Arena L, Banchini L, et al. Epidemiologic surveillance in occupational bladder cancer: a Tuscan experience. G Ital Med Lav Ergon. 2007 Jul-Sep; 29: 313-315
36. Lawrence MS, Stojanov P, Mermel CH, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014; 505: 495-501
37. Baker AM, Cereser B, Melton S, et al. Quantification of crypt and stem cell evolution in the normal and neoplastic human colon. Cell Rep 2014; 8: 940-947