The clonal relationships between pre-cancer and cancer revealed by ultra-deep sequencing

Journal of Pathology

Volumn 237, Issue 3, 2015, Pages 296-306

  Wood, Henry M ^a   Conway, Caroline ^a,d   Daly, Catherine ^a   Chalkley, Rebecca ^a   Berri, Stefano ^a,e   Senguven, Burcu ^a,f   Stead, Lucy ^a   Ross, Lisa ^a   Egan, Philip ^a   Chengot, Preetha ^b   Graham, Jennifer ^b   Sethi, Neeraj ^a   Ong, Thian K ^c   High, Alec ^b   Maclennan, Kenneth ^a   Rabbitts, Pamela ^a  

^a UNIVERSITY OF LEEDS   (United Kingdom)

^b ST JAMES S UNIVERSITY HOSPITAL   (United Kingdom)

^c LEEDS DENTAL INSTITUTE   (United Kingdom)

^d UNIVERSITY OF ULSTER   (United Kingdom)

^e ILLUMINA INC   (United States)

^f GAZI UNIVERSITY   (Turkey)

Author keywords

clonal evolution; oral cancer; pre cancer; tumour progression

Indexed keywords

DNA; TUMOR MARKER;

ARTICLE; CANCER GENETICS; CANCER LOCALIZATION; CANCER PATIENT; CANCER STAGING; CLINICAL ARTICLE; CLONAL EVOLUTION; CLONAL VARIATION; DNA LIBRARY; DNA SEQUENCE; DYSPLASIA; GENE FREQUENCY; GENE MUTATION; GENETIC HETEROGENEITY; GENOMICS; HUMAN; HUMAN GENOME; HUMAN TISSUE; METASTASIS; MOUTH CANCER; MOUTH CARCINOMA; MOUTH LESION; MULTIPLE CANCER; MUTATIONAL ANALYSIS; POINT MUTATION; PRECANCER; PRIMARY TUMOR; PRIORITY JOURNAL; SOMATIC MUTATION; TUMOR INVASION; ULTRA DEEP SEQUENCING; CARCINOMA; CELL LINEAGE; CELL MOTION; CELL PROLIFERATION; CELL TRANSFORMATION; DISEASE COURSE; GENE DOSAGE; GENETIC PREDISPOSITION; GENETICS; HIGH THROUGHPUT SEQUENCING; MOUTH TUMOR; MUTATION; PATHOLOGY; PHENOTYPE; PROCEDURES; SECONDARY;

BIOMARKERS, TUMOR; CARCINOMA; CELL LINEAGE; CELL MOVEMENT; CELL PROLIFERATION; CELL TRANSFORMATION, NEOPLASTIC; CLONAL EVOLUTION; DISEASE PROGRESSION; GENE DOSAGE; GENETIC PREDISPOSITION TO DISEASE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MOUTH NEOPLASMS; MUTATION; NEOPLASM INVASIVENESS; PHENOTYPE; PRECANCEROUS CONDITIONS; SEQUENCE ANALYSIS, DNA;

EID: 84945463873     PISSN: 00223417     EISSN: 10969896     Source Type: Journal    
DOI: 10.1002/path.4576     Document Type: Article

References (44)

1. Collins FS, Barker AD,. Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. Sci Am 2007; 296: 50-57.
2. Gerlinger M, Horswell S, Larkin J, et al., Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet 2014; 46: 225-233.
3. Nik-Zainal S, Alexandrov LB, Wedge DC, et al., Mutational processes molding the genomes of 21 breast cancers. Cell 2012; 149: 979-993.
4. Nik-Zainal S, Van Loo P, Wedge DC, et al., The life history of 21 breast cancers. Cell 2012; 149: 994-1007.
5. Walter MJ, Shen D, Ding L, et al., Clonal architecture of secondary acute myeloid leukemia. N Engl J Med 2012; 366: 1090-1098.
6. Mehanna HM, Rattay T, Smith J, et al., Treatment and follow-up of oral dysplasia-a systematic review and meta-analysis. Head Neck 2009; 31: 1600-1609.
7. Zhang L, Poh CF, Williams M, et al., Loss of heterozygosity (LOH) profiles-validated risk predictors for progression to oral cancer. Cancer Prev Res (Phila) 2012; 5: 1081-1089.
8. Califano J, Westra WH, Meininger G, et al., Genetic progression and clonal relationship of recurrent premalignant head and neck lesions. Clin Cancer Res 2000; 6: 347-352.
9. Tsui IF, Garnis C, Poh CF,. A dynamic oral cancer field: unraveling the underlying biology and its clinical implication. Am J Surg Pathol 2009; 33: 1732-1738.
10. Noutomi Y, Oga A, Uchida K, et al., Comparative genomic hybridization reveals genetic progression of oral squamous cell carcinoma from dysplasia via two different tumourigenic pathways. J Pathol 2006; 210: 67-74.
11. Tabor MP, Brakenhoff RH, Ruijter-Schippers HJ, et al., Multiple head and neck tumors frequently originate from a single preneoplastic lesion. Am J Pathol 2002; 161: 1051-1060.
12. Drmanac R, Sparks AB, Callow MJ, et al., Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327: 78-81.
13. Li H, Durbin R,. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25: 60.
14. McKenna A, Hanna M, Banks E, et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: 1297-1303.
15. Shah SP, Morin RD, Khattra J, et al., Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 2009; 461: 809-813.
16. Goya R, Sun MG, Morin RD, et al., SNVMix: predicting single nucleotide variants from next-generation sequencing of tumors. Bioinformatics 2010; 26: 730-736.
17. Koboldt DC, Zhang Q, Larson DE, et al., VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 2012; 22: 568-576.
18. McLaren W, Pritchard B, Rios D, et al., Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010; 26: 2069-2070.
19. Wong WC, Kim D, Carter H, et al., CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. Bioinformatics 2011; 27: 2147-2148.
20. Koressaar T, Remm M,. Enhancements and modifications of primer design program Primer3. Bioinformatics 2007; 23: 1289-1291.
21. Wood HM, Belvedere O, Conway C, et al., Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res 2010; 38: e151.
22. Gusnanto A, Wood HM, Pawitan Y, et al., Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics 2012; 28: 40-47.
23. Genomes Project C, Abecasis GR, Altshuler D, et al., A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061-1073.
24. Venkatraman ES, Olshen AB,. A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 2007; 23: 657-663.
25. Conway C, Chalkley R, High A, et al., Next-generation sequencing for simultaneous determination of human papillomavirus load, subtype, and associated genomic copy number changes in tumors. J Mol Diagn 2012; 14: 104-111.
26. Newburger DE, Kashef-Haghighi D, Weng Z, et al., Genome evolution during progression to breast cancer. Genome Res 2013; 23: 1097-1108.
27. Roth A, Khattra J, Yap D, et al., PyClone: statistical inference of clonal population structure in cancer. Nat Methods 2014; 11: 396-398.
28. Yost SE, Smith EN, Schwab RB, et al., Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res 2012; 40: e107.
29. Jiao W, Vembu S, Deshwar AG, et al., Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinformat 2014; 15: 35.
30. Fischer A, Vazquez-Garcia I, Illingworth CJ, et al., High-definition reconstruction of clonal composition in cancer. Cell Rep 2014; 7: 1740-1752.
31. Waridel F, Estreicher A, Bron L, et al., Field cancerisation and polyclonal p53 mutation in the upper aero-digestive tract. Oncogene 1997; 14: 163-169.
32. Rowley H, Sherrington P, Helliwell TR, et al., p53 expression and p53 gene mutation in oral cancer and dysplasia. Otolaryngol Head Neck Surg 1998; 118: 115-123.
33. Shahnavaz SA, Regezi JA, Bradley G, et al., p53 gene mutations in sequential oral epithelial dysplasias and squamous cell carcinomas. J Pathol 2000; 190: 417-422.
34. Stransky N, Egloff AM, Tward AD, et al., The mutational landscape of head and neck squamous cell carcinoma. Science 2011; 333: 1157-1160.
35. Ho MW, Risk JM, Woolgar JA, et al., The clinical determinants of malignant transformation in oral epithelial dysplasia. Oral Oncol 2012; 48: 969-976.
36. Ho MW, Field EA, Field JK, et al., Outcomes of oral squamous cell carcinoma arising from oral epithelial dysplasia: rationale for monitoring premalignant oral lesions in a multidisciplinary clinic. Br J Oral Maxillofac Surg 2013; 51: 594-599.
37. Brennan M, Migliorati CA, Lockhart PB, et al., Management of oral epithelial dysplasia: a review. Oral Surg Oral Med Oral Pathol Oral Radiol Endodont 2007; 103 (suppl): S19 e11-12.
38. Slaughter DP, Southwick HW, Smejkal W,. Field cancerization in oral stratified squamous epithelium; clinical implications of multicentric origin. Cancer 1953; 6: 963-968.
39. Johnson CE, Gorringe KL, Thompson ER, et al., Identification of copy number alterations associated with the progression of DCIS to invasive ductal carcinoma. Breast Cancer Res Treat 2012; 133: 889-898.
40. Bhattacharya A, Roy R, Snijders AM, et al., Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis. Clin Cancer Res 2011; 17: 7024-7034.
41. Koch WM, Lango M, Sewell D, et al., Head and neck cancer in nonsmokers: a distinct clinical and molecular entity. Laryngoscope 1999; 109: 1544-1551.
42. Chung CH, Parker JS, Karaca G, et al., Molecular classification of head and neck squamous cell carcinomas using patterns of gene expression. Cancer Cell 2004; 5: 489-500.
43. Cleary AS, Leonard TL, Gestl SA, et al., Tumour cell heterogeneity maintained by cooperating subclones in Wnt-driven mammary cancers. Nature 2014; 508: 113-117.
44. Pipinikas CP, Kiropoulos TS, Teixeira VH, et al., Cell migration leads to spatially distinct but clonally related airway cancer precursors. Thorax 2014; 69: 548-557.