Tumor heterogeneity: Next-generation sequencing enhances the view from the pathologist's microscope

Genome Biology

Volumn 15, Issue 9, 2014, Pages

  Aparicio, Samuel ^a,b   Mardis, Elaine ^c  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LONG UNTRANSLATED RNA; MICRORNA;

CANCER GENETICS; CANCER THERAPY; CELL HETEROGENEITY; DATA PROCESSING; DNA SEQUENCE; EDITORIAL; EPIGENETICS; EXPERIMENTAL STUDY; GENE EXPRESSION REGULATION; GENETIC HETEROGENEITY; HUMAN; METHODOLOGY; NEXT GENERATION SEQUENCING; RNA SEQUENCE; TUMOR CELL; DNA MUTATIONAL ANALYSIS; GENETICS; HIGH THROUGHPUT SEQUENCING; NEOPLASMS; SINGLE CELL ANALYSIS;

DNA MUTATIONAL ANALYSIS; GENETIC HETEROGENEITY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; SINGLE-CELL ANALYSIS;

EID: 84924550562     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/s13059-014-0463-6     Document Type: Editorial

References (22)

1. Hiley C, de Bruin EC, McGranahan N, Swanton C: Deciphering intratumor heterogeneity and temporal acquisition of driver events to refine precision medicine. Genome Biol 2014, 15:453.
2. Ali HR, Rueda OM, Chin SF, Curtis C, Dunning MJ, Aparicio SAJR, Caldas C: Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biol 2014, 15:431.
3. Fisher R, Horswell S, Rowan A, Salm M, De Bruin E, Gulati S, McGranahan N, Stares M, Gerlinger M, Varela I, Crockford A, Favero F, Quidville V, Andre F, Navas C, Gronroos E, Nicol D, Hazell S, Hrouda D, O'Brien T, Matthews N, Phillimore B, Begum S, Rabinowitz A, Biggs J, Bates PA, McDonald NQ, Stamp G, Spencer-Dene B, Hsieh JJ, et al: Development of synchronous VHL syndrome tumors reveals contingencies and constraints to tumor evolution. Genome Biol 2014, 15:433.
4. Nadauld LD, Garcia S, Natsoulis G, Bell JM, Miotke L, Hopmans ES, Xu H, Pai RK, Palm C, Regan JF, Chen H, Flaherty P, Ootani A, Zhang NR, Ford JM, Kuo CJ, Ji HP: Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer. Genome Biol 2014, 15:428.
5. Good BM, Ainscough BJ, McMichael JF, Su AI, Griffith OL: Organizing knowledge to enable personalization of medicine in cancer. Genome Biol 2014, 15:438.
6. Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RGW, Wheeler DA, Marth GT: SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol 2014, 15:443.
7. Zheng X, Zhao Q, Wu HJ, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P, Li F, Hou Y, He J, Wang J, Wang J, Zhang P, Zhang Y, Liu XS: MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biol 2014, 15:419.
8. Russnes HG, Lønning PE, Børresen-Dale AL, Lingjærde OC: The multitude of molecular analyses in cancer: the opening of Pandora's box. Genome Biol 2014, 15:447.
9. Navin NE: Cancer genomics: one cell at a time. Genome Biol 2014, 15:452.
10. Nana-Sinkam SP, Croce CM: MicroRNA regulation of tumorigenesis, cancer progression and interpatient heterogeneity: towards clinical use. Genome Biol 2014, 15:445.
11. White NM, Cabanski CR, Fisher-Silva JM, Dang HX, Govindan R, Maher CA: Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer. Genome Biol 2014, 15:429.
12. Wyatt AW, Mo F, Wang K, McConeghy B, Brahmbhatt S, Jong L, Mitchell DM, Johnston RL, Haegert A, Li E, Liew J, Yeung J, Shrestha R, Lapuk A, McPherson A, Shukin R, Bell RH, Anderson S, Bishop J, Hurtado-Coll A, Xiao H, Chinnaiyan AM, Mehra R, Lin D, Wang Y, Fazli L, Gleave ME, Volik SV, Collins CC: Heterogeneity in the inter-tumor transcriptome of high risk prostate cancer. Genome Biol 2014, 15:426.
13. Mayba O, Gilbert HN, Liu J, Haverty PM, Jhunjhunwala S, Jiang Z, Watanabe C, Zhang Z: MBASED: allele-specific expression detection in cancer tissues and cell lines. Genome Biol 2014, 15:405.
14. Lund K, Cole J, VanderKraats ND, McBryan T, Pchelintsev NA, Clark W, Copland M, Edwards JR, Adams PD: DNMT inhibitors reverse a specific signature of aberrant promoter DNA methylation and associated gene silencing in AML. Genome Biol 2014, 15:406.
15. Fleischer T, Frigessi A, Johnson KC, Edvardsen H, Touleimat N, Klajic J, Riis MLH, Haakensen V, Wärnberg F, Naume B, Helland Å, Børresen-Dale AL, Tost J, Christensen BC, Kristensen VN: Genome-wide DNA methylation profiles in progression to in situ and invasive carcinoma of the breast with impact on gene transcription and prognosis. Genome Biol 2014, 15:435.
16. Charlton J, Williams RD, Weeks M, Sebire NJ, Popov S, Vujanic G, Mifsud W, Alcaide-German M, Butcher LM, Beck S, Pritchard-Jones K: Methylome analysis identifies a Wilms tumor epigenetic biomarker detectable in blood. Genome Biol 2014, 15:434.
17. Varghese AM, Berger MF: Advancing clinical oncology through genome biology and technology. Genome Biol 2014, 15:427.
18. Mateo J, Gerlinger M, Rodrigues D, de Bono JS: The promise of circulating tumor cell analysis in cancer management. Genome Biol 2014, 15:448.
19. Siravegna G, Bardelli A: Genotyping cell-free tumor DNA in the blood to detect residual disease and drug resistance. Genome Biol 2014, 15:449.
20. Eiring AM, Deininger MW: Individualizing kinase-targeted cancer therapy: the paradigm of chronic myeloid leukemia. Genome Biol 2014, 15:461.
21. Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G: Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biol 2014, 15:462.
22. Kosseim P, Dove ES, Baggaley C, Meslin EM, Cate FH, Kaye J, Harris JR, Knoppers BM: Building a data sharing model for global genomic research. Genome Biol 2014, 15:430.