Genomic hallmarks of localized, non-indolent prostate cancer

Nature

Volumn 541, Issue 7637, 2017, Pages 359-364

  Fraser, Michael ^a   Sabelnykova, Veronica Y ^b   Yamaguchi, Takafumi N ^b   Heisler, Lawrence E ^b   Livingstone, Julie ^b   Huang, Vincent ^b   Shiah, Yu Jia ^b   Yousif, Fouad ^b   Lin, Xihui ^b   Masella, Andre P ^b   Fox, Natalie S ^b,c   Xie, Michael ^b   Prokopec, Stephenie D ^b   Berlin, Alejandro ^c   Lalonde, Emilie ^b,c   Ahmed, Musaddeque ^a   Trudel, Dominique ^d,j   Luo, Xuemei ^b   Beck, Timothy A ^b   Meng, Alice ^a   Zhang, Junyan ^a   D'Costa, Alister ^b   Denroche, Robert E ^b   Kong, Haiying ^b   Espiritu, Shadrielle Melijah G ^b   Chua, Melvin L K ^c   Wong, Ada ^b   Chong, Taryne ^b   Sam, Michelle ^b   Johns, Jeremy ^b   Timms, Lee ^b   Buchner, Nicholas B ^b   Orain, Michèle ^e   Picard, Valérie ^e   Hovington, Helène ^e   Murison, Alexander ^a   Kron, Ken ^a   Harding, Nicholas J ^b   P'ng, Christine ^b   Houlahan, Kathleen E ^b   Chu, Kenneth C ^b   Lo, Bryan ^b   Nguyen, Francis ^b   Li, Constance H ^b,c   Sun, Ren X ^b,f   De Borja, Richard ^b   Cooper, Christopher I ^b   Hopkins, Julia F ^b   Govind, Shaylan K ^b   Fung, Clement ^b   Waggott, Daryl ^b   Green, Jeffrey ^b   Haider, Syed ^b   Chan Seng Yue, Michelle A ^b   Jung, Esther ^b   Wang, Zhiyuan ^b   Bergeron, Alain ^e   Dal Pra, Alan ^c,k   Lacombe, Louis ^e   Collins, Colin C ^g,h   Sahinalp, Cenk ⁱ   Lupien, Mathieu ^a,c   Fleshner, Neil E ^a   He, Housheng H ^a,c   Fradet, Yves ^e   Tetu, Bernard ^e   Van Der Kwast, Theodorus ^d   McPherson, John D ^b,c   Bristow, Robert G ^a,c   Boutros, Paul C ^b,c,f   more..

^a PRINCESS MARGARET HOSPITAL   (Canada)

^b ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d TORONTO GENERAL HOSPITAL   (Canada)

^e LAVAL UNIVERSITY   (Canada)

^f UNIVERSITY OF TORONTO   (Canada)

^g UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^h VANCOUVER PROSTATE CENTRE   (Canada)

ⁱ SIMON FRASER UNIVERSITY   (Canada)

^j CENTRE HOSPITALIER DE L UNIVERSITÉ DE MONTRÉAL   (Canada)

^k UNIVERSITY OF BERN   (Switzerland)

more..

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA; TUMOR MARKER;

BIOMARKER; CANCER; DISEASE; DNA; GENOMICS; METHYLATION; RNA; TUMOR;

ARTICLE; CANCER PROGNOSIS; CANCER RECURRENCE; DNA METHYLATION; GENE REARRANGEMENT; GENE REPRESSION; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOMICS; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; METASTASIS; PRIORITY JOURNAL; PROSTATE CANCER; SOMATIC HYPERMUTATION; WHOLE EXOME SEQUENCING; WHOLE GENOME SEQUENCING; CASTRATION RESISTANT PROSTATE CANCER; CHROMOTHRIPSIS; COPY NUMBER VARIATION; EXOME; GENETICS; HUMAN GENOME; MUTATION; PATHOLOGY; PROGNOSIS; PROSTATE TUMOR; RECURRENT DISEASE;

CHROMOTHRIPSIS; DNA COPY NUMBER VARIATIONS; DNA METHYLATION; EXOME; GENOME, HUMAN; GENOMICS; HUMANS; MALE; MUTATION; NEOPLASM METASTASIS; PROGNOSIS; PROSTATIC NEOPLASMS; PROSTATIC NEOPLASMS, CASTRATION-RESISTANT; RECURRENCE;

EID: 85011688924     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature20788     Document Type: Article

References (61)

1. Lozano, R. et al. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet 380, 2095-2128 (2012).
2. Klotz, L. et al. Long-term follow-up of a large active surveillance cohort of patients with prostate cancer. J. Clin. Oncol. 33, 272-277 (2015).
3. D'Amico, A. V. et al. Cancer-specific mortality after surgery or radiation for patients with clinically localized prostate cancer managed during the prostate-specific antigen era. J. Clin. Oncol. 21, 2163-2172 (2003).
4. Boutros, P. C. et al. Spatial genomic heterogeneity within localized, multifocal prostate cancer. Nat. Genet. 47, 736-745 (2015).
5. Cooper, C. S. et al. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat. Genet. 47, 367-372 (2015).
6. Lalonde, E. et al. Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study. Lancet Oncol. 15, 1521-1532 (2014).
7. Buyyounouski, M. K., Pickles, T., Kestin, L. L., Allison, R. & Williams, S. G. Validating the interval to biochemical failure for the identification of potentially lethal prostate cancer. J. Clin. Oncol. 30, 1857-1863 (2012).
8. Robinson, D. et al. Integrative clinical genomics of advanced prostate cancer. Cell 161, 1215-1228 (2015).
9. Berger, M. F. et al. The genomic complexity of primary human prostate cancer. Nature 470, 214-220 (2011).
10. Baca, S. C. et al. Punctuated evolution of prostate cancer genomes. Cell 153, 666-677 (2013).
11. Weischenfeldt, J. et al. Integrative genomic analyses reveal an androgen-driven somatic alteration landscape in early-onset prostate cancer. Cancer Cell 23, 159-170 (2013).
12. Cancer Genome Atlas Research Network. The molecular taxonomy of primary prostate cancer. Cell 163, 1011-1025 (2015).
13. Barbieri, C. E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685-689 (2012).
14. Ewing, A. D. et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nat. Methods 12, 623-630 (2015).
15. Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495-501 (2014).
16. Ciriello, G. et al. Emerging landscape of oncogenic signatures across human cancers. Nat. Genet. 45, 1127-1133 (2013).
17. Zhou, J. & Troyanskaya, O. G. Predicting effects of noncoding variants with deep learning-based sequence model. Nat. Methods 12, 931-934 (2015).
18. Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013).
19. Gandhi, M., Evdokimova, V. & Nikiforov, Y. E. Frequency of close positioning of chromosomal loci detected by FRET correlates with their participation in carcinogenic rearrangements in human cells. Genes Chromosom. Cancer 51, 1037-1044 (2012).
20. Nikiforova, M. N. et al. Proximity of chromosomal loci that participate in radiation-induced rearrangements in human cells. Science 290, 138-141 (2000).
21. Rickman, D. S. et al. Oncogene-mediated alterations in chromatin conformation. Proc. Natl Acad. Sci. USA 109, 9083-9088 (2012).
22. Korbel, J. O. & Campbell, P. J. Criteria for inference of chromothripsis in cancer genomes. Cell 152, 1226-1236 (2013).
23. Govind, S. K. et al. ShatterProof: operational detection and quantification of chromothripsis. BMC Bioinformatics 15, 78 (2014).
24. Zafarana, G. et al. Copy number alterations of c-MYC and PTEN are prognostic factors for relapse after prostate cancer radiotherapy. Cancer 118, 4053-4062 (2012).
25. Hieronymus, H. et al. Copy number alteration burden predicts prostate cancer relapse. Proc. Natl Acad. Sci. USA 111, 11139-11144 (2014).
26. Mateo, J. et al. DNA-repair defects and olaparib in metastatic prostate cancer. N. Engl. J. Med. 373, 1697-1708 (2015).
27. Schiewer, M. J. et al. Dual roles of PARP-1 promote cancer growth and progression. Cancer Discov. 2, 1134-1149 (2012).
28. Feng, F. Y., de Bono, J. S., Rubin, M. A. & Knudsen, K. E. Chromatin to clinic: the molecular rationale for PARP1 inhibitor function. Mol. Cell 58, 925-934 (2015).
29. Gundem, G. et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353-357 (2015).
30. Graff, J. N. & Beer, T. M. Should docetaxel be administered earlier in prostate cancer therapy? Expert Rev. Anticancer Ther. 15, 977-979 (2015).
31. Fisher, S. et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1 (2011).
32. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
33. Wilkerson, M. D. & Hayes, D. N. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics 26, 1572-1573 (2010).
34. Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
35. Taylor, B. J. et al. DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. eLife 2, e00534 (2013).
36. Song, S. et al. qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS One 7, e45835 (2012).
37. Van Loo, P. et al. Analyzing cancer samples with SNP arrays. Methods Mol. Biol. 802, 57-72 (2012).
38. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
39. McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010).
40. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
41. Larson, D. E. et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 28, 311-317 (2012).
42. Cibulskis, K. et al. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics 27, 2601-2602 (2011).
43. Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
44. Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311 (2001).
45. Ouedraogo, M. et al. The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PLoS One 7, e50653 (2012).
46. Gerstein, M. B. et al. Architecture of the human regulatory network derived from ENCODE data. Nature 489, 91-100 (2012).
47. Fuentes Fajardo, K. V. et al. Detecting false-positive signals in exome sequencing. Hum. Mutat. 33, 609-613 (2012).
48. Forbes, S. A. et al. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805-D811 (2015).
49. Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333-i339 (2012).
50. Cingolani, P. 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) 6, 80-92 (2012).
51. Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645 (2009).
52. Pidsley, R. et al. A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics 14, 293 (2013).
53. Peters, T. J. et al. De novo identification of differentially methylated regions in the human genome. Epigenetics Chromatin 8, 6 (2015).
54. Chen, Y. A. et al. Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium Human Methylation450 microarray. Epigenetics 8, 203-209 (2013).
55. Aran, D., Sirota, M. & Butte, A. J. Systematic pan-cancer analysis of tumour purity. Nat. Commun. 6, 8971 (2015).
56. Brocks, D. et al. Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer. Cell Reports 8, 798-806 (2014).
57. Massie, C. E. et al. The androgen receptor fuels prostate cancer by regulating central metabolism and biosynthesis. EMBO J. 30, 2719-2733 (2011).
58. Crooks, G. E., Hon, G., Chandonia, J. M. & Brenner, S. E. WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190 (2004).
59. Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
60. Irizarry, R. A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003).
61. Yoshihara, K. et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat. Commun. 4, 2612 (2013).