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Prostate Cancer Research Center

PELICAN- Personalized Cancer Medicine <!--Bova-->

2020

  1. Bailey, MH, Meyerson, WU, Dursi, LJ, Wang, LB, Dong, G, Liang, WW et al.. Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020;11 (1):6232. doi: 10.1038/s41467-020-20128-w. PubMed PMID:33257764 PubMed Central PMC7705717.
  2. Woodcock, DJ, Riabchenko, E, Taavitsainen, S, Kankainen, M, Gundem, G, Brewer, DS et al.. Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy. Nat Commun. 2020;11 (1):5070. doi: 10.1038/s41467-020-18843-5. PubMed PMID:33033260 PubMed Central PMC7545111.
  3. Bailey, MH, Meyerson, WU, Dursi, LJ, Wang, LB, Dong, G, Liang, WW et al.. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020;11 (1):4748. doi: 10.1038/s41467-020-18151-y. PubMed PMID:32958763 PubMed Central PMC7505971.
  4. Li, CH, Prokopec, SD, Sun, RX, Yousif, F, Schmitz, N, PCAWG Tumour Subtypes and Clinical Translation et al.. Sex differences in oncogenic mutational processes. Nat Commun. 2020;11 (1):4330. doi: 10.1038/s41467-020-17359-2. PubMed PMID:32859912 PubMed Central PMC7455744.
  5. Gundem, G, Van Loo, P, Kremeyer, B, Alexandrov, LB, Tubio, JMC, Papaemmanuil, E et al.. Author Correction: The evolutionary history of lethal metastatic prostate cancer. Nature. 2020;584 (7820):E18. doi: 10.1038/s41586-020-2581-5. PubMed PMID:32728210 .
  6. PCAWG Transcriptome Core Group, Calabrese, C, Davidson, NR, Demircioğlu, D, Fonseca, NA, He, Y et al.. Genomic basis for RNA alterations in cancer. Nature. 2020;578 (7793):129-136. doi: 10.1038/s41586-020-1970-0. PubMed PMID:32025019 PubMed Central PMC7054216.
  7. Alexandrov, LB, Kim, J, Haradhvala, NJ, Huang, MN, Tian Ng, AW, Wu, Y et al.. The repertoire of mutational signatures in human cancer. Nature. 2020;578 (7793):94-101. doi: 10.1038/s41586-020-1943-3. PubMed PMID:32025018 PubMed Central PMC7054213.
  8. Rheinbay, E, Nielsen, MM, Abascal, F, Wala, JA, Shapira, O, Tiao, G et al.. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020;578 (7793):102-111. doi: 10.1038/s41586-020-1965-x. PubMed PMID:32025015 PubMed Central PMC7054214.
  9. Gerstung, M, Jolly, C, Leshchiner, I, Dentro, SC, Gonzalez, S, Rosebrock, D et al.. The evolutionary history of 2,658 cancers. Nature. 2020;578 (7793):122-128. doi: 10.1038/s41586-019-1907-7. PubMed PMID:32025013 PubMed Central PMC7054212.
  10. Li, Y, Roberts, ND, Wala, JA, Shapira, O, Schumacher, SE, Kumar, K et al.. Patterns of somatic structural variation in human cancer genomes. Nature. 2020;578 (7793):112-121. doi: 10.1038/s41586-019-1913-9. PubMed PMID:32025012 PubMed Central PMC7025897.
  11. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020;578 (7793):82-93. doi: 10.1038/s41586-020-1969-6. PubMed PMID:32025007 PubMed Central PMC7025898.
  12. Cortés-Ciriano, I, Lee, JJ, Xi, R, Jain, D, Jung, YL, Yang, L et al.. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2020;52 (3):331-341. doi: 10.1038/s41588-019-0576-7. PubMed PMID:32025003 PubMed Central PMC7058534.
  13. Zapatka, M, Borozan, I, Brewer, DS, Iskar, M, Grundhoff, A, Alawi, M et al.. The landscape of viral associations in human cancers. Nat Genet. 2020;52 (3):320-330. doi: 10.1038/s41588-019-0558-9. PubMed PMID:32025001 PubMed Central PMC8076016.
  14. Akdemir, KC, Le, VT, Chandran, S, Li, Y, Verhaak, RG, Beroukhim, R et al.. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet. 2020;52 (3):294-305. doi: 10.1038/s41588-019-0564-y. PubMed PMID:32024999 PubMed Central PMC7058537.
  15. Rodriguez-Martin, B, Alvarez, EG, Baez-Ortega, A, Zamora, J, Supek, F, Demeulemeester, J et al.. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020;52 (3):306-319. doi: 10.1038/s41588-019-0562-0. PubMed PMID:32024998 PubMed Central PMC7058536.
  16. Yuan, Y, Ju, YS, Kim, Y, Li, J, Wang, Y, Yoon, CJ et al.. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2020;52 (3):342-352. doi: 10.1038/s41588-019-0557-x. PubMed PMID:32024997 PubMed Central PMC7058535.
  17. Carlevaro-Fita, J, Lanzós, A, Feuerbach, L, Hong, C, Mas-Ponte, D, Pedersen, JS et al.. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol. 2020;3 (1):56. doi: 10.1038/s42003-019-0741-7. PubMed PMID:32024996 PubMed Central PMC7002399.
  18. Yakneen, S, Waszak, SM, PCAWG Technical Working Group, Gertz, M, Korbel, JO, PCAWG Consortium et al.. Butler enables rapid cloud-based analysis of thousands of human genomes. Nat Biotechnol. 2020;38 (3):288-292. doi: 10.1038/s41587-019-0360-3. PubMed PMID:32024987 PubMed Central PMC7062635.
  19. Reyna, MA, Haan, D, Paczkowska, M, Verbeke, LPC, Vazquez, M, Kahraman, A et al.. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020;11 (1):729. doi: 10.1038/s41467-020-14367-0. PubMed PMID:32024854 PubMed Central PMC7002574.
  20. Jiao, W, Atwal, G, Polak, P, Karlic, R, Cuppen, E, PCAWG Tumor Subtypes and Clinical Translation Working Group et al.. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nat Commun. 2020;11 (1):728. doi: 10.1038/s41467-019-13825-8. PubMed PMID:32024849 PubMed Central PMC7002586.
  21. Paczkowska, M, Barenboim, J, Sintupisut, N, Fox, NS, Zhu, H, Abd-Rabbo, D et al.. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2020;11 (1):735. doi: 10.1038/s41467-019-13983-9. PubMed PMID:32024846 PubMed Central PMC7002665.
  22. Cmero, M, Yuan, K, Ong, CS, Schröder, J, PCAWG Evolution and Heterogeneity Working Group, Corcoran, NM et al.. Inferring structural variant cancer cell fraction. Nat Commun. 2020;11 (1):730. doi: 10.1038/s41467-020-14351-8. PubMed PMID:32024845 PubMed Central PMC7002525.
  23. Rubanova, Y, Shi, R, Harrigan, CF, Li, R, Wintersinger, J, Sahin, N et al.. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun. 2020;11 (1):731. doi: 10.1038/s41467-020-14352-7. PubMed PMID:32024834 PubMed Central PMC7002414.
  24. Zhang, Y, Chen, F, Fonseca, NA, He, Y, Fujita, M, Nakagawa, H et al.. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020;11 (1):736. doi: 10.1038/s41467-019-13885-w. PubMed PMID:32024823 PubMed Central PMC7002524.
  25. Bhandari, V, Li, CH, Bristow, RG, Boutros, PC, PCAWG Consortium. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun. 2020;11 (1):737. doi: 10.1038/s41467-019-14052-x. PubMed PMID:32024819 PubMed Central PMC7002770.
  26. Shuai, S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger, S, Stein, LD, PCAWG Consortium. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun. 2020;11 (1):734. doi: 10.1038/s41467-019-13929-1. PubMed PMID:32024818 PubMed Central PMC7002750.
  27. Sieverling, L, Hong, C, Koser, SD, Ginsbach, P, Kleinheinz, K, Hutter, B et al.. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun. 2020;11 (1):733. doi: 10.1038/s41467-019-13824-9. PubMed PMID:32024817 PubMed Central PMC7002710.

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2019

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2018

  1. Kallio, HML, Hieta, R, Latonen, L, Brofeldt, A, Annala, M, Kivinummi, K et al.. Constitutively active androgen receptor splice variants AR-V3, AR-V7 and AR-V9 are co-expressed in castration-resistant prostate cancer metastases. Br J Cancer. 2018;119 (3):347-356. doi: 10.1038/s41416-018-0172-0. PubMed PMID:29988112 PubMed Central PMC6070921.
  2. Sainio, M, Visakorpi, T, Tolonen, T, Ilvesaro, J, Bova, GS. Expression of neuroendocrine differentiation markers in lethal metastatic castration-resistant prostate cancer. Pathol Res Pract. 2018;214 (6):848-856. doi: 10.1016/j.prp.2018.04.015. PubMed PMID:29728311 .
  3. Wedge, DC, Gundem, G, Mitchell, T, Woodcock, DJ, Martincorena, I, Ghori, M et al.. Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets. Nat Genet. 2018;50 (5):682-692. doi: 10.1038/s41588-018-0086-z. PubMed PMID:29662167 PubMed Central PMC6372064.
  4. Högnäs, G, Kivinummi, K, Kallio, HML, Hieta, R, Ruusuvuori, P, Koskenalho, A et al.. Feasibility of Prostate PAXgene Fixation for Molecular Research and Diagnostic Surgical Pathology: Comparison of Matched Fresh Frozen, FFPE, and PFPE Tissues. Am J Surg Pathol. 2018;42 (1):103-115. doi: 10.1097/PAS.0000000000000961. PubMed PMID:28984675 .

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2017

  1. Kivinummi, K, Urbanucci, A, Leinonen, K, Tammela, TLJ, Annala, M, Isaacs, WB et al.. The expression of AURKA is androgen regulated in castration-resistant prostate cancer. Sci Rep. 2017;7 (1):17978. doi: 10.1038/s41598-017-18210-3. PubMed PMID:29269934 PubMed Central PMC5740165.
  2. Camacho, N, Van Loo, P, Edwards, S, Kay, JD, Matthews, L, Haase, K et al.. Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data. PLoS Genet. 2017;13 (9):e1007001. doi: 10.1371/journal.pgen.1007001. PubMed PMID:28945760 PubMed Central PMC5628936.
  3. Bova, GS. Cancer genomics: Human metastases under scrutiny. Nature. 2017;548 (7667):287-288. doi: 10.1038/nature23535. PubMed PMID:28783720 .

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2016

  1. Behjati, S, Gundem, G, Wedge, DC, Roberts, ND, Tarpey, PS, Cooke, SL et al.. Mutational signatures of ionizing radiation in second malignancies. Nat Commun. 2016;7 :12605. doi: 10.1038/ncomms12605. PubMed PMID:27615322 PubMed Central PMC5027243.
  2. Ju, YS, Tubio, JM, Mifsud, W, Fu, B, Davies, HR, Ramakrishna, M et al.. Corrigendum: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome Res. 2016;26 (5):717.2. doi: 10.1101/gr.206557.116. PubMed PMID:27197245 PubMed Central PMC4864453.
  3. Bova, GS, Kallio, HM, Annala, M, Kivinummi, K, Högnäs, G, Häyrynen, S et al.. Integrated clinical, whole-genome, and transcriptome analysis of multisampled lethal metastatic prostate cancer. Cold Spring Harb Mol Case Stud. 2016;2 (3):a000752. doi: 10.1101/mcs.a000752. PubMed PMID:27148588 PubMed Central PMC4853517.
  4. Sjöblom, L, Saramäki, O, Annala, M, Leinonen, K, Nättinen, J, Tolonen, T et al.. Microseminoprotein-Beta Expression in Different Stages of Prostate Cancer. PLoS One. 2016;11 (3):e0150241. doi: 10.1371/journal.pone.0150241. PubMed PMID:26939004 PubMed Central PMC4777373.
  5. Myneni, S, Patel, VL, Bova, GS, Wang, J, Ackerman, CF, Berlinicke, CA et al.. Resolving complex research data management issues in biomedical laboratories: Qualitative study of an industry-academia collaboration. Comput Methods Programs Biomed. 2016;126 :160-70. doi: 10.1016/j.cmpb.2015.11.001. PubMed PMID:26652980 PubMed Central PMC4778387.

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2015

  1. Myneni, S, Patel, VL, Bova, GS, Wang, J, Ackerman, CF, Berlinicke, CA et al.. Resolving complex research data management issues in biomedical laboratories: Qualitative study of an industry-academia collaboration. Comput Methods Programs Biomed. 2016;126 :160-70. doi: 10.1016/j.cmpb.2015.11.001. PubMed PMID:26652980 PubMed Central PMC4778387.
  2. Gundem, G, Van Loo, P, Kremeyer, B, Alexandrov, LB, Tubio, JMC, Papaemmanuil, E et al.. The evolutionary history of lethal metastatic prostate cancer. Nature. 2015;520 (7547):353-357. doi: 10.1038/nature14347. PubMed PMID:25830880 PubMed Central PMC4413032.
  3. Cooper, CS, Eeles, R, Wedge, DC, Van Loo, P, Gundem, G, Alexandrov, LB 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. 2015;47 (4):367-372. doi: 10.1038/ng.3221. PubMed PMID:25730763 PubMed Central PMC4380509.

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