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PELICAN

Personalized Cancer Medicine

Publications (pubmed)

2024

  1. Kiviaho, A, Eerola, SK, Kallio, HML, Andersen, MK, Hoikka, M, Tiihonen, AM et al.. Single cell and spatial transcriptomics highlight the interaction of club-like cells with immunosuppressive myeloid cells in prostate cancer. Nat Commun. 2024;15 (1):9949. doi: 10.1038/s41467-024-54364-1. PubMed PMID:39550375 PubMed Central PMC11569175.
  2. Woodcock, DJ, Sahli, A, Teslo, R, Bhandari, V, Gruber, AJ, Ziubroniewicz, A et al.. Genomic evolution shapes prostate cancer disease type. Cell Genom. 2024;4 (3):100511. doi: 10.1016/j.xgen.2024.100511. PubMed PMID:38428419 PubMed Central PMC10943594.

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2023

  1. Kaljunen, H, Taavitsainen, S, Kaarijärvi, R, Takala, E, Paakinaho, V, Nykter, M et al.. Fanconi anemia pathway regulation by FANCI in prostate cancer. Front Oncol. 2023;13 :1260826. doi: 10.3389/fonc.2023.1260826. PubMed PMID:38023254 PubMed Central PMC10643534.
  2. Nurminen, A, Jaatinen, S, Taavitsainen, S, Högnäs, G, Lesluyes, T, Ansari-Pour, N et al.. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med. 2023;15 (1):82. doi: 10.1186/s13073-023-01242-y. PubMed PMID:37828555 PubMed Central PMC10571458.
  3. Sattari, M, Kohvakka, A, Moradi, E, Rauhala, H, Urhonen, H, Isaacs, WB et al.. Identification of long noncoding RNAs with aberrant expression in prostate cancer metastases. Endocr Relat Cancer. 2023;30 (8):. doi: 10.1530/ERC-22-0247. PubMed PMID:37140987 PubMed Central PMC10326635.
  4. Yakneen, S, Waszak, SM, PCAWG Technical Working Group, Gertz, M, Korbel, JO, PCAWG Consortium et al.. Author Correction: Butler enables rapid cloud-based analysis of thousands of human genomes. Nat Biotechnol. 2023;41 (4):577. doi: 10.1038/s41587-022-01554-1. PubMed PMID:36944844 PubMed Central PMC10110458.
  5. Rodriguez-Martin, B, Alvarez, EG, Baez-Ortega, A, Zamora, J, Supek, F, Demeulemeester, J et al.. Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2023;55 (6):1080. doi: 10.1038/s41588-023-01319-9. PubMed PMID:36944736 PubMed Central PMC10260396.
  6. Akdemir, KC, Le, VT, Chandran, S, Li, Y, Verhaak, RG, Beroukhim, R et al.. Author Correction: Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat Genet. 2023;55 (6):1079. doi: 10.1038/s41588-023-01318-w. PubMed PMID:36944735 PubMed Central PMC10260394.
  7. Zapatka, M, Borozan, I, Brewer, DS, Iskar, M, Grundhoff, A, Alawi, M et al.. Author Correction: The landscape of viral associations in human cancers. Nat Genet. 2023;55 (6):1077. doi: 10.1038/s41588-023-01316-y. PubMed PMID:36944734 PubMed Central PMC10260395.
  8. Cortés-Ciriano, I, Lee, JJ, Xi, R, Jain, D, Jung, YL, Yang, L et al.. Author Correction: Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat Genet. 2023;55 (6):1076. doi: 10.1038/s41588-023-01315-z. PubMed PMID:36944733 PubMed Central PMC10260391.
  9. Yuan, Y, Ju, YS, Kim, Y, Li, J, Wang, Y, Yoon, CJ et al.. Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2023;55 (6):1078. doi: 10.1038/s41588-023-01317-x. PubMed PMID:36944732 PubMed Central PMC10260393.
  10. Alexandrov, LB, Kim, J, Haradhvala, NJ, Huang, MN, Tian Ng, AW, Wu, Y et al.. Author Correction: The repertoire of mutational signatures in human cancer. Nature. 2023;614 (7948):E41. doi: 10.1038/s41586-022-05600-5. PubMed PMID:36697836 PubMed Central PMC9931578.
  11. Li, Y, Roberts, ND, Wala, JA, Shapira, O, Schumacher, SE, Kumar, K et al.. Author Correction: Patterns of somatic structural variation in human cancer genomes. Nature. 2023;614 (7948):E38. doi: 10.1038/s41586-022-05597-x. PubMed PMID:36697835 PubMed Central PMC9931568.
  12. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Author Correction: Pan-cancer analysis of whole genomes. Nature. 2023;614 (7948):E39. doi: 10.1038/s41586-022-05598-w. PubMed PMID:36697834 PubMed Central PMC9931570.
  13. Gerstung, M, Jolly, C, Leshchiner, I, Dentro, SC, Gonzalez, S, Rosebrock, D et al.. Author Correction: The evolutionary history of 2,658 cancers. Nature. 2023;614 (7948):E42. doi: 10.1038/s41586-022-05601-4. PubMed PMID:36697833 PubMed Central PMC9931577.
  14. Rheinbay, E, Nielsen, MM, Abascal, F, Wala, JA, Shapira, O, Tiao, G et al.. Author Correction: Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2023;614 (7948):E40. doi: 10.1038/s41586-022-05599-9. PubMed PMID:36697832 PubMed Central PMC9931557.
  15. PCAWG Transcriptome Core Group, Calabrese, C, Davidson, NR, Demircioğlu, D, Fonseca, NA, He, Y et al.. Author Correction: Genomic basis for RNA alterations in cancer. Nature. 2023;614 (7948):E37. doi: 10.1038/s41586-022-05596-y. PubMed PMID:36697831 PubMed Central PMC9931574.

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2022

  1. Carlevaro-Fita, J, Lanzós, A, Feuerbach, L, Hong, C, Mas-Ponte, D, Pedersen, JS et al.. Author Correction: Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol. 2022;5 (1):1347. doi: 10.1038/s42003-022-03769-z. PubMed PMID:36482178 PubMed Central PMC9732278.
  2. Rubanova, Y, Shi, R, Harrigan, CF, Li, R, Wintersinger, J, Sahin, N et al.. Author Correction: Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun. 2022;13 (1):7567. doi: 10.1038/s41467-022-32336-7. PubMed PMID:36482170 PubMed Central PMC9731941.
  3. Sieverling, L, Hong, C, Koser, SD, Ginsbach, P, Kleinheinz, K, Hutter, B et al.. Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun. 2022;13 (1):7574. doi: 10.1038/s41467-022-32328-7. PubMed PMID:36481818 PubMed Central PMC9731961.
  4. Shuai, S, PCAWG Drivers and Functional Interpretation Working Group, Gallinger, S, Stein, LD, PCAWG Consortium. Author Correction: Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun. 2022;13 (1):7571. doi: 10.1038/s41467-022-32343-8. PubMed PMID:36481739 PubMed Central PMC9732291.
  5. Cmero, M, Yuan, K, Ong, CS, Schröder, J, PCAWG Evolution and Heterogeneity Working Group, Corcoran, NM et al.. Author Correction: Inferring structural variant cancer cell fraction. Nat Commun. 2022;13 (1):7568. doi: 10.1038/s41467-022-32338-5. PubMed PMID:36481724 PubMed Central PMC9732297.
  6. Jiao, W, Atwal, G, Polak, P, Karlic, R, Cuppen, E, PCAWG Tumor Subtypes and Clinical Translation Working Group et al.. Author Correction: A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nat Commun. 2022;13 (1):7573. doi: 10.1038/s41467-022-32329-6. PubMed PMID:36481665 PubMed Central PMC9732335.
  7. Paczkowska, M, Barenboim, J, Sintupisut, N, Fox, NS, Zhu, H, Abd-Rabbo, D et al.. Author Correction: Integrative pathway enrichment analysis of multivariate omics data. Nat Commun. 2022;13 (1):7570. doi: 10.1038/s41467-022-32342-9. PubMed PMID:36481658 PubMed Central PMC9731958.
  8. Zhang, Y, Chen, F, Fonseca, NA, He, Y, Fujita, M, Nakagawa, H et al.. Author Correction: High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2022;13 (1):7572. doi: 10.1038/s41467-022-32333-w. PubMed PMID:36481652 PubMed Central PMC9732340.
  9. Bhandari, V, Li, CH, Bristow, RG, Boutros, PC, PCAWG Consortium. Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun. 2022;13 (1):7569. doi: 10.1038/s41467-022-32339-4. PubMed PMID:36481612 PubMed Central PMC9731962.
  10. Reyna, MA, Haan, D, Paczkowska, M, Verbeke, LPC, Vazquez, M, Kahraman, A et al.. Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2022;13 (1):7566. doi: 10.1038/s41467-022-32334-9. PubMed PMID:36481610 PubMed Central PMC9732045.
  11. Buhigas, C, Warren, AY, Leung, WK, Whitaker, HC, Luxton, HJ, Hawkins, S et al.. The architecture of clonal expansions in morphologically normal tissue from cancerous and non-cancerous prostates. Mol Cancer. 2022;21 (1):183. doi: 10.1186/s12943-022-01644-3. PubMed PMID:36131292 PubMed Central PMC9494848.
  12. Ouellet, V, Erickson, A, GAP1 UTMAs Contributing Investigators, Wiley, K, Morrissey, C, Berge, V et al.. The Movember Global Action Plan 1 (GAP1): Unique Prostate Cancer Tissue Microarray Resource. Cancer Epidemiol Biomarkers Prev. 2022;31 (4):715-727. doi: 10.1158/1055-9965.EPI-21-0600. PubMed PMID:35131885 PubMed Central PMC9381093.

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2021

  1. Li, QK, Chen, J, Hu, Y, Höti, N, Lih, TM, Thomas, SN et al.. Proteomic characterization of primary and metastatic prostate cancer reveals reduced proteinase activity in aggressive tumors. Sci Rep. 2021;11 (1):18936. doi: 10.1038/s41598-021-98410-0. PubMed PMID:34556748 PubMed Central PMC8460832.
  2. Ketola, K, Kaljunen, H, Taavitsainen, S, Kaarijärvi, R, Järvelä, E, Rodríguez-Martín, B et al.. Subclone Eradication Analysis Identifies Targets for Enhanced Cancer Therapy and Reveals L1 Retrotransposition as a Dynamic Source of Cancer Heterogeneity. Cancer Res. 2021;81 (19):4901-4909. doi: 10.1158/0008-5472.CAN-21-0371. PubMed PMID:34348967 PubMed Central PMC9397610.
  3. Jasu, J, Tolonen, T, Antonarakis, ES, Beltran, H, Halabi, S, Eisenberger, MA et al.. Combined Longitudinal Clinical and Autopsy Phenomic Assessment in Lethal Metastatic Prostate Cancer: Recommendations for Advancing Precision Medicine. Eur Urol Open Sci. 2021;30 :47-62. doi: 10.1016/j.euros.2021.05.011. PubMed PMID:34337548 PubMed Central PMC8317817.
  4. Valkonen, M, Hognas, G, Bova, GS, Ruusuvuori, P. Generalized Fixation Invariant Nuclei Detection Through Domain Adaptation Based Deep Learning. IEEE J Biomed Health Inform. 2021;25 (5):1747-1757. doi: 10.1109/JBHI.2020.3039414. PubMed PMID:33211668 .

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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:33033260PubMed 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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2018-2019

  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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