670 results on '"Berney, Daniel M."'
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2. Contemporary Updates on Sex Cord–stromal Tumors of the Testis
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Acosta, Andrés M., Idrees, Muhammad T., Berney, Daniel M., and Colecchia, Maurizio
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- 2024
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3. [11C]metomidate PET-CT versus adrenal vein sampling for diagnosing surgically curable primary aldosteronism: a prospective, within-patient trial
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Wu, Xilin, Senanayake, Russell, Goodchild, Emily, Bashari, Waiel A., Salsbury, Jackie, Cabrera, Claudia P., Argentesi, Giulia, O’Toole, Samuel M., Matson, Matthew, Koo, Brendan, Parvanta, Laila, Hilliard, Nick, Kosmoliaptsis, Vasilis, Marker, Alison, Berney, Daniel M., Tan, Wilson, Foo, Roger, Mein, Charles A., Wozniak, Eva, Savage, Emmanuel, Sahdev, Anju, Bird, Nicholas, Laycock, Kate, Boros, Istvan, Hader, Stefan, Warnes, Victoria, Gillett, Daniel, Dawnay, Anne, Adeyeye, Elizabeth, Prete, Alessandro, Taylor, Angela E., Arlt, Wiebke, Bhuva, Anish N., Aigbirhio, Franklin, Manisty, Charlotte, McIntosh, Alasdair, McConnachie, Alexander, Cruickshank, J. Kennedy, Cheow, Heok, Gurnell, Mark, Drake, William M., and Brown, Morris J.
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- 2023
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4. Pathologist-Level Grading of Prostate Biopsies with Artificial Intelligence
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Ström, Peter, Kartasalo, Kimmo, Olsson, Henrik, Solorzano, Leslie, Delahunt, Brett, Berney, Daniel M., Bostwick, David G., Evans, Andrew J., Grignon, David J., Humphrey, Peter A., Iczkowski, Kenneth A., Kench, James G., Kristiansen, Glen, van der Kwast, Theodorus H., Leite, Katia R. M., McKenney, Jesse K., Oxley, Jon, Pan, Chin-Chen, Samaratunga, Hemamali, Srigley, John R., Takahashi, Hiroyuki, Tsuzuki, Toyonori, Varma, Murali, Zhou, Ming, Lindberg, Johan, Bergström, Cecilia, Ruusuvuori, Pekka, Wählby, Carolina, Grönberg, Henrik, Rantalainen, Mattias, Egevad, Lars, and Eklund, Martin
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Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Artificial Intelligence ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
Background: An increasing volume of prostate biopsies and a world-wide shortage of uro-pathologists puts a strain on pathology departments. Additionally, the high intra- and inter-observer variability in grading can result in over- and undertreatment of prostate cancer. Artificial intelligence (AI) methods may alleviate these problems by assisting pathologists to reduce workload and harmonize grading. Methods: We digitized 6,682 needle biopsies from 976 participants in the population based STHLM3 diagnostic study to train deep neural networks for assessing prostate biopsies. The networks were evaluated by predicting the presence, extent, and Gleason grade of malignant tissue for an independent test set comprising 1,631 biopsies from 245 men. We additionally evaluated grading performance on 87 biopsies individually graded by 23 experienced urological pathologists from the International Society of Urological Pathology. We assessed discriminatory performance by receiver operating characteristics (ROC) and tumor extent predictions by correlating predicted millimeter cancer length against measurements by the reporting pathologist. We quantified the concordance between grades assigned by the AI and the expert urological pathologists using Cohen's kappa. Results: The performance of the AI to detect and grade cancer in prostate needle biopsy samples was comparable to that of international experts in prostate pathology. The AI achieved an area under the ROC curve of 0.997 for distinguishing between benign and malignant biopsy cores, and 0.999 for distinguishing between men with or without prostate cancer. The correlation between millimeter cancer predicted by the AI and assigned by the reporting pathologist was 0.96. For assigning Gleason grades, the AI achieved an average pairwise kappa of 0.62. This was within the range of the corresponding values for the expert pathologists (0.60 to 0.73)., Comment: 45 pages, 11 figures
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- 2019
5. Testicular Tumors: New Developments in Germ Cell and Sex Cord Stromal Tumors
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Dashora, Abhishek, Wagner, Thomas, and Berney, Daniel M.
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- 2022
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6. The 2022 World Health Organization Classification of Tumors of the Urinary System and Male Genital Organs—Part B: Prostate and Urinary Tract Tumors
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Netto, George J., Amin, Mahul B., Berney, Daniel M., Compérat, Eva M., Gill, Anthony J., Hartmann, Arndt, Menon, Santosh, Raspollini, Maria R., Rubin, Mark A., Srigley, John R., Hoon Tan, Puay, Tickoo, Satish K., Tsuzuki, Toyonori, Turajlic, Samra, Cree, Ian, and Moch, Holger
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- 2022
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7. The 2022 World Health Organization Classification of Tumours of the Urinary System and Male Genital Organs—Part A: Renal, Penile, and Testicular Tumours
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Moch, Holger, Amin, Mahul B., Berney, Daniel M., Compérat, Eva M., Gill, Anthony J., Hartmann, Arndt, Menon, Santosh, Raspollini, Maria R., Rubin, Mark A., Srigley, John R., Hoon Tan, Puay, Tickoo, Satish K., Tsuzuki, Toyonori, Turajlic, Samra, Cree, Ian, and Netto, George J.
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- 2022
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8. Accumulation of copy number alterations and clinical progression across advanced prostate cancer
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Grist, Emily, Friedrich, Stefanie, Brawley, Christopher, Mendes, Larissa, Parry, Marina, Ali, Adnan, Haran, Aine, Hoyle, Alex, Gilson, Claire, Lall, Sharanpreet, Zakka, Leila, Bautista, Carla, Landless, Alex, Nowakowska, Karolina, Wingate, Anna, Wetterskog, Daniel, Hasan, A. M. Mahedi, Akato, Nafisah B., Richmond, Malissa, Ishaq, Sofeya, Matthews, Nik, Hamid, Anis A., Sweeney, Christopher J., Sydes, Matthew R., Berney, Daniel M., Lise, Stefano, Parmar, Mahesh K. B., Clarke, Noel W., James, Nicholas D., Cremaschi, Paolo, Brown, Louise C., and Attard, Gerhardt
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- 2022
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9. Somatic mutations of GNA11 and GNAQ in CTNNB1-mutant aldosterone-producing adenomas presenting in puberty, pregnancy or menopause
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Zhou, Junhua, Azizan, Elena A. B., Cabrera, Claudia P., Fernandes-Rosa, Fabio L., Boulkroun, Sheerazed, Argentesi, Giulia, Cottrell, Emily, Amar, Laurence, Wu, Xilin, O’Toole, Sam, Goodchild, Emily, Marker, Alison, Senanayake, Russell, Garg, Sumedha, Åkerström, Tobias, Backman, Samuel, Jordan, Suzanne, Polubothu, Satyamaanasa, Berney, Daniel M., Gluck, Anna, Lines, Kate E., Thakker, Rajesh V., Tuthill, Antoinette, Joyce, Caroline, Kaski, Juan Pablo, Karet Frankl, Fiona E., Metherell, Lou A., Teo, Ada E. D., Gurnell, Mark, Parvanta, Laila, Drake, William M., Wozniak, Eva, Klinzing, David, Kuan, Jyn Ling, Tiang, Zenia, Gomez Sanchez, Celso E., Hellman, Per, Foo, Roger S. Y., Mein, Charles A., Kinsler, Veronica A., Björklund, Peyman, Storr, Helen L., Zennaro, Maria-Christina, and Brown, Morris J.
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- 2021
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10. Cribriform prostate cancer: Morphologic criteria enabling a diagnosis, based on survey of experts
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Iczkowski, Kenneth A., van Leenders, Geert J.L.H., Tarima, Sergey, Wu, Ruizhe, Van der Kwast, Theodorus, Berney, Daniel M., Evans, Andrew J., Wheeler, Thomas M., Ro, Jae Y., Samaratunga, Hemamali, Delahunt, Brett, Srigley, John, Varma, Murali, Tsuzuki, Toyonori, and Egevad, Lars
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- 2021
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11. Pathological predictors of metastatic disease in testicular non-seminomatous germ cell tumors: which tumor-node-metastasis staging system?
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Scandura, Glenda, Wagner, Thomas, Beltran, Luis, Alifrangis, Constantine, Shamash, Jonathan, and Berney, Daniel M.
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- 2021
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12. Granular necrosis: a distinctive form of cell death in malignant tumours
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Samaratunga, Hemamali, Delahunt, Brett, Srigley, John R., Berney, Daniel M., Cheng, Liang, Evans, Andrew, Furusato, Bungo, Leite, Katia R.M., MacLennan, Gregory T., Martignoni, Guido, Moch, Holger, Pan, Chin-Chen, Paner, Gladell, Ro, Jae, Thunders, Michelle, Tsuzuki, Toyonori, Wheeler, Thomas, van der Kwast, Theodorus, Varma, Murali, Williamson, Sean R., Yaxley, John W., and Egevad, Lars
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- 2020
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13. Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study
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Ström, Peter, Kartasalo, Kimmo, Olsson, Henrik, Solorzano, Leslie, Delahunt, Brett, Berney, Daniel M, Bostwick, David G, Evans, Andrew J, Grignon, David J, Humphrey, Peter A, Iczkowski, Kenneth A, Kench, James G, Kristiansen, Glen, van der Kwast, Theodorus H, Leite, Katia R M, McKenney, Jesse K, Oxley, Jon, Pan, Chin-Chen, Samaratunga, Hemamali, Srigley, John R, Takahashi, Hiroyuki, Tsuzuki, Toyonori, Varma, Murali, Zhou, Ming, Lindberg, Johan, Lindskog, Cecilia, Ruusuvuori, Pekka, Wählby, Carolina, Grönberg, Henrik, Rantalainen, Mattias, Egevad, Lars, and Eklund, Martin
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- 2020
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14. Contemporary Updates on Sex Cord–stromal Tumors of the Testis
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Acosta, Andrés M., primary, Idrees, Muhammad T., additional, Berney, Daniel M., additional, and Colecchia, Maurizio, additional
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- 2023
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15. Proposal for a reappraisal of the current classification of so‐called "somatic‐type" malignancies arising in germ cell tumours.
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Acosta, Andres M, Berney, Daniel M, Lobo, João, Idrees, Muhammad T, and Ulbright, Thomas M
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SINGLE nucleotide polymorphisms , *GERM cell tumors , *BIOLOGICAL classification , *GERM cells , *TESTICULAR cancer - Abstract
This article proposes a reappraisal of the current classification of "somatic-type" malignancies that arise in germ cell tumors. These malignancies, which occur in about 7% of germ cell tumors, are currently classified as "teratoma with somatic-type malignancy." However, the authors argue that this classification is suboptimal and does not align with the growing body of evidence that suggests these malignancies are significantly different from true somatic neoplasms. The authors propose an alternative classification that is more in line with current biological concepts and refers to these neoplasms as "sarcoma-like tumor, (adeno)carcinoma-like tumor, leukemia-like tumor, nephroblastoma-like tumor, or embryonic-type neuroectodermal tumor of germ cell origin." They believe that adopting this terminology is important for accuracy and to prevent inappropriate treatments. [Extracted from the article]
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- 2024
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16. Phospholipase D2 in prostate cancer: protein expression changes with Gleason score
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Noble, Amanda R., Hogg, Karen, Suman, Rakesh, Berney, Daniel M., Bourgoin, Sylvain, Maitland, Norman J., and Rumsby, Martin G.
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- 2019
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17. 2019 Gleason grading recommendations from ISUP and GUPS: broadly concordant but with significant differences
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Varma, Murali, Shah, Rajal B., Williamson, Sean R., and Berney, Daniel M.
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- 2021
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18. Ki-67 is an independent predictor of prostate cancer death in routine needle biopsy samples: proving utility for routine assessments
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Kammerer-Jacquet, Solène-Florence, Ahmad, Amar, Møller, Henrik, Sandu, Holly, Scardino, Peter, Soosay, Geraldine, Beltran, Luis, Cuzick, Jack, and Berney, Daniel M.
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- 2019
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19. Genomic analysis of spermatocytic tumors demonstrates recurrent molecular alterations in cases with malignant clinical behavior
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Gupta, Sounak, primary, Sholl, Lynette M, additional, Yang, Yiying, additional, Osunkoya, Adeboye O, additional, Gordetsky, Jennifer B, additional, Cornejo, Kristine M, additional, Michalova, Kvetoslava, additional, Maclean, Fiona, additional, Dvindenko, Eugénia, additional, Snuderl, Matija, additional, Hirsch, Michelle S, additional, Anderson, William J, additional, Rowsey, Ross A, additional, Jimenez, Rafael E, additional, Cheville, John C, additional, Sadow, Peter M, additional, Colecchia, Maurizio, additional, Ricci, Costantino, additional, Ulbright, Thomas M, additional, Berney, Daniel M, additional, and Acosta, Andres Martin, additional
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- 2023
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20. OR02-02 Pre-operative Blood Pressure Response To Aldosterone Antagonists And Urinary Hybrid Steroid Ratios Predict Clinical Outcomes In Unilateral Primary Aldosteronism For At Least 2 Years Post-adrenalectomy
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Wu, Xilin, primary, Goodchild, Emily, additional, Senanayake, Russell, additional, Bashari, Waiel, additional, Salsbury, Jackie, additional, Cabrera, Claudia P, additional, Argentesi, Giulia, additional, O’Toole, Samuel M, additional, McFarlane, James, additional, Matson, Matthew, additional, Parvanta, Laila, additional, Hilliard, Nicholas, additional, Kosmoliaptsis, Vasilis, additional, Marker, Alison, additional, Berney, Daniel M, additional, Tan, Wilson, additional, Foo, Roger, additional, Mein, Charles A, additional, Wozniak, Eva, additional, Sahdev, Anju, additional, Bird, Nicholas, additional, Laycock, Kate, additional, Adeyeye, Elizabeth, additional, Dawnay, Anne, additional, Gillett, Daniel, additional, Prete, Alessandro, additional, Taylor, Angela E, additional, Arlt, Wiebke, additional, Bhuva, Anish N, additional, Manisty, Charlotte, additional, Cruickshank, Kennedy J, additional, Cheow, Heok, additional, Mark, Gurnell, additional, Drake, William, additional, and Brown, Morris J, additional
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- 2023
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21. The urinary tract and male reproductive system
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Beltran, Luis, primary and Berney, Daniel M., additional
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- 2020
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22. Personalized histopathology reporting for personalized medicine: a plea for improved communication
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Varma, Murali, Delahunt, Brett, McCluggage, W. Glenn, Shah, Varsha I., and Berney, Daniel M.
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- 2020
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23. The molecular pathogenesis of penile carcinoma—current developments and understanding
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Emmanuel, Anthony, Nettleton, Jeremy, Watkin, Nick, and Berney, Daniel M.
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- 2019
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24. Genomic analysis of spermatocytic tumors demonstrates recurrent molecular alterations in cases with malignant clinical behavior.
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Gupta, Sounak, Sholl, Lynette M, Yang, Yiying, Osunkoya, Adeboye O, Gordetsky, Jennifer B, Cornejo, Kristine M, Michalova, Kvetoslava, Maclean, Fiona, Dvindenko, Eugénia, Snuderl, Matija, Hirsch, Michelle S, Anderson, William J, Rowsey, Ross A, Jimenez, Rafael E, Cheville, John C, Sadow, Peter M, Colecchia, Maurizio, Ricci, Costantino, Ulbright, Thomas M, and Berney, Daniel M
- Subjects
GENOMICS ,OLDER men ,TUMORS ,DNA sequencing - Abstract
Spermatocytic tumor (ST) is a rare type of germ cell tumor that occurs exclusively in the postpubertal testis and typically affects elderly men. Most STs are benign, but rare cases exhibit aggressive clinical behavior, often in association with transition to sarcomatoid histology. Limited molecular analyses have been performed on STs; therefore, their genomic and epigenomic features remain incompletely described. Twenty‐seven samples from 25 individual patients were analyzed with a combination of DNA sequencing panels, genomic methylation profiling, SNP array, isochromosome (12p) [i(12p)] FISH, and immunohistochemistry. The series included five metastasizing tumors (three with sarcomatoid transformation, one anaplastic, and one conventional) and 20 non‐metastasizing tumors (14 anaplastic and six conventional). Anaplastic tumors comprised a monomorphic population of intermediate‐sized neoplastic cells, as previously described. Multiomic analyses demonstrated that there were two genomic subgroups of STs: one with diploid genomes and hotspot RAS/RAF variants and the other with global ploidy shift and absence of recurrent mutations. Relative gain of chromosome 9 was a consistent finding in both subgroups. A comparison of metastasizing and non‐metastasizing cases demonstrated that aggressive behavior was associated with the acquisition of pathogenic TP53 mutations and/or relative gains of 12p/i(12p). In cases with sarcomatoid transformation, TP53 mutations seem to underlie the transition to sarcomatoid histology. Genomic methylation analysis demonstrated that aggressive cases with gains of 12p cluster closer to pure seminomas than to STs without gains of 12p. In conclusion, STs include two genomic subgroups, characterized by global ploidy shifts without recurrent mutations and diploid genomes with RAS/RAF hotspot mutations, respectively. Biologic progression was associated with relative gains of 12p and TP53 mutations. The findings in STs with relative gains of 12p suggest that they may exhibit biologic characteristics akin to those seen in germ cell neoplasia in situ‐related germ cell tumors rather than non‐germ cell neoplasia in situ‐derived STs. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]
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- 2024
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25. Difficult or Newly Described Morphologic Entities in Testicular Neoplasia
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Berney, Daniel M., Ulbright, Thomas M., Magi-Galluzzi, Cristina, editor, and Przybycin, Christopher G., editor
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- 2015
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26. Testicular Cancer Reporting on Radical Orchiectomy and Retroperitoneal Lymph Node Dissection After Treatment
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Berney, Daniel M., Magi-Galluzzi, Cristina, editor, and Przybycin, Christopher G., editor
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- 2015
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27. Anatomy of the Testis and Staging of its Cancers: Implications for Diagnosis
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Berney, Daniel M., Ulbright, Thomas M., Magi-Galluzzi, Cristina, editor, and Przybycin, Christopher G., editor
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- 2015
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28. Handling and reporting of transperineal template prostate biopsy in Europe: a web-based survey by the European Network of Uropathology (ENUP)
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Kammerer-Jacquet, Solene-Florence, Compérat, Eva, Egevad, Lars, Hes, Ondra, Oxley, Jon, Varma, Murali, Kristiansen, Glen, and Berney, Daniel M.
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- 2018
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29. Phospholipase D inhibitors reduce human prostate cancer cell proliferation and colony formation
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Noble, Amanda R, Maitland, Norman J, Berney, Daniel M, and Rumsby, Martin G
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- 2018
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30. Corrigendum to “Pathological predictors of metastatic disease in testicular non-seminomatous germ cell tumors: which tumor-node-metastasis staging system?”
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Scandura, Glenda, primary, Wagner, Thomas, additional, Beltran, Luis, additional, Alifrangis, Constantine, additional, Shamash, Jonathan, additional, and Berney, Daniel M., additional
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- 2023
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31. Prostate Adenocarcinoma Grade Group 1: Rationale for Retaining a Cancer Label in the 2022 World Health Organization Classification
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Netto, George J., primary, Amin, Mahul B., additional, Compérat, Eva M., additional, Gill, Anthony J., additional, Hartmann, Arndt, additional, Moch, Holger, additional, Menon, Santosh, additional, Raspollini, Maria R., additional, Rubin, Mark A., additional, Srigley, John R., additional, Hoon Tan, Puay, additional, Tickoo, Satish K., additional, Tsuzuki, Toyonori, additional, Turajlic, Samra, additional, Cree, Ian, additional, and Berney, Daniel M., additional
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- 2023
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32. A Validated Algorithm for Register-Based Identification of Patients with Relapse of Clinical Stage I Testicular Cancer
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Wagner, Thomas, primary, Lauritsen, Jakob, additional, Bandak, Mikkel, additional, Rasmussen, Linda Aagaard, additional, Bakker, Johannes, additional, Hovaldt, Hanna Birkbak, additional, Larsson, Heidi, additional, Christensen, Ib Jarle, additional, Toft, Birgitte Grønkær, additional, Agerbæk, Mads, additional, Dysager, Lars, additional, Kreiberg, Michael, additional, Rosenvilde, Josephine Julie, additional, Engvad, Birte, additional, Berney, Daniel M, additional, and Daugaard, Gedske, additional
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- 2023
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33. Supplementary Figure 2 from SOX9 Elevation in the Prostate Promotes Proliferation and Cooperates with PTEN Loss to Drive Tumor Formation
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Thomsen, Martin K., primary, Ambroisine, Laurence, primary, Wynn, Sarah, primary, Cheah, Kathryn S.E., primary, Foster, Christopher S., primary, Fisher, Gabrielle, primary, Berney, Daniel M., primary, Møller, Henrik, primary, Reuter, Victor E., primary, Scardino, Peter, primary, Cuzick, Jack, primary, Ragavan, Narasimhan, primary, Singh, Paras B., primary, Martin, Francis L., primary, Butler, Christopher M., primary, Cooper, Colin S., primary, and Swain, Amanda, primary
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- 2023
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34. Data from Androgen-Induced TMPRSS2:ERG Fusion in Nonmalignant Prostate Epithelial Cells
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Bastus, Nuria Coll, primary, Boyd, Lara K., primary, Mao, Xueying, primary, Stankiewicz, Elzbieta, primary, Kudahetti, Sakunthala C., primary, Oliver, R. Tim D., primary, Berney, Daniel M., primary, and Lu, Yong-Jie, primary
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- 2023
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35. Supplementary Figure 1 from SOX9 Elevation in the Prostate Promotes Proliferation and Cooperates with PTEN Loss to Drive Tumor Formation
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Thomsen, Martin K., primary, Ambroisine, Laurence, primary, Wynn, Sarah, primary, Cheah, Kathryn S.E., primary, Foster, Christopher S., primary, Fisher, Gabrielle, primary, Berney, Daniel M., primary, Møller, Henrik, primary, Reuter, Victor E., primary, Scardino, Peter, primary, Cuzick, Jack, primary, Ragavan, Narasimhan, primary, Singh, Paras B., primary, Martin, Francis L., primary, Butler, Christopher M., primary, Cooper, Colin S., primary, and Swain, Amanda, primary
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- 2023
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36. Supplementary Figures 1-2, Tables 1-8 from Distinct Genomic Alterations in Prostate Cancers in Chinese and Western Populations Suggest Alternative Pathways of Prostate Carcinogenesis
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Mao, Xueying, primary, Yu, Yongwei, primary, Boyd, Lara K., primary, Ren, Guoping, primary, Lin, Dongmei, primary, Chaplin, Tracy, primary, Kudahetti, Sakunthala C., primary, Stankiewicz, Elzbieta, primary, Xue, Liyan, primary, Beltran, Luis, primary, Gupta, Manu, primary, Oliver, R. Tim D., primary, Lemoine, Nick R., primary, Berney, Daniel M., primary, Young, Bryan D., primary, and Lu, Yong-Jie, primary
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- 2023
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37. Data from SOX9 Elevation in the Prostate Promotes Proliferation and Cooperates with PTEN Loss to Drive Tumor Formation
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Thomsen, Martin K., primary, Ambroisine, Laurence, primary, Wynn, Sarah, primary, Cheah, Kathryn S.E., primary, Foster, Christopher S., primary, Fisher, Gabrielle, primary, Berney, Daniel M., primary, Møller, Henrik, primary, Reuter, Victor E., primary, Scardino, Peter, primary, Cuzick, Jack, primary, Ragavan, Narasimhan, primary, Singh, Paras B., primary, Martin, Francis L., primary, Butler, Christopher M., primary, Cooper, Colin S., primary, and Swain, Amanda, primary
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- 2023
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38. Supplementary Figure 3 from SOX9 Elevation in the Prostate Promotes Proliferation and Cooperates with PTEN Loss to Drive Tumor Formation
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Thomsen, Martin K., primary, Ambroisine, Laurence, primary, Wynn, Sarah, primary, Cheah, Kathryn S.E., primary, Foster, Christopher S., primary, Fisher, Gabrielle, primary, Berney, Daniel M., primary, Møller, Henrik, primary, Reuter, Victor E., primary, Scardino, Peter, primary, Cuzick, Jack, primary, Ragavan, Narasimhan, primary, Singh, Paras B., primary, Martin, Francis L., primary, Butler, Christopher M., primary, Cooper, Colin S., primary, and Swain, Amanda, primary
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- 2023
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39. Supplementary Figures 1-3, Tables 1-2 from Androgen-Induced TMPRSS2:ERG Fusion in Nonmalignant Prostate Epithelial Cells
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Bastus, Nuria Coll, primary, Boyd, Lara K., primary, Mao, Xueying, primary, Stankiewicz, Elzbieta, primary, Kudahetti, Sakunthala C., primary, Oliver, R. Tim D., primary, Berney, Daniel M., primary, and Lu, Yong-Jie, primary
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- 2023
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40. Data from Distinct Genomic Alterations in Prostate Cancers in Chinese and Western Populations Suggest Alternative Pathways of Prostate Carcinogenesis
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Mao, Xueying, primary, Yu, Yongwei, primary, Boyd, Lara K., primary, Ren, Guoping, primary, Lin, Dongmei, primary, Chaplin, Tracy, primary, Kudahetti, Sakunthala C., primary, Stankiewicz, Elzbieta, primary, Xue, Liyan, primary, Beltran, Luis, primary, Gupta, Manu, primary, Oliver, R. Tim D., primary, Lemoine, Nick R., primary, Berney, Daniel M., primary, Young, Bryan D., primary, and Lu, Yong-Jie, primary
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- 2023
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41. A Validated Algorithm for Register-Based Identification of Patients with Relapse of Clinical Stage I Testicular Cancer
- Author
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Wagner,Thomas, Lauritsen,Jakob, Bandak,Mikkel, Rasmussen,Linda Aagaard, Bakker,Johannes, Hovaldt,Hanna Birkbak, Larsson,Heidi, Christensen,Ib Jarle, Toft,Birgitte Grønkær, Agerbæk,Mads, Dysager,Lars, Kreiberg,Michael, Rosenvilde,Josephine Julie, Engvad,Birte, Berney,Daniel M, Daugaard,Gedske, Wagner,Thomas, Lauritsen,Jakob, Bandak,Mikkel, Rasmussen,Linda Aagaard, Bakker,Johannes, Hovaldt,Hanna Birkbak, Larsson,Heidi, Christensen,Ib Jarle, Toft,Birgitte Grønkær, Agerbæk,Mads, Dysager,Lars, Kreiberg,Michael, Rosenvilde,Josephine Julie, Engvad,Birte, Berney,Daniel M, and Daugaard,Gedske
- Abstract
Thomas Wagner,1,2 Jakob Lauritsen,1 Mikkel Bandak,1 Linda Aagaard Rasmussen,3 Johannes Bakker,4 Hanna Birkbak Hovaldt,4 Heidi Larsson,4 Ib Jarle Christensen,1 Birgitte Grønkær Toft,2 Mads Agerbæk,5 Lars Dysager,6 Michael Kreiberg,1 Josephine Julie Rosenvilde,1 Birte Engvad,7 Daniel M Berney,8 Gedske Daugaard1 1Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark; 2Department of Pathology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark; 3Research Unit for General Practice, Aarhus, Denmark; 4The Danish Clinical Quality Program â National Clinical Registries (RKKP), Aarhus, Odense and Copenhagen, Denmark; 5Department of Oncology, Aarhus University Hospital, Aarhus, Denmark; 6Department of Oncology, Odense University Hospital, Odense, Denmark; 7Department of Pathology, Odense University Hospital, Odense, Denmark; 8Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, UKCorrespondence: Thomas Wagner, Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Blegdamsvej 9, Copenhagen, 2100, Denmark, Tel +45 35459682, Email thomas.wagner.nielsen@regionh.dkPurpose: The Danish Testicular Cancer (DaTeCa) database aims to monitor and improve quality of care for testicular cancer patients. Relapse data registered in the DaTeCa database rely on manual registration. Currently, some safeguarding against missing registrations is attempted by a non-validated register-based algorithm. However, this algorithm is inaccurate and entails time-consuming medical record reviews. We aimed (1) to validate relapse data as registered in the DaTeCa database, and (2) to develop and validate an improved register-based algorithm identifying patients diagnosed with relapse of clinical stage I testicular cancer.Patients and Methods: Patients registered in the DaTeCa database with clinical stage I testicular cancer from 2013 to 2018 were included. Medical record i
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- 2023
42. A Validated Algorithm for Register-Based Identification of Patients with Relapse of Clinical Stage I Testicular Cancer
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Wagner, Thomas, Lauritsen, Jakob, Bandak, Mikkel, Rasmussen, Linda Aagaard, Bakker, Johannes, Hovaldt, Hanna Birkbak, Larsson, Heidi, Christensen, Ib Jarle, Toft, Birgitte Grønkær, Agerbæk, Mads, Dysager, Lars, Kreiberg, Michael, Rosenvilde, Josephine Julie, Engvad, Birte, Berney, Daniel M., Daugaard, Gedske, Wagner, Thomas, Lauritsen, Jakob, Bandak, Mikkel, Rasmussen, Linda Aagaard, Bakker, Johannes, Hovaldt, Hanna Birkbak, Larsson, Heidi, Christensen, Ib Jarle, Toft, Birgitte Grønkær, Agerbæk, Mads, Dysager, Lars, Kreiberg, Michael, Rosenvilde, Josephine Julie, Engvad, Birte, Berney, Daniel M., and Daugaard, Gedske
- Abstract
Purpose: The Danish Testicular Cancer (DaTeCa) database aims to monitor and improve quality of care for testicular cancer patients. Relapse data registered in the DaTeCa database rely on manual registration. Currently, some safeguarding against missing registrations is attempted by a non-validated register-based algorithm. However, this algorithm is inaccurate and entails time-consuming medical record reviews. We aimed (1) to validate relapse data as registered in the DaTeCa database, and (2) to develop and validate an improved register-based algorithm identifying patients diagnosed with relapse of clinical stage I testicular cancer. Patients and Methods: Patients registered in the DaTeCa database with clinical stage I testicular cancer from 2013 to 2018 were included. Medical record information on relapse data served as a gold standard. A pre-specified algorithm to identify relapse was tested and optimized on a random sample of 250 patients. Indicators of relapse were obtained from pathology codes in the Danish National Pathology Register and from diagnosis and procedure codes in the Danish National Patient Register. We applied the final algorithm to the remaining study population to validate its performance. Results: Of the 1377 included patients, 284 patients relapsed according to the gold standard during a median follow-up time of 5.9 years. The completeness of relapse data registered in the DaTeCa database was 97.2% (95% confidence interval (CI): 95.2– 99.1). The algorithm achieved a sensitivity of 99.6% (95% CI: 98.7– 100), a specificity of 98.9% (95% CI: 98.2– 99.6), and a positive predictive value of 95.9% (95% CI: 93.4– 98.4) in the validation cohort (n = 1127, 233 relapses). Conclusion: The registration of relapse data in the DaTeCa database is accurate, confirming the database as a reliable source for ongoing clinical quality assessments. Applying the provided algorithm to the DaTeCa database will optimize the accuracy of relapse data further, Purpose: The Danish Testicular Cancer (DaTeCa) database aims to monitor and improve quality of care for testicular cancer patients. Relapse data registered in the DaTeCa database rely on manual registration. Currently, some safeguarding against missing registrations is attempted by a non-validated register-based algorithm. However, this algorithm is inaccurate and entails time-consuming medical record reviews. We aimed (1) to validate relapse data as registered in the DaTeCa database, and (2) to develop and validate an improved register-based algorithm identifying patients diagnosed with relapse of clinical stage I testicular cancer. Patients and Methods: Patients registered in the DaTeCa database with clinical stage I testicular cancer from 2013 to 2018 were included. Medical record information on relapse data served as a gold standard. A pre-specified algorithm to identify relapse was tested and optimized on a random sample of 250 patients. Indicators of relapse were obtained from pathology codes in the Danish National Pathology Register and from diagnosis and procedure codes in the Danish National Patient Register. We applied the final algorithm to the remaining study population to validate its performance. Results: Of the 1377 included patients, 284 patients relapsed according to the gold standard during a median follow-up time of 5.9 years. The completeness of relapse data registered in the DaTeCa database was 97.2% (95% confidence interval (CI): 95.2–99.1). The algorithm achieved a sensitivity of 99.6% (95% CI: 98.7–100), a specificity of 98.9% (95% CI: 98.2–99.6), and a positive predictive value of 95.9% (95% CI: 93.4–98.4) in the validation cohort (n = 1127, 233 relapses). Conclusion: The registration of relapse data in the DaTeCa database is accurate, confirming the database as a reliable source for ongoing clinical quality assessments. Applying the provided algorithm to the DaTeCa database will optimize the accuracy of relapse data further, decrease tim
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- 2023
43. Tumors of the Testis: Morphologic Features and Molecular Alterations
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Howitt, Brooke E. and Berney, Daniel M.
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- 2015
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44. Histopathologic False-positive Diagnoses of Prostate Cancer in the Age of Immunohistochemistry
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Beltran, Luis, Ahmad, Amar S., Sandu, Holly, Kudahetti, Sakunthala, Soosay, Geraldine, Møller, Henrik, Cuzick, Jack, and Berney, Daniel M.
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- 2019
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45. Seminoma and dysgerminoma: evidence for alignment of clinical trials and de-escalation of systemic chemotherapy.
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Wood, Georgina E., Bunting, Christopher P., Veli, Mesel, Arora, Rupali, Berney, Daniel M., Alifrangis, Constantine, MacDonald, Nicola D., Miller, Rowan E., Shamash, Jonathan, Stoneham, Sara, and Lockley, Michelle
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CANCER chemotherapy ,SEMINOMA ,CLINICAL trials ,GERM cells ,GENE expression ,CANCER cells - Abstract
Malignant germ cell tumours are a group of rare cancers whose incidence peaks in late adolescence and early adulthood. Dysgerminomas of the ovary and seminomas of the testis are analogous diseases, but seminomas have a 10-fold higher incidence. The two tumours are morphologically identical and are only differentiated by surrounding organ-specific tissue or testicular germ cell neoplasia in situ. They share genetic features including KIT and RAS mutations, amplification of chromosome 12p, and expression of pluripotency markers (NANOG (Nanog homeobox), OCT3/4 (Octamer-binding transcription factor 3/4), and SAL4 (Spalt-like trascription factor 4)). Both histologies are exquisitely sensitive to platinum chemotherapy, and the combination of bleomycin, etoposide, and cisplatin (BEP) yields survival rates greater than 90%. However, BEP causes significant, lifelong toxicity (cardiovascular, renal, respiratory, and neurological) in these young patients with an expectation of cure. Here, we comprehensively review the biological features of dysgerminoma and seminoma to demonstrate that they are biologically analogous diseases. We present available clinical trial data supporting de-escalation of chemotherapy treatment. Finally, we propose that future trials should enrol men, women, and children to benefit all patients regardless of age or sex. [ABSTRACT FROM AUTHOR]
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- 2023
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46. Fumarate hydratase‐deficient testicular sex cord‐stromal tumour (FH‐TSCST): proposal for reclassification of a subset of Leydig cell tumours with distinct molecular and clinicopathologic features
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Acosta, Andres M, primary, Colecchia, Maurizio, additional, and Berney, Daniel M, additional
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- 2023
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47. Testicular cancer
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Cheng, Liang, Albers, Peter, Berney, Daniel M., Feldman, Darren R., Daugaard, Gedske, Gilligan, Timothy, and Looijenga, Leendert H. J.
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- 2018
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48. Testicular Tumors
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Dashora, Abhishek, primary, Wagner, Thomas, additional, and Berney, Daniel M., additional
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- 2022
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49. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
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Jiao, Wei, Atwal, Gurnit, Polak, Paz, Karlic, Rosa, Cuppen, Edwin, Al-Shahrour, Fatima, Bailey, Peter J, Biankin, Andrew V, Boutros, Paul C, Campbell, Peter J, Chang, David K, Cooke, Susanna L, Deshpande, Vikram, Faltas, Bishoy M, Faquin, William C, Garraway, Levi, Getz, Gad, Grimmond, Sean M, Haider, Syed, Hoadley, Katherine A, Kaiser, Vera B, Kato, Mamoru, Kübler, Kirsten, Lazar, Alexander J, Li, Constance H, Louis, David N, Margolin, Adam, Martin, Sancha, Nahal-Bose, Hardeep K, Nielsen, G Petur, Nik-Zainal, Serena, Omberg, Larsson, P’ng, Christine, Perry, Marc D, Rheinbay, Esther, Rubin, Mark A, Semple, Colin A, Sgroi, Dennis C, Shibata, Tatsuhiro, Siebert, Reiner, Smith, Jaclyn, Stein, Lincoln D, Stobbe, Miranda D, Sun, Ren X, Thai, Kevin, Wright, Derek W, Wu, Chin-Lee, Yuan, Ke, Zhang, Junjun, Danyi, Alexandra, de Ridder, Jeroen, van Herpen, Carla, Lolkema, Martijn P, Steeghs, Neeltje, Morris, Quaid D, Aaltonen, Lauri A, Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J, Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C, Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B, Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G, Amary, Fernanda, Amin, Samirkumar B, Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J, Ang, Yeng, Antonello, Davide, Anur, Pavana, Aparicio, Samuel, Appelbaum, Elizabeth L, Arai, Yasuhito, Aretz, Axel, Arihiro, Koji, Ariizumi, Shun-ichi, Armenia, Joshua, Arnould, Laurent, Asa, Sylvia, Assenov, Yassen, Aukema, Sietse, Auman, J Todd, Aure, Miriam RR, Awadalla, Philip, Aymerich, Marta, Bader, Gary D, Baez-Ortega, Adrian, Bailey, Matthew H, Balasundaram, Miruna, Balu, Saianand, Bandopadhayay, Pratiti, Banks, Rosamonde E, Barbi, Stefano, Barbour, Andrew P, Barenboim, Jonathan, Barnholtz-Sloan, Jill, Barr, Hugh, Barrera, Elisabet, Bartlett, John, Bartolome, Javier, Bassi, Claudio, Bathe, Oliver F, Baumhoer, Daniel, Bavi, Prashant, Baylin, Stephen B, Bazant, Wojciech, Beardsmore, Duncan, Beck, Timothy A, Behjati, Sam, Behren, Andreas, Niu, Beifang, Bell, Cindy, Beltran, Sergi, Benz, Christopher, Berchuck, Andrew, Bergmann, Anke K, Bergstrom, Erik N, Berman, Benjamin P, Berney, Daniel M, Bernhart, Stephan H, Beroukhim, Rameen, Berrios, Mario, Bersani, Samantha, Bertl, Johanna, Betancourt, Miguel, Bhandari, Vinayak, Bhosle, Shriram G, Bieg, Matthias, Bigner, Darell, Binder, Hans, Birney, Ewan, Birrer, Michael, Biswas, Nidhan K, Bjerkehagen, Bodil, Bodenheimer, Tom, Boice, Lori, Bonizzato, Giada, De Bono, Johann S, Boot, Arnoud, Bootwalla, Moiz S, Borg, Ake, Borkhardt, Arndt, Boroevich, Keith A, Borozan, Ivan, Borst, Christoph, Bosenberg, Marcus, Bosio, Mattia, Boultwood, Jacqueline, Bourque, Guillaume, Bova, G Steven, Bowen, David T, Bowlby, Reanne, Bowtell, David DL, Boyault, Sandrine, Boyce, Rich, Boyd, Jeffrey, Brazma, Alvis, Brennan, Paul, Brewer, Daniel S, Brinkman, Arie B, Bristow, Robert G, Broaddus, Russell R, Brock, Jane E, Brock, Malcolm, Broeks, Annegien, Brooks, Angela N, Brooks, Denise, Brors, Benedikt, Brunak, Søren, Bruxner, Timothy JC, Bruzos, Alicia L, Buchanan, Alex, Buchhalter, Ivo, Buchholz, Christiane, Bullman, Susan, Burke, Hazel, Burkhardt, Birgit, Burns, Kathleen H, Busanovich, John, Bustamante, Carlos D, Butler, Adam P, Butte, Atul J, Byrne, Niall J, Børresen-Dale, Anne-Lise, Caesar-Johnson, Samantha J, Cafferkey, Andy, Cahill, Declan, Calabrese, Claudia, Caldas, Carlos, Calvo, Fabien, Camacho, Niedzica, Campo, Elias, Cantù, Cinzia, Cao, Shaolong, Carey, Thomas E, Carlevaro-Fita, Joana, Carlsen, Rebecca, Cataldo, Ivana, Cazzola, Mario, Cebon, Jonathan, Cerfolio, Robert, Chadwick, Dianne E, Chakravarty, Dimple, Chalmers, Don, Chan, Calvin Wing Yiu, Chan, Kin, Chan-Seng-Yue, Michelle, Chandan, Vishal S, Chanock, Stephen J, Chantrill, Lorraine A, Chateigner, Aurélien, Chatterjee, Nilanjan, Chayama, Kazuaki, Chen, Hsiao-Wei, Chen, Jieming, Chen, Ken, Chen, Yiwen, Chen, Zhaohong, Cherniack, Andrew D, Chien, Jeremy, Chiew, Yoke-Eng, Chin, Suet-Feung, Cho, Juok, Cho, Sunghoon, Choi, Jung Kyoon, Choi, Wan, Chomienne, Christine, Chong, Zechen, Choo, Su Pin, Chou, Angela, Christ, Angelika N, Christie, Elizabeth L, Chuah, Eric, Cibulskis, Carrie, Cibulskis, Kristian, Cingarlini, Sara, Clapham, Peter, Claviez, Alexander, Cleary, Sean, Cloonan, Nicole, Cmero, Marek, Collins, Colin C, Connor, Ashton A, Cooper, Colin S, Cope, Leslie, Corbo, Vincenzo, Cordes, Matthew G, Cordner, Stephen M, Cortés-Ciriano, Isidro, Covington, Kyle, Cowin, Prue A, Craft, Brian, Craft, David, Creighton, Chad J, Cun, Yupeng, Curley, Erin, Cutcutache, Ioana, Czajka, Karolina, Czerniak, Bogdan, Dagg, Rebecca A, Danilova, Ludmila, Davi, Maria Vittoria, Davidson, Natalie R, Davies, Helen, Davis, Ian J, Davis-Dusenbery, Brandi N, Dawson, Kevin J, De La Vega, Francisco M, De Paoli-Iseppi, Ricardo, Defreitas, Timothy, Dei Tos, Angelo P, Delaneau, Olivier, Demchok, John A, Demeulemeester, Jonas, Demidov, German M, Demircioğlu, Deniz, Dennis, Nening M, Denroche, Robert E, Dentro, Stefan C, Desai, Nikita, Deshwar, Amit G, Desmedt, Christine, Deu-Pons, Jordi, Dhalla, Noreen, Dhani, Neesha C, Dhingra, Priyanka, Dhir, Rajiv, DiBiase, Anthony, Diamanti, Klev, Ding, Li, Ding, Shuai, Dinh, Huy Q, Dirix, Luc, Doddapaneni, HarshaVardhan, Donmez, Nilgun, Dow, Michelle T, Drapkin, Ronny, Drechsel, Oliver, Drews, Ruben M, Serge, Serge, Dudderidge, Tim, Dueso-Barroso, Ana, Dunford, Andrew J, Dunn, Michael, Dursi, Lewis Jonathan, Duthie, Fraser R, Dutton-Regester, Ken, Eagles, Jenna, Easton, Douglas F, Edmonds, Stuart, Edwards, Paul A, Edwards, Sandra E, Eeles, Rosalind A, Ehinger, Anna, Eils, Juergen, Eils, Roland, El-Naggar, Adel, Eldridge, Matthew, Ellrott, Kyle, Erkek, Serap, Escaramis, Georgia, Espiritu, Shadrielle MG, Estivill, Xavier, Etemadmoghadam, Dariush, Eyfjord, Jorunn E, Fan, Daiming, Fan, Yu, Farcas, Claudiu, Fassan, Matteo, Fatima, Aquila, Favero, Francesco, Fayzullaev, Nodirjon, Felau, Ina, Fereday, Sian, Ferguson, Martin L, Ferretti, Vincent, Feuerbach, Lars, Field, Matthew A, Fink, J Lynn, Finocchiaro, Gaetano, Fisher, Cyril, Fittall, Matthew W, Fitzgerald, Anna, Fitzgerald, Rebecca C, Flanagan, Adrienne M, Fleshner, Neil E, Flicek, Paul, Foekens, John A, Fong, Kwun M, Fonseca, Nuno A, Foster, Christopher S, Fox, Natalie S, Fraser, Michael, Frazer, Scott, Frenkel-Morgenstern, Milana, Friedman, William, Frigola, Joan, Fronick, Catrina C, Fujimoto, Akihiro, Fujita, Masashi, Fukayama, Masashi, Fulton, Lucinda A, Fulton, Robert S, Furuta, Mayuko, Futreal, P Andrew, Füllgrabe, Anja, Gabriel, Stacey B, Gallinger, Steven, Gambacorti-Passerini, Carlo, Gao, Jianjiong, Gao, Shengjie, Garred, Øystein, Garrison, Erik, Garsed, Dale W, Gehlenborg, Nils, Gelpi, Josep LL, George, Joshy, Gerhard, Daniela S, Gerhauser, Clarissa, Gershenwald, Jeffrey E, Gerstein, Mark, Gerstung, Moritz, Ghori, Mohammed, Ghossein, Ronald, Giama, Nasra H, Gibbs, Richard A, Gibson, Bob, Gill, Anthony J, Gill, Pelvender, Giri, Dilip D, Glodzik, Dominik, Gnanapragasam, Vincent J, Goebler, Maria Elisabeth, Goldman, Mary J, Gomez, Carmen, Gonzalez, Santiago, Gonzalez-Perez, Abel, Gordenin, Dmitry A, Gossage, James, Gotoh, Kunihito, Govindan, Ramaswamy, Grabau, Dorthe, Graham, Janet S, Grant, Robert C, Green, Anthony R, Green, Eric, Greger, Liliana, Grehan, Nicola, Grimaldi, Sonia, Grossman, Robert L, Grundhoff, Adam, Gundem, Gunes, Guo, Qianyun, Gupta, Manaswi, Gupta, Shailja, Gut, Ivo G, Gut, Marta, Göke, Jonathan, Ha, Gavin, Haake, Andrea, Haan, David, Haas, Siegfried, Haase, Kerstin, Haber, James E, Habermann, Nina, Hach, Faraz, Hama, Natsuko, Hamdy, Freddie C, Hamilton, Anne, Hamilton, Mark P, Han, Leng, Hanna, George B, Hansmann, Martin, Haradhvala, Nicholas J, Harismendy, Olivier, Harliwong, Ivon, Harmanci, Arif O, Harrington, Eoghan, Hasegawa, Takanori, Haussler, David, Hawkins, Steve, Hayami, Shinya, Hayashi, Shuto, Hayes, D Neil, Hayes, Stephen J, Hayward, Nicholas K, Hazell, Steven, He, Yao, Heath, Allison P, Heath, Simon C, Hedley, David, Hegde, Apurva M, Heiman, David I, Heinold, Michael C, Heins, Zachary, Heisler, Lawrence E, Hellstrom-Lindberg, Eva, Helmy, Mohamed, Heo, Seong Gu, Hepperla, Austin J, Heredia-Genestar, José María, Herrmann, Carl, Hersey, Peter, Hess, Julian M, Hilmarsdottir, Holmfridur, Hinton, Jonathan, Hirano, Satoshi, Hiraoka, Nobuyoshi, Hobolth, Asger, Hodzic, Ermin, Hoell, Jessica I, Hoffmann, Steve, Hofmann, Oliver, Holbrook, Andrea, Holik, Aliaksei Z, Hollingsworth, Michael A, Holmes, Oliver, Holt, Robert A, Hong, Chen, Hong, Eun Pyo, Hong, Jongwhi H, Hooijer, Gerrit K, Hornshøj, Henrik, Hosoda, Fumie, Hou, Yong, Hovestadt, Volker, Howat, William, Hoyle, Alan P, Hruban, Ralph H, Hu, Jianhong, Hu, Taobo, Hua, Xing, Huang, Kuan-lin, Huang, Mei, Huang, Mi Ni, Huang, Vincent, Huang, Yi, Huber, Wolfgang, Hudson, Thomas J, Hummel, Michael, Hung, Jillian A, Huntsman, David, Hupp, Ted R, Huse, Jason, Huska, Matthew R, Hutter, Barbara, Hutter, Carolyn M, Hübschmann, Daniel, Iacobuzio-Donahue, Christine A, Imbusch, Charles David, Imielinski, Marcin, Imoto, Seiya, Isaacs, William B, Isaev, Keren, Ishikawa, Shumpei, Iskar, Murat, Islam, SM Ashiqul, Ittmann, Michael, Ivkovic, Sinisa, Izarzugaza, Jose MG, Jacquemier, Jocelyne, Jakrot, Valerie, Jamieson, Nigel B, Jang, Gun Ho, Jang, Se Jin, Jayaseelan, Joy C, Jayasinghe, Reyka, Jefferys, Stuart R, Jegalian, Karine, Jennings, Jennifer L, Jeon, Seung-Hyup, Jerman, Lara, Ji, Yuan, Johansson, Peter A, Johns, Amber L, Johns, Jeremy, Johnson, Rory, Johnson, Todd A, Jolly, Clemency, Joly, Yann, Jonasson, Jon G, Jones, Corbin D, Jones, David R, Jones, David TW, Jones, Nic, Jones, Steven JM, Jonkers, Jos, Ju, Young Seok, Juhl, Hartmut, Jung, Jongsun, Juul, Malene, Juul, Randi Istrup, Juul, Sissel, Jäger, Natalie, Kabbe, Rolf, Kahles, Andre, Kahraman, Abdullah, Kakavand, Hojabr, Kalimuthu, Sangeetha, von Kalle, Christof, Kang, Koo Jeong, Karaszi, Katalin, Karlan, Beth, Karlić, Rosa, Karsch, Dennis, Kasaian, Katayoon, Kassahn, Karin S, Katai, Hitoshi, Katoh, Hiroto, Kawakami, Yoshiiku, Kay, Jonathan D, Kazakoff, Stephen H, Kazanov, Marat D, Keays, Maria, Kebebew, Electron, Kefford, Richard F, Kellis, Manolis, Kench, James G, Kennedy, Catherine J, Kerssemakers, Jules NA, Khoo, David, Khoo, Vincent, Khuntikeo, Narong, Khurana, Ekta, Kilpinen, Helena, Kim, Hark Kyun, Kim, Hyung-Lae, Kim, Hyung-Yong, Kim, Hyunghwan, Kim, Jaegil, Kim, Jihoon, Kim, Jong K, Kim, Youngwook, King, Tari A, Klapper, Wolfram, Kleinheinz, Kortine, Klimczak, Leszek J, Knappskog, Stian, Kneba, Michael, Knoppers, Bartha M, Koh, Youngil, Komorowski, Jan, Komura, Daisuke, Komura, Mitsuhiro, Kong, Gu, Kool, Marcel, Korbel, Jan O, Korchina, Viktoriya, Korshunov, Andrey, Koscher, Michael, Koster, Roelof, Kote-Jarai, Zsofia, Koures, Antonios, Kovacevic, Milena, Kremeyer, Barbara, Kretzmer, Helene, Kreuz, Markus, Krishnamurthy, Savitri, Kube, Dieter, Kumar, Kiran, Kumar, Pardeep, Kumar, Sushant, Kumar, Yogesh, Kundra, Ritika, Küppers, Ralf, Lagergren, Jesper, Lai, Phillip H, Laird, Peter W, Lakhani, Sunil R, Lalansingh, Christopher M, Lalonde, Emilie, Lamaze, Fabien C, Lambert, Adam, Lander, Eric, Landgraf, Pablo, Landoni, Luca, Langerød, Anita, Lanzós, Andrés, Larsimont, Denis, Larsson, Erik, Lathrop, Mark, Lau, Loretta MS, Lawerenz, Chris, Lawlor, Rita T, Lawrence, Michael S, Lazic, Ana Mijalkovic, Le, Xuan, Lee, Darlene, Lee, Donghoon, Lee, Eunjung Alice, Lee, Hee Jin, Lee, Jake June-Koo, Lee, Jeong-Yeon, Lee, Juhee, Lee, Ming Ta Michael, Lee-Six, Henry, Lehmann, Kjong-Van, Lehrach, Hans, Lenze, Dido, Leonard, Conrad R, Leongamornlert, Daniel A, Leshchiner, Ignaty, Letourneau, Louis, Letunic, Ivica, Levine, Douglas A, Lewis, Lora, Ley, Tim, Li, Chang, Li, Haiyan Irene, Li, Jun, Li, Lin, Li, Shantao, Li, Siliang, Li, Xiaobo, Li, Xiaotong, Li, Xinyue, Li, Yilong, Liang, Han, Liang, Sheng-Ben, Lichter, Peter, Lin, Pei, Lin, Ziao, Linehan, WM, Lingjærde, Ole Christian, Liu, Dongbing, Liu, Eric Minwei, Liu, Fei-Fei Fei, Liu, Fenglin, Liu, Jia, Liu, Xingmin, Livingstone, Julie, Livitz, Dimitri, Livni, Naomi, Lochovsky, Lucas, Loeffler, Markus, Long, Georgina V, Lopez-Guillermo, Armando, Lou, Shaoke, Lovat, Laurence B, Lu, Yiling, Lu, Yong-Jie, Lu, Youyong, Luchini, Claudio, Lungu, Ilinca, Luo, Xuemei, Luxton, Hayley J, Lynch, Andy G, Lype, Lisa, López, Cristina, López-Otín, Carlos, Z, Eric, Ma, Yussanne, MacGrogan, Gaetan, MacRae, Shona, Macintyre, Geoff, Madsen, Tobias, Maejima, Kazuhiro, Mafficini, Andrea, Maglinte, Dennis T, Maitra, Arindam, Majumder, Partha P, Malcovati, Luca, Malikic, Salem, Malleo, Giuseppe, Mann, Graham J, Mantovani-Löffler, Luisa, Marchal, Kathleen, Marchegiani, Giovanni, Mardis, Elaine R, Margolin, Adam A, Marin, Maximillian G, Markowetz, Florian, Markowski, Julia, Marks, Jeffrey, Marques-Bonet, Tomas, Marra, Marco A, Marsden, Luke, Martens, John WM, Martin-Subero, Jose I, Martincorena, Iñigo, Martinez-Fundichely, Alexander, Maruvka, Yosef E, Mashl, R Jay, Massie, Charlie E, Matthew, Thomas J, Matthews, Lucy, Mayer, Erik, Mayes, Simon, Mayo, Michael, Mbabaali, Faridah, McCune, Karen, McDermott, Ultan, McGillivray, Patrick D, McLellan, Michael D, McPherson, John D, McPherson, John R, McPherson, Treasa A, Meier, Samuel R, Meng, Alice, Meng, Shaowu, Menzies, Andrew, Merrett, Neil D, Merson, Sue, Meyerson, Matthew, Meyerson, William, Mieczkowski, Piotr A, Mihaiescu, George L, Mijalkovic, Sanja, Mikkelsen, Tom, Milella, Michele, Mileshkin, Linda, Miller, Christopher A, Miller, David K, Miller, Jessica K, Mills, Gordon B, Milovanovic, Ana, Minner, Sarah, Miotto, Marco, Arnau, Gisela Mir, Mirabello, Lisa, Mitchell, Chris, Mitchell, Thomas J, Miyano, Satoru, Miyoshi, Naoki, Mizuno, Shinichi, Molnár-Gábor, Fruzsina, Moore, Malcolm J, Moore, Richard A, Morganella, Sandro, Morrison, Carl, Mose, Lisle E, Moser, Catherine D, Muiños, Ferran, Mularoni, Loris, Mungall, Andrew J, Mungall, 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Deurzen, Carolien HM, van de Vijver, Marc J, Veer, L van’t, and von Mering, Christian
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Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA.
- Published
- 2023
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50. Combined burden and functional impact tests for cancer driver discovery using DriverPower
- Author
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- Subjects
Human Biology & Physiology ,Ecology,Evolution & Ethology ,Tumour Biology ,Genetics & Genomics ,Structural Biology & Biophysics ,Computational & Systems Biology - Abstract
The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2658 cancers across 38 tumour types, we describe DriverPower, a software package that uses mutational burden and functional impact evidence to identify driver mutations in coding and non-coding sites within cancer whole genomes. Using a total of 1373 genomic features derived from public sources, DriverPower’s background mutation model explains up to 93% of the regional variance in the mutation rate across multiple tumour types. By incorporating functional impact scores, we are able to further increase the accuracy of driver discovery. Testing across a collection of 2583 cancer genomes from the PCAWG project, DriverPower identifies 217 coding and 95 non-coding driver candidates. Comparing to six published methods used by the PCAWG Drivers and Functional Interpretation Working Group, DriverPower has the highest F1 score for both coding and non-coding driver discovery. This demonstrates that DriverPower is an effective framework for computational driver discovery.
- Published
- 2023
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