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5. Abstracts from the 3rd Conference on Aneuploidy and Cancer: Clinical and Experimental Aspects

Author

Cornish-Bowden, Athel, Rasnick, David, Heng, Henry H, Horne, Steven, Abdallah, Batoul, Liu, Guo, Ye, Christine J, Bloomfield, Mathew, Vincent, Mark D, Aldaz, C Marcelo, Karlsson, Jenny, Valind, Anders, Jansson, Caroline, Gisselsson, David, Graves, Jennifer A Marshall, Stepanenko, Aleksei A, Andreieva, Svitlana V, Korets, Kateryna V, Mykytenko, Dmytro O, Huleyuk, Nataliya L, Baklaushev, Vladimir P, Kovaleva, Oksana A, Chekhonin, Vladimir P, Vassetzky, Yegor S, Avdieiev, Stanislav S, Bakker, Bjorn, Taudt, Aaron S, Belderbos, Mirjam E, Porubsky, David, Spierings, Diana CJ, de Jong, Tristan V, Halsema, Nancy, Kazemier, Hinke G, Hoekstra-Wakker, Karina, Bradley, Allan, de Bont, Eveline SJM, van den Berg, Anke, Guryev, Victor, Lansdorp, Peter M, Tatché, Maria Colomé, Foijer, Floris, Liehr, Thomas, Baudoin, Nicolaas C, Nicholson, Joshua M, Soto, Kimberly, Quintanilla, Isabel, Camps, Jordi, Cimini, Daniela, Dürrbaum, M, Donnelly, N, Passerini, V, Kruse, C, Habermann, B, Storchová, Z, Mandrioli, Daniele, Belpoggi, Fiorella, Silbergeld, Ellen K, Perry, Melissa J, Skotheim, Rolf I, Løvf, Marthe, Johannessen, Bjarne, Hoff, Andreas M, Zhao, Sen, SveeStrømme, Jonas M, Sveen, Anita, Lothe, Ragnhild A, Hehlmann, R, Voskanyan, A, Fabarius, A, Böcking, Alfred, Biesterfeld, Stefan, Berynskyy, Leonid, Börgermann, Christof, Engers, Rainer, Dietz, Josef, Fritz, A, Sehgal, N, Vecerova, J, Stojkovicz, B, Ding, H, Page, N, Tye, C, Bhattacharya, S, Xu, J, Stein, G, Stein, J, Berezney, R, Gong, Xue, Grasedieck, Sarah, Swoboda, Julian, Rücker, Frank G, Bullinger, Lars, Pollack, Jonathan R, Roumelioti, Fani-Marlen, Chiourea, Maria, Raftopoulou, Christina, Gagos, Sarantis, Duesberg, Peter, and Bloomfield, Mat

Subjects
Genetics
Published
2017

6. Evolutionary mode and timing of dissemination of high-grade serous carcinomas

Author

Sveen, Anita, primary, Johannessen, Bjarne, additional, Klokkerud, Solveig M.K., additional, Kraggerud, Sigrid M., additional, Meza-Zepeda, Leonardo A., additional, Bjørnslett, Merete, additional, Bischof, Katharina, additional, Myklebost, Ola, additional, Taskén, Kjetil, additional, Skotheim, Rolf I., additional, Dørum, Anne, additional, Davidson, Ben, additional, and Lothe, Ragnhild A., additional

Published
2024
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7. Identification of 22 susceptibility loci associated with testicular germ cell tumors

Author

Pluta, John, Pyle, Louise C., Nead, Kevin T., Wilf, Rona, Li, Mingyao, Mitra, Nandita, Weathers, Benita, D’Andrea, Kurt, Almstrup, Kristian, Anson-Cartwright, Lynn, Benitez, Javier, Brown, Christopher D., Chanock, Stephen, Chen, Chu, Cortessis, Victoria K., Ferlin, Alberto, Foresta, Carlo, Gamulin, Marija, Gietema, Jourik A., Grasso, Chiara, Greene, Mark H., Grotmol, Tom, Hamilton, Robert J., Haugen, Trine B., Hauser, Russ, Hildebrandt, Michelle A. T., Johnson, Matthew E., Karlsson, Robert, Kiemeney, Lambertus A., Lessel, Davor, Lothe, Ragnhild A., Loud, Jennifer T., Loveday, Chey, Martin-Gimeno, Paloma, Meijer, Coby, Nsengimana, Jérémie, Quinn, David I., Rafnar, Thorunn, Ramdas, Shweta, Richiardi, Lorenzo, Skotheim, Rolf I., Stefansson, Kari, Turnbull, Clare, Vaughn, David J., Wiklund, Fredrik, Wu, Xifeng, Yang, Daphne, Zheng, Tongzhang, Wells, Andrew D., Grant, Struan F. A., Rajpert-De Meyts, Ewa, Schwartz, Stephen M., Bishop, D. Timothy, McGlynn, Katherine A., Kanetsky, Peter A., and Nathanson, Katherine L.

Published
2021
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12. 'High proliferative cribriform prostate cancer' defines a patient subgroup with an inferior prognosis.

Author

Bogaard, Mari, Skotheim, Rolf I, Maltau, Aase V, Kidd, Susanne G, Lothe, Ragnhild A, Axcrona, Karol, and Axcrona, Ulrika

Subjects
*PROSTATE cancer, *RADICAL prostatectomy, *PROGNOSIS, *DISEASE risk factors, *PROGRESSION-free survival
Abstract

Aims: A cribriform pattern, reactive stroma (RS), PTEN, Ki67 and ERG are promising prognostic biomarkers in primary prostate cancer (PCa). We aim to determine the relative contribution of these factors and the Cancer of the Prostate Risk Assessment Postsurgical (CAPRA‐S) score in predicting PCa prognosis. Methods and results: We included 475 patients who underwent radical prostatectomy (2010–12, median follow‐up = 8.7 years). Cribriform pattern was identified in 57% of patients, PTEN loss in 55%, ERG expression in 51%, RS in 39% and high Ki67 in 9%. In patients with multiple samples from the same malignant focus and either PTEN loss or high Ki67, intrafocal heterogeneity for PTEN and Ki67 expression was detected in 55% and 89%, respectively. In patients with samples from two or more foci, interfocal heterogeneity was detected in 46% for PTEN and 6% for Ki67. A cribriform pattern and Ki67 were independent predictors of biochemical recurrence (BCR) and clinical recurrence (CR), whereas ERG expression was an independent predictor of CR. Besides CAPRA‐S, a cribriform pattern provided the highest relative proportion of explained variation for predicting BCR (11%), and Ki67 provided the highest relative proportion of explained variation for CR (21%). In patients with a cribriform pattern, high Ki67 was associated with a higher risk of BCR [hazard ratio (HR) = 2.83, P < 0.001] and CR (HR = 4.35, P < 0.001). Conclusions: High Ki67 in patients with a cribriform pattern identifies a patient subgroup with particularly poor prognosis, which we termed 'high proliferative cribriform prostate cancer'. These results support reporting a cribriform pattern in pathology reports, and advocate implementing Ki67. [ABSTRACT FROM AUTHOR]

Published
2023
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13. Supplemental Materials, Figures S1-6, Tables S1-4 from Regulator of Chromosome Condensation 2 Identifies High-Risk Patients within Both Major Phenotypes of Colorectal Cancer

Author

Bruun, Jarle, primary, Kolberg, Matthias, primary, Ahlquist, Terje C., primary, Røyrvik, Ellen C., primary, Nome, Torfinn, primary, Leithe, Edward, primary, Lind, Guro E., primary, Merok, Marianne A., primary, Rognum, Torleiv O., primary, Bjørkøy, Geir, primary, Johansen, Terje, primary, Lindblom, Annika, primary, Sun, Xiao-Feng, primary, Svindland, Aud, primary, Liestøl, Knut, primary, Nesbakken, Arild, primary, Skotheim, Rolf I., primary, and Lothe, Ragnhild A., primary

Published
2023
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15. Supplementary Data from Three Epigenetic Biomarkers, GDF15, TMEFF2, and VIM, Accurately Predict Bladder Cancer from DNA-Based Analyses of Urine Samples

Author

Costa, Vera L., primary, Henrique, Rui, primary, Danielsen, Stine A., primary, Duarte-Pereira, Sara, primary, Eknaes, Mette, primary, Skotheim, Rolf I., primary, Rodrigues, Ângelo, primary, Magalhães, José S., primary, Oliveira, Jorge, primary, Lothe, Ragnhild A., primary, Teixeira, Manuel R., primary, Jerónimo, Carmen, primary, and Lind, Guro E., primary

Published
2023
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16. Supplementary Table S1 from TMPRSS2 Fusions with Oncogenic ETS Factors in Prostate Cancer Involve Unbalanced Genomic Rearrangements and Are Associated with HDAC1 and Epigenetic Reprogramming

Author

Iljin, Kristiina, primary, Wolf, Maija, primary, Edgren, Henrik, primary, Gupta, Santosh, primary, Kilpinen, Sami, primary, Skotheim, Rolf I., primary, Peltola, Mari, primary, Smit, Frank, primary, Verhaegh, Gerald, primary, Schalken, Jack, primary, Nees, Matthias, primary, and Kallioniemi, Olli, primary

Published
2023
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20. Supplementary Table 2A from Differentiation of Human Embryonal Carcinomas In vitro and In vivo Reveals Expression Profiles Relevant to Normal Development

Author

Skotheim, Rolf I., primary, Lind, Guro E., primary, Monni, Outi, primary, Nesland, Jahn M., primary, Abeler, Vera M., primary, Fosså, Sophie D., primary, Duale, Nur, primary, Brunborg, Gunnar, primary, Kallioniemi, Olli, primary, Andrews, Peter W., primary, and Lothe, Ragnhild A., primary

Published
2023
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21. Supplementary Figure S1 from TMPRSS2 Fusions with Oncogenic ETS Factors in Prostate Cancer Involve Unbalanced Genomic Rearrangements and Are Associated with HDAC1 and Epigenetic Reprogramming

Author

Iljin, Kristiina, primary, Wolf, Maija, primary, Edgren, Henrik, primary, Gupta, Santosh, primary, Kilpinen, Sami, primary, Skotheim, Rolf I., primary, Peltola, Mari, primary, Smit, Frank, primary, Verhaegh, Gerald, primary, Schalken, Jack, primary, Nees, Matthias, primary, and Kallioniemi, Olli, primary

Published
2023
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22. Data from Oncogenicity of the Developmental Transcription Factor Sox9

Author

Matheu, Ander, primary, Collado, Manuel, primary, Wise, Clare, primary, Manterola, Lorea, primary, Cekaite, Lina, primary, Tye, Angela J., primary, Canamero, Marta, primary, Bujanda, Luis, primary, Schedl, Andreas, primary, Cheah, Kathryn S.E., primary, Skotheim, Rolf I., primary, Lothe, Ragnhild A., primary, López de Munain, Adolfo, primary, Briscoe, James, primary, Serrano, Manuel, primary, and Lovell-Badge, Robin, primary

Published
2023
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23. Supplementary Figures 1-2 from Differentiation of Human Embryonal Carcinomas In vitro and In vivo Reveals Expression Profiles Relevant to Normal Development

Author

Skotheim, Rolf I., primary, Lind, Guro E., primary, Monni, Outi, primary, Nesland, Jahn M., primary, Abeler, Vera M., primary, Fosså, Sophie D., primary, Duale, Nur, primary, Brunborg, Gunnar, primary, Kallioniemi, Olli, primary, Andrews, Peter W., primary, and Lothe, Ragnhild A., primary

Published
2023
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24. Supplementary Methods, Tables 1-3, Figure Legends 1-9 from Oncogenicity of the Developmental Transcription Factor Sox9

Author

Matheu, Ander, primary, Collado, Manuel, primary, Wise, Clare, primary, Manterola, Lorea, primary, Cekaite, Lina, primary, Tye, Angela J., primary, Canamero, Marta, primary, Bujanda, Luis, primary, Schedl, Andreas, primary, Cheah, Kathryn S.E., primary, Skotheim, Rolf I., primary, Lothe, Ragnhild A., primary, López de Munain, Adolfo, primary, Briscoe, James, primary, Serrano, Manuel, primary, and Lovell-Badge, Robin, primary

Published
2023
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27. Supplementary Figures 1-9 from Oncogenicity of the Developmental Transcription Factor Sox9

Author

Matheu, Ander, primary, Collado, Manuel, primary, Wise, Clare, primary, Manterola, Lorea, primary, Cekaite, Lina, primary, Tye, Angela J., primary, Canamero, Marta, primary, Bujanda, Luis, primary, Schedl, Andreas, primary, Cheah, Kathryn S.E., primary, Skotheim, Rolf I., primary, Lothe, Ragnhild A., primary, López de Munain, Adolfo, primary, Briscoe, James, primary, Serrano, Manuel, primary, and Lovell-Badge, Robin, primary

Published
2023
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28. Supplementary Table S4-S6 from TMPRSS2 Fusions with Oncogenic ETS Factors in Prostate Cancer Involve Unbalanced Genomic Rearrangements and Are Associated with HDAC1 and Epigenetic Reprogramming

Author

Iljin, Kristiina, primary, Wolf, Maija, primary, Edgren, Henrik, primary, Gupta, Santosh, primary, Kilpinen, Sami, primary, Skotheim, Rolf I., primary, Peltola, Mari, primary, Smit, Frank, primary, Verhaegh, Gerald, primary, Schalken, Jack, primary, Nees, Matthias, primary, and Kallioniemi, Olli, primary

Published
2023
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36. Association Study between Polymorphisms in DNA Methylation-Related Genes and Testicular Germ Cell Tumor Risk

Author

Grasso, Chiara, Popovic, Maja, Isaevska, Elena, Lazzarato, Fulvio, Fiano, Valentina, Zugna, Daniela, Pluta, John, Weathers, Benita, D'Andrea, Kurt, Almstrup, Kristian, Anson-Cartwright, Lynn, Bishop, D. Timothy, Chanock, Stephen J., Chen, Chu, Cortessis, Victoria K., Dalgaard, Marlene D., Daneshmand, Siamak, Ferlin, Alberto, Foresta, Carlo, Frone, Megan N., Gamulin, Marija, Gietema, Jourik A., Greene, Mark H., Grotmol, Tom, Hamilton, Robert J., Haugen, Trine B., Hauser, Russ, Karlsson, Robert, Kiemeney, Lambertus A., Lesse, Davor, Lista, Patrizia, Lothe, Ragnhild A., Loveday, Chey, Meijer, Coby, Nead, Kevin T., Nsengimana, Jérémie, Skotheim, Rolf I., Turnbull, Clare, Vaughn, David J., Wiklund, Fredrik, Zheng, Tongzhang, Zitella, Andrea, Schwartz, Stephen M., McGlynn, Katherine A., Kanetsky, Peter A., Nathanson, Katherine L., Richiardi, Lorenzo, Grasso, Chiara, Popovic, Maja, Isaevska, Elena, Lazzarato, Fulvio, Fiano, Valentina, Zugna, Daniela, Pluta, John, Weathers, Benita, D'Andrea, Kurt, Almstrup, Kristian, Anson-Cartwright, Lynn, Bishop, D. Timothy, Chanock, Stephen J., Chen, Chu, Cortessis, Victoria K., Dalgaard, Marlene D., Daneshmand, Siamak, Ferlin, Alberto, Foresta, Carlo, Frone, Megan N., Gamulin, Marija, Gietema, Jourik A., Greene, Mark H., Grotmol, Tom, Hamilton, Robert J., Haugen, Trine B., Hauser, Russ, Karlsson, Robert, Kiemeney, Lambertus A., Lesse, Davor, Lista, Patrizia, Lothe, Ragnhild A., Loveday, Chey, Meijer, Coby, Nead, Kevin T., Nsengimana, Jérémie, Skotheim, Rolf I., Turnbull, Clare, Vaughn, David J., Wiklund, Fredrik, Zheng, Tongzhang, Zitella, Andrea, Schwartz, Stephen M., McGlynn, Katherine A., Kanetsky, Peter A., Nathanson, Katherine L., and Richiardi, Lorenzo

Abstract

Background: Testicular germ cell tumors (TGCT), histologically classified as seminomas and nonseminomas, are believed to arise from primordial gonocytes, with the maturation process blocked when they are subjected to DNA methylation reprogramming. SNPs in DNA methylation machinery and folate-dependent one-carbon metabolism genes have been postulated to influence the proper establishment of DNA methylation. Methods: In this pathway-focused investigation, we evaluated the association between 273 selected tag SNPs from 28 DNA methylation-related genes and TGCT risk. We carried out association analysis at individual SNP and gene-based level using summary statistics from the Genome Wide Association Study meta-analysis recently conducted by the international Testicular Cancer Consortium on 10,156 TGCT cases and 179,683 controls. Results: In individual SNP analyses, seven SNPs, four mapping within MTHFR, were associated with TGCT risk after correction for multiple testing (q = 0.05). Queries of public databases showed that three of these SNPs were associated with MTHFR changes in enzymatic activity (rs1801133) or expression level in testis tissue (rs12121543, rs1476413). Gene-based analyses revealed MTHFR (q = 8.4 × 10-4), methyl-CpG-binding protein 2 (MECP2; q = 2 × 10-3), and ZBTB4 (q = 0.03) as the top TGCT-associated genes. Stratifying by tumor histology, four MTHFR SNPs were associated with seminoma. In gene-based analysis MTHFR was associated with risk of seminoma (q = 2.8 × 10-4), but not with nonseminomatous tumors (q = 0.22). Conclusions: Genetic variants within MTHFR, potentially having an impact on the DNA methylation pattern, are associated with TGCT risk. Impact: This finding suggests that TGCT pathogenesis could be associated with the folate cycle status, and this relation could be partly due to here

Published
2022

38. Association Study between Polymorphisms in DNA Methylation–Related Genes and Testicular Germ Cell Tumor Risk

Author

Grasso, Chiara, primary, Popovic, Maja, additional, Isaevska, Elena, additional, Lazzarato, Fulvio, additional, Fiano, Valentina, additional, Zugna, Daniela, additional, Pluta, John, additional, Weathers, Benita, additional, D'Andrea, Kurt, additional, Almstrup, Kristian, additional, Anson-Cartwright, Lynn, additional, Bishop, D. Timothy, additional, Chanock, Stephen J., additional, Chen, Chu, additional, Cortessis, Victoria K., additional, Dalgaard, Marlene D., additional, Daneshmand, Siamak, additional, Ferlin, Alberto, additional, Foresta, Carlo, additional, Frone, Megan N., additional, Gamulin, Marija, additional, Gietema, Jourik A., additional, Greene, Mark H., additional, Grotmol, Tom, additional, Hamilton, Robert J., additional, Haugen, Trine B., additional, Hauser, Russ, additional, Karlsson, Robert, additional, Kiemeney, Lambertus A., additional, Lessel, Davor, additional, Lista, Patrizia, additional, Lothe, Ragnhild A., additional, Loveday, Chey, additional, Meijer, Coby, additional, Nead, Kevin T., additional, Nsengimana, Jérémie, additional, Skotheim, Rolf I., additional, Turnbull, Clare, additional, Vaughn, David J., additional, Wiklund, Fredrik, additional, Zheng, Tongzhang, additional, Zitella, Andrea, additional, Schwartz, Stephen M., additional, McGlynn, Katherine A., additional, Kanetsky, Peter A., additional, Nathanson, Katherine L., additional, and Richiardi, Lorenzo, additional

Published
2022
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39. NRF2 drives an oxidative stress response predictive of breast cancer

Author

Wolowczyk, Camilla, primary, Neckmann, Ulrike, additional, Aure, Miriam Ragle, additional, Hall, Martina, additional, Johannessen, Bjarne, additional, Zhao, Sen, additional, Skotheim, Rolf I., additional, Andersen, Sonja B., additional, Zwiggelaar, Rosalie, additional, Steigedal, Tonje S., additional, Lingjærde, Ole Christian, additional, Sahlberg, Kristine Kleivi, additional, Almaas, Eivind, additional, and Bjørkøy, Geir, additional

Published
2022
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41. Collision tumors revealed by prospectively assessing subtype-defining molecular alterations in 904 individual prostate cancer foci

Author

Fontugne, Jacqueline, primary, Cai, Peter Y., additional, Alnajar, Hussein, additional, Bhinder, Bhavneet, additional, Park, Kyung, additional, Ye, Huihui, additional, Beg, Shaham, additional, Sailer, Verena, additional, Siddiqui, Javed, additional, Blattner-Johnson, Mirjam, additional, Croyle, Jaclyn A., additional, Noorzad, Zohal, additional, Calagua, Carla, additional, MacDonald, Theresa Y., additional, Axcrona, Ulrika, additional, Bogaard, Mari, additional, Axcrona, Karol, additional, Scherr, Douglas S., additional, Sanda, Martin G., additional, Johannessen, Bjarne, additional, Chinnaiyan, Arul M., additional, Elemento, Olivier, additional, Skotheim, Rolf I., additional, Rubin, Mark A., additional, Barbieri, Christopher E., additional, and Mosquera, Juan Miguel, additional

Published
2022
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42. Somatic mutations reveal complex metastatic seeding from multifocal primary prostate cancer.

Author

Carm, Kristina T., Johannessen, Bjarne, Bogaard, Mari, Bakken, Anne Cathrine, Maltau, Aase V., Hoff, Andreas M., Axcrona, Ulrika, Axcrona, Karol, Lothe, Ragnhild A., and Skotheim, Rolf I.

Subjects
SOMATIC mutation, PROSTATE cancer, CIRCULATING tumor DNA, PROSTATE cancer patients, SOWING, METASTASIS
Abstract

Primary prostate cancer shows a striking intraorgan molecular heterogeneity, with multiple spatially separated malignant foci in the majority of patients. Metastatic prostate cancer, however, typically reveals more homogenous molecular profiles, suggesting a monoclonal origin of the metastatic lesions. Longitudinal mutational spectra, comparing multiple primary lesions with metastases from the same patients remain poorly defined. We have here analyzed somatic mutations in multisampled, spatio‐temporal biobanked lesions (38 samples from primary foci and 1 sample from each of 8 metastases from seven prostate cancer patients) applying a custom‐designed panel targeting 68 prostate cancer relevant genes. The metastatic samples were taken at time of primary surgery and up to 7 years later, and sampling included circulating tumor DNA in plasma or solid metastatic tissue samples. A total of 282 somatic mutations were detected, with a range of 0 to 25 mutations per sample. Although seven samples had solely private mutations, the remaining 39 samples had both private and shared mutations. Seventy‐four percent of mutations in metastases were not found in any primary samples, and vice versa, 96% of mutations in primary cancers were not found in any metastatic samples. However, for three patients, shared mutations were found suggesting the focus of origin, including mutations in AKT1, FOXA1, HOXB13, RB1 and TP53. In conclusion, the spatio‐temporal heterogeneous nature of multifocal disease is emphasized in our study, and underlines the importance of testing a recent sample in genomics‐based precision medicine for metastatic prostate cancer. [ABSTRACT FROM AUTHOR]

Published
2023
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43. Long‐term first‐in‐man Phase I/II study of an adjuvant dendritic cell vaccine in patients with high‐risk prostate cancer after radical prostatectomy

Author

Tryggestad, Anne M. A., primary, Axcrona, Karol, additional, Axcrona, Ulrika, additional, Bigalke, Iris, additional, Brennhovd, Bjørn, additional, Inderberg, Else M., additional, Hønnåshagen, Turid K., additional, Skoge, Lisbeth J., additional, Solum, Guri, additional, Sæbøe‐Larssen, Stein, additional, Josefsen, Dag, additional, Olaussen, Richard W., additional, Aamdal, Steinar, additional, Skotheim, Rolf I., additional, Myklebust, Tor Å., additional, Schendel, Dolores J., additional, Lilleby, Wolfgang, additional, Dueland, Svein, additional, and Kvalheim, Gunnar, additional

Published
2021
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45. Additional file 2 of The expressed mutational landscape of microsatellite stable colorectal cancers

Author

Sveen, Anita, Johannessen, Bjarne, Eilertsen, Ina A., Røsok, Bård I., Gulla, Marie, Eide, Peter W., Bruun, Jarle, Kryeziu, Kushtrim, Meza-Zepeda, Leonardo A., Myklebost, Ola, Bjørnbeth, Bjørn A., Skotheim, Rolf I., Nesbakken, Arild, and Lothe, Ragnhild A.

Abstract

Additional file 2: Figure S1. TMB and expressed TMB relative to sequencing coverage and tumor purity. Figure S2. Gene-wise mutation frequency among microsatellite stable CRCs. Figure S3. Gene set enrichment analyses of expressed mutations. Figure S4. Validation of mutation expression frequencies in TCGA. Figure S5. Heatmap of expressed mutations per gene and tumor sample. Figure S6. Logistic PCA of the expressed mutation matrix. Figure S7. Genes with frequent non-expressed mutations. Figure S8. Genes with frequent non-expressed mutated alleles. Figure S9. Genes with both expression and silencing of the mutated allele among tumors. Figure S10. Illustration of estimates used to describe relative allelic expression of mutations. Figure S11. RNA and DNA level MAFs in primary MSS CRCs in the in-house series. Figure S12. RNA MAF versus DNA MAF in TCGA. Figure S13. Genes with high relative allelic expression of mutations. Figure S14. RNA MAF versus DNA MAF in in-house series according to mutation/target gene category. Figure S15. Relative allelic mutation expression in TCGA data according to allelic copy number balance. Figure S16. Allele-specific expression of TP53 and KRAS mutations among 241 primary colon cancers in the TCGA validation series. Figure S17. Allele-specific expression of APC mutations in the in-house series of primary CRCs. Figure S18. Allele-specific mutation expression and drug sensitivity in CRC cell lines. Figure S19. Minimal evolutionary changes in mutation expression during metastasis. Figure S20. Comparisons of DNA MAFs among multiple tumor samples from each of 4 patients. Figure S21. Comparisons of RNA MAFs among multiple tumor samples from each of 4 patients. Figure S22. Comparisons of ΔMAF RNA|DNA among multiple tumor samples from each of 4 patients. Figure S23. Comparisons of RNA read counts of mutated alleles among multiple tumor samples from each of 4 patients.

Published
2021
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47. Identification of 22 novel loci associated with susceptibility to testicular germ cell tumors

Author

Pluta, John B., Pyle, Louise C., Bishop, D. Timothy, Benitez, Javier, Cortessis, Victoria K., Ferlin, Alberto, Gietema, Jourik A., Greene, Mark H., Grotmol, Tom, Gupta, Ramneek, Hamilton, Robert M, Hildebrandt, Michelle, Kiemeney, Lambertus A, Lessel, Davor, Rafnar, Thorunn, Richiardi, Lorenzo, Skotheim, Rolf I., Turnbull, Clare, Wiklund, Fredrik, Zheng, Tongzhang, Rajpert-De Meyts, Ewa, Schwartz, Stephen M., McGlynn, Katherine A., Kanetsky, Peter A, Nathanson, Katherine L., Guided Treatment in Optimal Selected Cancer Patients (GUTS), and Damage and Repair in Cancer Development and Cancer Treatment (DARE)

Abstract

Background: Testicular germ cell tumors (TGCT) are the most common cancers in young men of European ancestry aged 20 to 39 years. The incidence of TGCT has doubled over the past 20 years, yet no robust environmental risk factors for disease have been identified. Although TGCTs are treatable by surgery, radiation, and platinum-based chemotherapy, multiple long-term toxicities of treatment often occur impacting morbidity and mortality. Due to their high heritability and homogenous cell of origin, TGCTs are well suited to genome-wide association methods. The Testicular Cancer Consortium (TECAC) has brought together the largest genome-wise association study (GWAS) study of TGCT to date. Methods: We conducted a GWAS of 5,602 cases and 5,006 controls aggregated from 12 locations in the US and Europe. Logistic regression models adjusted for study center and genomic ancestry. Genotypes were imputed against the Human Haplotype Reference Consortium. Meta-analysis was performed to combine GWAS results with summary statistics from five previously published TGCT studies, UK Biobank, deCODE Genetics, and an independent set of cases and controls, for a total of 10,156 cases and 179,683 controls. Biologic function of loci was explored using PAINTOR annotated with ATAC-seq data of four TGCT cell lines, SPATIAL-seq data of the NTERA2 TGCT cell-line, and publicly available data from ENCODE. Polygenic risk scores (PRS) were computed using subject-level data from the 5,602 cases and 5,006 controls, and effect sizes of the novel hits derived from the meta-analysis. Results: 22 novel and 45 previously reported loci associated with TGCT surpassed genome-wide significance (p < 5e-08). We discovered additional markers in known susceptibility loci and identified novel regions associated with germ cell development and sex determination (e.g., BCL11, AR), immune function (e.g., TNXB, ITIH5), and for the first time identified genes associated with kinetochore activity (e.g., PPP2R5A, ANAPC2). All identified risk SNPs to date account for 42.3% of heritability. Men in the highest 1% of PRS had over a 15-fold increased risk of TGCT compared to those at the median PRS, and PRS overall had an AUC of 74.29%. Conclusions: Results from our TGCT meta-analysis continue to provide insights into biological pathways affecting germ cell specification, expression, and epigenetic reprogramming, and sex determination. Our results also uniquely place TGCT as the only cancer type in which inherited variants implicating kinetochore activity, critical for chromosomal segregation, have been identified. Citation Format: John Pluta, Louisa Pyle, Timothy Bishop, Javier Benitez, Victoria Cortessis, Alberto Ferlin, Jourik Gietema, Mark Greene, Thomas Grotmol, Ramneek Gupta, Robert Hamilton, Michelle Hildebrandt, Lambertus Kiemeney, Davor Lessel, Thorunn Rafnar, Lorenzo Richiardi, Rolf Skotheim, Clare Turnbull, Fredrik Wiklund, Tongzhang Zheng, Ewa Rajpert- De Meyts, Stephen Schwartz, Katherine McGlynn, Peter Kanetsky, Katherine Nathanson. Identification of 22 novel loci associated with susceptibility to testicular germ cell tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1203.

Published
2020

48. Testicular germ cell tumor susceptibility associated with the UCK2 locus on chromosome 1q23

Author

Schumacher, Fredrick R., Wang, Zhaoming, Skotheim, Rolf I., Koster, Roelof, Chung, Charles C., Hildebrandt, Michelle A. T., Kratz, Christian P., Bakken, Anne C., Timothy Bishop, D., Cook, Michael B., Erickson, R. Loren, Fosså, Sophie D., Greene, Mark H., Jacobs, Kevin B., Kanetsky, Peter A., Kolonel, Laurence N., Loud, Jennifer T., Korde, Larissa A., Le Marchand, Loic, Pablo Lewinger, Juan, Lothe, Ragnhild A., Pike, Malcolm C., Rahman, Nazneen, Rubertone, Mark V., Schwartz, Stephen M., Siegmund, Kimberly D., Skinner, Eila C., Turnbull, Clare, Van Den Berg, David J., Wu, Xifeng, Yeager, Meredith, Nathanson, Katherine L., Chanock, Stephen J., Cortessis, Victoria K., and McGlynn, Katherine A.

Published
2013
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