Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration.

Autor: Smid M; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., Rodríguez-González FG; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., Sieuwerts AM; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., Salgado R; Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium.; Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium., Prager-Van der Smissen WJ; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., Vlugt-Daane MV; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., van Galen A; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., Nik-Zainal S; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK.; East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK., Staaf J; Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden., Brinkman AB; Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands., van de Vijver MJ; Department of Pathology, Academic Medical Center, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands., Richardson AL; Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.; Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA., Fatima A; Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., Berentsen K; Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands., Butler A; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK., Martin S; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK., Davies HR; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK., Debets R; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., Gelder ME; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., van Deurzen CH; Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., MacGrogan G; Département de Biopathologie,Institut Bergonié, CS 61283 33076 Bordeaux, France., Van den Eynden GG; Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium.; Molecular Immunology Unit, Jules Bordet Institute, B-1000 Brussels, Belgium., Purdie C; Department of Pathology, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK., Thompson AM; Department of Pathology, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK., Caldas C; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK., Span PN; Department of Radiation Oncology, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands.; Department of Laboratory Medicine, Radboud University Medical Center, 6525GA, Nijmegen, The Netherlands., Simpson PT; The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane 4029, Australia., Lakhani SR; The University of Queensland: UQ Centre for Clinical Research and School of Medicine, Brisbane 4029, Australia.; Pathology Queensland, The Royal Brisbane and Women's Hospital, Brisbane 4029, Australia., Van Laere S; Center for Oncological Research, University of Antwerp &GZA Hospitals Sint-Augustinus, 2610 Wilrijk, Belgium., Desmedt C; Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, Bd de Waterloo 121, B-1000 Brussels, Belgium., Ringnér M; Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden., Tommasi S; IRCCS Istituto Tumori 'Giovanni Paolo II', 70124 Bari, Italy., Eyford J; Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland., Broeks A; The Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands., Vincent-Salomon A; Department of Pathology and INSERM U934, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France., Futreal PA; Department of Genomic Medicine, UT MD Anderson Cancer Center, Houston, TX, 77230, USA., Knappskog S; Department of Clinical Science, University of Bergen, 5020 Bergen, Norway.; Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway., King T; Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, New York 10065, USA., Thomas G; Synergie Lyon Cancer,Centre Léon Bérard, 28 rue Laënnec, Cedex 08 Lyon, France., Viari A; Synergie Lyon Cancer,Centre Léon Bérard, 28 rue Laënnec, Cedex 08 Lyon, France.; Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655, Av. de l'Europe, 38330 Montbonnot-Saint Martin, France., Langerød A; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital, 0310, Oslo, Norway.; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, 0310 Oslo, Norway., Børresen-Dale AL; Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radiumhospital, 0310, Oslo, Norway.; K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, 0310 Oslo, Norway., Birney E; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton CB10 1SD, Cambridgeshire, UK., Stunnenberg HG; Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA, Nijmegen, The Netherlands., Stratton M; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, Cambridge, UK., Foekens JA; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands., Martens JW; Department of Medical Oncology, Erasmus MC Cancer Institute and Cancer Genomics Netherlands, Erasmus University Medical Center, 3015CN Rotterdam, The Netherlands.

Publikováno v: Nature communications [Nat Commun] 2016 Sep 26; Vol. 7, pp. 12910. Date of Electronic Publication: 2016 Sep 26.

Efficient feature extraction from highly sparse binary genotype data for cancer prognosis prediction using an auto-encoder.

Autor: Junjie Shen, Huijun Li, Xinghao Yu, Lu Bai, Yongfei Dong, Jianping Cao, Ke Lu, Zaixiang Tang

Publikováno v: Frontiers in Oncology; 1/10/2023, Vol. 12, p1-12, 12p

Characterization of Frequently Mutated Cancer Genes and Tumor Mutation Burden in Chinese Breast Cancer.

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Publikováno v: Frontiers in Oncology; 4/21/2021, Vol. 11, pN.PAG-N.PAG, 10p

Mutant POLQ and POLZ/REV3L DNA polymerases may contribute to the favorable survival of patients with tumors with POLE mutations outside the exonuclease domain.

Autor: Huang, Fangjin¹ (AUTHOR), Tanaka, Hisashi^1,2,3 (AUTHOR), Knudsen, Beatrice S.^1,2,4,5 (AUTHOR) Beatrice.Knudsen@path.utah.edu, Rutgers, Joanne K.⁴ (AUTHOR)

Publikováno v: BMC Medical Genetics. 8/24/2020, Vol. 21 Issue 1, pN.PAG-N.PAG. 1p.

Integrative genomic analyses of APOBEC-mutational signature, expression and germline deletion of APOBEC3 genes, and immunogenicity in multiple cancer types.

Autor: Chen, Zhishan¹ (AUTHOR) Zhishan.chen@vumc.org, Wen, Wanqing¹ (AUTHOR) Wanqing.wen@vumc.org, Bao, Jiandong¹ (AUTHOR) baojd@fafu.efu.cn, Kuhs, Krystle L.¹ (AUTHOR) krystle.kuhs@vumc.org, Cai, Qiuyin¹ (AUTHOR) qiuyin.cai@vumc.org, Long, Jirong¹ (AUTHOR) Jirong.long@vumc.org, Shu, Xiao-ou¹ (AUTHOR) xiao-ou.shu@vumc.org, Zheng, Wei¹ (AUTHOR) wei.zheng@vanderbilt.edu, Guo, Xingyi¹ (AUTHOR) Xingyi.guo@vumc.org

Publikováno v: BMC Medical Genomics. 9/18/2019, Vol. 12 Issue 1, pN.PAG-N.PAG. 1p.