Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning.

Autor: Nieboer MM; Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands.; Oncode Institute, Utrecht, The Netherlands., Nguyen L; Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands.; Oncode Institute, Utrecht, The Netherlands., de Ridder J; Center for Molecular Medicine, University Medical Center Utrecht, 3584 CG, Utrecht, The Netherlands. J.deRidder-4@umcutrecht.nl.; Oncode Institute, Utrecht, The Netherlands. J.deRidder-4@umcutrecht.nl.

Publikováno v: Scientific reports [Sci Rep] 2021 Jul 13; Vol. 11 (1), pp. 14411. Date of Electronic Publication: 2021 Jul 13.

Molecular heterogeneity and early metastatic clone selection in testicular germ cell cancer development.

Autor: Dorssers LCJ; Department of Pathology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands. l.dorssers@erasmusmc.nl., Gillis AJM; Department of Pathology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands., Stoop H; Department of Pathology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands., van Marion R; Department of Pathology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands., Nieboer MM; University Medical Center Utrecht, Universiteitsweg 100, STR 1.305, Utrecht, 3584 CG, The Netherlands., van Riet J; Cancer Computational Biology Center, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.; Department of Urology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands., van de Werken HJG; Cancer Computational Biology Center, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.; Department of Urology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands., Oosterhuis JW; Department of Pathology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands., de Ridder J; University Medical Center Utrecht, Universiteitsweg 100, STR 1.305, Utrecht, 3584 CG, The Netherlands., Looijenga LHJ; Department of Pathology, Wytemaweg 80, 3015 CN, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands. l.looijenga@erasmusmc.nl.; Princess Maxima Center for Pediatric Oncology, Utrecht, The Netherlands. l.looijenga@erasmusmc.nl.

Publikováno v: British journal of cancer [Br J Cancer] 2019 Feb; Vol. 120 (4), pp. 444-452. Date of Electronic Publication: 2019 Feb 11.

Mapping and phasing of structural variation in patient genomes using nanopore sequencing.

Autor: Cretu Stancu M; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., van Roosmalen MJ; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., Renkens I; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., Nieboer MM; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., Middelkamp S; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., de Ligt J; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., Pregno G; Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, 10043, Italy., Giachino D; Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, 10043, Italy., Mandrile G; Medical Genetics Unit, Department of Clinical and Biological Sciences, University of Torino, Orbassano, 10043, Italy., Espejo Valle-Inclan J; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., Korzelius J; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., de Bruijn E; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., Cuppen E; Department of Genetics and Cancer Genomics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., Talkowski ME; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.; Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA.; Program in Population and Medical Genetics and Stanley Center for Psychiatric Research, The Broad Institute of M.I.T. and Harvard, Cambridge, MA, 02142, USA., Marschall T; Center for Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.; Max Planck Institute for Informatics, 66123, Saarbrücken, Germany., de Ridder J; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands., Kloosterman WP; Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG, Utrecht, The Netherlands. w.kloosterman@umcutrecht.nl.

Publikováno v: Nature communications [Nat Commun] 2017 Nov 06; Vol. 8 (1), pp. 1326. Date of Electronic Publication: 2017 Nov 06.