DKFZ-HIPO Publications



Dietz S et al.; Serial liquid biopsies for detection of treatment failure and profiling of resistance mechanisms in KLC1–ALK-rearranged lung cancer; Cold Spring Harbor, Molecular Case Studies 2019; DOI: 10.1101/mcs.a004630

Smits M et al.; Follicular T helper cells shape the HCV-specific CD4 T cell repertoire after viral elimination; J Clin Invest 2019; DOI: 10.1172/JCI129642

Reinhardt A et al.; Tumors diagnosed as cerebellar glioblastoma comprise distinct molecular entities; acta neuropathol commun 2019; DOI: 10.1186/s40478-019-0801-8

Weinberg F et al.; Identification and characterization of a BRAF fusion oncoprotein with retained autoinhibitory domains; Oncogene 2019; DOI: 10.1038/s41388-019-1021-1

Aslam M et al.; Segregation and potential functional impact of a rare stop-gain PABPC4L variant in familial atypical Parkinsonism. Sci Rep. 2019; DOI: 10.1038/s41598-019-50102-6

Heeke S et al.; In-house Implementation of Tumor Mutational Burden Testing to Predict Durable Clinical Benefit in Non-small Cell Lung Cancer and Melanoma Patients; Cancers (Basel). 2019; DOI: 10.3390/cancers11091271

Tirier SM et al.; Pheno-seq - linking visual features and gene expression in 3D cell culture systems; Sci Rep. 2019; DOI: 10.1038/s41598-019-48771-4

Allgayer et al.; Defining the "Metastasome": Perspectives from the genome and molecular landscape in colorectal cancer for metastasis evolution and clinical consequences; Sem Cancer Biol 2019; DOI: 10.1016/j.semcancer.2019.07.018

Jia M et al.; A prognostic CpG score derived from epigenome-wide profiling of tumor tissue was independently associated with colorectal cancer survival; Clin Epigenetics. 2019; DOI: 10.1186/s13148-019-0703-4

Kazdal D et al.; Spatial and Temporal Heterogeneity of Panel-Based Tumor Mutational Burden in Pulmonary Adenocarcinoma: Separating Biology From Technical Artifacts; J Thorac Oncol 2019; DOI: 10.1016/j.jtho.2019.07.006

Suarez-Carmona M et al.; CCR5 status and metastatic progression in colorectal cancer; Oncoimmunology 2019; DOI: 10.1080/2162402X.2019.1626193

Hüllein J et al.; MDM4 Targeted by 1q Gain and Drives Disease in Burkitt Lymphoma; Cancer Res. 2019; DOI: 10.1158/0008-5472

Schmitt K et al.; Somatic mutations and promotor methylation of the ryanodine receptor 2 is a common event in the pathogenesis of head and neck cancer; Int J Cancer 2019; DOI: 10.1002/ijc.32481

Mallm JP et al.; Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks; Mol Syst Biol 2019; DOI: 10.15252/msb.20188339

Paramasivam N et al.; Mutational patterns and regulatory networks in epigenetic subgroups of meningioma; Acta Neuropat 2019; DOI: 10.1007/s00401-019-02008-w

Leichsenring J et al.; Variant classification in precision oncology; Int J Cancer 2019; DOI: 10.1002/ijc.32358

Gröschel S et al.; Defective homologous recombination DNA repair as therapeutic target in advanced chordoma; Nat Commun 2019; DOI: 10.1038/s41467-019-09633-9

Körber et al.; Evolutionary trajectories of IDH-wildtype glioblastomas reveal a common path of early tumorigenesis instigated years ahead of initial diagnosis; Cancer Cell 2019; DOI: 10.1016/j.ccell.2019.02.007

Kalamakis G et al.; Quiescence Modulates Stem Cell Maintenance and Regenerative Capacity in the Aging Brain; Cell. 2019; DOI: 10.1016/j.cell.2019.01.040

Horak P et al.; Response to olaparib in a PALB2 germline mutated prostate cancer and genetic events associated with resistance; Cold Spring Harbor, Molecular Case Studies 2019; DOI: 10.1101/mcs.a003657

Hübschmann D, Schlesner M ; Evaluation of Whole Genome Sequencing Data; In: Küppers R. (eds) Lymphoma. Methods in Molecular Biology, vol 1956. Humana Press, New York, NY, 2019; DOI: 10.1007/978-1-4939-9151-8_15

Fremd C et al.; Mismatch Repair Deficiency Drives Durable Complete Remission by Targeting Programmed Death Receptor 1 in a Metastatic Luminal Breast Cancer Patient; Breast Care 2019; DOI: 10.1159/000492580

Allgayer H; Editorial Comment: Deciphering the "Metastasome" Leads to Novel Hypotheses on Understanding the Evolution of Metastasis and Implications Consequences for Metastasis

Therapy and Prevention; Cancer Microenviron. 2019; DOI: 10.1007/s12307-019-00221-5

Haller F et al.; Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands; Nat Commun 2019; DOI: 10.1038/s41467-018-08069-x

Christopoulos et al.; Detection of TP53 Mutations in Tissue or Liquid Rebiopsies at Progression Identifies ALK+ Lung Cancer Patients with Poor Survival; Cancers 2019; DOI: 10.3390/cancers11010124

Erkek S et al.; Comprehensive Analysis of Chromatin States in Atypical Teratoid/Rhabdoid Tumor Identifies Diverging Roles for SWI/SNF and Polycomb in Gene Regulation; Cancer Cell. 2019; DOI: 10.1016/j.ccell.2018.11.014



Wick et al.; N2M2 (NOA-20) phase I/II trial of molecularly matched targeted therapies plus radiotherapy in patients with newly diagnosed non-MGMT hypermethylated glioblastoma ; Neuro Oncol. 2018

Kesch C et al.; Correlation between genomic index lesions and mpMRI and 68Ga-PSMAPET/CT imaging features in primary prostate cancer; Sci. Rep. 2018

Ishaque N et al.; Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer; Nat. Comm. 2018

Junge KM et al.; MEST mediates the impact of prenatal bisphenol A exposure on long-term body weight development; Clin Epigenetics. 2018

Gröbner SM et al.; The landscape of genomic alterations across childhood cancers; Nature 2018

Waszak SM et al.; Spectrum and prevalence of genetic predisposition in medulloblastoma: a retrospective genetic study and prospective validation in a clinical trial cohort; Lancet Oncol. 2018

Capper D et al.; DNA methylation-based classification of central nervous system tumours; Nature 2018

Abba ML et al.; Prevention of carcinogenesis and metastasis by Artemisinin-type drugs; Cancer Lett. 2018

Dieffenbacher S et al.; Prospective single center trial of next-generation sequencing analysis in metastatic renal cell cancer: the MORE-TRIAL; Future Sci OA 2018

Heining C et al.; NRG1 Fusions in KRAS Wild-type Pancreatic Cancer; Cancer Discov. 2018; DOI:10.1158/2159-8290.CD-18-0036

Chudasama P. et al.; Integrative genomic and transcriptomic analysis of leiomyosarcoma; Nat. Commun 2018; DOI: 10.1038/s41467-017-02602-0

Dietrich S et al. Drug-perturbation-based stratification of blood cancer. J Clin Invest. 2018; DOI:10.1172/JCI93801

Gu Z et al.; EnrichedHeatmap: an R/Bioconductor package for comprehensive visualization of genomic signal associations; BMC Genomics. 2018; DOI: 10.1186/s12864-018-4625-x



Thürmann L et al.; Early-onset childhood atopic dermatitis is related to NLRP2 repression; J Allergy Clin Immunol. 2017. DOI: 10.1016/j.jaci.2017.11.018

Pfaff E et al.; Feasibility of real-time molecular profiling for patients with newly diagnosed glioblastoma without MGMT promoter-hypermethylation - the NCT Neuro Master Match (N2M2) pilot study. Neuro Oncol. 2017; DOI: 10.1093/neuonc/nox216

Czink E et al.; Successful immune checkpoint blockade in a patient with advanced stage microsatellite-unstable biliary tract cancer; Cold Spring Harb Mol Case Stud. 2017; DOI:10.1101/mcs.a001974

Reisinger E et al.; OTP: An automatized system for managing and processing NGS data; J Biotechnol. 2017; DOI: 10.1016/j.jbiotec.2017.08.006

Wu B et al.; MED12 mutations and NOTCH signalling in chronic lymphocytic leukaemia; Br J Haematol. 2017; DOI: 10.1111/bjh.14869

Wolf C. et al.; NFATC1 activation by DNA hypomethylation in chronic lymphocytic leukemia correlates with clinical staging and can be inhibited by ibrutini; Int J Cancer. 2017;DOI:10.1002/ijc.31057

Brinkler TJ et al.; A Dermatologist's Ammunition in the War Against Smoking: A Photoaging App; J Med Internet Res 2017;  DOI: 10.2196/jmir.8743

Huang Z et al.; confFuse: High-Confidence Fusion Gene Detection across Tumor Entities; Front Genet. 2017; DOI: 10.3389/fgene.2017.00137

Dalacher M et al.; Genome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues; Nat. Immunol. 2017; DOI: 10.1038/ni.3799

Korshunov A et al.; H3-/IDH-wild type pediatric glioblastoma is comprised of molecularly and prognostically distinct subtypes with associated oncogenic drivers; Acta Neuropathol 2017;  DOI: 10.1007/s00401-017-1710-1

Northcott PA et al.; The whole-genome landscape of medulloblastoma subtypes; Nature 2017; DOI: 10.1038/nature22973

Sahm F. et al.; DNA methylation-based classification and grading system for meningioma: a multicentre, retrospective analysis; Lancet Oncol. 2017; DOI: 10.1016/S1470-2045(17)30155-9

Wegert, J, Vokuhl C, Ziegler C, Ernestus C, Leuschner I, Furtwängler R, Graf N, Gessler M. TP53 alterations in Wilms tumor represent progression events with strong intratumor heterogeneity that are closely linked, but not limited to anaplasia. The Journal of Pathology: Clinical Research 2017

Espinet E et al.; Cellular deconvolution and expression analysis of Stromal and Epithelial cells directly isolated from human Pancreatic Ductal Adenocarcinoma (PDAC); Pancreatology 2017

Lichter P. and von Kalle C.; Special Section: From Genes to Bedside and Back; Int J Cancer 2017; DOI: 10.1002/ijc.30836

Dietz S et al.; Patient-specific molecular alterations are associated with metastatic clear cell renal cell cancer progressing under tyrosine kinase inhibitor therapy; Oncotarget 2017; DOI: 10.18632/oncotarget.18200

Horak P et al.; Precision oncology based on omics data: The NCT Heidelberg experience; Int J Cancer 2017; DOI: 10.1002/ijc.30828

Sahm F et al.; Meningiomas induced by low-dose radiation carry structural variants of NF2 and a distinct mutational signature; Acta Neuropathol 2017; DOI: 10.1007/s00401-017-1715-9

Gröschel S et al.; Integration of genomics and histology revises diagnosis and enables effective therapy of refractory cancer of unknown primary with PDL1 amplification; Cold Spring Harb Mol Case Stud. 2017; DOI: 10.1101/mcs.a001180

Drennan S et al.; IL-10 production by CLL cells is enhanced in the anergic IGHV mutated subset and associates with reduced DNA methylation of the IL10 locus; Leukemia 2017; DOI: 10.1038/leu.2016.356

Chudasama P et al.; Targeting fibroblast growth factor receptor 1 for treatment of soft-tissue sarcoma; Clin Cancer Res 2017; DOI: 10.1158/1078-0432.CCR-16-0860

Dieter SM et al.; Patient‐derived Xenografts of Gastrointestinal Cancers Are Susceptible to Rapid and Delayed B‐Lymphoproliferation; Int J Cancer 2017; DOI: 10.1002/ijc.30561

Abba M et al.; MicroRNAs as novel targets and tools in cancer therapy, Cancer Letters 2017; DOI:10.1016/j.canlet.2016.03.043

Dieter SM et al.; Mutant KIT as Imatinib-Sensitive Target in Metastatic Sinonasal Carcinoma; Ann Oncol 2017; DOI: 10.1093/annonc/mdw446




El-Daly SM et al., miRs-134 and -370 function as tumor suppressors in colorectal cancer by independently suppressing EGFR and PI3K signalling; Sci. Rep. 2016; DOI: 10.1038/srep24720

Fan F et al.; The AP-1 transcription factor JunB is essential for multiple myeloma cell proliferation and drug resistance in the bone marrow microenvironment; Leukemia 2016; DOI: 10.1038/leu.2016.358

Vita F et al.; Aromatic and proteomic analyses corroborate the distinction between Mediterranean landraces and modern varieties of durum wheat; Sci. Rep. 2016; DOI: 10.1038/srep34619

Bartram CR et al.; Position Paper: Cornerstones for an ethically and legally informed practice of whole genome sequencing: code of conduct and patient consent models; Forum Marsilius-Kolleg 2016; DOI:

International Cancer Genome Consortium PedBrain Tumor Project; Recurrent MET fusion genes represent a drug target in pediatric glioblastoma; Nature Medicine 2016; DOI: 10.1038/nm.4204

Kosaloglu, Zeynep, et al. In silico SNP analysis of the breast cancer antigen NY-BR-1; BMC Cancer 2016; DOI: 10.1186/s12885-016-2924-7

Johann PD et al.; Cribriform neuroepithelial tumor: Molecular characterization of a SMARCB1‐deficient non‐rhabdoid tumor with favorable long‐term outcome; Brain Pathology 2016; DOI: 10.1111/bpa.12413

Thomas C et al.; Methylation profiling of choroid plexus tumors reveals 3 clinically distinct subgroups; Neuro Oncol 2016; DOI: 10.1093/neuonc/nov322

Junge KM et al.; Increased vitamin D levels at birth and in early infancy increase offspring allergy risk-evidence for involvement of epigenetic mechanisms; J Allergy Clin Immunol 2016; DOI: 10.1016/j.jaci.2015.06.040

Czink E et al.; Durable remission under dual HER2 blockade with trastuzumab and pertuzumab in a patient with metastatic gallbladder cancer; Z Gastroenterol 2016; DOI: 10.1055/s-0042-103498

Bochtler T. et al.; Evolution of a FLT3-TKD mutated subclone at meningeal relapse in acute promyelocytic leukemia; Cold Spring Harb Mol Case Stud 2016; DOI: 10.1101/mcs.a001123

Gröschel S et al.; Integration of genomics and histology revises diagnosis and enables effective therapy of refractory cancer of unknown primary with PDL1 amplification; Cold Spring Harb Mol Case Stud 2016; DOI: 10.1101/mcs.a001180

Trump S et al.; Prenatal maternal stress and wheeze in children: novel insights into epigenetic regulation; Scientific Reports 2016; DOI: 10.1038/srep28616

Gu Z et al.; gtrellis: an R/Bioconductor package for making genome-level Trellis graphics; BMC Bioinformatics 2016; DOI: 10.1186/s12859-016-1051-4

Gu Z et al; HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data; Bioinformatics 2016; DOI: 10.1093/bioinformatics/btw161

Gu Z et al.; Complex heatmaps  reveal  patterns  and  correlations in multidimensional genomic data; Bioinformatics 2016; DOI: 10.1093/bioinformatics/btw313

Bauer T et al; Environment‐induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their children, Mol. Syst. Biol. 2016; DOI: 10.15252/msb.20156520

Johann PD et al.; Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes, Cancer Cell 2016; DOI: 10.1016/j.ccell.2016.02.001

Sturm D et al.; New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs; Cell 2016; DOI: 10.1016/j.cell.2016.01.015

Oakes CC et al.; DNA methylation dynamics during B cell maturation underlie a continuum of disease phenotypes in chronic lymphocytic leukemia; Nature Genet 2016; DOI: 10.1038/ng.3488

Kordes M et al.; Cooperation of BRAFF595L and mutant HRAS in histiocytic sarcoma provides new insights into oncogenic BRAF signaling; Leukemia 2016; DOI: 10.1038/leu.2015.319

Noll EM et al.; CYP3A5 mediates basal and acquired therapy resistance in different subtypes of pancreatic ductal adenocarcinoma; Nat. Med. 2016; DOI: 10.1038/nm.4038




Abba M et al.;MicroRNAs — from metastasis prediction to metastasis prevention?; Mol Cell Oncol 2015; DOI: 10.1080/23723556.2015.1074336

Mudduluru G. et al.; A Systematic Approach to Defining the microRNA Landscape in Metastasis; Cancer Res. 2015; DOI: 10.1158/0008-5472.CAN-15-0997

Alioto TS et al.; A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing; Nat Commun 2015; DOI: 10.1038/ncomms10001

Sahm F et al.; Next-generation sequencing in routine brain tumor diagnostics enables an integrated diagnosis and identifies actionable targets; Acta Neuropathol. 2015; DOI: 10.1007/s00401-015-1519-8

Kretzmer H et al.; DNA methylome analysis in Burkitt and follicular lymphomas identifies differentially methylated regions linked to somatic mutation and transcriptional control; Nat. Genet. 2015; DOI: 10.1038/ng.3413

Ruggiero E et al.; High-resolution analysis of the human T-cell receptor repertoire, Nat. Commun. 2015; DOI: 10.1038/ncomms9081

Heim S et al.; Papillary tumor of the Pineal Region: A Distinct Molecular Entity, Brain Pathol. 2015; DOI: 10.1111/bpa.12282

Korshunov A et al.; Integrated analysis of pediatric glioblastoma reveals a subset of biologically favorable tumors with associated molecular prognostic markers; Acta Neuropathol. 2015; DOI: 10.1007/s00401-015-1405-4

Gu L et al.; BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence; Nat. Genet. 2015; DOI: 10.1038/ng.3165

Pajtler KW et al.; Molecular Classification of Ependymal Tumors across all CNS Compartments, Histopathological Grades, and Age Groups; Cancer Cell 2015; DOI: 10.1016/j.ccell.2015.04.002

Haller F et al.; Recurrent Mutations within the amino-Terminal region of β-Catenin Are Probable Key Molecular Driver Events in Sinonasal Hemangiopericytoma; Am J Pathol. 2015; DOI: 10.1016/j.ajpath.2014.10.019

Dietrich S et al.; Recurrent CDKN1B (p27) mutations in hairy cell leukemia; Blood 2015; DOI: 10.1182/blood-2015-04-643361

Schlesner M and Eils R; Hypermutation takes the driver`s seat; Genome Med. 2015; DOI: 10.1186/s13073-015-0159-x

Wegert J et al.; Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors; Cancer Cell 2015; DOI: 10.1016/j.ccell.2015.01.002




Northcott PA et al.; Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma; Nature 2014; DOI: 10.1038/nature13379

Gu Z et al.; circlize Implements and enhances circular visualization in R, Bioinformatics 2014; DOI: 10.1093/bioinformatics/btu393

Wiestler B et al.; Integrated DNA methylation and copy-number profiling identify three clinically and biologically relevant groups of anaplastic glioma; Acta Neuropathol. 2014; DOI: 10.1007/s00401-014-1315-x

Hutter S et al.; Whole exome sequencing reveals that the majority of schwannomatosis cases remain unexplained after excluding SMARCB1 and LZTR1 germline variants; Acta Neuropathol. 2014; DOI: 10.1007/s00401-014-1311-1

Oakes CC et al.; Evolution of DNA methylation is linked to genetic aberrations in chronic lymphocytic leukemia; Cancer Discov. 2014; DOI: 10.1158/2159-8290.CD-13-0349

Barthelmeß S et al.; Solitary fibrous tumors/hemangiopericytomas with different variants of the NAB2-STAT6 gene fusion are characterized by specific histomorphology and distinct clinicopathological features; Am J Pathol. 2014; DOI: 10.1016/j.ajpath.2013.12.016

Haller F et al.; Aberrant DNA hypermethylation of SDHC: a novel mechanism of tumor development in Carney triad;  Endocr. Relat. Cancer 2014; DOI: 10.1530/ERC-14-0254

Olins AL et al.; Retrotransposon Alu is enriched in the epichromatin of HL-60 cells; Nucleus 2014; DOI: 10.4161/nucl.29141

Hovestadt V et al.; Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing; Nature 2014; DOI: 10.1038/nature13268

Wick et al.; A phase II, randomized, study of weekly APG101+reirradiation versus reirradiation in progressive glioblastoma; Clin Cancer Res 2014; DOI: 10.1158/1078-0432.CCR-14-0951-T

Ball CR et al.; Clonal succession of transiently active tumor-initiating cell clones in human pancreatic cancer drives cancer progression in vivo; Oncol Res Treat 2014; DOI: 10.15252/emmm.201607354

Yaktapour et al.; BRAF inhibitor-associated ERK activation drives development of chronic lymphocytic leukemia; J Clin Invest 2014; DOI: 10.1172/JCI76539


Dietrich S et al.; Continued response off treatment after BRAF inhibition in refractory hairy cell leukemia; J Clin Oncol 2013; DOI: 10.1200/JCO.2012.45.9495

Jäger N et al.; Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer; Cell 2013; DOI: 10.1016/j.cell.2013.09.042

Jethwa A et al.; Targeted resequencing for analysis of clonal composition of recurrent gene mutations in chronic lymphocytic leukaemia; BJH 2013; DOI: 10.1111/bjh.12539

Jones DT et al.; Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma; Nat. Genet. 2013; DOI: 10.1038/ng.2682


Jones DT et al.; Dissecting the genomic complexity underlying medulloblastoma; Nature 2012; DOI: 10.1038/nature11284


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