NCT/DKFZ MASTER handbook of interpreting whole-genome, transcriptome, and methylome data for precision oncology

Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC)

(2022) Peter Horak et al.   GENETICS IN MEDICINE

Methylation classifiers: Brain tumors, sarcomas, and what's next

(2022) Christian Koelsche et al.   GENES CHROMOSOMES & CANCER

Lessons learned: the first consecutive 1000 patients of the CCCMunichLMU Molecular Tumor Board

(2022) Kathrin Heinrich et al.   JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY

A pan-cancer compendium of chromosomal instability

(2022) Ruben M. Drews et al.   NATURE

Signatures of copy number alterations in human cancer

(2022) Christopher D. Steele et al.   NATURE

Comprehensive genomic and epigenomic analysis in cancer of unknown primary guides molecularly-informed therapies despite heterogeneity

(2022) Lino Möhrmann et al.   Nature Communications

1490MO CDK4/6 inhibition in locally advanced/metastatic chordoma (NCT PMO-1601)

(2022) M-V. Teleanu et al.   ANNALS OF ONCOLOGY

Comprehensive cancer predisposition testing within the prospective MASTER trial identifies hereditary cancer patients and supports treatment decisions for rare cancers

(2022) A. Jahn et al.   ANNALS OF ONCOLOGY

Accurate and efficient detection of gene fusions from RNA sequencing data

(2021) Sebastian Uhrig et al.   GENOME RESEARCH

Sarcoma classification by DNA methylation profiling

(2021) Christian Koelsche et al.   Nature Communications

Knowledge bases and software support for variant interpretation in precision oncology

(2021) Florian Borchert et al.   BRIEFINGS IN BIOINFORMATICS

Assigning evidence to actionability: An introduction to variant interpretation in precision cancer medicine

(2021) Peter Horak et al.   GENES CHROMOSOMES & CANCER

Comprehensive Genomic and Transcriptomic Analysis for Guiding Therapeutic Decisions in Patients with Rare Cancers

(2021) Peter Horak et al.   Cancer Discovery

EGFR and PI3K Pathway Activities Might Guide Drug Repurposing in HPV-Negative Head and Neck Cancers

(2021) Andreas Mock et al.   Frontiers in Oncology

Rationale and design of the CRAFT (Continuous ReAssessment with Flexible ExTension in Rare Malignancies) multicenter phase II trial

(2021) C.E. Heilig et al.   ESMO Open

Molecular profiling for precision cancer therapies

(2020) Eoghan R. Malone et al.   Genome Medicine

Milademetan, an oral MDM2 inhibitor, in well-differentiated/ dedifferentiated liposarcoma: results from a phase 1 study in patients with solid tumors or lymphomas

(2020) M.M. Gounder et al.   EUROPEAN JOURNAL OF CANCER

Integrating proteomics into precision oncology

(2020) Leonie W. Wahjudi et al.   INTERNATIONAL JOURNAL OF CANCER

Analysis of mutational signatures with yet another package for signature analysis

(2020) Daniel Hübschmann et al.   GENES CHROMOSOMES & CANCER

S2k-Leitlinie Humangenetische Diagnostik und Genetische Beratung

(2019)   Medizinische Genetik

The Status and Impact of Clinical Tumor Genome Sequencing

(2019) Kenna R. Mills Shaw et al.   Annual Review of Genomics and Human Genetics

Variant classification in precision oncology

(2019) Jonas Leichsenring et al.   INTERNATIONAL JOURNAL OF CANCER

Immunogenic neoantigens derived from gene fusions stimulate T cell responses

(2019) Wei Yang et al.   NATURE MEDICINE

Molecular profiling in precision medicine oncology

(2019) Christophe Le Tourneau et al.   NATURE MEDICINE

TelomereHunter – in silico estimation of telomere content and composition from cancer genomes

(2019) Lars Feuerbach et al.   BMC BIOINFORMATICS

Palbociclib and cetuximab in platinum-resistant and in cetuximab-resistant human papillomavirus-unrelated head and neck cancer: a multicentre, multigroup, phase 2 trial

(2019) Douglas Adkins et al.   LANCET ONCOLOGY

Maintenance Olaparib for Germline BRCA-Mutated Metastatic Pancreatic Cancer

(2019) Talia Golan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Defective homologous recombination DNA repair as therapeutic target in advanced chordoma

(2019) Stefan Gröschel et al.   Nature Communications

Rogaratinib in patients with advanced cancers selected by FGFR mRNA expression: a phase 1 dose-escalation and dose-expansion study

(2019) Martin Schuler et al.   LANCET ONCOLOGY

ClinVar: improvements to accessing data

(2019) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Standard operating procedure for curation and clinical interpretation of variants in cancer

(2019) Arpad M. Danos et al.   Genome Medicine

The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma

(2018) Matthew J. McBride et al.   CANCER CELL

Pathogenic Germline Variants in 10,389 Adult Cancers

(2018) Kuan-lin Huang et al.   CELL

DNA methylation-based classification of central nervous system tumours

(2018) David Capper et al.   NATURE

Integrative genomic and transcriptomic analysis of leiomyosarcoma

(2018) Priya Chudasama et al.   Nature Communications

Perturbation-response genes reveal signaling footprints in cancer gene expression

(2018) Michael Schubert et al.   Nature Communications

NRG1 Fusions in KRAS Wild-type Pancreatic Cancer

(2018) Christoph Heining et al.   Cancer Discovery

VarSome: the human genomic variant search engine

(2018) Christos Kopanos et al.   BIOINFORMATICS

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Precision oncology based on omics data: The NCT Heidelberg experience

(2017) Peter Horak et al.   INTERNATIONAL JOURNAL OF CANCER

OTP: An automatized system for managing and processing NGS data

(2017) Eva Reisinger et al.   JOURNAL OF BIOTECHNOLOGY

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

(2017) Marilyn M. Li et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Multi-dimensional genomic analysis of myoepithelial carcinoma identifies prevalent oncogenic gene fusions

(2017) Martin G. Dalin et al.   Nature Communications

Accelerating Discovery of Functional Mutant Alleles in Cancer

(2017) Matthew T. Chang et al.   Cancer Discovery

Whole-Genome and Epigenomic Landscapes of Etiologically Distinct Subtypes of Cholangiocarcinoma

(2017) Apinya Jusakul et al.   Cancer Discovery

KIT Oncogenic Mutations: Biologic Insights, Therapeutic Advances, and Future Directions

(2016) Jonathan A. Fletcher   CANCER RESEARCH

Phase I trial of palbociclib, a selective cyclin dependent kinase 4/6 inhibitor, in combination with cetuximab in patients with recurrent/metastatic head and neck squamous cell carcinoma

(2016) Loren Michel et al.   ORAL ONCOLOGY

Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors

(2016) D. Williams Parsons et al.   JAMA Oncology

Receptor Tyrosine Kinase Expression Predicts Response to Sunitinib in Breast Cancer

(2015) Philip M. Spanheimer et al.   ANNALS OF SURGICAL ONCOLOGY

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

ClinGen — The Clinical Genome Resource

(2015) Heidi L. Rehm et al.   NEW ENGLAND JOURNAL OF MEDICINE

Personalized genomic analyses for cancer mutation discovery and interpretation

(2015) Siân Jones et al.   Science Translational Medicine

Genomic landscape of liposarcoma

(2015) Deepika Kanojia et al.   Oncotarget

Molecular Tumor Board: The University of California San Diego Moores Cancer Center Experience

(2014) M. Schwaederle et al.   ONCOLOGIST

MSIsensor: microsatellite instability detection using paired tumor-normal sequence data

(2013) Beifang Niu et al.   BIOINFORMATICS

Enhanced Sensitivity for Detection of Low-Level Germline MosaicRB1Mutations in Sporadic Retinoblastoma Cases Using Deep Semiconductor Sequencing

(2013) Zhao Chen et al.   HUMAN MUTATION

Imatinib for Melanomas Harboring Mutationally Activated or Amplified KIT Arising on Mucosal, Acral, and Chronically Sun-Damaged Skin

(2013) F. Stephen Hodi et al.   JOURNAL OF CLINICAL ONCOLOGY

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer

(2012) V Abkevich et al.   BRITISH JOURNAL OF CANCER

Ploidy and Large-Scale Genomic Instability Consistently Identify Basal-like Breast Carcinomas with BRCA1/2 Inactivation

(2012) T. Popova et al.   CANCER RESEARCH

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

Rare cancers are not so rare: The rare cancer burden in Europe

(2011) Gemma Gatta et al.   EUROPEAN JOURNAL OF CANCER