Multiscale heterogeneity in gastric adenocarcinoma evolution is an obstacle to precision medicine

The evolutionary history of 2,658 cancers

(2020) Moritz Gerstung et al.   NATURE

Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer

(2020) Katharina von Loga et al.   Nature Communications

The landscape of selection in 551 esophageal adenocarcinomas defines genomic biomarkers for the clinic

(2019) Alexander M. Frankell et al.   NATURE GENETICS

How many samples are needed to infer truly clonal mutations from heterogenous tumours?

(2019) Luka Opasic et al.   BMC CANCER

Tumor genomic profiling guides metastatic gastric cancer patients to targeted treatment: The VIKTORY Umbrella Trial

(2019) Jeeyun Lee et al.   Cancer Discovery

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data

(2019) Ketevan Chkhaidze et al.   PLoS Computational Biology

Intratumoral heterogeneity and loss of ARID1A expression in gastric cancer correlates with increased PD-L1 expression in Western patients

(2019) Julia Maria Tober et al.   HUMAN PATHOLOGY

Palimpsest: an R package for studying mutational and structural variant signatures along clonal evolution in cancer

(2018) Jayendra Shinde et al.   BIOINFORMATICS

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal

(2018) Samra Turajlic et al.   CELL

Smad4/DPC4

(2018) Aoife J McCarthy et al.   JOURNAL OF CLINICAL PATHOLOGY

Quantification of subclonal selection in cancer from bulk sequencing data

(2018) Marc J. Williams et al.   NATURE GENETICS

Mutation heterogeneity between primary gastric cancers and their matched lymph node metastases

(2018) Han Hong Lee et al.   Gastric Cancer

COSMIC: the Catalogue Of Somatic Mutations In Cancer

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

Typing tumors using pathways selected by somatic evolution

(2018) Sheng Wang et al.   Nature Communications

Cellular senescence regulated by SWI/SNF complex subunits through p53/p21 and p16/pRB pathway

(2017) Ling He et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma

(2017) Eirini Pectasides et al.   Cancer Discovery

Clinicopathologic Characteristics of Microsatellite Instable Gastric Carcinomas Revisited

(2017) Micaela Mathiak et al.   APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY

Gastric adenocarcinoma

(2017) Jaffer A. Ajani et al.   Nature Reviews Disease Primers

Detecting truly clonal alterations from multi-region profiling of tumours

(2017) Benjamin Werner et al.   Scientific Reports

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Identification of neutral tumor evolution across cancer types

(2016) Marc J Williams et al.   NATURE GENETICS

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

The chronological sequence of somatic mutations in early gastric carcinogenesis inferred from multiregion sequencing of gastric adenomas

(2016) Chul-Hyun Lim et al.   Oncotarget

CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing

(2016) Eric Talevich et al.   PLoS Computational Biology

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data

(2015) Konstantin Okonechnikov et al.   BIOINFORMATICS

Validating the prognostic and discriminating value of the TNM-classification for gastric cancer – A critical appraisal

(2015) C. Röcken et al.   EUROPEAN JOURNAL OF CANCER

MET in gastric cancer - discarding a 10% cutoff rule

(2015) Marie-Luise Metzger et al.   HISTOPATHOLOGY

Fast and scalable inference of multi-sample cancer lineages

(2015) Victoria Popic et al.   GENOME BIOLOGY

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data

(2014) F. Favero et al.   ANNALS OF ONCOLOGY

ABRA: improved coding indel detection via assembly-based realignment

(2014) Lisle E. Mose et al.   BIOINFORMATICS

Cooperativity of E-cadherin and Smad4 Loss to Promote Diffuse-Type Gastric Adenocarcinoma and Metastasis

(2014) Jun Won Park et al.   MOLECULAR CANCER RESEARCH

Comprehensive molecular characterization of gastric adenocarcinoma

(2014) Adam J. Bass et al.   NATURE

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer

(2014) Kai Wang et al.   NATURE GENETICS

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

(2013) Beifang Niu et al.   BIOINFORMATICS

Prognostic and Putative Predictive Biomarkers of Gastric Cancer for Personalized Medicine

(2013) Viktoria S. Warneke et al.   DIAGNOSTIC MOLECULAR PATHOLOGY

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Her2/neu testing in gastric cancer: evaluating the risk of sampling errors

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Detecting false-positive signals in exome sequencing

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ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

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