2021
Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer
Sheng T, Ho S, Ooi W, Xu C, Xing M, Padmanabhan N, Huang K, Ma L, Ray M, Guo Y, Sim N, Anene-Nzelu C, Chang M, Razavi-Mohseni M, Beer M, Foo R, Sundar R, Chan Y, Tan A, Ong X, Skanderup A, White K, Jha S, Tan P. Integrative epigenomic and high-throughput functional enhancer profiling reveals determinants of enhancer heterogeneity in gastric cancer. Genome Medicine 2021, 13: 158. PMID: 34635154, PMCID: PMC8504099, DOI: 10.1186/s13073-021-00970-3.Peer-Reviewed Original ResearchMeSH KeywordsAcetylationADP-Ribosylation FactorsCell Line, TumorCell ProliferationChromatinEnhancer Elements, GeneticEpigenomicsGene Expression Regulation, NeoplasticGenomicsHistonesHumansInhibitor of Growth Protein 1OncogenesPromoter Regions, GeneticRNA-SeqStomach NeoplasmsTranscriptomeWhole Genome SequencingConceptsSingle nucleotide polymorphismsActivity-by-contactEnhancer-promoter interactionsSomatic copy number alterationsGermline single nucleotide polymorphismsHistone modificationsDistal cis-regulatory elementsLow somatic mutation rateCell-specific gene expressionCis-regulatory elementsFunctional enhancer activityHistone modification profilesWhole-genome sequencingRegulatory region sequencingCell fate determinationSuper-enhancer regionsCopy number alterationsGenome copy numberEffect of histone acetylationSomatic mutation rateCancer-relevant genesFunctional assay dataEnhanced activityGC cell linesRegion sequences
2018
Biomarkers for Homologous Recombination Deficiency in Cancer
Hoppe M, Sundar R, Tan D, Jeyasekharan A. Biomarkers for Homologous Recombination Deficiency in Cancer. Journal Of The National Cancer Institute 2018, 110: 704-713. PMID: 29788099, DOI: 10.1093/jnci/djy085.Peer-Reviewed Original ResearchConceptsPoly-ADP-ribose polymeraseArray-based comparative genomic hybridizationSingle nucleotide polymorphismsHomologous recombination deficiencyPoly-ADP ribose polymerase inhibitorsComparative genomic hybridizationHomologous recombination genesNext-generation sequencingDNA repair pathwaysRecombination deficiencyClinical trialsGenomic hybridizationGermline BRCA1/2 mutation statusClinical development of PARP inhibitorsDefective DNA repairGenomic scarsResponse to platinum-based therapyHomologous recombinationDevelopment of PARP inhibitorsRecombinant genesNucleotide polymorphismsPlatinum-based therapyRibose polymeraseBRCA1/2 mutation statusDNA repair