2023
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Movassagh M, Schiff S, Paulson J. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023, 39: btad565. PMID: 37707523, PMCID: PMC10516520, DOI: 10.1093/bioinformatics/btad565.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsRNA sequencingMicrobial abundance dataQuantitative trait lociSingle nucleotide polymorphism dataRibosomal RNA sequencingField of genomicsWhole-genome sequencingEvidence of interplayMutational profileTrait lociMicrobial communitiesMicrobial abundancePolymorphism dataMicrobial populationsGenome sequencingAbundance dataFirst R packageHuman geneticsBioconductor packageGenetic variantsMicrobiome dataSequencingR packageAbundance
2022
Prognostic mutational subtyping in de novo diffuse large B-cell lymphoma
Kim E, Jiang Y, Xu T, Bazeos A, Knapp A, Bolen C, Humphrey K, Nielsen T, Penuel E, Paulson J. Prognostic mutational subtyping in de novo diffuse large B-cell lymphoma. BMC Cancer 2022, 22: 231. PMID: 35236331, PMCID: PMC8892802, DOI: 10.1186/s12885-022-09237-5.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAntineoplastic Combined Chemotherapy ProtocolsBridged Bicyclo Compounds, HeterocyclicClinical Trials, Phase II as TopicClinical Trials, Phase III as TopicEnhancer of Zeste Homolog 2 ProteinExome SequencingFemaleHumansLymphoma, Large B-Cell, DiffuseMaleMiddle AgedMutationPrognosisProto-Oncogene Proteins c-bcl-2RNA-SeqSulfonamidesTreatment OutcomeConceptsSequence dataWhole-exome sequencing dataExome-sequencing dataTargeted sequencing platformsExome sequencing dataTargeted sequencing dataBackgroundDiffuse large B-cell lymphomaLarge B-cell lymphomaSequencing platformsRNA-seqDe novo DLBCLImproved overall survivalTarget sequenceB-cell lymphomaVenetoclax therapyMutation subtypesPrognostic subsetsMutationsOverall survivalMolecular subsetsSubset distributionMutation groupSurvival outcomesMutation profilesClinical associations
2019
Prognostic impact of somatic mutations in diffuse large B-cell lymphoma and relationship to cell-of-origin: data from the phase III GOYA study
Bolen C, Klanova M, Trneny M, Sehn L, He J, Tong J, Paulson J, Kim E, Vitolo U, Di Rocco A, Fingerle-Rowson G, Nielsen T, Lenz G, Oestergaard M. Prognostic impact of somatic mutations in diffuse large B-cell lymphoma and relationship to cell-of-origin: data from the phase III GOYA study. Haematologica 2019, 105: 2298-2307. PMID: 33054054, PMCID: PMC7556630, DOI: 10.3324/haematol.2019.227892.Peer-Reviewed Original ResearchConceptsDiffuse large B-cell lymphomaLarge B-cell lymphomaB-cell lymphomaPrognostic impact of somatic mutationsCell-of-origin subtypesBCL2 alterationsCell of originPrognostic impactImpact of somatic mutationsMolecular heterogeneity of diffuse large B-cell lymphomaGerminal center B-cell-like diffuse large B-cell lymphomaHeterogeneity of diffuse large B-cell lymphomaTargeted DNA next-generation sequencingAssociated with shorter progression-free survivalShorter progression-free survivalSomatic mutationsDNA next-generation sequencingParaffin-embedded tissue biopsiesProgression-free survivalMultivariate Cox regressionBCL2 translocationsUntreated patientsPotential treatment targetPrognostic differencesPrognostic effect
2018
Cancer subtype identification using somatic mutation data
Kuijjer M, Paulson J, Salzman P, Ding W, Quackenbush J. Cancer subtype identification using somatic mutation data. British Journal Of Cancer 2018, 118: 1492-1501. PMID: 29765148, PMCID: PMC5988673, DOI: 10.1038/s41416-018-0109-7.Peer-Reviewed Original ResearchConceptsSomatic mutation dataAssociated with mutationsNext-generation sequencing technologiesMutation dataBiological pathwaysSets of mutationsSignal transduction pathwaysCancer typesPan-cancer subtypesSequencing technologiesPhenotypic dataCancer Genome AtlasCancer subtype identificationTransduction pathwaysMutational driversSomatic mutationsSubgroup of patientsTargeted treatment optionsMutationsMutation patternsGenome AtlasClassification of patientsMutation profilesPrimary tumorPrognostic subtypes