2016
A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data
Cui A, Di Niro R, Vander Heiden JA, Briggs AW, Adams K, Gilbert T, O'Connor KC, Vigneault F, Shlomchik MJ, Kleinstein SH. A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data. The Journal Of Immunology 2016, 197: 3566-3574. PMID: 27707999, PMCID: PMC5161250, DOI: 10.4049/jimmunol.1502263.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsB-LymphocytesCells, CulturedClonal Selection, Antigen-MediatedDNA RepairFemaleGerminal CenterHigh-Throughput Nucleotide SequencingHumansImmunoglobulin Heavy ChainsImmunoglobulin Variable RegionMiceMice, Inbred BALB CMice, TransgenicModels, GeneticMutationMutation RateSomatic Hypermutation, ImmunoglobulinConceptsSpecific DNA motifsSimilar biological processesObserved mutation patternDNA repair activityIg sequencesNonfunctional sequencesDNA motifsMutation patternsHigh mutation frequencySelection pressureUnselected mutationsSequencing dataBiological processesFunctional sequencesRepair activityTransition mutationsSomatic hypermutation patternsGerminal center B cellsSomatic hypermutationNext-generation methodsHypermutation patternsMutation frequencyMutationsSequenceMotif
2015
A model of somatic hypermutation targeting in mice based on high-throughput immunoglobulin sequencing data (TECH2P.910)
Cui A, Diniro R, Briggs A, Adams K, Vander Heiden J, O'Connor K, Vigneault F, Shlomchik M, Kleinstein S. A model of somatic hypermutation targeting in mice based on high-throughput immunoglobulin sequencing data (TECH2P.910). The Journal Of Immunology 2015, 194: 206.20-206.20. DOI: 10.4049/jimmunol.194.supp.206.20.Peer-Reviewed Original ResearchSimilar biological processesNon-functional sequencesObserved mutation patternDNA repair activityMutation patternsDNA motifsNext-generation sequencingHigh mutation frequencyUnselected mutationsSelection pressureSequencing dataBiological processesFunctional sequencesImmunoglobulin genesRepair activitySomatic hypermutation patternsSomatic hypermutationHypermutation patternsMutation frequencyIg sequencesT transitionSequenceHeavy chain transgenic miceMotifTransgenic mice
2013
Models of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data
Yaari G, Vander Heiden J, Uduman M, Gadala-Maria D, Gupta N, Stern JN, O’Connor K, Hafler DA, Laserson U, Vigneault F, Kleinstein SH. Models of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data. Frontiers In Immunology 2013, 4: 358. PMID: 24298272, PMCID: PMC3828525, DOI: 10.3389/fimmu.2013.00358.Peer-Reviewed Original ResearchAccurate background modelSynonymous mutationsNon-coding regionsParticular codon usageNon-functional sequencesComputational analysis methodsObserved mutation patternExisting modelsBackground modelInfluence of selectionCodon usageSHM targetingBase compositionImproved modelSequencing dataNucleotide substitutionsAnalysis methodStatistical analysisFunctional sequencesMutation targetingB-cell cancersModelSomatic hypermutation patternsMutationsHypermutation patterns
2011
Somatic hypermutation targeting is influenced by location within the immunoglobulin V region
Cohen RM, Kleinstein SH, Louzoun Y. Somatic hypermutation targeting is influenced by location within the immunoglobulin V region. Molecular Immunology 2011, 48: 1477-1483. PMID: 21592579, PMCID: PMC3109224, DOI: 10.1016/j.molimm.2011.04.002.Peer-Reviewed Original ResearchConceptsObserved mutation patternSpecific DNA motifsBiased codon usageImmunoglobulin V genesMutation accumulationGene positionCodon usageMutation patternsDNA motifsPositive selectionPosition-specific effectsImmunoglobulin V regionsNegative selectionB cellsMutationsMutation frequencyV geneGenesPeripheral B cellsSubstitution typeV regionsTargetingSpecific targetingCellsSequence