2016
The Link Between CD6 and Autoimmunity: Genetic and Cellular Associations.
Kofler DM, Farkas A, von Bergwelt-Baildon M, Hafler DA. The Link Between CD6 and Autoimmunity: Genetic and Cellular Associations. Current Drug Targets 2016, 17: 651-65. PMID: 26844569, DOI: 10.2174/1389450117666160201105934.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CDAntigens, Differentiation, T-LymphocyteArthritis, RheumatoidAutoimmunityCD4-Positive T-LymphocytesCell Adhesion Molecules, NeuronalClinical Trials as TopicDisease Models, AnimalFetal ProteinsGenetic Predisposition to DiseaseHumansMultiple SclerosisPolymorphism, Single NucleotideConceptsMultiple sclerosisRheumatoid arthritisCentral nervous systemNervous systemSingle nucleotide polymorphismsDevelopment of MSTreatment of RARole of CD6T cell traffickingT cell functionGenetic risk factorsEndothelial cell barrierCD6 geneClinical responseGenetic associationClinical featuresAutoimmune diseasesSynovial cellsRisk factorsTumor necrosisSynovial fibroblastsPossible common mechanismT cellsT lymphocytesLeukocyte trafficking
2011
Genome‐wide meta‐analysis identifies novel multiple sclerosis susceptibility loci
Patsopoulos NA, Esposito F, Reischl J, Lehr S, Bauer D, Heubach J, Sandbrink R, Pohl C, Edan G, Kappos L, Miller D, Montalbán J, Polman C, Freedman M, Hartung H, Arnason B, Comi G, Cook S, Filippi M, Goodin D, Jeffery D, O'Connor P, Ebers G, Langdon D, Reder A, Traboulsee A, Zipp F, Schimrigk S, Hillert J, Bahlo M, Booth D, Broadley S, Brown M, Browning B, Browning S, Butzkueven H, Carroll W, Chapman C, Foote S, Griffiths L, Kermode A, Kilpatrick T, Lechner-Scott J, Marriott M, Mason D, Moscato P, Heard R, Pender M, Perreau V, Perera D, Rubio J, Scott R, Slee M, Stankovich J, Stewart G, Taylor B, Tubridy N, Willoughby E, Wiley J, Matthews P, Boneschi F, Compston A, Haines J, Hauser S, McCauley J, Ivinson A, Oksenberg J, Pericak-Vance M, Sawcer S, De Jager P, Hafler D, de Bakker P. Genome‐wide meta‐analysis identifies novel multiple sclerosis susceptibility loci. Annals Of Neurology 2011, 70: 897-912. PMID: 22190364, PMCID: PMC3247076, DOI: 10.1002/ana.22609.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsSusceptibility lociHapMap Phase IIUnique single nucleotide polymorphismsGene discovery effortsNew susceptibility lociStrongest cis effectsMS genome-wide association studiesQuantitative trait analysisFlanking genesGenetic architectureRNA expression dataMultiple sclerosis susceptibility lociIntergenic regionSecond intronNew lociNovel susceptibility allelesAdditional lociTrait analysisAssociation studiesExpression dataChromosome 2p21LociFunctional consequencesGenome-Wide Assessment for Genetic Variants Associated with Ventricular Dysfunction after Primary Coronary Artery Bypass Graft Surgery
Fox AA, Pretorius M, Liu KY, Collard CD, Perry TE, Shernan SK, De Jager PL, Hafler DA, Herman DS, DePalma SR, Roden DM, Muehlschlegel JD, Donahue BS, Darbar D, Seidman JG, Body SC, Seidman CE. Genome-Wide Assessment for Genetic Variants Associated with Ventricular Dysfunction after Primary Coronary Artery Bypass Graft Surgery. PLOS ONE 2011, 6: e24593. PMID: 21980348, PMCID: PMC3184087, DOI: 10.1371/journal.pone.0024593.Peer-Reviewed Original ResearchConceptsCABG surgeryPostoperative ventricular dysfunctionVentricular dysfunctionSingle nucleotide polymorphismsPrimary coronary artery bypass graft surgeryCoronary artery bypass graft surgeryArtery bypass graft surgeryPrimary CABG surgeryBypass graft surgeryClinical risk factorsMechanical ventricular supportPatient risk stratificationGenetic variantsCABG cohortGraft surgeryPostoperative morbiditySurgical patientsCardiopulmonary bypassRisk stratificationVentricular supportRisk factorsLarge cohortPrevention strategiesSurgeryMale subjectsThe CD6 Multiple Sclerosis Susceptibility Allele Is Associated with Alterations in CD4+ T Cell Proliferation
Kofler DM, Severson CA, Mousissian N, De Jager PL, Hafler DA. The CD6 Multiple Sclerosis Susceptibility Allele Is Associated with Alterations in CD4+ T Cell Proliferation. The Journal Of Immunology 2011, 187: 3286-3291. PMID: 21849685, DOI: 10.4049/jimmunol.1100626.Peer-Reviewed Original ResearchMeSH KeywordsAllelesAntigens, CDAntigens, Differentiation, T-LymphocyteCD4-Positive T-LymphocytesCD8-Positive T-LymphocytesCell ProliferationCell SeparationCells, CulturedFemaleFlow CytometryGenetic Predisposition to DiseaseGenotypeHumansMaleMultiple SclerosisPhenotypeReverse Transcriptase Polymerase Chain ReactionRisk FactorsRNA, Small InterferingConceptsGenome-wide association studiesAssociation studiesAllelic variantsNew susceptibility lociSusceptibility allelesRisk allelesProliferation defectExon 5Risk-associated allelesSingle nucleotide polymorphismsExtracellular binding sitesCD6 geneSusceptibility lociLinkage disequilibriumMS risk alleleSelective knockdownT cell activationNucleotide polymorphismsAltered proliferationCell proliferationGenetic associationAllelesLong-term activationBinding sitesMS susceptibility allelesPervasive Sharing of Genetic Effects in Autoimmune Disease
Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, Wallace C, Abecasis GR, Barrett JC, Behrens T, Cho J, De Jager PL, Elder JT, Graham RR, Gregersen P, Klareskog L, Siminovitch KA, van Heel DA, Wijmenga C, Worthington J, Todd JA, Hafler DA, Rich SS, Daly MJ, . Pervasive Sharing of Genetic Effects in Autoimmune Disease. PLOS Genetics 2011, 7: e1002254. PMID: 21852963, PMCID: PMC3154137, DOI: 10.1371/journal.pgen.1002254.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsSystemic lupus erythematosusImmune-mediated diseasesType 1 diabetesGenetic risk factorsMajor histocompatibility locusCommon autoimmuneCommon single nucleotide polymorphismsLupus erythematosusCrohn's diseaseRheumatoid arthritisClinical evidenceMultiple sclerosisAutoimmune diseasesRisk single nucleotide polymorphismsCeliac diseaseInflammatory diseasesRisk factorsMeta-AnalysisDisease riskDiseaseHistocompatibility locusUnderlying mechanismGenetic associationNucleotide polymorphismsInterrogating the complex role of chromosome 16p13.13 in multiple sclerosis susceptibility: independent genetic signals in the CIITA–CLEC16A–SOCS1 gene complex
Zuvich RL, Bush WS, McCauley JL, Beecham AH, De Jager PL, Consortium T, Ivinson A, Compston A, Hafler D, Hauser S, Sawcer S, Pericak-Vance M, Barcellos L, Mortlock D, Haines J. Interrogating the complex role of chromosome 16p13.13 in multiple sclerosis susceptibility: independent genetic signals in the CIITA–CLEC16A–SOCS1 gene complex. Human Molecular Genetics 2011, 20: 3517-3524. PMID: 21653641, PMCID: PMC3153306, DOI: 10.1093/hmg/ddr250.Peer-Reviewed Original ResearchMeSH KeywordsCCCTC-Binding FactorChromosomes, Human, Pair 16FemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyGenotypeHumansLectins, C-TypeLinkage DisequilibriumLogistic ModelsMaleMonosaccharide Transport ProteinsMultiple SclerosisQuantitative Trait LociRepressor ProteinsSuppressor of Cytokine Signaling 1 ProteinSuppressor of Cytokine Signaling ProteinsConceptsIndependent genetic signalsGenetic signalsLymphoblastoid cell linesChromosome 16p13Cis expression QTLsOpen chromatin configurationCell linesLinkage disequilibrium patternsExpression array dataH3K27 methylationHistone modificationsGenomic regionsKb stretchStrong genetic componentSingle nucleotide polymorphismsChromatin configurationExpression correlationGene complexDisequilibrium patternsDisease locusGenesCorrelated expressionGenetic componentFunctional mechanismsLoci
2010
A Major Histocompatibility Class I Locus Contributes to Multiple Sclerosis Susceptibility Independently from HLA-DRB1*15:01
Cree BA, Rioux JD, McCauley JL, Gourraud PA, Goyette P, McElroy J, De Jager P, Santaniello A, Vyse TJ, Gregersen PK, Mirel D, Hafler DA, Haines JL, Pericak-Vance MA, Compston A, Sawcer SJ, Oksenberg JR, Hauser SL, , . A Major Histocompatibility Class I Locus Contributes to Multiple Sclerosis Susceptibility Independently from HLA-DRB1*15:01. PLOS ONE 2010, 5: e11296. PMID: 20593013, PMCID: PMC2892470, DOI: 10.1371/journal.pone.0011296.Peer-Reviewed Original ResearchConceptsCase-control analysisMS susceptibilityMultiple sclerosisSingle nucleotide polymorphismsClass IMS susceptibility allelesMultiple sclerosis susceptibilityMajor histocompatibility class ICochran-Armitage trend testLogistic regression modelingHLA-G geneMHC class IReplication datasetDiscovery datasetHistocompatibility class IArmitage trend testHLASignificant associationClass IIGenetic susceptibilityMajor histocompatibility complex (MHC) genesRegression modelingSusceptibility allelesP-valueMHCVariation Within DNA Repair Pathway Genes and Risk of Multiple Sclerosis
Briggs FB, Goldstein BA, McCauley JL, Zuvich RL, De Jager PL, Rioux JD, Ivinson AJ, Compston A, Hafler DA, Hauser SL, Oksenberg JR, Sawcer SJ, Pericak-Vance MA, Haines JL, Barcellos LF, Consortium F. Variation Within DNA Repair Pathway Genes and Risk of Multiple Sclerosis. American Journal Of Epidemiology 2010, 172: 217-224. PMID: 20522537, PMCID: PMC3658128, DOI: 10.1093/aje/kwq086.Peer-Reviewed Original ResearchConceptsDNA repair pathway genesPathway genesMultiple sclerosisExcision repairGeneral transcription factor IIHDouble-strand break repairTranscription factor IIHDNA repair pathwaysNucleotide excision repairRisk of MSBase excision repairPrimary genetic risk factorProminent genetic componentHuman leukocyte antigenComplex autoimmune diseaseSingle nucleotide polymorphism (SNP) variantsCentral nervous systemLogistic regression modelingGenetic risk factorsSingle nucleotide polymorphismsBreak repairRepair pathwaysCandidate genesAutoimmune diseasesGenesGenetic variation in the IL7RA/IL7 pathway increases multiple sclerosis susceptibility
Zuvich RL, McCauley JL, Oksenberg JR, Sawcer SJ, De Jager PL, International Multiple Sclerosis Genetics Consortium, Aubin C, Cross AH, Piccio L, Aggarwal NT, Evans D, Hafler DA, Compston A, Hauser SL, Pericak-Vance MA, Haines JL. Genetic variation in the IL7RA/IL7 pathway increases multiple sclerosis susceptibility. Human Genetics 2010, 127: 525-535. PMID: 20112030, PMCID: PMC2854871, DOI: 10.1007/s00439-010-0789-4.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsGene regionCase-control data setsPutative functional relationshipsNovel gene regionsIndependent case-control data setDense SNP mapReceptor alpha-chain geneIllumina Infinium BeadChipExperiment-wise significanceNovel associationsAlpha chain geneGenetic architectureComplex traitsStrong genetic componentGenetic variationSNP mapInfinium BeadChipAffordable genotypingBiological pathwaysGenesGenetic componentChain geneTYK2 geneNumerous family studies
2009
Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci
, , McCauley J, Zuvich R, Beecham A, De Jager P, Konidari I, Whitehead P, Aubin C, Ban M, Pobywajlo S, Briskin R, Romano S, Aggarwal N, Piccio L, McArdle W, Strachan D, Evans D, Cross A, Cree B, Rioux J, Barcellos L, Ivinson A, Compston A, Hafler D, Hauser S, Oksenberg J, Sawcer S, Pericak-Vance M, Haines J. Comprehensive follow-up of the first genome-wide association study of multiple sclerosis identifies KIF21B and TMEM39A as susceptibility loci. Human Molecular Genetics 2009, 19: 953-962. PMID: 20007504, PMCID: PMC2816610, DOI: 10.1093/hmg/ddp542.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphismsAssociation studiesFirst genome-wide association studyGenome-wide association screenNumerous complex diseasesSusceptibility lociInitial genome-wide association studyGenome-wide significanceNovel susceptibility lociComplex genetic diseasesHundreds of associationsSNP hitsGWAS studiesGenetic diseasesLociComplex diseasesOriginal screenTMEM39AInitial associationIndependent data setsReplicationKIF21BInitial replicationScreenReplication analysis identifies TYK2 as a multiple sclerosis susceptibility factor
Ban M, Goris A, Lorentzen Å, Baker A, Mihalova T, Ingram G, Booth DR, Heard RN, Stewart GJ, Bogaert E, Dubois B, Harbo HF, Celius EG, Spurkland A, Strange R, Hawkins C, Robertson NP, Dudbridge F, Wason J, De Jager PL, Hafler D, Rioux JD, Ivinson AJ, McCauley JL, Pericak-Vance M, Oksenberg JR, Hauser SL, Sexton D, Haines J, Sawcer S. Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor. European Journal Of Human Genetics 2009, 17: 1309-1313. PMID: 19293837, PMCID: PMC2782567, DOI: 10.1038/ejhg.2009.41.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesNon-synonymous single nucleotide polymorphismsRecent genome-wide association studiesLevel of phosphorylationAmino acid substitutionsTyrosine kinase 2 geneKinase 2 geneSingle-nucleotide polymorphism resultsSingle nucleotide polymorphismsKinase domainMultiple sclerosis susceptibility genesAssociation studiesAcid substitutionsFunctional roleSusceptibility genesNucleotide polymorphismsPolymorphism resultsTrio familiesReplication analysisGenesLociTYK2Susceptibility factorsPhosphorylationMultiple sclerosis
2007
Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study
Hafler D, Compston A, Sawcer S, Lander E, Daly M, De Jager P, de Bakker P, Gabriel S, Mirel D, Ivinson A, Pericak-Vance M, Gregory S, Rioux J, McCauley J, Haines J, Barcellos L, Cree B, Oksenberg J, Hauser S. Risk Alleles for Multiple Sclerosis Identified by a Genomewide Study. New England Journal Of Medicine 2007, 357: 851-862. PMID: 17660530, DOI: 10.1056/nejmoa073493.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedAllelesFemaleGenetic Predisposition to DiseaseGenome, HumanHLA-DR alpha-ChainsHLA-DR AntigensHumansInterleukin-2 Receptor alpha SubunitInterleukin-7 Receptor alpha SubunitLinkage DisequilibriumMaleMiddle AgedMultiple SclerosisMutationOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideRisk FactorsConceptsMultiple sclerosisReceptor alpha geneSingle nucleotide polymorphismsControl subjectsCase subjectsInterleukin-7 receptor alpha geneHeritable risk factorsAlpha geneRisk factorsFamily triosSclerosisRisk allelesHLA lociHLA-DRA locusTransmission disequilibrium testStringent P valueP-valueEffect sizeSignificant heritable componentInterleukin-2 receptor alpha geneNonsynonymous single nucleotide polymorphismsGenomewide association studiesMultiple single nucleotide polymorphismsSubjectsAssociationA second major histocompatibility complex susceptibility locus for multiple sclerosis
Yeo TW, De Jager PL, Gregory SG, Barcellos LF, Walton A, Goris A, Fenoglio C, Ban M, Taylor CJ, Goodman RS, Walsh E, Wolfish CS, Horton R, Traherne J, Beck S, Trowsdale J, Caillier SJ, Ivinson AJ, Green T, Pobywajlo S, Lander ES, Pericak-Vance MA, Haines JL, Daly MJ, Oksenberg JR, Hauser SL, Compston A, Hafler DA, Rioux JD, Sawcer S, . A second major histocompatibility complex susceptibility locus for multiple sclerosis. Annals Of Neurology 2007, 61: 228-236. PMID: 17252545, PMCID: PMC2737610, DOI: 10.1002/ana.21063.Peer-Reviewed Original ResearchConceptsMajor histocompatibility complexMultiple sclerosisHLA-C geneHLA-DRB1 geneHuman leukocyte antigen (HLA) typingResidual associationHLA-DRB1 locusComplex susceptibility lociTight linkage disequilibriumControl subjectsAntigen typingProtective effectSclerosisClass II regionHistocompatibility complexHLA lociRisk haplotypeClassical HLA lociSingle nucleotide polymorphismsIndependent effectsChromosome 6p21AssociationNucleotide polymorphismsTrio familiesSusceptibility loci
2004
A High-Density Admixture Map for Disease Gene Discovery in African Americans
Smith MW, Patterson N, Lautenberger JA, Truelove AL, McDonald GJ, Waliszewska A, Kessing BD, Malasky MJ, Scafe C, Le E, De Jager PL, Mignault AA, Yi Z, de Thé G, Essex M, Sankalé J, Moore JH, Poku K, Phair JP, Goedert JJ, Vlahov D, Williams SM, Tishkoff SA, Winkler CA, De La Vega FM, Woodage T, Sninsky JJ, Hafler DA, Altshuler D, Gilbert DA, O’Brien S, Reich D. A High-Density Admixture Map for Disease Gene Discovery in African Americans. American Journal Of Human Genetics 2004, 74: 1001-1013. PMID: 15088270, PMCID: PMC1181963, DOI: 10.1086/420856.Peer-Reviewed Original Research