2024
Genetic mapping across autoimmune diseases reveals shared associations and mechanisms
Lincoln M, Connally N, Axisa P, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers I, Padyukov L, Rich S, Graham R, Gaffney P, Langefeld C, Vyse T, Hafler D, Chun S, Sunyaev S, Cotsapas C. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nature Genetics 2024, 56: 838-845. PMID: 38741015, DOI: 10.1038/s41588-024-01732-8.Peer-Reviewed Original ResearchConceptsGenetic mapResolution of genetic mappingExpression quantitative trait lociFine-mapping resolutionQuantitative trait lociGenomic lociTrait lociPolygenic disorderAllelesRisk allelesLociPathogenic mechanismsImmune systemAutoimmune mechanismsAutoimmune diseasesInflammatory diseasesTraitsMechanismDiseaseSample collectionExpression
2019
Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility
Patsopoulos N, Baranzini S, Santaniello A, Shoostari P, Cotsapas C, Wong G, Beecham A, James T, Replogle J, Vlachos I, McCabe C, Pers T, Brandes A, White C, Keenan B, Cimpean M, Winn P, Panteliadis I, Robbins A, Andlauer T, Zarzycki O, Dubois B, Goris A, Søndergaard H, Sellebjerg F, Sorensen P, Ullum H, Thørner L, Saarela J, Cournu-Rebeix I, Damotte V, Fontaine B, Guillot-Noel L, Lathrop M, Vukusic S, Berthele A, Pongratz V, Buck D, Gasperi C, Graetz C, Grummel V, Hemmer B, Hoshi M, Knier B, Korn T, Lill C, Luessi F, Mühlau M, Zipp F, Dardiotis E, Agliardi C, Amoroso A, Barizzone N, Benedetti M, Bernardinelli L, Cavalla P, Clarelli F, Comi G, Cusi D, Esposito F, Ferrè L, Galimberti D, Guaschino C, Leone M, Martinelli V, Moiola L, Salvetti M, Sorosina M, Vecchio D, Zauli A, Santoro S, Mancini N, Zuccalà M, Mescheriakova J, van Duijn C, Bos S, Celius E, Spurkland A, Comabella M, Montalban X, Alfredsson L, Bomfim I, Gomez-Cabrero D, Hillert J, Jagodic M, Lindén M, Piehl F, Jelčić I, Martin R, Sospedra M, Baker A, Ban M, Hawkins C, Hysi P, Kalra S, Karpe F, Khadake J, Lachance G, Molyneux P, Neville M, Thorpe J, Bradshaw E, Caillier S, Calabresi P, Cree B, Cross A, Davis M, de Bakker P, Delgado S, Dembele M, Edwards K, Fitzgerald K, Frohlich I, Gourraud P, Haines J, Hakonarson H, Kimbrough D, Isobe N, Konidari I, Lathi E, Lee M, Li T, An D, Zimmer A, Madireddy L, Manrique C, Mitrovic M, Olah M, Patrick E, Pericak-Vance M, Piccio L, Schaefer C, Weiner H, Lage K, Compston A, Hafler D, Harbo H, Hauser S, Stewart G, D’Alfonso S, Hadjigeorgiou G, Taylor B, Barcellos L, Booth D, Hintzen R, Kockum I, Martinelli-Boneschi F, McCauley J, Oksenberg J, Oturai A, Sawcer S, Ivinson A, Olsson T, De Jager P. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility. Science 2019, 365 PMID: 31604244, PMCID: PMC7241648, DOI: 10.1126/science.aav7188.Peer-Reviewed Original ResearchMeSH KeywordsCase-Control StudiesCell Cycle ProteinsChromosome MappingChromosomes, Human, XGene FrequencyGenetic LociGenome-Wide Association StudyGenomicsGTPase-Activating ProteinsHumansInheritance PatternsMajor Histocompatibility ComplexMicrogliaMultiple SclerosisPolymorphism, Single NucleotideQuantitative Trait LociRNA-SeqTranscriptomeConceptsMajor histocompatibility complexMultiple sclerosisImmune cellsBrain-resident immune cellsPeripheral immune cellsPeripheral immune responseCentral nervous systemExtended major histocompatibility complexAutoimmune processControl subjectsHuman microgliaImmune responseNervous systemImmune systemHistocompatibility complexPutative susceptibility genesMicrogliaX variantGenetic architectureSusceptibility genesGenomic mapGenetic dataExpression profilesM geneSusceptibility variants
2013
Fine-Mapping the Genetic Association of the Major Histocompatibility Complex in Multiple Sclerosis: HLA and Non-HLA Effects
Patsopoulos NA, Barcellos LF, Hintzen RQ, Schaefer C, van Duijn CM, Noble JA, Raj T, , , Gourraud PA, Stranger BE, Oksenberg J, Olsson T, Taylor BV, Sawcer S, Hafler DA, Carrington M, De Jager PL, de Bakker PI. Fine-Mapping the Genetic Association of the Major Histocompatibility Complex in Multiple Sclerosis: HLA and Non-HLA Effects. PLOS Genetics 2013, 9: e1003926. PMID: 24278027, PMCID: PMC3836799, DOI: 10.1371/journal.pgen.1003926.Peer-Reviewed Original ResearchMeSH KeywordsAllelesChromosome MappingGenetic Predisposition to DiseaseGenome-Wide Association StudyHaplotypesHistocompatibility Antigens Class IHLA-DP beta-ChainsHLA-DRB1 ChainsHumansIntracellular Signaling Peptides and ProteinsLinkage DisequilibriumMajor Histocompatibility ComplexMembrane ProteinsMultiple SclerosisPolymorphism, Single NucleotideReceptors, Tumor Necrosis Factor, Type IConceptsHuman leukocyte antigenNon-HLA risk allelesRisk allelesClassical human leukocyte antigenClass IMultiple sclerosis susceptibilityHLA class IIndependent effectsMS susceptibility geneMajor histocompatibility complexMajor histocompatibility complex regionHLA effectMultiple sclerosisLeukocyte antigenHLA-DRB1MS susceptibilityMultiple risk allelesDPB1 allelesClass IIPeptide-binding grooveHistocompatibility complexPolymorphic amino acid positionsTNF geneClassical allelesSusceptibility genes
2010
A non-synonymous SNP within membrane metalloendopeptidase-like 1 (MMEL1) is associated with multiple sclerosis
Ban M, McCauley JL, Zuvich R, Baker A, Bergamaschi L, Cox M, Kemppinen A, D'Alfonso S, Guerini FR, Lechner-Scott J, Dudbridge F, Wason J, Robertson NP, De Jager PL, Hafler DA, Barcellos LF, Ivinson AJ, Sexton D, Oksenberg JR, Hauser SL, Pericak-Vance MA, Haines J, Compston A, Sawcer S. A non-synonymous SNP within membrane metalloendopeptidase-like 1 (MMEL1) is associated with multiple sclerosis. Genes & Immunity 2010, 11: 660-664. PMID: 20574445, PMCID: PMC2946966, DOI: 10.1038/gene.2010.36.Peer-Reviewed Original Research
2009
Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases
Rioux J, Goyette P, Vyse T, Hammarström L, Fernando M, Green T, De Jager P, Foisy S, Wang J, de Bakker P, Leslie S, McVean G, Padyukov L, Alfredsson L, Annese V, Hafler D, Pan-Hammarström Q, Matell R, Sawcer S, Compston A, Cree B, Mirel D, Daly M, Behrens T, Klareskog L, Gregersen P, Oksenberg J, Hauser S. Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 18680-18685. PMID: 19846760, PMCID: PMC2773992, DOI: 10.1073/pnas.0909307106.Peer-Reviewed Original ResearchConceptsAutoimmune diseasesSystemic lupus erythematosusSelective IgA deficiencyStrong susceptibility locusNon-HLA genesMHC regionLupus erythematosusMyasthenia gravisUlcerative colitisCrohn's diseaseRheumatoid arthritisIgA deficiencyMultiple sclerosisMultiple susceptibility variantsMHC associationsDiseaseAppropriate control samplesPrimary association signalStrong linkage disequilibriumIndependent association signalsHuman MHCSusceptibility variantsSusceptibility lociAssociation signalsMost studiesThe role of the CD58 locus in multiple sclerosis
De Jager PL, Baecher-Allan C, Maier LM, Arthur AT, Ottoboni L, Barcellos L, McCauley JL, Sawcer S, Goris A, Saarela J, Yelensky R, Price A, Leppa V, Patterson N, de Bakker PI, Tran D, Aubin C, Pobywajlo S, Rossin E, Hu X, Ashley CW, Choy E, Rioux JD, Pericak-Vance MA, Ivinson A, Booth DR, Stewart GJ, Palotie A, Peltonen L, Dubois B, Haines JL, Weiner HL, Compston A, Hauser SL, Daly MJ, Reich D, Oksenberg JR, Hafler DA. The role of the CD58 locus in multiple sclerosis. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 5264-5269. PMID: 19237575, PMCID: PMC2664005, DOI: 10.1073/pnas.0813310106.Peer-Reviewed Original ResearchConceptsMultiple sclerosisMS subjectsMononuclear cellsCD58 expressionProtective effectMRNA expressionPeripheral blood mononuclear cellsRegulatory T cellsBlood mononuclear cellsTranscription factor Foxp3Dose-dependent increaseCentral nervous systemLymphoblastic cell linesClinical remissionAxonal lossControl subjectsInflammatory diseasesFactor Foxp3T cellsWhole-genome association scansLFA-3Nervous systemProtective allelesPotential mechanismsSclerosis
2005
A whole-genome admixture scan finds a candidate locus for multiple sclerosis susceptibility
Reich D, Patterson N, Jager P, McDonald GJ, Waliszewska A, Tandon A, Lincoln RR, DeLoa C, Fruhan SA, Cabre P, Bera O, Semana G, Kelly MA, Francis DA, Ardlie K, Khan O, Cree BA, Hauser SL, Oksenberg JR, Hafler DA. A whole-genome admixture scan finds a candidate locus for multiple sclerosis susceptibility. Nature Genetics 2005, 37: 1113-1118. PMID: 16186815, DOI: 10.1038/ng1646.Peer-Reviewed Original ResearchMeSH KeywordsBlack or African AmericanChromosome MappingChromosomes, Human, Pair 1Genetic Predisposition to DiseaseGenome, HumanHumansMultiple SclerosisA High-Density Screen for Linkage in Multiple Sclerosis
Sawcer S, Ban M, Maranian M, Yeo TW, Compston A, Kirby A, Daly MJ, De Jager PL, Walsh E, Lander ES, Rioux JD, Hafler DA, Ivinson A, Rimmler J, Gregory SG, Schmidt S, Pericak-Vance MA, Akesson E, Hillert J, Datta P, Oturai A, Ryder LP, Harbo HF, Spurkland A, Myhr KM, Laaksonen M, Booth D, Heard R, Stewart G, Lincoln R, Barcellos LF, Hauser SL, Oksenberg JR, Kenealy SJ, Haines JL. A High-Density Screen for Linkage in Multiple Sclerosis. American Journal Of Human Genetics 2005, 77: 454-467. PMID: 16080120, PMCID: PMC1226210, DOI: 10.1086/444547.Peer-Reviewed Original ResearchApplying a new generation of genetic maps to understand human inflammatory disease
Hafler DA, Jager P. Applying a new generation of genetic maps to understand human inflammatory disease. Nature Reviews Immunology 2005, 5: 83-91. PMID: 15630431, DOI: 10.1038/nri1532.Peer-Reviewed Original ResearchMeSH KeywordsChromosome MappingHaplotypesHumansInflammationMajor Histocompatibility ComplexMultiple SclerosisPolymorphism, Single Nucleotide
2004
Enhancing linkage analysis of complex disorders: an evaluation of high-density genotyping
Sawcer SJ, Maranian M, Singlehurst S, Yeo T, Compston A, Daly MJ, De Jager PL, Gabriel S, Hafler DA, Ivinson AJ, Lander ES, Rioux JD, Walsh E, Gregory SG, Schmidt S, Pericak-Vance MA, Barcellos L, Hauser SL, Oksenberg JR, Kenealy SJ, Haines JL. Enhancing linkage analysis of complex disorders: an evaluation of high-density genotyping. Human Molecular Genetics 2004, 13: 1943-1949. PMID: 15238506, DOI: 10.1093/hmg/ddh202.Peer-Reviewed Original ResearchA 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 ResearchMethods for High-Density Admixture Mapping of Disease Genes
Patterson N, Hattangadi N, Lane B, Lohmueller KE, Hafler DA, Oksenberg JR, Hauser SL, Smith MW, O’Brien S, Altshuler D, Daly MJ, Reich D. Methods for High-Density Admixture Mapping of Disease Genes. American Journal Of Human Genetics 2004, 74: 979-1000. PMID: 15088269, PMCID: PMC1181990, DOI: 10.1086/420871.Peer-Reviewed Original Research