2018
Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk
Consortium I, Mitrovič M, Patsopoulos N, Beecham A, Dankowski T, Goris A, Dubois B, D’hooghe M, Lemmens R, Van Damme P, Søndergaard H, Sellebjerg F, Sorensen P, Ullum H, Thørner L, Werge T, Saarela J, Cournu-Rebeix I, Damotte V, Fontaine B, Guillot-Noel L, Lathrop M, Vukusik S, Gourraud P, Andlauer T, Pongratz V, Buck D, Gasperi C, Bayas A, Heesen C, Kümpfel T, Linker R, Paul F, Stangel M, Tackenberg B, Bergh F, Warnke C, Wiendl H, Wildemann B, Zettl U, Ziemann U, Tumani H, Gold R, Grummel V, Hemmer B, Knier B, Lill C, Luessi F, Dardiotis E, Agliardi C, Barizzone N, Mascia E, Bernardinelli L, Comi G, Cusi D, Esposito F, Ferrè L, Comi C, Galimberti D, Leone M, Sorosina M, Mescheriakova J, Hintzen R, van Duijn C, Theunissen C, Bos S, Myhr K, Celius E, Lie B, Spurkland A, Comabella M, Montalban X, Alfredsson L, Stridh P, Hillert J, Jagodic M, Piehl F, Jelčić I, Martin R, Sospedra M, Ban M, Hawkins C, Hysi P, Kalra S, Karpe F, Khadake J, Lachance G, Neville M, Santaniello A, Caillier S, Calabresi P, Cree B, Cross A, Davis M, Haines J, de Bakker P, Delgado S, Dembele M, Edwards K, Fitzgerald K, Hakonarson H, Konidari I, Lathi E, Manrique C, Pericak-Vance M, Piccio L, Schaefer C, McCabe C, Weiner H, Goldstein J, Olsson T, Hadjigeorgiou G, Taylor B, Tajouri L, Charlesworth J, Booth D, Harbo H, Ivinson A, Hauser S, Compston A, Stewart G, Zipp F, Barcellos L, Baranzini S, Martinelli-Boneschi F, D’Alfonso S, Ziegler A, Oturai A, McCauley J, Sawcer S, Oksenberg J, De Jager P, Kockum I, Hafler D, Cotsapas C. Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk. Cell 2018, 175: 1679-1687.e7. PMID: 30343897, PMCID: PMC6269166, DOI: 10.1016/j.cell.2018.09.049.Peer-Reviewed Original ResearchConceptsRare coding variationsGenome-wide association studiesNon-coding variationCommon variant signalsSubstantial linkage disequilibriumLow-frequency variantsNovel genesCell homeostasisAssociation studiesComplex neurological diseasesLinkage disequilibriumGenetic variantsCommon variantsHeritabilityRich resourceGenesVariantsKey pathogenic roleIndividual familiesEpistasisAdditive effectBiologyHomeostasisMutationsNeurological diseases
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 genesNetwork-Based Multiple Sclerosis Pathway Analysis with GWAS Data from 15,000 Cases and 30,000 Controls
Consortium I, Baranzini S, Khankhanian P, Patsopoulos N, Li M, Stankovich J, Cotsapas C, Søndergaard H, Ban M, Barizzone N, Bergamaschi L, Booth D, Buck D, Cavalla P, Celius E, Comabella M, Comi G, Compston A, Cournu-Rebeix I, D’alfonso S, Damotte V, Din L, Dubois B, Elovaara I, Esposito F, Fontaine B, Franke A, Goris A, Gourraud P, Graetz C, Guerini F, Guillot-Noel L, Hafler D, Hakonarson H, Hall P, Hamsten A, Harbo H, Hemmer B, Hillert J, Kemppinen A, Kockum I, Koivisto K, Larsson M, Lathrop M, Leone M, Lill C, Macciardi F, Martin R, Martinelli V, Martinelli-Boneschi F, McCauley J, Myhr K, Naldi P, Olsson T, Oturai A, Pericak-Vance M, Perla F, Reunanen M, Saarela J, Saker-Delye S, Salvetti M, Sellebjerg F, Sørensen P, Spurkland A, Stewart G, Taylor B, Tienari P, Winkelmann J, Consortium W, Zipp F, Ivinson A, Haines J, Sawcer S, DeJager P, Hauser S, Oksenberg J. Network-Based Multiple Sclerosis Pathway Analysis with GWAS Data from 15,000 Cases and 30,000 Controls. American Journal Of Human Genetics 2013, 92: 854-865. PMID: 23731539, PMCID: PMC3958952, DOI: 10.1016/j.ajhg.2013.04.019.Peer-Reviewed Original ResearchConceptsPathway analysisNetwork-based pathway analysisGenome-wide association studiesSubnetworks of genesExtended linkage disequilibriumNon-HLA susceptibility lociHigh-confidence candidatesSubsequent genetic studiesComplex traitsSubstantial genetic componentSignificant lociGWAS dataAssociation studiesGene levelGenetic studiesNominal statistical evidenceSusceptibility lociGenesLinkage disequilibriumSusceptibility variantsGenetic componentRelated pathwaysLociHuman leukocyte antigen (HLA) regionPowerful approach
2011
Interrogating 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-valueMHCA 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 ResearchGenome-wide Association Study in a High-Risk Isolate for Multiple Sclerosis Reveals Associated Variants in STAT3 Gene
Jakkula E, Leppä V, Sulonen AM, Varilo T, Kallio S, Kemppinen A, Purcell S, Koivisto K, Tienari P, Sumelahti ML, Elovaara I, Pirttilä T, Reunanen M, Aromaa A, Oturai AB, Søndergaard HB, Harbo HF, Mero IL, Gabriel SB, Mirel DB, Hauser SL, Kappos L, Polman C, De Jager PL, Hafler DA, Daly MJ, Palotie A, Saarela J, Peltonen L. Genome-wide Association Study in a High-Risk Isolate for Multiple Sclerosis Reveals Associated Variants in STAT3 Gene. American Journal Of Human Genetics 2010, 86: 285-291. PMID: 20159113, PMCID: PMC2820168, DOI: 10.1016/j.ajhg.2010.01.017.Peer-Reviewed Original ResearchConceptsSTAT3 geneGenome-wide association studiesRare risk allelesComplex traitsRisk lociRisk allelesAssociated variantsAssociation studiesRecent GWASInternal isolateLociCommon variantsGenetic riskGenesAllelesCritical roleSTAT3Small odds ratiosHeterogeneous populationVariantsGWASIsolatesProtective haplotypeTraitsSNPs
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 polymorphismsSubjectsAssociation
2004
Methods 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 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 Research