2025
Exome sequencing reveals low-frequency and rare variant contributions to multiple sclerosis susceptibility in Turkish families
Büyükgöl F, Gürdamar B, Aluçlu M, Beckmann Y, Bilguvar K, Boz C, Bülbül A, Bünül S, Çetin Ö, Demir C, Demir S, Duman T, Efendi H, Ekmekçi Ö, Ertetik U, Ethemoğlu Ö, Everest E, Gümüş H, Gündüz T, Karabudak R, Karaman B, Kürtüncü M, Mutluer M, Reda M, Saip S, Seferoğlu M, Sever E, Sezerman O, Şen S, Taşdelen B, Tecellioğlu M, Terzi M, Tuncer A, Turan Ö, Tütüncü M, Uncu G, Uygunoğlu U, Uzunköprü C, Voyvoda U, Yetkin M, Yüceyar N, Siva A, Turanlı E. Exome sequencing reveals low-frequency and rare variant contributions to multiple sclerosis susceptibility in Turkish families. Scientific Reports 2025, 15: 11682. PMID: 40188234, PMCID: PMC11972333, DOI: 10.1038/s41598-025-94691-x.Peer-Reviewed Original ResearchConceptsSegregation analysisExome sequencingGene-based burden testsGene-based burden analysisRare Coding VariantsVariants associated with MSWhole-exome sequencingPathway enrichment analysisMultiplex MS familiesHuman leukocyte antigen lociContribution of low-frequencyAdmixed populationsBurden testsHemidesmosome assemblyMultiple sclerosis susceptibilityAllele frequenciesAntigen lociEnrichment analysisBurden analysisMS familiesGenesTurkish familyExtracellular matrixProgressive neurodegenerationITPR1 geneInvestigating the Contribution of Coding Variants in Alcohol Use Disorder Using Whole-Exome Sequencing Across Ancestries
Wang L, Kranzler H, Gelernter J, Zhou H. Investigating the Contribution of Coding Variants in Alcohol Use Disorder Using Whole-Exome Sequencing Across Ancestries. Biological Psychiatry 2025, 98: 46-55. PMID: 39892688, PMCID: PMC12167164, DOI: 10.1016/j.biopsych.2025.01.020.Peer-Reviewed Original ResearchContribution of coding variantsGene-based collapsing testAlcohol use disorderAnalyzed whole-exome sequencing dataEuropean ancestryContribution of rare coding variantsRare loss-of-functionWhole-exome sequencing dataWhole-exome sequencing studiesRare Coding VariantsAfrican ancestryWhole-exome sequencingLoss-of-functionGenetic architectureSequence dataAllelic heterogeneityMissense variantsGenetic variantsAllele frequenciesRare variantsYale-PennStudy of alcohol use disorderUK BiobankUK Biobank cohortVariants
2024
Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis
Ghouse J, Sveinbjörnsson G, Vujkovic M, Seidelin A, Gellert-Kristensen H, Ahlberg G, Tragante V, Rand S, Brancale J, Vilarinho S, Lundegaard P, Sørensen E, Erikstrup C, Bruun M, Jensen B, Brunak S, Banasik K, Ullum H, Verweij N, Lotta L, Baras A, Mirshahi T, Carey D, Kaplan D, Lynch J, Morgan T, Schwantes-An T, Dochtermann D, Pyarajan S, Tsao P, Laisk T, Mägi R, Kozlitina J, Tybjærg-Hansen A, Jones D, Knowlton K, Nadauld L, Ferkingstad E, Björnsson E, Ulfarsson M, Sturluson Á, Sulem P, Pedersen O, Ostrowski S, Gudbjartsson D, Stefansson K, Olesen M, Chang K, Holm H, Bundgaard H, Stender S. Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis. Nature Genetics 2024, 56: 827-837. PMID: 38632349, PMCID: PMC11096111, DOI: 10.1038/s41588-024-01720-y.Peer-Reviewed Original ResearchMeSH KeywordsAlanine TransaminaseCarcinoma, HepatocellularCase-Control StudiesCohort StudiesFemalegamma-GlutamyltransferaseGenetic Predisposition to DiseaseGenetic VariationGenome-Wide Association StudyHumansLipaseLiver CirrhosisLiver NeoplasmsMaleMembrane ProteinsMultifactorial InheritancePolymorphism, Single NucleotideRisk FactorsConceptsMulti-ancestry genome-wide association studyPolygenic risk scoresRare variant analysisVariant analysisGenome-wide association studiesRare Coding VariantsHepatocellular carcinomaLow alanine aminotransferaseRisk associationAlcohol intakePrioritized genesGenetic architectureNear genesAlanine aminotransferaseRisk scoreHepatic lipid metabolismAssociation studiesLiver cirrhosisGenetic underpinningsPNPLA3 p.Cirrhosis to hepatocellular carcinomaRisk of cirrhosisLiver function testsLipid metabolismGenesRare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer’s disease
Bhattarai P, Gunasekaran T, Belloy M, Reyes-Dumeyer D, Jülich D, Tayran H, Yilmaz E, Flaherty D, Turgutalp B, Sukumar G, Alba C, McGrath E, Hupalo D, Bacikova D, Le Guen Y, Lantigua R, Medrano M, Rivera D, Recio P, Nuriel T, Ertekin-Taner N, Teich A, Dickson D, Holley S, Greicius M, Dalgard C, Zody M, Mayeux R, Kizil C, Vardarajan B. Rare genetic variation in fibronectin 1 (FN1) protects against APOEε4 in Alzheimer’s disease. Acta Neuropathologica 2024, 147: 70. PMID: 38598053, PMCID: PMC11006751, DOI: 10.1007/s00401-024-02721-1.Peer-Reviewed Original ResearchConceptsLoss-of-functionWhole-genome sequencingFibronectin 1Genetic variationAlzheimer's diseaseAD riskRare Coding VariantsLoss-of-function variantsRare genetic variationGene Ontology termsFamily based studyIn vivo functional studiesAD-related pathologyAlpha 2 chainOntology termsPresence of cellular mechanismsProtective variantsECM proteinsAD pathologyPathway analysisFunctional studiesUnaffected carriersZebrafish modelAPOEe4 alleleProtein levelsWhole-exome sequencing in UK Biobank reveals rare genetic architecture for depression
Tian R, Ge T, Kweon H, Rocha D, Lam M, Liu J, Singh K, Levey D, Gelernter J, Stein M, Tsai E, Huang H, Chabris C, Lencz T, Runz H, Chen C. Whole-exome sequencing in UK Biobank reveals rare genetic architecture for depression. Nature Communications 2024, 15: 1755. PMID: 38409228, PMCID: PMC10897433, DOI: 10.1038/s41467-024-45774-2.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesRare Coding VariantsWhole-exome sequencingGenetic architectureGenetic relationshipsLoss-of-function intolerant genesContribution of rare coding variantsRare damagingAssociated with risk of depressionElectronic health recordsUK Biobank participantsPolygenic risk scoresRisk of depressionAssociated with riskIntolerant genesRisk lociAssociation studiesCoding variantsBiobank participantsHealth recordsUK BiobankDepression definitionsDepression riskBurden analysisRare variants
2015
Rare Coding Variation and Risk of Intracerebral Hemorrhage
Radmanesh F, Falcone GJ, Anderson CD, McWilliams D, Devan WJ, Brown WM, Battey TW, Ayres AM, Raffeld MR, Schwab K, Sun G, Deka R, Viswanathan A, Goldstein JN, Greenberg SM, Tirschwell DL, Silliman SL, Selim M, Meschia JF, Brown DL, Worrall BB, Langefeld CD, Woo D, Rosand J. Rare Coding Variation and Risk of Intracerebral Hemorrhage. Stroke 2015, 46: 2299-2301. PMID: 26111891, PMCID: PMC4519408, DOI: 10.1161/strokeaha.115.009838.Peer-Reviewed Original ResearchConceptsGenome-wide significance levelRare coding variationsGene-based association testingSusceptibility lociGene-based associationRare Coding VariantsGenome-wide significanceIllumina HumanExome BeadChipGenetic susceptibility lociSubstantial genetic componentCoding variationsChromosome 19q13APOE epsilon allelesHumanExome BeadChipGenetic componentCoding variantAssociation testingLociCommon variantsEpsilon allelesLarge effectVariantsBeadChipGenesTOMM40
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