2025
Targeted analysis of dyslexia-associated regions on chromosomes 6, 12 and 15 in large multigenerational cohorts
Chapman N, Navas P, Dorschner M, Mehaffey M, Wigg K, Price K, Naumova O, Kerr E, Guger S, Lovett M, Grigorenko E, Berninger V, Barr C, Wijsman E, Raskind W. Targeted analysis of dyslexia-associated regions on chromosomes 6, 12 and 15 in large multigenerational cohorts. PLOS ONE 2025, 20: e0324006. PMID: 40424442, PMCID: PMC12112411, DOI: 10.1371/journal.pone.0324006.Peer-Reviewed Original ResearchConceptsEvidence of associationLarge-scale sequencing studiesCis-acting regulatory regionsGenome-wide association studiesAggregating rare variantsRare exonic variantsDetected significant evidenceSingle nucleotide polymorphismsGenomic variationDeleterious variantsAssociated with reduced performanceAssociation studiesLarge-effectRegulatory elementsTranscriptional regulationRegulatory regionsQuantitative phenotypesCandidate genesExonic variantsChromosome 6Sequencing studiesSingle variantsCoding exonsMultiple traitsGenetic basis
2024
The genetics of severe depression
Franklin C, Achtyes E, Altinay M, Bailey K, Bhati M, Carr B, Conroy S, Husain M, Khurshid K, Lencz T, McDonald W, Mickey B, Murrough J, Nestor S, Nickl-Jockschat T, Nikayin S, Reeves K, Reti I, Selek S, Sanacora G, Trapp N, Viswanath B, Wright J, Sullivan P, Zandi P, Potash J. The genetics of severe depression. Molecular Psychiatry 2024, 30: 1117-1126. PMID: 39406997, DOI: 10.1038/s41380-024-02731-1.Peer-Reviewed Original ResearchGenome-wide association studiesSevere depressionGenome-wide significant lociWhole-exome sequencing studiesAssociated with dysphoriaGenome-wide lociGenome-wide interrogationExome sequencing studiesEarly-onset illnessDegree of impairmentDepressive disorderMDD phenotypesSignificant lociAssociation studiesClinical markers of severitySequencing studiesMDDLociRare variantsClinically actionable findingsEstimates of heritabilityDepressionFamily-basedSevere formGeneticsSemi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies
Shyr D, Dey R, Li X, Zhou H, Boerwinkle E, Buyske S, Daly M, Gibbs R, Hall I, Matise T, Reeves C, Stitziel N, Zody M, Neale B, Lin X. Semi-supervised machine learning method for predicting homogeneous ancestry groups to assess Hardy-Weinberg equilibrium in diverse whole-genome sequencing studies. American Journal Of Human Genetics 2024, 111: 2129-2138. PMID: 39270648, PMCID: PMC11480788, DOI: 10.1016/j.ajhg.2024.08.018.Peer-Reviewed Original ResearchHardy-Weinberg equilibriumWhole-genome sequencing studiesWhole-genome sequencingHomogeneous ancestryWGS studiesDownstream analysisAssociation analysisPresence of population structureAncestry groupsGenetic ancestry groupsPopulation structureSequencing studiesSelf-reported raceGenetic researchQuality variantsAncestrySubsets of samplesProgram centersVariantsIncreasing diversityHeterogeneous sampleAncestralAssociationGeneticsSequenceWhole genome sequencing study of identical twins discordant for psychosis
Ormond C, Ryan N, Hedman A, Cannon T, Sullivan P, Gill M, Hultman C, Heron E, Johansson V, Corvin A. Whole genome sequencing study of identical twins discordant for psychosis. Translational Psychiatry 2024, 14: 313. PMID: 39080272, PMCID: PMC11289105, DOI: 10.1038/s41398-024-02982-0.Peer-Reviewed Original ResearchConceptsCopy number variantsSequencing studiesGenic copy number variantsWhole-genome sequencing studiesRare genic copy number variantsDeleterious missense variantsWhole-genome sequencingExome sequencing studiesGenome sequencing studiesMZ twinsPost-zygotic eventsPairs of MZ twinsGenome sequenceIdentical genomesDNA variantsMissense variantsOverlapped genesPsychotic phenotypesPsychotic disordersBipolar disorderRare variantsMZ twin studiesPhenotypic discordanceTwin studiesTwin pairsThe genetics of trichotillomania and excoriation disorder: A systematic review
Reid M, Lin A, Farhat L, Fernandez T, Olfson E. The genetics of trichotillomania and excoriation disorder: A systematic review. Comprehensive Psychiatry 2024, 133: 152506. PMID: 38833896, PMCID: PMC11513794, DOI: 10.1016/j.comppsych.2024.152506.Peer-Reviewed Original ResearchSystematic reviewGenome-wide researchGenome-wide associationDNA sequencing studiesDiscovery of risk genesWeb of ScienceGenetic factorsObsessive-compulsive disorderGenetic epidemiologyGenetic risk factorsSequencing studiesRisk genesGeneral populationMolecular geneticsExcoriation disorderRisk factorsGeneticsFirst-line medicationPsychiatric disordersObsessive-compulsive related disordersObsessive-compulsive disorder spectrumBody-focused repetitive behaviorsDevelopment of trichotillomaniaPsycINFOGenome
2023
Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD
Wang S, Wang B, Drury V, Drake S, Sun N, Alkhairo H, Arbelaez J, Duhn C, Bal V, Langley K, Martin J, Hoekstra P, Dietrich A, Xing J, Heiman G, Tischfield J, Fernandez T, Owen M, O’Donovan M, Thapar A, State M, Willsey A. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD. Nature Communications 2023, 14: 8077. PMID: 38057346, PMCID: PMC10700338, DOI: 10.1038/s41467-023-43776-0.Peer-Reviewed Original ResearchConceptsDamaging variantsHigh-confidence ASD risk genesExome-wide significanceRare genetic variationASD risk genesRare damaging variantsHemizygous natureWhole-exome sequencing studiesExome sequencing studiesGene discoveryMultiple neurodevelopmental disordersGenetic variationGenetic mechanismsChr XMale sex biasSequencing studiesChromosome XRisk genesTransmission disequilibrium testAttention-deficit/hyperactivity disorderASD probandsAutism spectrum disorderASD familiesSex biasInformative recombinationsThe molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research
Nakamura T, Takata A. The molecular pathology of schizophrenia: an overview of existing knowledge and new directions for future research. Molecular Psychiatry 2023, 28: 1868-1889. PMID: 36878965, PMCID: PMC10575785, DOI: 10.1038/s41380-023-02005-2.Peer-Reviewed Original ResearchConceptsMolecular pathology of schizophreniaCopy number variantsDiscovery of copy number variantsLarge-scale exome sequencing studiesMolecular pathologyExome sequencing studiesDNA sequencesPathology of schizophreniaEpigenomic analysesSequencing studiesSingle genesGenetic variantsRare mutationsMultiple disease modelsGenesGenetic pathologyDisease modelsCurrent knowledgeSchizophrenia brainDisease riskVariantsPostmortem tissueBiological alterationsDNAEtiological validity
2022
Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes
Ganesh S, Vemula A, Bhattacharjee S, Mathew K, Ithal D, Navin K, Nadella R, Viswanath B, Sullivan P, Jain S, Purushottam M. Whole exome sequencing in dense families suggests genetic pleiotropy amongst Mendelian and complex neuropsychiatric syndromes. Scientific Reports 2022, 12: 21128. PMID: 36476812, PMCID: PMC9729597, DOI: 10.1038/s41598-022-25664-7.Peer-Reviewed Original ResearchConceptsSequence kernel association testKernel association testWhole-exome sequencing studiesExome sequencing studiesUnique genesGenetic architectureCase-control association analysisDeleterious variantsSequencing studiesWhole-exome sequencingMendelian syndromesAssociation analysisCriteria of rarityPleiotropic influenceGenesWES studyFunctional consequencesSignificant overrepresentationGenetic pleiotropyExome sequencingAffected individualsFamilyImportant insightsUnrelated controlsAssociation TestMolecular genetics of human developmental neurocranial anomalies: towards “precision surgery”
Duy PQ, Timberlake AT, Lifton RP, Kahle KT. Molecular genetics of human developmental neurocranial anomalies: towards “precision surgery”. Cerebral Cortex 2022, 33: 2912-2918. PMID: 35739418, PMCID: PMC10016031, DOI: 10.1093/cercor/bhac249.Peer-Reviewed Original ResearchConceptsFuture clinical trialsSurgical treatmentClinical trialsCongenital hydrocephalusWhole-exome sequencing studiesDisease classification systemDevelopmental anomaliesNeuropsychiatric diseasesNonsyndromic craniosynostosisGenetic counselingPrecision surgeryHuman brainNovel disease genesClassification systemMolecular nomenclatureSequencing studiesHydrocephalusSurgeryPathogenesisTherapyMolecular geneticsPrognosticationDiseaseTrialsBrainInsights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension
Kelly TN, Sun X, He KY, Brown MR, Taliun SAG, Hellwege JN, Irvin MR, Mi X, Brody JA, Franceschini N, Guo X, Hwang SJ, de Vries PS, Gao Y, Moscati A, Nadkarni GN, Yanek LR, Elfassy T, Smith JA, Chung RH, Beitelshees AL, Patki A, Aslibekyan S, Blobner BM, Peralta JM, Assimes TL, Palmas WR, Liu C, Bress AP, Huang Z, Becker LC, Hwa CM, O’Connell J, Carlson JC, Warren HR, Das S, Giri A, Martin LW, Johnson W, Fox ER, Bottinger EP, Razavi AC, Vaidya D, Chuang LM, Chang YC, Naseri T, Jain D, Kang HM, Hung AM, Srinivasasainagendra V, Snively BM, Gu D, Montasser ME, Reupena M, Heavner BD, LeFaive J, Hixson JE, Rice KM, Wang FF, Nielsen JB, Huang J, Khan AT, Zhou W, Nierenberg JL, Laurie CC, Armstrong ND, Shi M, Pan Y, Stilp AM, Emery L, Wong Q, Hawley NL, Minster RL, Curran JE, Munroe PB, Weeks DE, North KE, Tracy RP, Kenny EE, Shimbo D, Chakravarti A, Rich SS, Reiner AP, Blangero J, Redline S, Mitchell BD, Rao DC, Chen Y, Kardia SLR, Kaplan RC, Mathias RA, He J, Psaty BM, Fornage M, Loos RJF, Correa A, Boerwinkle E, Rotter JI, Kooperberg C, Edwards TL, Abecasis GR, Zhu X, Levy D, Arnett DK, Morrison AC. Insights From a Large-Scale Whole-Genome Sequencing Study of Systolic Blood Pressure, Diastolic Blood Pressure, and Hypertension. Hypertension 2022, 79: 1656-1667. PMID: 35652341, PMCID: PMC9593435, DOI: 10.1161/hypertensionaha.122.19324.Peer-Reviewed Original ResearchConceptsDiastolic blood pressureSystolic blood pressureBlood pressureSequencing dataNovel common variantsWhole-genome sequencing dataGenome-wide significanceAllele frequency spectrumGenome sequencing studiesWhole-genome sequencing analysisLower systolic blood pressureWhole-exome sequencing dataStage 1Future blood pressureNovel lociTrans-OmicsIntergenic variantsVariant findingsSequencing studiesMillion Veteran ProgramUK Biobank participantsSequencing analysisCommon variantsBlood pressure signalsStroke participants
2021
Analyzing gut microbiota composition in individual Anopheles mosquitoes after experimental treatment
Fofana A, Gendrin M, Romoli O, Yarbanga G, Ouédraogo G, Yerbanga R, Ouédraogo J. Analyzing gut microbiota composition in individual Anopheles mosquitoes after experimental treatment. IScience 2021, 24: 103416. PMID: 34901787, PMCID: PMC8637483, DOI: 10.1016/j.isci.2021.103416.Peer-Reviewed Original ResearchMosquito microbiotaHigh-throughput sequencing studiesHigh-throughput sequencingMosquito microbiomeMicrobiota compositionBlood digestionSemi-field conditionsMajor generaSequencing studiesGut samplesReduced microbial loadRelative abundanceMalaria transmissionOverall microbiota compositionBlood mealGut microbiota compositionInfluence of amoxicillinAnopheles mosquitoesAdult femalesNegative control dataMicrobiotaAntibiotic treatmentSpecific decreaseAmoxicillin preparationsMicrobial loadSignaling Pathways and Sex Differential Processes in Autism Spectrum Disorder
Enriquez KD, Gupta AR, Hoffman EJ. Signaling Pathways and Sex Differential Processes in Autism Spectrum Disorder. Frontiers In Psychiatry 2021, 12: 716673. PMID: 34690830, PMCID: PMC8531220, DOI: 10.3389/fpsyt.2021.716673.Peer-Reviewed Original ResearchASD genetic studiesBiological pathwaysGenetic studiesRisk gene discoveryCellular pathways downstreamASD risk genesWhole-exome sequencing studiesCommon biological pathwaysGene discoveryPathways downstreamGene expressionSequencing studiesRisk genesMale biasPathwayGenesNeuronal communicationCommon pathwayPotential roleFemale protective effectNeurodevelopmental disordersRecent analysisTranscriptomicsGenomicsRecent investigationsExome Sequencing Analysis on Products of Conception: A Cohort Study to Evaluate Clinical Utility and Genetic Etiology for Pregnancy Loss
Zhao C, Chai H, Zhou Q, Wen J, Reddy U, Kastury R, Jiang Y, Mak W, Bale A, Zhang H, Li P. Exome Sequencing Analysis on Products of Conception: A Cohort Study to Evaluate Clinical Utility and Genetic Etiology for Pregnancy Loss. Obstetrical & Gynecological Survey 2021, 76: 468-469. DOI: 10.1097/01.ogx.0000791680.43228.b1.Peer-Reviewed Original ResearchA microProtein repressor complex in the shoot meristem controls the transition to flowering
Rodrigues VL, Dolde U, Sun B, Blaakmeer A, Straub D, Eguen T, Botterweg-Paredes E, Hong S, Graeff M, Li MW, Gendron JM, Wenkel S. A microProtein repressor complex in the shoot meristem controls the transition to flowering. Plant Physiology 2021, 187: 187-202. PMID: 34015131, PMCID: PMC8418433, DOI: 10.1093/plphys/kiab235.Peer-Reviewed Original ResearchConceptsShoot apical meristemEarly flowering phenotypeGenetic suppressor screenPost-translational regulatorFloral repressionSuppressor screenChromatin modificationsFloral transitionFloral meristemRepressive complexesShoot meristemRepressor complexGenetic interactionsApical meristemCONSTANSEarly floweringShoot apexUndifferentiated stateJMJ14Sequencing studiesMeristemAdditional roleSum1MicroproteinsPlants
2020
Cutting-edge genetics in obsessive-compulsive disorder
Saraiva L, Cappi C, Simpson H, Stein D, Viswanath B, van den Heuvel O, Reddy Y, Miguel E, Shavitt R. Cutting-edge genetics in obsessive-compulsive disorder. Faculty Reviews 2020, 9: 30. PMID: 33659962, PMCID: PMC7886082, DOI: 10.12703/r/9-30.Peer-Reviewed Original ResearchGenetic architectureWide association studyNumber variation studiesCutting-edge geneticsWhole-exome sequencing studiesUnderlying biological pathwaysHuman cell modelsGene networksStudy of endophenotypesGene expressionBiological pathwaysSequencing studiesAssociation studiesAnimal systemsGeneticsGene-environment interactionsCell modelBiological basisPolygenic risk scoresEvidence pointsSynaptic transmissionRecent advancesVariation studiesExperimental animal systemsNeuropsychiatric disordersCoding functions of “noncoding” RNAs
Wei LH, Guo JU. Coding functions of “noncoding” RNAs. Science 2020, 367: 1074-1075. PMID: 32139529, DOI: 10.1126/science.aba6117.Commentaries, Editorials and LettersConceptsRNA regionsProtein-coding functionProtein-coding sequencesDistinct biological processesRNA sequencing studiesLong noncoding RNAPervasive transcriptionFunctional peptidesPervasive translationHuman genomeNoncoding RNAsTranslation eventsBiological processesSequencing studiesCell growthRNATranscriptomeGenomeTranscriptionLncRNAsPeptidesMicroproteinsTranslationSubsequent studiesRegion
2019
Bi-Functional Chicken Immunoglobulin-Like Receptors With a Single Extracellular Domain (ChIR-AB1): Potential Framework Genes Among a Relatively Stable Number of Genes Per Haplotype
Meziane E, Potts N, Viertlboeck B, Løvlie H, Krupa A, Burke T, Brown S, Watson K, Richardson D, Pizzari T, Göbel T, Kaufman J. Bi-Functional Chicken Immunoglobulin-Like Receptors With a Single Extracellular Domain (ChIR-AB1): Potential Framework Genes Among a Relatively Stable Number of Genes Per Haplotype. Frontiers In Immunology 2019, 10: 2222. PMID: 31620133, PMCID: PMC6760009, DOI: 10.3389/fimmu.2019.02222.Peer-Reviewed Original ResearchConceptsLeukocyte receptor complexRed junglefowlIg-like receptorsChicken Ig-like receptorsLeukocyte Ig-like receptorsCHIR-AB1Chicken linesExtracellular domainImmunoglobulin-like (Ig-likeHighly-related genesTrios of parentsExtracellular Ig-like domainsStrand-mediated conformational analysisIg-like domainsCommercial chicken linesPositively-charged residuesKiller Ig-like receptorsExperimental chicken linesCytoplasmic tailSequencing studiesIg-likeFramework genesTransmembrane regionSequence relationshipsEgg-laying chickensWhole-Exome Sequencing in Evaluation of Thrombophilia: Characterization of Novel Genetic Variants
Gu S, Shevell L, Tormey C, Rinder H, Lee A. Whole-Exome Sequencing in Evaluation of Thrombophilia: Characterization of Novel Genetic Variants. American Journal Of Clinical Pathology 2019, 152: s35-s35. DOI: 10.1093/ajcp/aqz112.066.Peer-Reviewed Original ResearchWhole-exome sequencingMultiple sequence alignment analysisVenous thromboembolismGenetic variantsSequence alignment analysisDisease-causing genetic variantsVon Willebrand factorRegions of proteinsNovel genetic variantsNext-generation sequencing studiesAmino acid substitutionsGenetic factorsNovel VUSAlignment analysisMajority of VTESequencing studiesAcid substitutionsSilico mutagenesisConformational changesEvaluation of thrombophiliaDeep venous thrombosisNonsynonymous variantsProthrombin gene mutationFactor V LeidenEnzymatic activityGeometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape
Hie B, Cho H, DeMeo B, Bryson B, Berger B. Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape. Cell Systems 2019, 8: 483-493.e7. PMID: 31176620, PMCID: PMC6597305, DOI: 10.1016/j.cels.2019.05.003.Peer-Reviewed Original ResearchConceptsSingle-cell transcriptomic landscapeSingle-cell RNA sequencing studiesSingle-cell omicsCell typesSeq data integrationSingle-cell data analysisRare cell typesRNA sequencing studiesScRNA-seq dataTranscriptional diversityTranscriptomic landscapeBiological cell typesTranscriptomic heterogeneitySequencing studiesRare subpopulationAnalysis pipelineCellsUmbilical cord bloodEssential stepInflammatory macrophagesOmicsComprehensive visualizationDiversityGeometric sketchHundreds of thousandsMulti-platform discovery of haplotype-resolved structural variation in human genomes
Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications 2019, 10: 1784. PMID: 30992455, PMCID: PMC6467913, DOI: 10.1038/s41467-018-08148-z.Peer-Reviewed Original ResearchConceptsStructural variantsSequencing studiesHigh-throughput sequencing studiesHuman genetic diversityHuman genetic variationGenome sequencing studiesGenetic diversityHuman genomeGenetic variationSequencing technologiesGenome ProjectSV detectionGenomeIndel variantsSV callsetsStructural variationsRecurrent microdeletionsDisease associationsMicroduplication syndromesOptical mappingVariantsSevenfold increaseDiversityCritical regionCallsets
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