2025
Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes
Sierant M, Jin S, Bilguvar K, Morton S, Dong W, Jiang W, Lu Z, Li B, López-Giráldez F, Tikhonova I, Zeng X, Lu Q, Choi J, Zhang J, Nelson-Williams C, Knight J, Zhao H, Cao J, Mane S, Sedore S, Gruber P, Lek M, Goldmuntz E, Deanfield J, Giardini A, Mital S, Russell M, Gaynor J, King E, Wagner M, Srivastava D, Shen Y, Bernstein D, Porter G, Newburger J, Seidman J, Roberts A, Yandell M, Yost H, Tristani-Firouzi M, Kim R, Chung W, Gelb B, Seidman C, Brueckner M, Lifton R. Genomic analysis of 11,555 probands identifies 60 dominant congenital heart disease genes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2420343122. PMID: 40127276, PMCID: PMC12002227, DOI: 10.1073/pnas.2420343122.Peer-Reviewed Original ResearchConceptsCongenital heart disease genesCongenital heart diseaseDamaging variantsMissense variantsAnalyzing de novo mutationsCHD probandsEpidermal growth factor (EGF)-like domainsNeurodevelopmental delayLoss of function variantsParent-offspring triosSyndromic congenital heart diseaseHeart disease genesDisease genesGenomic analysisCongenital heart disease subtypesAssociated with neurodevelopmental delayTetralogy of FallotFunctional variantsIncomplete penetranceCHD phenotypesGenesAssociated with developmentGenetic testingMolecular diagnosticsExtracardiac abnormalities
2024
Quantitative correlation of ENPP1 pathogenic variants with disease phenotype
Ansh A, Stabach P, Ciccone C, Cao W, De La Cruz E, Sabbagh Y, Carpenter T, Ferreira C, Braddock D. Quantitative correlation of ENPP1 pathogenic variants with disease phenotype. Bone 2024, 186: 117136. PMID: 38806089, PMCID: PMC11227391, DOI: 10.1016/j.bone.2024.117136.Peer-Reviewed Original ResearchEctonucleotide pyrophosphatase/phosphodiesterase 1Pathogenic variantsDisease phenotypeEnzyme velocityCompound heterozygotesEnzyme activityVariable enzyme activityAutosomal dominant phenotypeHigh-throughput assayAutosomal recessive formInnate immune responseENPP1 variantsDamaging variantsENPP1 deficiencyCole diseaseDominant phenotypeAutosomal dominant diseaseCatalytic velocityRecessive formEnzymePhenotypeWT levelsBio-active moleculesClinical phenotypeDominant disease
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 recombinationsMutation of key signaling regulators of cerebrovascular development in vein of Galen malformations
Zhao S, Mekbib K, van der Ent M, Allington G, Prendergast A, Chau J, Smith H, Shohfi J, Ocken J, Duran D, Furey C, Hao L, Duy P, Reeves B, Zhang J, Nelson-Williams C, Chen D, Li B, Nottoli T, Bai S, Rolle M, Zeng X, Dong W, Fu P, Wang Y, Mane S, Piwowarczyk P, Fehnel K, See A, Iskandar B, Aagaard-Kienitz B, Moyer Q, Dennis E, Kiziltug E, Kundishora A, DeSpenza T, Greenberg A, Kidanemariam S, Hale A, Johnston J, Jackson E, Storm P, Lang S, Butler W, Carter B, Chapman P, Stapleton C, Patel A, Rodesch G, Smajda S, Berenstein A, Barak T, Erson-Omay E, Zhao H, Moreno-De-Luca A, Proctor M, Smith E, Orbach D, Alper S, Nicoli S, Boggon T, Lifton R, Gunel M, King P, Jin S, Kahle K. Mutation of key signaling regulators of cerebrovascular development in vein of Galen malformations. Nature Communications 2023, 14: 7452. PMID: 37978175, PMCID: PMC10656524, DOI: 10.1038/s41467-023-43062-z.Peer-Reviewed Original ResearchConceptsEphrin receptor B4Galen malformationBrain arteriovenous malformationsP120 RasGAPTransmitted variantsArteriovenous malformationsDe novo variantsSingle-cell transcriptomesSignificant burdenCerebrovascular developmentIntegrative genomic analysisEndothelial cellsVenous networkAdditional probandsMalformationsNovo variantsMissense variantsGenomic analysisDevelopmental angiogenesisVascular developmentDamaging variantsVeinRasGAPIntegrated analysisPatientsPrimary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene
Fernandez T, Williams Z, Kline T, Rajendran S, Augustine F, Wright N, Sullivan C, Olfson E, Abdallah S, Liu W, Hoffman E, Gupta A, Singer H. Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene. PLOS ONE 2023, 18: e0291978. PMID: 37788244, PMCID: PMC10547198, DOI: 10.1371/journal.pone.0291978.Peer-Reviewed Original ResearchConceptsRisk genesDe novo damaging variantsGene expression patternsWhole-exome DNA sequencingMid-fetal developmentAdditional risk genesHigh-confidence risk genesParent-child triosGene OntologyCell signalingExpression patternsCalcium ion transportFunctional convergenceCell cycleDamaging variantsGenesDNA sequencingDe novoASD probandsGenetic etiologyBiological mechanismsSequencingDNANetwork analysisIon transport
2022
Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia
Dong W, Wong KHY, Liu Y, Levy-Sakin M, Hung WC, Li M, Li B, Jin SC, Choi J, Lopez-Giraldez F, Vaka D, Poon A, Chu C, Lao R, Balamir M, Movsesyan I, Malloy MJ, Zhao H, Kwok PY, Kane JP, Lifton RP, Pullinger CR. Whole-exome sequencing reveals damaging gene variants associated with hypoalphalipoproteinemia. Journal Of Lipid Research 2022, 63: 100209. PMID: 35460704, PMCID: PMC9126845, DOI: 10.1016/j.jlr.2022.100209.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingCandidate genesDamaging variantsGenome-wide association studiesGenome-wide significanceDamaging rare variantsCandidate gene listGene burden testingHDL-C levelsGene variantsGene listsAssociation studiesLDLR geneGenesBurden testingCancer biologySequencingFunction variantsABCA1Mean HDL-C levelsRare variantsDiscovery studiesCoronary heart diseaseHDL deficiencyRisk of cancerWhole‐exome DNA sequencing in childhood anxiety disorders identifies rare de novo damaging coding variants
Olfson E, Lebowitz ER, Hommel G, Pashankar N, Silverman WK, Fernandez TV. Whole‐exome DNA sequencing in childhood anxiety disorders identifies rare de novo damaging coding variants. Depression And Anxiety 2022, 39: 474-484. PMID: 35312124, PMCID: PMC9246845, DOI: 10.1002/da.23251.Peer-Reviewed Original ResearchConceptsWhole-exome DNA sequencingRisk genesDNA sequencingCanonical biological pathwaysMissense genetic variantsNovo variantsGenetic variant detectionParent-child triosGenomic approachesDe novo variantsLikely geneBiologic pathwaysDeleterious variantsBiological pathwaysDamaging variantsGenesGenetic variantsPathwayVariant detectionSequencingNetwork analysisGenetic factorsUnderlying biologyVariantsEnrichment
2021
What is the role of synaptic protein TRIO's spectrin repeats?
Corcoran E, Bircher J, Koleske A. What is the role of synaptic protein TRIO's spectrin repeats? The FASEB Journal 2021, 35 DOI: 10.1096/fasebj.2021.35.s1.01837.Peer-Reviewed Original ResearchSpectrin repeatsProper neuronal developmentSpectrin repeat domainRare damaging variantsDisease-associated mutationsAccessory domainsCatalytic domainRepeat domainRegulatory proteinsRepeat functionDe novo missense mutationsSignaling mechanismDamaging mutationsNeuronal developmentDamaging variantsDisease mutationsBiochemical eventsNovo missense mutationNeurodevelopmental disordersMissense mutationsSpectrinRepeatsMutationsDomainTherapeutic strategiesAssociation of Damaging Variants in Genes With Increased Cancer Risk Among Patients With Congenital Heart Disease
Morton SU, Shimamura A, Newburger PE, Opotowsky AR, Quiat D, Pereira AC, Jin SC, Gurvitz M, Brueckner M, Chung WK, Shen Y, Bernstein D, Gelb BD, Giardini A, Goldmuntz E, Kim RW, Lifton RP, Porter GA, Srivastava D, Tristani-Firouzi M, Newburger JW, Seidman JG, Seidman CE. Association of Damaging Variants in Genes With Increased Cancer Risk Among Patients With Congenital Heart Disease. JAMA Cardiology 2021, 6: 457-462. PMID: 33084842, PMCID: PMC7578917, DOI: 10.1001/jamacardio.2020.4947.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAgedAged, 80 and overCase-Control StudiesChildChild, PreschoolFemaleGene Expression RegulationGene FrequencyGenes, NeoplasmGenetic Predisposition to DiseaseGenetic VariationHeart Defects, CongenitalHumansInfantInfant, NewbornLoss of Function MutationMaleMiddle AgedNeoplasmsYoung AdultConceptsCongenital heart diseaseCancer risk genesCancer riskLoF variantsControl participantsHeart diseaseRisk genesMulticenter case-control studyStructural cardiac anomaliesTime of enrollmentCase-control studyDamaging variantsExtracardiac anomaliesExtracardiac manifestationsCardiac anomaliesClinical variablesNeurodevelopmental delayLongitudinal surveillanceMAIN OUTCOMEParent studyCommon birth defectsPatientsEarly interventionFunction variantsMultiple patients
2020
Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal Neuralgia
Dong W, Jin SC, Allocco A, Zeng X, Sheth AH, Panchagnula S, Castonguay A, Lorenzo LÉ, Islam B, Brindle G, Bachand K, Hu J, Sularz A, Gaillard J, Choi J, Dunbar A, Nelson-Williams C, Kiziltug E, Furey CG, Conine S, Duy PQ, Kundishora AJ, Loring E, Li B, Lu Q, Zhou G, Liu W, Li X, Sierant MC, Mane S, Castaldi C, López-Giráldez F, Knight JR, Sekula RF, Simard JM, Eskandar EN, Gottschalk C, Moliterno J, Günel M, Gerrard JL, Dib-Hajj S, Waxman SG, Barker FG, Alper SL, Chahine M, Haider S, De Koninck Y, Lifton RP, Kahle KT. Exome Sequencing Implicates Impaired GABA Signaling and Neuronal Ion Transport in Trigeminal Neuralgia. IScience 2020, 23: 101552. PMID: 33083721, PMCID: PMC7554653, DOI: 10.1016/j.isci.2020.101552.Peer-Reviewed Original ResearchTrigeminal neuralgiaNeuronal ion transportImpairment of GABAVoltage-gated CaMechanical allodyniaTN pathogenesisPain syndromePain behaviorGABA signalingReceptor ClDisease pathogenesisTN casesFamilial clusteringExome sequencingGenetic factorsVariant burdenNeuralgiaRare damaging variantsPathogenesisGABAChannel CaDamaging variantsProbandsParent-offspring triosLarge-scale genomic studiesDe novo Damaging Variants, Clinical Phenotypes and Post-Operative Outcomes in Congenital Heart Disease
Boskovski MT, Homsy J, Nathan M, Sleeper LA, Morton S, Manheimer KB, Tai A, Gorham J, Lewis M, Swartz M, Alfieris GM, Bacha EA, Karimi M, Meyer D, Nguyen K, Bernstein D, Romano-Adesman A, Porter GA, Goldmuntz E, Chung WK, Srivastava D, Kaltman JR, Tristani-Firouzi M, Lifton R, Roberts AE, Gaynor JW, Gelb BD, Kim R, Seidman JG, Brueckner M, Mayer JE, Newburger JW, Seidman CE. De novo Damaging Variants, Clinical Phenotypes and Post-Operative Outcomes in Congenital Heart Disease. Circulation Genomic And Precision Medicine 2020, 13: e002836-e002836. PMID: 32812804, PMCID: PMC7439931, DOI: 10.1161/circgen.119.002836.Peer-Reviewed Original ResearchConceptsWorse transplant-free survivalTransplant-free survivalExtra-cardiac anomaliesCongenital heart diseaseDe novo variantsHeart diseaseFinal extubationNovo variantsFirst operationPost-operative outcomesOpen heart surgeryPreoperative genetic testingRoutine clinical practiceDamaging variantsWhole-exome sequencingHeart transplantationAdverse outcomesSurgical dataPatientsClinical practiceCardiac repairClinical phenotypeDe novoGenetic testingGenetic abnormalitiesDe novo damaging variants associated with congenital heart diseases contribute to the connectome
Ji W, Ferdman D, Copel J, Scheinost D, Shabanova V, Brueckner M, Khokha MK, Ment LR. De novo damaging variants associated with congenital heart diseases contribute to the connectome. Scientific Reports 2020, 10: 7046. PMID: 32341405, PMCID: PMC7184603, DOI: 10.1038/s41598-020-63928-2.Peer-Reviewed Original ResearchMeSH KeywordsConnectomeDNA HelicasesDNA-Binding ProteinsExomeFemaleHeart Defects, CongenitalHistone-Lysine N-MethyltransferaseHomeodomain ProteinsHumansMaleMi-2 Nucleosome Remodeling and Deacetylase ComplexMutationMutation, MissenseMyeloid-Lymphoid Leukemia ProteinNerve Tissue ProteinsProtein Tyrosine Phosphatase, Non-Receptor Type 11Receptor, Notch1ConceptsDe novo variantsNDD genesCardiac patterningDe novo damaging variantsDamaging de novo variantsCHD genesDamaging variantsGenesProtein truncatingGenetic originNovo variantsGene mutationsPatterningRecent studiesDendritic developmentVariantsMutationsNeurogenesisSynaptogenesisBonferroni correction
2019
De Novo Damaging DNA Coding Mutations Are Associated With Obsessive-Compulsive Disorder and Overlap With Tourette’s Disorder and Autism
Cappi C, Oliphant ME, Péter Z, Zai G, Conceição do Rosário M, Sullivan CAW, Gupta AR, Hoffman EJ, Virdee M, Olfson E, Abdallah SB, Willsey AJ, Shavitt RG, Miguel EC, Kennedy JL, Richter MA, Fernandez TV. De Novo Damaging DNA Coding Mutations Are Associated With Obsessive-Compulsive Disorder and Overlap With Tourette’s Disorder and Autism. Biological Psychiatry 2019, 87: 1035-1044. PMID: 31771860, PMCID: PMC7160031, DOI: 10.1016/j.biopsych.2019.09.029.Peer-Reviewed Original Research
2018
De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis
Wang S, Mandell JD, Kumar Y, Sun N, Morris MT, Arbelaez J, Nasello C, Dong S, Duhn C, Zhao X, Yang Z, Padmanabhuni SS, Yu D, King RA, Dietrich A, Khalifa N, Dahl N, Huang AY, Neale BM, Coppola G, Mathews CA, Scharf JM, Study T, Abdulkadir M, Arbelaez J, Bodmer B, Bromberg Y, Brown L, Cheon K, Coffey B, Deng L, Dietrich A, Dong S, Duhn C, Elzerman L, Fernandez T, Fremer C, Garcia-Delgar B, Gilbert D, Grice D, Hagstrøm J, Hedderly T, Heiman G, Heyman I, Hoekstra P, Hong H, Huyser C, Kim E, Kim Y, Kim Y, King R, Koh Y, Kook S, Kuperman S, Leventhal B, Ludolph A, Madruga-Garrido M, Mandell J, Maras A, Mir P, Morer A, Morris M, Müller-Vahl K, Münchau A, Murphy T, Nasello C, Plessen K, Poisner H, Roessner V, Sanders S, Shin E, Song D, Song J, State M, Sun N, Thackray J, Tischfield J, Tübing J, Visscher F, Wanderer S, Wang S, Willsey A, Woods M, Xing J, Zhang Y, Zhao X, Zinner S, Initiative T, Androutsos C, Barta C, Farkas L, Fichna J, Georgitsi M, Janik P, Karagiannidis I, Koumoula A, Nagy P, Paschou P, Puchala J, Rizzo R, Szejko N, Szymanska U, Tarnok Z, Tsironi V, Wolanczyk T, Zekanowski C, Genetics T, Barr C, Batterson J, Berlin C, Bruun R, Budman C, Cath D, Chouinard S, Coppola G, Cox N, Darrow S, Davis L, Dion Y, Freimer N, Grados M, Hirschtritt M, Huang A, Illmann C, Kurlan R, Leckman J, Lyon G, Malaty I, Mathews C, MacMahon W, Neale B, Okun M, Osiecki L, Pauls D, Posthuma D, Ramensky V, Robertson M, Rouleau G, Sandor P, Scharf J, Singer H, Smit J, Sul J, Yu D, Fernandez T, Buxbaum J, De Rubeis S, Grice D, Xing J, Heiman G, Tischfield J, Paschou P, Willsey A, State M. De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis. Cell Reports 2018, 24: 3441-3454.e12. PMID: 30257206, PMCID: PMC6475626, DOI: 10.1016/j.celrep.2018.08.082.Peer-Reviewed Original ResearchConceptsCell polarityNumber variantsSequence variantsDe novo damaging variantsDe novoDe novo sequencesCopy number variantsNovo sequencesWhole-exome sequencingDamaging variantsRisk genesGenesCommon pathwayNovoSignificant overlapVariantsTriosGenetic riskSequencingCELSR3PathwayPolaritySequenceSignificant excessFamily
2017
De Novo Coding Variants Are Strongly Associated with Tourette Disorder
Willsey AJ, Fernandez TV, Yu D, King RA, Dietrich A, Xing J, Sanders SJ, Mandell JD, Huang AY, Richer P, Smith L, Dong S, Samocha KE, Genetics T, Abdulkadir M, Bohnenpoll J, Bromberg Y, Brown L, Cheon K, Coffey B, Deng L, Dietrich A, Dong S, Elzerman L, Fernandez T, Fründt O, Garcia-Delgar B, Gedvilaite E, Gilbert D, Grice D, Hagstrøm J, Hedderly T, Heiman G, Heyman I, Hoekstra P, Hong H, Huyser C, Ibanez-Gomez L, Kim Y, Kim Y, King R, Koh Y, Kook S, Kuperman S, Lamerz A, Leventhal B, Ludolph A, da Silva C, Madruga-Garrido M, Mandell J, Maras A, Mir P, Morer A, Münchau A, Murphy T, Nasello C, Openneer T, Plessen K, Richer P, Roessner V, Sanders S, Shin E, Sival D, Smith L, Song D, Song J, State M, Stolte A, Sun N, Tischfield J, Tübing J, Visscher F, Walker M, Wanderer S, Wang S, Willsey A, Woods M, Xing J, Zhang Y, Zhou A, Zinner S, Genetics T, Barr C, Batterson J, Berlin C, Bruun R, Budman C, Cath D, Chouinard S, Coppola G, Cox N, Darrow S, Davis L, Dion Y, Freimer N, Grados M, Hirschtritt M, Huang A, Illmann C, Kurlan R, Leckman J, Lyon G, Malaty I, Mathews C, MaMahon W, Neale B, Okun M, Osiecki L, Pauls D, Posthuma D, Ramensky V, Robertson M, Rouleau G, Sandor P, Scharf J, Singer H, Smit J, Sul J, Yu D, Neale B, Coppola G, Mathews C, Tischfield J, Scharf J, State M, Heiman G. De Novo Coding Variants Are Strongly Associated with Tourette Disorder. Neuron 2017, 94: 486-499.e9. PMID: 28472652, PMCID: PMC5769876, DOI: 10.1016/j.neuron.2017.04.024.Peer-Reviewed Original ResearchConceptsWhole-exome sequencingTourette's disorderDamaging variantsLikely gene-disrupting variantsComplex neurodevelopmental disorderClinical casesUnrelated probandsNeurodevelopmental disordersDe novo damaging variantsDisordersRisk genesGenetic cohortsConsistent evidenceCoding variantReplication sampleProbandsInternational ConsortiumCohortVariants
2015
Exome sequencing links mutations in PARN and RTEL1 with familial pulmonary fibrosis and telomere shortening
Stuart BD, Choi J, Zaidi S, Xing C, Holohan B, Chen R, Choi M, Dharwadkar P, Torres F, Girod CE, Weissler J, Fitzgerald J, Kershaw C, Klesney-Tait J, Mageto Y, Shay JW, Ji W, Bilguvar K, Mane S, Lifton RP, Garcia CK. Exome sequencing links mutations in PARN and RTEL1 with familial pulmonary fibrosis and telomere shortening. Nature Genetics 2015, 47: 512-517. PMID: 25848748, PMCID: PMC4414891, DOI: 10.1038/ng.3278.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAged, 80 and overAmino Acid SequenceCase-Control StudiesCells, CulturedDNA HelicasesDNA Mutational AnalysisExomeExoribonucleasesFemaleGenetic Association StudiesGenetic Predisposition to DiseaseHumansIdiopathic Pulmonary FibrosisLeukocytesLod ScoreMaleMiddle AgedMolecular Sequence DataPedigreeTelomereTelomere Shortening
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