Featured Publications
A retrospective cohort analysis of the Yale pediatric genomics discovery program
Al‐Ali S, Jeffries L, Faustino EVS, Ji W, Mis E, Konstantino M, Zerillo C, Jiang Y, Spencer‐Manzon M, Bale A, Zhang H, McGlynn J, McGrath JM, Tremblay T, Brodsky NN, Lucas CL, Pierce R, Deniz E, Khokha MK, Lakhani SA. A retrospective cohort analysis of the Yale pediatric genomics discovery program. American Journal Of Medical Genetics Part A 2022, 188: 2869-2878. PMID: 35899841, PMCID: PMC9474639, DOI: 10.1002/ajmg.a.62918.Peer-Reviewed Original ResearchConceptsRetrospective cohort analysisNext-generation sequencingCohort analysisSystem abnormalitiesImmune system abnormalitiesCardiovascular system abnormalitiesFunctional molecular analysesNovel genesPrecise molecular diagnosisClinical characteristicsFurther genetic evaluationDiscovery programsComplex patientsMultisystem diseaseDisease genesPediatric providersRare genetic diseaseNew diagnosisPhenotype relationshipsPatientsGenetic diseasesMolecular analysisDiagnosisParticipant demographicsNGS resultsRethinking what constitutes a diagnosis in the genomics era: a critical illness perspective.
Lakhani SA, Pierce R. Rethinking what constitutes a diagnosis in the genomics era: a critical illness perspective. Current Opinion In Pediatrics 2019, 31: 317-321. PMID: 31090571, DOI: 10.1097/mop.0000000000000754.Peer-Reviewed Original ResearchConceptsPediatric intensivistsIll childrenCritical care pediatriciansFirst clinical diagnosisTypes of patientsWhole-exome sequencingSevere congenital diseaseUnderlying genetic causePatient's conditionIllness perspectiveUndiagnosed diseasePatientsDescriptive diagnosisClinical diagnosisCongenital diseaseGenetic testingGenetic abnormalitiesDiagnosisExome sequencingGenetic causeNext-generation sequencingClinical geneticistsIntensivistsGenetic diagnosisDiseaseDe novo pathogenic variants in neuronal differentiation factor 2 (NEUROD2) cause a form of early infantile epileptic encephalopathy
Sega AG, Mis EK, Lindstrom K, Mercimek-Andrews S, Ji W, Cho MT, Juusola J, Konstantino M, Jeffries L, Khokha MK, Lakhani SA. De novo pathogenic variants in neuronal differentiation factor 2 (NEUROD2) cause a form of early infantile epileptic encephalopathy. Journal Of Medical Genetics 2018, 56: 113. PMID: 30323019, DOI: 10.1136/jmedgenet-2018-105322.Peer-Reviewed Original ResearchConceptsEarly infantile epileptic encephalopathyInfantile epileptic encephalopathyEpileptic encephalopathyPatient variantsDe novo pathogenic variantsNovel de novo variantNovo pathogenic variantsEarly-onset refractory seizuresDifferentiation factor 2Whole-exome sequencingNeuronal differentiation factorRefractory seizuresSignificant developmental delaySpontaneous seizuresUnderlying etiologyEctopic neuronsDe novo variantsPatient's conditionEncephalopathyPathogenic variantsSevere disordersDevelopmental delayUnrelated childrenExome sequencingGene mutations
2024
CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow
Kim A, Sakin I, Viviano S, Tuncel G, Aguilera S, Goles G, Jeffries L, Ji W, Lakhani S, Kose C, Silan F, Oner S, Kaplan O, Group M, Ergoren M, Mishra-Gorur K, Gunel M, Sag S, Temel S, Deniz E. CC2D1A causes ciliopathy, intellectual disability, heterotaxy, renal dysplasia, and abnormal CSF flow. Life Science Alliance 2024, 7: e202402708. PMID: 39168639, PMCID: PMC11339347, DOI: 10.26508/lsa.202402708.Peer-Reviewed Original ResearchConceptsDevelopmental disabilitiesIntellectual disabilityPatient-derived fibroblastsMidbrain regionsBrain developmentDefective ciliogenesisCSF circulationDisabilityCSF flowAbnormal CSF flowNervous system developmentMutant tadpolesCiliated tissuesMultiple model systemsVariant functionPronephric ductUnrelated familiesCC2D1AExpression patternsCiliogenesisRenal dysplasiaLeft-right organizerFunctional analysisDisease mechanismsBrainUnraveling the genetic tapestry of pediatric sarcomeric cardiomyopathies and masquerading phenocopies in Jordan
Azab B, Aburizeg D, Shaaban S, Ji W, Mustafa L, Isbeih N, Al-Akily A, Mohammad H, Jeffries L, Khokha M, Lakhani S, Al-Ammouri I. Unraveling the genetic tapestry of pediatric sarcomeric cardiomyopathies and masquerading phenocopies in Jordan. Scientific Reports 2024, 14: 15141. PMID: 38956129, PMCID: PMC11219879, DOI: 10.1038/s41598-024-64921-9.Peer-Reviewed Original ResearchConceptsExome sequencingSarcomere-related genesMitochondrial-related diseasesAt-risk family membersGenetic architectureGenetic landscapePathogenic variantsGene panelPediatric cardiomyopathyMolecular underpinningsGenetic testingPhenocopiesSarcomeric cardiomyopathiesGenesSequenceStorage disorderFamily membersAt-riskVariantsEarly interventionExomeFamilyGlycogen storage disorderHypertrophic cardiomyopathyCardiomyopathyA metabolic signature for NADSYN1-dependent congenital NAD deficiency disorder
Szot J, Cuny H, Martin E, Sheng D, Iyer K, Portelli S, Nguyen V, Gereis J, Alankarage D, Chitayat D, Chong K, Wentzensen I, Vincent-Delormé C, Lermine A, Burkitt-Wright E, Ji W, Jeffries L, Pais L, Tan T, Pitt J, Wise C, Wright H, Andrews I, Pruniski B, Grebe T, Corsten-Janssen N, Bouman K, Poulton C, Prakash S, Keren B, Brown N, Hunter M, Heath O, Lakhani S, McDermott J, Ascher D, Chapman G, Bozon K, Dunwoodie S. A metabolic signature for NADSYN1-dependent congenital NAD deficiency disorder. Journal Of Clinical Investigation 2024, 134: e174824. PMID: 38357931, PMCID: PMC10866660, DOI: 10.1172/jci174824.Peer-Reviewed Original ResearchConceptsCongenital NAD deficiency disorderNicotinamide adenine dinucleotideBiallelic loss-of-function variantsLoss-of-function variantsPrecursor supplementationNAD precursor supplementationStructures modelled in silicoNonredundant enzymesMetabolic signaturesNAD metabolomeNicotinamide adenine dinucleotide levelsDeficiency disordersPrevent adverse pregnancy outcomesSynthesis pathwayAdverse pregnancy outcomesModel in silicoNAD precursorsMetabolic blockEmbryonic developmentImproving clinical diagnosticsAdenine dinucleotideAbsence of malformationsPregnancy outcomesCongenital malformationsMalformations“Deficiency in ELF4, X-Linked”: a Monogenic Disease Entity Resembling Behçet’s Syndrome and Inflammatory Bowel Disease
Olyha S, O’Connor S, Kribis M, Bucklin M, Uthaya Kumar D, Tyler P, Alam F, Jones K, Sheikha H, Konnikova L, Lakhani S, Montgomery R, Catanzaro J, Du H, DiGiacomo D, Rothermel H, Moran C, Fiedler K, Warner N, Hoppenreijs E, van der Made C, Hoischen A, Olbrich P, Neth O, Rodríguez-Martínez A, Lucena Soto J, van Rossum A, Dalm V, Muise A, Lucas C. “Deficiency in ELF4, X-Linked”: a Monogenic Disease Entity Resembling Behçet’s Syndrome and Inflammatory Bowel Disease. Journal Of Clinical Immunology 2024, 44: 44. PMID: 38231408, PMCID: PMC10929603, DOI: 10.1007/s10875-023-01610-8.Peer-Reviewed Original ResearchConceptsDEX patientsClass-switched memory B cellsInborn errors of immunityTreated with anti-inflammatory agentsLow natural killerX-linkedMemory B cellsErrors of immunityCohort of patientsIncreased inflammatory cytokinesLoss-of-function variantsHeterogeneous clinical phenotypesInflammatory bowel diseaseTargeted therapeutic interventionsNatural killerAnti-inflammatory agentsAphthous ulcersTherapeutic responseAutoinflammatory syndromeInflammatory markersClinical manifestationsB cellsBehcet's syndromeGastrointestinal symptomsMechanisms of disease
2023
Sequence variants in different genes underlying Bardet-Biedl syndrome in four consanguineous families
Ali A, Abdullah, Bilal M, Mis E, Lakhani S, Ahmad W, Ullah I. Sequence variants in different genes underlying Bardet-Biedl syndrome in four consanguineous families. Molecular Biology Reports 2023, 50: 9963-9970. PMID: 37897612, DOI: 10.1007/s11033-023-08816-4.Peer-Reviewed Original ResearchConceptsUnique inheritance patternConsanguineous familyPakistani consanguineous familyMKK genesDifferent genesBBS7 geneBardet-Biedl syndromeWhole-exome sequencingRod-cone dystrophyBBS genesGenesCompound heterozygous variantsNovel homozygous variantHeterogeneous congenital disorderInheritance patternRelated phenotypesExome sequencingClinical manifestationsMutational screeningRenal abnormalitiesMutation spectrumCognitive impairmentHeterozygous variantsPakistani populationHomozygous variantSequence variants in DLX5, HOXD13 and 445 kb‐microduplication surrounding BTRC cause split‐hand/foot malformation in three different families
Abdullah, Hussain S, Ji W, Khan H, Mis E, Mushtaq R, Chodhary M, Raza M, Jan A, Ullah I, Khokha M, Lakhani S, Ahmad W. Sequence variants in DLX5, HOXD13 and 445 kb‐microduplication surrounding BTRC cause split‐hand/foot malformation in three different families. Clinical Genetics 2023, 105: 109-111. PMID: 37776184, DOI: 10.1111/cge.14430.Peer-Reviewed Original ResearchClinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta
Caron V, Chassaing N, Ragge N, Boschann F, Ngu A, Meloche E, Chorfi S, Lakhani S, Ji W, Steiner L, Marcadier J, Jansen P, van de Pol L, van Hagen J, Russi A, Le Guyader G, Nordenskjöld M, Nordgren A, Anderlid B, Plaisancié J, Stoltenburg C, Horn D, Drenckhahn A, Hamdan F, Lefebvre M, Attie-Bitach T, Forey P, Smirnov V, Ernould F, Jacquemont M, Grotto S, Alcantud A, Coret A, Ferrer-Avargues R, Srivastava S, Vincent-Delorme C, Romoser S, Safina N, Saade D, Lupski J, Calame D, Geneviève D, Chatron N, Schluth-Bolard C, Myers K, Dobyns W, Calvas P, Study T, Salmon C, Holt R, Elmslie F, Allaire M, Prigozhin D, Tremblay A, Michaud J. Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta. Genetics In Medicine 2023, 25: 100856. PMID: 37092537, PMCID: PMC10757562, DOI: 10.1016/j.gim.2023.100856.Peer-Reviewed Original ResearchConceptsPathogenic variantsLikely pathogenic variantsRetinoic acid receptor betaDevelopmental eye anomaliesGlobal developmental delayAcid receptor betaRetinoic acid receptor beta geneExtensive clinical heterogeneityClinical spectrumClinical dataEye anomaliesMotor impairmentCardinal featuresClinical heterogeneityReceptor betaNormal responseBirth anomaliesDevelopmental delayFunction variantsSyndromic formsAffected individualsDominant variantVariable phenotypeFunctional heterogeneityBeta gene
2021
Human autoinflammatory disease reveals ELF4 as a transcriptional regulator of inflammation
Tyler PM, Bucklin ML, Zhao M, Maher TJ, Rice AJ, Ji W, Warner N, Pan J, Morotti R, McCarthy P, Griffiths A, van Rossum AMC, Hollink IHIM, Dalm VASH, Catanzaro J, Lakhani SA, Muise AM, Lucas CL. Human autoinflammatory disease reveals ELF4 as a transcriptional regulator of inflammation. Nature Immunology 2021, 22: 1118-1126. PMID: 34326534, PMCID: PMC8985851, DOI: 10.1038/s41590-021-00984-4.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCalgranulin ADNA-Binding ProteinsFemaleGene Expression RegulationHereditary Autoinflammatory DiseasesHumansInflammatory Bowel DiseasesInterleukin 1 Receptor Antagonist ProteinLipocalin-2LipopolysaccharidesMacrophagesMaleMiceMice, Inbred C57BLMice, KnockoutTh17 CellsTranscription FactorsTranscription, GeneticTriggering Receptor Expressed on Myeloid Cells-1ConceptsInterleukin-1Inflammatory bowel disease (IBD) characteristicsInflammatory immune cellsHuman inflammatory disordersAnti-inflammatory genesTumor necrosis factorHuman autoinflammatory diseasesInnate stimuliHyperinflammatory responseMale patientsNeutrophil chemoattractantDisease characteristicsInflammatory disordersMucosal diseaseImmune cellsInflammation amplifierNecrosis factorUnrelated male patientsAutoinflammatory diseasesMouse modelBroad translational relevanceTranslational relevanceInflammationFunction variantsMouse macrophagesFunctional testing for variant prioritization in a family with long QT syndrome
Najari Beidokhti M, Bertalovitz AC, Ji W, McCormack J, Jeffries L, Sempou E, Khokha MK, McDonald TV, Lakhani SA. Functional testing for variant prioritization in a family with long QT syndrome. Molecular Genetics And Genomics 2021, 296: 823-836. PMID: 33876311, DOI: 10.1007/s00438-021-01780-3.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionAMP-Activated Protein KinasesDNA Mutational AnalysisElectrocardiographyERG1 Potassium ChannelExome SequencingFamilyFemaleGenetic TestingHeart Function TestsHEK293 CellsHumansKCNQ1 Potassium ChannelLong QT SyndromeMiddle AgedMutationPedigreePhenotypePolymerase Chain ReactionPolymorphism, Single NucleotideProtein Serine-Threonine KinasesConceptsWhole-exome sequencingFunctional characterizationSilico analysisPrecise genetic etiologyHeterologous expression systemNext-generation sequencing platformsNovel genetic variantsDeleterious phenotypesFunction phenotypesExpression systemSequencing platformsSecond individualHeritable diseaseVariant prioritizationGenetic variantsLong QT syndromeExome sequencingGenetic etiologyGenetic settingClinical genetics settingPhenotypeFamilyGene panelFamily membersVariantsExpansion of NEUROD2 phenotypes to include developmental delay without seizures
Mis EK, Sega AG, Signer RH, Cartwright T, Ji W, Martinez‐Agosto J, Nelson SF, Palmer CGS, Lee H, Mitzelfelt T, Konstantino M, Network U, Jeffries L, Khokha MK, Marco E, Martin MG, Lakhani SA. Expansion of NEUROD2 phenotypes to include developmental delay without seizures. American Journal Of Medical Genetics Part A 2021, 185: 1076-1080. PMID: 33438828, PMCID: PMC8212414, DOI: 10.1002/ajmg.a.62064.Peer-Reviewed Original ResearchConceptsDevelopmental delayEarly-onset seizuresDe novo heterozygous variantsNovo heterozygous variantsDifferentiation factor 2Xenopus laevis tadpolesHeterozygous variantsSeizuresNeuronal differentiationParental studiesFunctional testingMissense variantsPatient variantsFunctional evidenceFactor 2Vivo assaysLaevis tadpolesVariant pathogenicityFunction effectsAdolescentsVariantsUncontrolled Epstein-Barr Virus as an Atypical Presentation of Deficiency in ADA2 (DADA2)
Brooks JP, Rice AJ, Ji W, Lanahan SM, Konstantino M, Dara J, Hershfield MS, Cruickshank A, Dokmeci E, Lakhani S, Lucas CL. Uncontrolled Epstein-Barr Virus as an Atypical Presentation of Deficiency in ADA2 (DADA2). Journal Of Clinical Immunology 2021, 41: 680-683. PMID: 33394316, DOI: 10.1007/s10875-020-00940-1.Peer-Reviewed Original ResearchAdenosine DeaminaseAntiviral AgentsBiomarkersBiopsyChildDisease ManagementDisease SusceptibilityDNA Mutational AnalysisEpstein-Barr Virus InfectionsExome SequencingFemaleHematopoietic Stem Cell TransplantationHumansIntercellular Signaling Peptides and ProteinsSevere Combined ImmunodeficiencySiblingsSymptom AssessmentTomography, X-Ray ComputedTreatment Outcome
2020
The latest FADS: Functional analysis of GLDN patient variants and classification of GLDN‐associated AMC as a type of viable fetal akinesia deformation sequence
Mis EK, Al‐Ali S, Ji W, Spencer‐Manzon M, Konstantino M, Khokha MK, Jeffries L, Lakhani SA. The latest FADS: Functional analysis of GLDN patient variants and classification of GLDN‐associated AMC as a type of viable fetal akinesia deformation sequence. American Journal Of Medical Genetics Part A 2020, 182: 2291-2296. PMID: 32812332, DOI: 10.1002/ajmg.a.61783.Peer-Reviewed Original ResearchConceptsFetal akinesia deformation sequenceArthrogryposis multiplex congenitaCohort of patientsScope of illnessPulmonary hypoplasiaAdditional patientsClinical featuresNeonatal supportNervous system developmentMultiplex congenitaCongenital contracturesPatientsHeterogenous conditionRecessive variantsPatient variantsFunctional evidenceCohortNovel variantsContractureFunctional dataSyndromeHypoplasiaIllnessVariantsFindingsDYNC1H1‐related disorders: A description of four new unrelated patients and a comprehensive review of previously reported variants
Amabile S, Jeffries L, McGrath JM, Ji W, Spencer‐Manzon M, Zhang H, Lakhani SA. DYNC1H1‐related disorders: A description of four new unrelated patients and a comprehensive review of previously reported variants. American Journal Of Medical Genetics Part A 2020, 182: 2049-2057. PMID: 32656949, DOI: 10.1002/ajmg.a.61729.Peer-Reviewed Original ResearchConceptsSpinal muscular atrophyIntellectual disabilityUnrelated patientsSingle-center experienceNew unrelated patientsCenter experienceDYNC1H1 geneCNS disordersCombined disordersCortical developmentDisease-causing variantsVariable syndromeNeuromuscular diseaseNeuromuscular phenotypePatientsMuscular atrophyHeterozygous variantsDYNC1H1Medical literatureCharcot-MarieDisordersType 20Novel variantsPhenotypeReportNovel compound heterozygous variants in NHLRC2 in a patient with FINCA syndrome
Brodsky NN, Boyarchuk O, Kovalchuk T, Hariyan T, Rice A, Ji W, Khokha M, Lakhani S, Lucas CL. Novel compound heterozygous variants in NHLRC2 in a patient with FINCA syndrome. Journal Of Human Genetics 2020, 65: 911-915. PMID: 32435055, DOI: 10.1038/s10038-020-0776-0.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAngiomatosisBrain NeoplasmsCardiomegalyChild, PreschoolExome SequencingFibrosisHeterozygoteHumansIntracellular Signaling Peptides and ProteinsLung DiseasesMaleModels, MolecularNeurodegenerative DiseasesPedigreePoint MutationProtein ConformationProtein DomainsSequence AlignmentSequence Homology, Amino AcidSyndromeConceptsWhole-exome sequencingNovel compound heterozygous variantsCompound heterozygous variantsUkrainian patientsClinical featuresNovel variantsNew patientsHealthy humansCompound heterozygous combinationPatientsHeterozygous variantsSyndromeFinnish childrenNHLRC2Sanger sequencingFibrosisDiseaseGnomAD databaseN-terminal thioredoxinCentral regulatorVariantsNeurodegenerationNovel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome
Alharatani R, Ververi A, Beleza-Meireles A, Ji W, Mis E, Patterson QT, Griffin JN, Bhujel N, Chang CA, Dixit A, Konstantino M, Healy C, Hannan S, Neo N, Cash A, Li D, Bhoj E, Zackai EH, Cleaver R, Baralle D, McEntagart M, Newbury-Ecob R, Scott R, Hurst JA, Au PYB, Hosey MT, Khokha M, Marciano DK, Lakhani SA, Liu KJ. Novel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome. Human Molecular Genetics 2020, 29: 1900-1921. PMID: 32196547, PMCID: PMC7372553, DOI: 10.1093/hmg/ddaa050.Peer-Reviewed Original ResearchConceptsCell-cell junctionsNovel protein-truncating variantsP120-catenin proteinProtein-truncating variantsNext-generation sequencingTranscriptional signalingP120-cateninCRISPR/Epithelial-mesenchymal transitionSubset of phenotypesDevelopmental roleLimb dysmorphologiesAdditional phenotypesHuman diseasesCTNND1Conditional deletionDe novoTruncating mutationsBlepharocheilodontic syndromeEpithelial integrityNovel truncating mutationCraniofacial dysmorphismPhenotypeCleft palateNeurodevelopmental disorders
2019
Siblings with lethal primary pulmonary hypoplasia and compound heterozygous variants in the AARS2 gene: further delineation of the phenotypic spectrum
Kiraly-Borri C, Jevon G, Ji W, Jeffries L, Ricciardi JL, Konstantino M, Ackerman KG, Lakhani SA. Siblings with lethal primary pulmonary hypoplasia and compound heterozygous variants in the AARS2 gene: further delineation of the phenotypic spectrum. Molecular Case Studies 2019, 5: a003699. PMID: 30819764, PMCID: PMC6549552, DOI: 10.1101/mcs.a003699.Peer-Reviewed Original ResearchConceptsPrimary pulmonary hypoplasiaPulmonary hypoplasiaPhenotypic spectrumEvidence of cardiomyopathyPremature ovarian insufficiencyAbsence of cardiomyopathyCompound heterozygous variantsWhole-exome sequencingOvarian insufficiencyAARS2 geneCompound HeterozygousHeterozygous variantsCardiomyopathyNewborn siblingsCarrier statusFurther delineationHypoplasiaUnaffected siblingsMitochondrial cardiomyopathySiblingsFirst reportLeukoencephalopathy
2018
A homozygous variant in RRM2B is associated with severe metabolic acidosis and early neonatal death
Penque BA, Su L, Wang J, Ji W, Bale A, Luh F, Fulbright RK, Sarmast U, Sega AG, Konstantino M, Spencer-Manzon M, Pierce R, Yen Y, Lakhani SA. A homozygous variant in RRM2B is associated with severe metabolic acidosis and early neonatal death. European Journal Of Medical Genetics 2018, 62: 103574. PMID: 30439532, DOI: 10.1016/j.ejmg.2018.11.008.Peer-Reviewed Original Research