Jia Di Wen, MD, PhD, FACMG
Assistant ProfessorCards
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Research
Publications
2025
Decoding the genetic complexity in a pediatric case of B-ALL through long-read genomic sequencing and RNA sequencing
Chong M, Ng S, Chai H, Diadamo A, Flagg A, Owen N, Li P, Wen J. Decoding the genetic complexity in a pediatric case of B-ALL through long-read genomic sequencing and RNA sequencing. Cancer Genetics 2025, 298: 274-279. PMID: 41232304, PMCID: PMC12666982, DOI: 10.1016/j.cancergen.2025.11.002.Peer-Reviewed Original ResearchConceptsLong-read genome sequencingB-cell acute lymphoblastic leukemiaGenome sequenceRNA sequencingTyrosine kinase inhibitorsGenetic alterationsCopy number aberrationsChromosomal microarray analysisPediatric casesHigh-risk B-cell acute lymphoblastic leukemiaCases of B-cell acute lymphoblastic leukemiaTCRB locusOncogenic gene fusionsSequencing approachClinically actionable targetsGenetic complexityABL1 genePartial deletionCytogenetic methodsGene fusionsAcute lymphoblastic leukemiaMicroarray analysisHeterogeneous hematologic malignancyABL1 fusionsSequencePrognostic impact of cytogenetic abnormalities in aggressive T-cell lymphomas: Defining high-risk subgroups through conventional karyotyping.
Kiwan A, Diadamo A, Wen J, Kewan T, Siddon A, Kothari S, Isufi I, Seropian S, Huntington S, Montanari F, Xu M, Li P, Girardi M, Sethi T, Foss F. Prognostic impact of cytogenetic abnormalities in aggressive T-cell lymphomas: Defining high-risk subgroups through conventional karyotyping. Blood 2025, 146: 1759-1759. DOI: 10.1182/blood-2025-1759.Peer-Reviewed Original ResearchT-cell lymphomaMature T-cell lymphomasAggressive T-cell lymphomaUnivariate Cox proportional hazardsMonosomy 9Overall survivalPeripheral bloodMonosomy 5Nodal PTCLBone marrowHigh-risk subgroupsPrognostic significancePlatelet countCox proportional hazardsCytogenetic abnormalitiesPrognostic impactComplex karyotypeT cellsMarker chromosomesPrognostic impact of cytogenetic abnormalitiesPredictor of poor OSImpact of cytogenetic abnormalitiesMultivariate CPH modelChromosomal lesionsPresence of marker chromosomesUnravelling ring chromosome structures and formation mechanisms by short-read and long-read genomic sequencing
Chong M, Burssed B, Chen Z, Wen J, Ng E, Szewczyk B, Wang G, Chua K, Liehr T, Zou Y, Murry J, Sheth F, Li P, Melaragno M. Unravelling ring chromosome structures and formation mechanisms by short-read and long-read genomic sequencing. Genetics In Medicine Open 2025, 103475. DOI: 10.1016/j.gimo.2025.103475.Peer-Reviewed Original ResearchLong-read genome sequencingShort-read genome sequencingMicrohomology-mediated break-induced replicationCopy number variantsMicrohomology-mediated end joiningNon-Homologous End JoiningGenome sequenceRing chromosomesEnd joiningTelomere-to-telomereNucleotide-level resolutionSingle-copy sequencesBreak-induced replicationLoss of euchromatinReference genomeShort readsGenomic rearrangementsRepetitive sequencesTelomeric regionsChromosome structureCell cycleChromosomal instabilitySequenceGenomeChromosomeCopy Number Variants of Uncertain Significance by Chromosome Microarray Analysis from Consecutive Pediatric Patients: Reevaluation Following Current Guidelines and Reanalysis by Genome Sequencing
Li W, Xie X, Chai H, DiAdamo A, Bistline E, Li P, Dai Y, Knight J, Avni-Singer A, Burger J, Ment L, Spencer-Manzon M, Zhang H, Wen J. Copy Number Variants of Uncertain Significance by Chromosome Microarray Analysis from Consecutive Pediatric Patients: Reevaluation Following Current Guidelines and Reanalysis by Genome Sequencing. Genes 2025, 16: 874. PMID: 40869922, PMCID: PMC12385847, DOI: 10.3390/genes16080874.Peer-Reviewed Original ResearchConceptsWhole-genome sequencingChromosomal microarray analysisCopy number variantsGenome sequenceMicroarray analysisCausative genetic variantsDiagnostic valueClinical cytogenetics laboratoryPediatric casesConsecutive pediatric casesConsecutive pediatric patientsPathogenic CNVsGenetic variantsBenign CNVsGenetic counselorsClinical geneticistsRate of reclassificationLaboratory reevaluationCytogenetic laboratoriesPediatric patientsChromosomeClinical impactSequenceVariantsCopyA Concordance Study among 26 NGS Laboratories Participating in the NCI Molecular Analysis for Therapy Choice Clinical Trial.
Zane L, Yee L, Chang T, Sklar J, Yang G, Wen J, Li P, Harrington R, Sims D, Harper K, Trent J, LoBello J, Szelinger S, Benson K, Zeng J, Poorman K, Xu D, Frampton G, Pavlick D, Miller V, Tandon B, Swat W, Weiss L, Funari V, Conroy J, Prescott J, Chandra P, Ma C, Champion K, Baschkopf G, Fesko Y, Freitas T, Tomlins S, Hovelson D, White K, Sorrells S, Tell R, Beaubier N, King D, Li L, Kelly K, Uvalic J, Meyers B, Kolhe R, Lindeman N, Baltay M, Sholl L, Lopategui J, Vail E, Zhang W, Telatar M, Afkhami M, Hsiao S, Mansukhani M, Adams E, Jiang L, Aldape K, Raffeld M, Xi L, Stehr H, Segal J, Aisner D, Davies K, Brown N, Livingston R, Konnick E, Song W, Solomon J, Walther Z, McShane L, Harris L, Chen A, Tsongalis G, Hamilton S, Flaherty K, O'Dwyer P, Conley B, Patton D, Iafrate A, Williams P, Tricoli J, Karlovich C. A Concordance Study among 26 NGS Laboratories Participating in the NCI Molecular Analysis for Therapy Choice Clinical Trial. Clinical Cancer Research 2025, 31: 3512-3525. PMID: 40465838, PMCID: PMC12284871, DOI: 10.1158/1078-0432.ccr-24-2188.Peer-Reviewed Original ResearchVariant detectionVariant reportingEstimates of copy numberTarget enrichment methodLow-complexity regionsCentral laboratoryNational Cancer Institute-Molecular AnalysisNCI-MATCH trialVariant interpretationVariant classesCopy numberBioinformatics analysisCNV reporterNGS assayCLIA-certified laboratoryEnrichment methodNGSHybridization captureIndelsNCI-MATCHTumor profiling testsCell linesTherapy choiceClinical samplesSNVsP685: A single-center reevaluation and reanalysis of copy number variants of uncertain significance detected by chromosome microarray from consecutive pediatric patients
Li W, Chai H, Diadamo A, Dai Y, Li P, Spencer-Manzon M, Zhang H, Wen J. P685: A single-center reevaluation and reanalysis of copy number variants of uncertain significance detected by chromosome microarray from consecutive pediatric patients. Genetics In Medicine Open 2025, 3: 103054. DOI: 10.1016/j.gimo.2025.103054.Peer-Reviewed Original Research
2024
Patterns of Cytogenomic Findings from a Case Series of Recurrent Pregnancy Loss Provide Insight into the Extent of Genetic Defects Causing Miscarriages
DiAdamo A, Chai H, Chong M, Wang G, Wen J, Jiang Y, Li P. Patterns of Cytogenomic Findings from a Case Series of Recurrent Pregnancy Loss Provide Insight into the Extent of Genetic Defects Causing Miscarriages. Global Medical Genetics 2024, 11: 123-131. PMID: 38560483, PMCID: PMC10980555, DOI: 10.1055/s-0044-1785227.Peer-Reviewed Original ResearchRecurrent pregnancy lossProducts of conceptionAbnormal karyotypeConsecutive miscarriagesCase seriesCytogenomic abnormalitiesCA groupCytogenomic findingsRoutine cytogenetic analysisCopy number variantsMonosomy XNormal karyotypeRetrospective studyPregnancy lossCytogenetic analysisPathogenic variantsMiscarriageSA groupAneuploidyKaryotypeLethal variantWomenAbnormalitiesGenome sequenceAbstract BackgroundRing Chromosome 12
Taylor H, Wen J. Ring Chromosome 12. 2024, 191-199. DOI: 10.1007/978-3-031-47530-6_16.Peer-Reviewed Original ResearchRing Chromosome 19
Wen J, Chong M. Ring Chromosome 19. 2024, 271-278. DOI: 10.1007/978-3-031-47530-6_23.Peer-Reviewed Original ResearchPercentage of mosaicismRare chromosomal aberrationGenotype-phenotype correlationSeverity of clinical featuresGenomic investigationsChromosome 19Genetic imbalanceVariable clinical manifestationsRare genetic abnormalitySurvive into adulthoodCarrier parentsSevere phenotypeClinical featuresLaboratory findingsInherited casesClinical manifestationsGenetic abnormalitiesChromosomal aberrationsClinical implicationsMosaicismFamilial transmissionPhenotypeComprehensive understandingIntellectual disabilityPatientsAcquired Ring Chromosomes in Solid Tumors
Wen J, Chong M. Acquired Ring Chromosomes in Solid Tumors. 2024, 475-490. DOI: 10.1007/978-3-031-47530-6_32.Peer-Reviewed Original ResearchPrevalence of ARCHuman solid tumorsSolid tumorsTumor typesRing chromosomesManagement of solid tumorsSoft tissue tumorsTumor suppressor geneTumor siteMalignant cellsTissue tumorsMitelman databaseChromosome analysisTumorTumor formationTreatment managementQuality of bandingMolecular consequencesSecondary findingsGene fusionsPrevalence
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