2024
Rare germline variants in cancer-relevant genes are associated with breast cancer risk in young women with high-risk family history
Rozenblit M, Qing T, Ye Y, Zhao H, Hofstatter E, Singh V, Reisenbichler E, Murray M, Pusztai L. Rare germline variants in cancer-relevant genes are associated with breast cancer risk in young women with high-risk family history. Breast Cancer Research And Treatment 2024, 209: 21-26. PMID: 39602012, DOI: 10.1007/s10549-024-07560-y.Peer-Reviewed Original ResearchHigh-risk family historyFamily historyRare germline variantsCancer riskSNP-set kernel association testAssociated with breast cancer riskCancer casesContribution of family historyEarly-onset breast cancerCancer prevention clinicBreast cancerBreast cancer riskKernel association testBreast cancer casesCancer-predisposing genesGermline variantsGermline pathogenic variantsYoung womenPrevention clinicSKAT-OBurden testsPathogenic variantsExome sequencing dataAssociation TestLevel alterationsMitochondrial Heteroplasmy Is a Novel Predictor of Chronic Lymphocytic Leukemia Risk
Pasca S, Hong Y, Shi W, Puiu D, Lake N, Lek M, Guallar E, Arking D, Gondek L. Mitochondrial Heteroplasmy Is a Novel Predictor of Chronic Lymphocytic Leukemia Risk. Blood 2024, 144: 4054-4054. DOI: 10.1182/blood-2024-210250.Peer-Reviewed Original ResearchMitochondrial heteroplasmyClonal hematopoiesis of indeterminate potentialMtDNA heteroplasmyWhole-exome sequencing dataSomatic mutationsPresence of somatic mutationsExome sequencing dataCancer-associated genesClonal hematopoiesisClonal expansionVariant allele frequencyAssociated with myeloid malignanciesMtDNA variantsMitochondrial DNAPresence of mutationsSequence dataUK Biobank (UKBBiologically significant roleDeleterious mutationsHeteroplasmyChronic lymphocytic leukemia riskAllele frequenciesOncogenic transformationMitochondrial functionMyeloid genesAXIN1 mutations in nonsyndromic craniosynostosis.
Timberlake A, Hemal K, Gustafson J, Hao L, Valenzuela I, Slavotinek A, Cunningham M, Kahle K, Lifton R, Persing J. AXIN1 mutations in nonsyndromic craniosynostosis. Journal Of Neurosurgery Pediatrics 2024, 34: 246-251. PMID: 38905707, PMCID: PMC11200303, DOI: 10.3171/2024.5.peds24115.Peer-Reviewed Original ResearchSequence dataAXIN1 mutationsCase-parent triosGenome-wide significanceCS casesNonsyndromic CSGenome sequencing projectsWnt signalingExome sequencing dataRNA sequencing dataPhenotypes associated with mutationsSequencing projectsGenetic testingInhibitor of Wnt signalingLive birthsNonsyndromic casesGenetic etiologyGenetic causeCS patientsAXIN1Nonsyndromic craniosynostosisMutationsHealthy controlsBirth defectsExome
2023
Clinical and genomic differences in supratentorial versus infratentorial NF2 mutant meningiomas.
Tabor J, O'Brien J, Vasandani S, Vetsa S, Lei H, Jalal M, Marianayagam N, Jin L, Millares Chavez M, Haynes J, Dincer A, Yalcin K, Aguilera S, Omay S, Mishra-Gorur K, McGuone D, Morales-Valero S, Fulbright R, Gunel M, Erson-Omay E, Moliterno J. Clinical and genomic differences in supratentorial versus infratentorial NF2 mutant meningiomas. Journal Of Neurosurgery 2023, 139: 1648-1656. PMID: 37243548, DOI: 10.3171/2023.4.jns222929.Peer-Reviewed Original ResearchConceptsSubtotal resectionSupratentorial tumorsElevated Ki-67High-risk featuresProgression-free survivalChromosome 1p deletionInfratentorial counterpartsInfratentorial tumorsPostoperative managementSomatic driver mutationsCerebral convexityGrade IIInfratentorial meningiomasKi-67Posterior fossaLoss of heterozygosityMeningiomasResectionTumorsWhole-exome sequencing dataDriver mutationsHigh gradeSignificant differencesExome sequencing dataSporadic meningiomasKidneyNetwork: using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease
Boulogne F, Claus L, Wiersma H, Oelen R, Schukking F, de Klein N, Li S, Westra H, van der Zwaag B, van Reekum F, Sierks D, Schönauer R, Li Z, Bijlsma E, Bos W, Halbritter J, Knoers N, Besse W, Deelen P, Franke L, van Eerde A. KidneyNetwork: using kidney-derived gene expression data to predict and prioritize novel genes involved in kidney disease. European Journal Of Human Genetics 2023, 31: 1300-1308. PMID: 36807342, PMCID: PMC10620423, DOI: 10.1038/s41431-023-01296-x.Peer-Reviewed Original ResearchConceptsCo-expression networkTissue-specific expressionCandidate genesGene functionPhenotypic consequences of genetic variationPathogenic variantsConsequences of genetic variationInterpretation of genetic variantsGenetic causeRare variantsGene-phenotype associationsHereditary kidney diseaseExome sequencing dataDisease-associated genesGene expression dataPlausible candidate genesCandidate gene prioritizationKidney disease phenotypesUnbiased mannerCystic kidneysNovel genesGenetic variationPhenotypic consequencesGene prioritizationSequence data
2022
EPCO-40. INFRATENTORIAL NF2 MUTANT SPORADIC MENINGIOMAS DIFFER FROM THOSE IN SUPRATENTORIAL LOCATIONS AND ARE MORE BENIGN
Vasandani S, Vetsa S, Jalal M, Yalcin K, Marianayagam N, Nadar A, Jin L, Fulbright R, Erson-Omay E, Günel M, Moliterno J. EPCO-40. INFRATENTORIAL NF2 MUTANT SPORADIC MENINGIOMAS DIFFER FROM THOSE IN SUPRATENTORIAL LOCATIONS AND ARE MORE BENIGN. Neuro-Oncology 2022, 24: vii125-vii125. DOI: 10.1093/neuonc/noac209.474.Peer-Reviewed Original ResearchSupratentorial locationWhole-exome sequencing dataHigh-risk clinical featuresLonger progression-free survivalProgression-free survivalExtent of resectionShorter overall survivalDifferent intracranial locationsChromosome 1p deletionOverall survivalClinical featuresInfratentorial tumorsAggressive featuresClinical manifestationsClinical behaviorKi-67Intracranial locationMeningiomasTumorsUnstable tumorsNF2 lossResectionGenomic profilesPatientsExome sequencing dataPrognostic mutational subtyping in de novo diffuse large B-cell lymphoma
Kim E, Jiang Y, Xu T, Bazeos A, Knapp A, Bolen C, Humphrey K, Nielsen T, Penuel E, Paulson J. Prognostic mutational subtyping in de novo diffuse large B-cell lymphoma. BMC Cancer 2022, 22: 231. PMID: 35236331, PMCID: PMC8892802, DOI: 10.1186/s12885-022-09237-5.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAntineoplastic Combined Chemotherapy ProtocolsBridged Bicyclo Compounds, HeterocyclicClinical Trials, Phase II as TopicClinical Trials, Phase III as TopicEnhancer of Zeste Homolog 2 ProteinExome SequencingFemaleHumansLymphoma, Large B-Cell, DiffuseMaleMiddle AgedMutationPrognosisProto-Oncogene Proteins c-bcl-2RNA-SeqSulfonamidesTreatment OutcomeConceptsSequence dataWhole-exome sequencing dataExome-sequencing dataTargeted sequencing platformsExome sequencing dataTargeted sequencing dataBackgroundDiffuse large B-cell lymphomaLarge B-cell lymphomaSequencing platformsRNA-seqDe novo DLBCLImproved overall survivalTarget sequenceB-cell lymphomaVenetoclax therapyMutation subtypesPrognostic subsetsMutationsOverall survivalMolecular subsetsSubset distributionMutation groupSurvival outcomesMutation profilesClinical associations
2021
Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences
Ganel L, Chen L, Christ R, Vangipurapu J, Young E, Das I, Kanchi K, Larson D, Regier A, Abel H, Kang CJ, Scott A, Havulinna A, Chiang CWK, Service S, Freimer N, Palotie A, Ripatti S, Kuusisto J, Boehnke M, Laakso M, Locke A, Stitziel NO, Hall IM. Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences. Human Genomics 2021, 15: 34. PMID: 34099068, PMCID: PMC8185936, DOI: 10.1186/s40246-021-00335-2.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedApoptosis Regulatory ProteinsCell LineageDNA Copy Number VariationsDNA, MitochondrialExome SequencingFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyGenome, MitochondrialGTP-Binding ProteinsHumansMaleMembrane ProteinsMendelian Randomization AnalysisMiddle AgedPhenotypePolymorphism, Single NucleotideProto-Oncogene Proteins c-mybSequence Analysis, DNAConceptsCell type compositionGenome copy numberBlood-derived DNAMitochondrial genome copy numberCombination of genomesCopy numberBulk DNA sequencingDNA sequencingPolygenic risk scoresNumber of mitochondriaExome sequencing dataRelated traitsSequencing dataMetabolic traitsTraitsCommon variantsLociRare variantsSequencingDNAFinnish individualsMendelian randomization frameworkUK BiobankMetS traitsGenome
2019
Assessment of tumor mutation burden calculation from gene panel sequencing data
Xu Z, Dai J, Wang D, Lu H, Dai H, Ye H, Gu J, Chen S, Huang B. Assessment of tumor mutation burden calculation from gene panel sequencing data. OncoTargets And Therapy 2019, 12: 3401-3409. PMID: 31123404, PMCID: PMC6510391, DOI: 10.2147/ott.s196638.Peer-Reviewed Original ResearchTumor mutation burdenNon-small cell lung cancerHigh tumor mutation burdenImmune checkpoint blockadeCell lung cancerCancer Genome AtlasCheckpoint blockadeLung cancerClinical trialsSelection biomarkerMutation burdenCancer typesWhole-exome sequencing dataGenome AtlasPanel sequencing dataTargeted sequencingClinical applicationExome sequencing dataBurden calculationsWhole-genome sequencingMutation levelsSomatic mutation data
2018
Whole Exome Sequencing Reveals a Monogenic Cause of Disease in ≈43% of 35 Families With Midaortic Syndrome
Warejko JK, Schueler M, Vivante A, Tan W, Daga A, Lawson JA, Braun DA, Shril S, Amann K, Somers MJG, Rodig NM, Baum MA, Daouk G, Traum AZ, Kim HB, Vakili K, Porras D, Lock J, Rivkin MJ, Chaudry G, Smoot LB, Singh MN, Smith ER, Mane SM, Lifton RP, Stein DR, Ferguson MA, Hildebrandt F. Whole Exome Sequencing Reveals a Monogenic Cause of Disease in ≈43% of 35 Families With Midaortic Syndrome. Hypertension 2018, 71: 691-699. PMID: 29483232, PMCID: PMC5843550, DOI: 10.1161/hypertensionaha.117.10296.Peer-Reviewed Original ResearchConceptsMidaortic syndromeWhole-exome sequencingExome sequencingVascular diseaseMonogenic causesExtensive vascular diseaseSevere childhood hypertensionGenotype/phenotype correlationChildhood hypertensionRare causeEtiologic diagnosisInflammatory diseasesAbdominal aortaMolecular genetic diagnosisGenetic syndromesSyndromic diseaseWhole-exome sequencing dataDiseaseSyndromePhenotype correlationGenetic diagnosisExome sequencing dataDiagnosisCauseHigh percentageA noncoding variant in GANAB explains isolated polycystic liver disease (PCLD) in a large family
Besse W, Choi J, Ahram D, Mane S, Sanna‐Cherchi S, Torres V, Somlo S. A noncoding variant in GANAB explains isolated polycystic liver disease (PCLD) in a large family. Human Mutation 2018, 39: 378-382. PMID: 29243290, PMCID: PMC5805583, DOI: 10.1002/humu.23383.Peer-Reviewed Original ResearchConceptsLoss-of-function variantsSequence analysis pipelineWhole-exome sequencing analysisExome sequencing dataExome sequencing analysisBase pair deletionSkipping of exonIsolated polycystic liver diseaseNoncoding variantsLinkage analysisDisease genesSequence dataGene discoveryMinigene assayLinkage disequilibriumCoding regionSNP genotypingSequence analysisGenomic evaluationPolycystic liver diseaseSplice donorIdentified mutationsMutation detectionPair deletionGANAB
2017
Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders
Nguyen H, Bryois J, Kim A, Dobbyn A, Huckins L, Munoz-Manchado A, Ruderfer D, Genovese G, Fromer M, Xu X, Pinto D, Linnarsson S, Verhage M, Smit A, Hjerling-Leffler J, Buxbaum J, Hultman C, Sklar P, Purcell S, Lage K, He X, Sullivan P, Stahl E. Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders. Genome Medicine 2017, 9: 114. PMID: 29262854, PMCID: PMC5738153, DOI: 10.1186/s13073-017-0497-y.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsDD risk genesRisk genesRisk-geneGene set enrichment resultsProtein-protein interaction subnetworksStudy of rare variationWhole-exome sequencing dataNeurodevelopmental disorder genesPost-transcriptional gene regulationExome sequencing dataSets of genesRare exonic variantsGene set enrichmentRare variationNeurodevelopmental disordersAutism spectrum disorderGene subnetworksGenetic architectureSequence dataRNA-seqTrio familiesGene regulationExonic variantsPathway enrichmentRare‐variant association tests in longitudinal studies, with an application to the Multi‐Ethnic Study of Atherosclerosis (MESA)
He Z, Lee S, Zhang M, Smith J, Guo X, Palmas W, Kardia S, Ionita‐Laza I, Mukherjee B. Rare‐variant association tests in longitudinal studies, with an application to the Multi‐Ethnic Study of Atherosclerosis (MESA). Genetic Epidemiology 2017, 41: 801-810. PMID: 29076270, PMCID: PMC5696115, DOI: 10.1002/gepi.22081.Peer-Reviewed Original ResearchConceptsMulti-Ethnic Study of AtherosclerosisMulti-Ethnic StudyStudy of atherosclerosisType I error rateRare-variant association testsRare variantsGene-based association testsRare-variant associationsAssociation TestLongitudinal outcomesLongitudinal studyExome sequencing dataMeasurement of blood pressureGenomic regionsSequence dataTrait heritabilitySequencing studiesMeasured outcomesGenetic variantsVariant analysisModerate sample sizesIndividual variantsRobust to misspecificationWithin-subject correlationStatistical powerLandscape and variation of novel retroduplications in 26 human populations
Zhang Y, Li S, Abyzov A, Gerstein MB. Landscape and variation of novel retroduplications in 26 human populations. PLOS Computational Biology 2017, 13: e1005567. PMID: 28662076, PMCID: PMC5510864, DOI: 10.1371/journal.pcbi.1005567.Peer-Reviewed Original ResearchConceptsParent genesSequencing dataHigh-coverage exomesLow-coverage whole-genome sequencing dataHuman populationWhole-genome sequencing dataExon-exon junctionsGenomes Phase 3Young L1 elementsPaired-end readsPotential disease associationsRetrotranspositional activityGenomic elementsNucleosome positioningPhylogenetic treeRetroduplicationExome sequencing dataReference genomeGenomic featuresInsertion eventsL1 elementsComprehensive discoveryPopulation markersSNP callingFunctional regionsATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism
Desai R, Frazier A, Durigon R, Patel H, Jones A, Rosa I, Lake N, Compton A, Mountford H, Tucker E, Mitchell A, Jackson D, Sesay A, Di Re M, van den Heuvel L, Burke D, Francis D, Lunke S, McGillivray G, Mandelstam S, Mochel F, Keren B, Jardel C, Turner A, Andrews P, Smeitink J, Spelbrink J, Heales S, Kohda M, Ohtake A, Murayama K, Okazaki Y, Lombès A, Holt I, Thorburn D, Spinazzola A. ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism. Brain 2017, 140: 1595-1610. PMID: 28549128, PMCID: PMC5445257, DOI: 10.1093/brain/awx094.Peer-Reviewed Original ResearchConceptsATAD3A geneHigh-throughput sequencing technologyIntegration of mitochondriaMitochondrial DNA organizationCholesterol homeostasisCellular cholesterol homeostasisSingle nucleotide polymorphism arrayMitochondrial DNA abnormalitiesNiemann-Pick type C diseaseNucleotide polymorphism arrayWhole-exome sequencing dataDNA organizationExome sequencing dataMitochondrial DNACausal genesCholesterol metabolismGenomic analysisGenomic rearrangementsSequencing technologiesHigh homologySequencing dataType C diseaseDrug-induced perturbationsGene cluster deletionsGenes
2016
Discovery of the First Pathogenic Human EPO Mutation Provides Mechanistic Insight into Cytokine Signaling
Kim A, Ulirsch J, Wilmes S, Unal E, Moraga I, Karakukcu M, Yuan D, Kazerounian S, Gupta N, Gabriel S, Lander E, Patiroglu T, Ozcan A, Ozdemir M, Garcia C, Piehler J, Gazda H, Klein D, Sankaran V. Discovery of the First Pathogenic Human EPO Mutation Provides Mechanistic Insight into Cytokine Signaling. Blood 2016, 128: 331. DOI: 10.1182/blood.v128.22.331.331.Peer-Reviewed Original ResearchDiamond-Blackfan anemiaWhole-exome sequencing dataEPO receptorPotent concentrationAllogeneic bone marrow transplantBone marrow transplantBone marrow failure disordersYears of ageIntracellular flow cytometryMarrow failure disordersSerum EPO levelsExome sequencing dataMajority of casesAnemia correctionHost diseaseSevere graftDonor chimerismRed blood cellsMarrow transplantResultant complicationsLow doseRare caseSide effectsPatientsBone marrowPatterns of genic intolerance of rare copy number variation in 59,898 human exomes
Ruderfer DM, Hamamsy T, Lek M, Karczewski KJ, Kavanagh D, Samocha KE, Daly M, MacArthur D, Fromer M, Purcell S. Patterns of genic intolerance of rare copy number variation in 59,898 human exomes. Nature Genetics 2016, 48: 1107-1111. PMID: 27533299, PMCID: PMC5042837, DOI: 10.1038/ng.3638.Peer-Reviewed Original ResearchConceptsGenic copy number variantsHuman genetic variationExome Aggregation ConsortiumRare copy number variationsCopy number variationsCopy number variantsExome sequencing dataGenetic variationGenic intoleranceHuman exomeSequencing dataPersonal genomesNumber variationsNumber variantsGenomeIntegrated databaseExomeVariationVariantsConsortiumConstitutive mismatch repair defect syndrome: New insights from whole exome sequencing data and functional studies
Caglayan A, Omay Z, Koksal Y, Coskun S, Unal E, Per H, Bilguvar K, Yasuno K, Ostergaard J, Gunel M. Constitutive mismatch repair defect syndrome: New insights from whole exome sequencing data and functional studies. Journal Of Biotechnology 2016, 231: s12. DOI: 10.1016/j.jbiotec.2016.05.067.Peer-Reviewed Original Research
2015
Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci
Sanders SJ, He X, Willsey AJ, Ercan-Sencicek AG, Samocha KE, Cicek AE, Murtha MT, Bal VH, Bishop SL, Dong S, Goldberg AP, Jinlu C, Keaney JF, Klei L, Mandell JD, Moreno-De-Luca D, Poultney CS, Robinson EB, Smith L, Solli-Nowlan T, Su MY, Teran NA, Walker MF, Werling DM, Beaudet AL, Cantor RM, Fombonne E, Geschwind DH, Grice DE, Lord C, Lowe JK, Mane SM, Martin DM, Morrow EM, Talkowski ME, Sutcliffe JS, Walsh CA, Yu TW, Consortium A, Ledbetter DH, Martin CL, Cook EH, Buxbaum JD, Daly MJ, Devlin B, Roeder K, State MW. Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci. Neuron 2015, 87: 1215-1233. PMID: 26402605, PMCID: PMC4624267, DOI: 10.1016/j.neuron.2015.09.016.Peer-Reviewed Original ResearchConceptsAutism Genome ProjectAutism Sequencing ConsortiumRisk lociRisk genesSimons Simplex CollectionASD risk lociDe novo CNVsGenomic architectureSequencing ConsortiumExome sequencing dataDe novo deletionsCNV regionsDe novo mutationsGenome ProjectSequencing dataNovo deletionGenesCNV dataLociNovo mutationsDeletionAssociation TestBiologyMutationsStrong evidence
2013
The Role and Challenges of Exome Sequencing in Studies of Human Diseases
Wang Z, Liu X, Yang BZ, Gelernter J. The Role and Challenges of Exome Sequencing in Studies of Human Diseases. Frontiers In Genetics 2013, 4: 160. PMID: 24032039, PMCID: PMC3752524, DOI: 10.3389/fgene.2013.00160.Peer-Reviewed Original ResearchHuman diseasesSequencing dataExome sequencingGenetic studiesProtein-coding portionNext-generation sequencing technologiesLow-frequency variantsComplex traitsExome sequencing dataHuman genomeSequencing technologiesExonic regionsTarget enrichmentFrequency variantsMendelian disordersSequencingTargeted sequencingVariant callsTarget regionRare variantsGenotype concordanceVariantsGenomeRecent advancesOverall consistency rate
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