2024
A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children
de Smith A, Wahlster L, Jeon S, Kachuri L, Black S, Langie J, Cato L, Nakatsuka N, Chan T, Xia G, Mazumder S, Yang W, Gazal S, Eng C, Hu D, Burchard E, Ziv E, Metayer C, Mancuso N, Yang J, Ma X, Wiemels J, Yu F, Chiang C, Sankaran V. A noncoding regulatory variant in IKZF1 increases acute lymphoblastic leukemia risk in Hispanic/Latino children. Cell Genomics 2024, 4: 100526. PMID: 38537633, PMCID: PMC11019360, DOI: 10.1016/j.xgen.2024.100526.Peer-Reviewed Original ResearchHispanic/Latino childrenNon-Hispanic white individualsHigher risk of acute lymphoblastic leukemiaRisk of acute lymphoblastic leukemiaNoncoding regulatory variantsFine-mapping analysisAcute lymphoblastic leukemia riskAcute lymphoblastic leukemiaEvidence of selectionIndigenous American ancestryReduced enhancer activityRisk allele frequenciesIncreased ALL riskRegulatory variantsHispanic/Latino individualsPro-B CellsHispanic/Latino populationRacial/ethnic groupsDownstream enhancerGenetic basisLeukemia riskWhite individualsAllele frequenciesAmerican ancestryALL risk
2018
Genome-wide Association Study Identifies a Regulatory Variant of RGMA Associated With Opioid Dependence in European Americans
Cheng Z, Zhou H, Sherva R, Farrer LA, Kranzler HR, Gelernter J. Genome-wide Association Study Identifies a Regulatory Variant of RGMA Associated With Opioid Dependence in European Americans. Biological Psychiatry 2018, 84: 762-770. PMID: 29478698, PMCID: PMC6041180, DOI: 10.1016/j.biopsych.2017.12.016.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesAssociation studiesHomologous mouse geneMouse geneAxon guidance proteinRegulatory variantsCoexpression analysisOpioid dependenceTranscript variantsGenetic studiesChromosome 15Guidance proteinsRNA expressionNominal significanceMessenger RNA expressionGenesRepulsive guidance molecule AHigh expressionRGMaRisk allelesChronic morphine injectionDSM-IV diagnosisExpressionNew leadsMorphine injection
2017
Mapping regulatory variants in hiPSC models
Hoffman GE, Brennand KJ. Mapping regulatory variants in hiPSC models. Nature Genetics 2017, 50: 1-2. PMID: 29273803, DOI: 10.1038/s41588-017-0017-4.Peer-Reviewed Original ResearchA sequence-based method to predict the impact of regulatory variants using random forest
Liu Q, Gan M, Jiang R. A sequence-based method to predict the impact of regulatory variants using random forest. BMC Systems Biology 2017, 11: 7. PMID: 28361702, PMCID: PMC5374684, DOI: 10.1186/s12918-017-0389-1.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsGenome-wide association studiesK-mer featuresK-mersGenome sequenceChromatin regionsDNA sequencesGenetic variantsImpact of regulatory variantsRandom genomic sequencesSequence conservation featuresIdentification of genetic risk factorsDisease-Associated VariantsSequence-based methodsK-mer countingImpact of single nucleotide polymorphismsBreast cancer cell linesRegulatory variantsGenetic risk factorsNoncoding regionsComplex traitsAssociation studiesRegulatory elementsCancer cell linesPermutation experiments
2014
Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes
Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL. Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes. Science 2014, 344: 519-523. PMID: 24786080, PMCID: PMC4910825, DOI: 10.1126/science.1249547.Peer-Reviewed Original ResearchMeSH KeywordsAdaptive ImmunityAllelesAlzheimer DiseaseAutoimmune DiseasesAutoimmunityCD4-Positive T-LymphocytesEthnicityGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansImmunity, InnateMonocytesMultiple SclerosisNeurodegenerative DiseasesParkinson DiseasePolymorphism, Single NucleotideQuantitative Trait LociRheumatic FeverTranscriptomeConceptsSpecific immune cell typesHuman immune functionImmune cell typesMulti-ethnic cohortCell-autonomous effectsAutoimmune diseasesT cellsImmune functionParkinson's diseaseHealthy individualsInnate immunityRisk allelesDiseaseExpression quantitative trait loci (eQTL) studiesQuantitative trait loci studiesSusceptibility allelesPutative functional assignmentsCausal regulatory variantsDisease-associated lociDisease susceptibility variantsCell typesSusceptibility variantsTrans-eQTLsFunctional assignmentRegulatory variants
2009
A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells
Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM. A Robust Approach to Identifying Tissue-Specific Gene Expression Regulatory Variants Using Personalized Human Induced Pluripotent Stem Cells. PLOS Genetics 2009, 5: e1000718. PMID: 19911041, PMCID: PMC2766639, DOI: 10.1371/journal.pgen.1000718.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCell DifferentiationCell LineCells, CulturedCluster AnalysisComputational BiologyDNA, ComplementaryFlow CytometryGene Expression RegulationHuman Genome ProjectHumansInduced Pluripotent Stem CellsNucleic Acid Amplification TechniquesOrgan SpecificityRegulatory Elements, TranscriptionalReproducibility of ResultsConceptsCis-regulatory variantsPluripotent stem cellsRegulatory polymorphismsGene expressionAllele-specific gene expressionIPS cellsPrimary fibroblastsCell typesAllele-specific expressionHigh-throughput sequencingStem cellsHuman iPS cellsSkin primary fibroblastsRegulatory variantsTissue-specific variantsX chromosomeDifferentiated derivativesExpression locusCell differentiationSpecific tissuesLymphoblastoid cellsDigital-RNAPadlock probesExpressionCells
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