2024
Evaluation of imputation performance of multiple reference panels in a Pakistani population
Xu J, Liu D, Hassan A, Genovese G, Cote A, Fennessy B, Cheng E, Charney A, Knowles J, Ayub M, Peterson R, Bigdeli T, Huckins L. Evaluation of imputation performance of multiple reference panels in a Pakistani population. Human Genetics And Genomics Advances 2024, 6: 100395. PMID: 39696820, PMCID: PMC11759560, DOI: 10.1016/j.xhgg.2024.100395.Peer-Reviewed Original ResearchGenome-wide association studiesReference panelImputation accuracyMultiple reference panelsPakistani individualsGenotype imputationAssociation studiesGenotype dataAncestry compositionEuropean individualsSample sizeTOPMedDiverse populationsPakistani populationImputationGenomeAncestryIndividualsGenotypesPopulationVariantsFuture panels
2022
Nyssorhynchus darlingi genome-wide studies related to microgeographic dispersion and blood-seeking behavior
Alvarez M, Alonso D, Kadri S, Rufalco-Moutinho P, Bernardes I, de Mello A, Souto A, Carrasco-Escobar G, Moreno M, Gamboa D, Vinetz J, Conn J, Ribolla P. Nyssorhynchus darlingi genome-wide studies related to microgeographic dispersion and blood-seeking behavior. Parasites & Vectors 2022, 15: 106. PMID: 35346342, PMCID: PMC8961893, DOI: 10.1186/s13071-022-05219-5.Peer-Reviewed Original ResearchConceptsGenome-wide association studiesSingle nucleotide polymorphism (SNP) markersGenome-wide studiesLow-coverage whole-genome sequencingGenomic sequencing dataMajor malaria vectorCircadian rhythm genesFemale timingPopulation stratification analysisWhole-genome sequencingMicrogeographic scaleSNP markersPolymorphism markersPopulation structureSequencing dataAssociation studiesInsecticide resistanceDusk/dawnRhythm genesGenotype imputationGenesFemale mosquitoesMalaria vectorsBlood mealGenetic association
2021
Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation
Kim M, Harmanci A, Bossuat J, Carpov S, Cheon J, Chillotti I, Cho W, Froelicher D, Gama N, Georgieva M, Hong S, Hubaux J, Kim D, Lauter K, Ma Y, Ohno-Machado L, Sofia H, Son Y, Song Y, Troncoso-Pastoriza J, Jiang X. Ultrafast homomorphic encryption models enable secure outsourcing of genotype imputation. Cell Systems 2021, 12: 1108-1120.e4. PMID: 34464590, PMCID: PMC9898842, DOI: 10.1016/j.cels.2021.07.010.Peer-Reviewed Original ResearchConceptsHomomorphic encryption techniqueResource-intensive computationsSecure outsourcingGenomic data analysisData securityEncryption modelEncryption techniquePrivacy concernsSource codeMemory requirementsGenetic data analysisData analysisComparable accuracyFundamental stepGenotype imputationImputationDownloadSecurityOutsourcingComputationCodeServicesRequirementsAccuracyMethodPrivacy-preserving genotype imputation in a trusted execution environment
Dokmai N, Kockan C, Zhu K, Wang X, Sahinalp S, Cho H. Privacy-preserving genotype imputation in a trusted execution environment. Cell Systems 2021, 12: 983-993.e7. PMID: 34450045, PMCID: PMC8542641, DOI: 10.1016/j.cels.2021.08.001.Peer-Reviewed Original ResearchConceptsTrusted Execution EnvironmentExecution environmentHardware-based solutionsSide-channel attacksIntel SGXEnhanced securityPrivacy concernsAnalysis servicesImputation ServerServer limitData resourcesImputation algorithmSGXServerImputation softwareGenomic data resourcesImputation accuracyGenotype imputationImputation strategiesServicesDownstream analysisScalabilityImputationEssential toolSecurityThe genetic structure of the Turkish population reveals high levels of variation and admixture
Kars ME, Başak AN, Onat OE, Bilguvar K, Choi J, Itan Y, Çağlar C, Palvadeau R, Casanova JL, Cooper DN, Stenson PD, Yavuz A, Buluş H, Günel M, Friedman JM, Özçelik T. The genetic structure of the Turkish population reveals high levels of variation and admixture. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2026076118. PMID: 34426522, PMCID: PMC8433500, DOI: 10.1073/pnas.2026076118.Peer-Reviewed Original ResearchConceptsGenetic structureTR populationGenome-wide association studiesRuns of homozygosityGenomes Project populationsHigh inbreeding coefficientsDisease gene discoveryHigh-quality haplotypesPotential medical relevanceGene discoveryExtensive admixturePhenotypic consequencesWhole genomeGenetic basisInbreeding coefficientSpecific genesRare rangeGenome variantsAssociation studiesGenetic relationshipsFunctional consequencesWhole exomeSpecific phenotypesGenotype imputationMedical relevance
2016
A Genome-Wide Association Study to Identify Single-Nucleotide Polymorphisms for Acute Kidney Injury
Zhao B, Lu Q, Cheng Y, Belcher JM, Siew ED, Leaf DE, Body SC, Fox AA, Waikar SS, Collard CD, Thiessen-Philbrook H, Ikizler TA, Ware LB, Edelstein CL, Garg AX, Choi M, Schaub JA, Zhao H, Lifton RP, Parikh CR. A Genome-Wide Association Study to Identify Single-Nucleotide Polymorphisms for Acute Kidney Injury. American Journal Of Respiratory And Critical Care Medicine 2016, 195: 482-490. PMID: 27576016, PMCID: PMC5378420, DOI: 10.1164/rccm.201603-0518oc.Peer-Reviewed Original ResearchMeSH KeywordsAcute Kidney InjuryAdultAgedApolipoprotein L1ApolipoproteinsBiomarkersCardiac Surgical ProceduresCase-Control StudiesCritical IllnessFemaleGenetic Predisposition to DiseaseGenome-Wide Association StudyGenotypeHumansIntensive Care UnitsInterferon Regulatory Factor-2Lipoproteins, HDLMaleMiddle AgedPolymorphism, Single NucleotidePostoperative ComplicationsRisk FactorsStatistics, NonparametricT-Box Domain ProteinsConceptsAcute kidney injuryGenome-wide association studiesSingle nucleotide polymorphismsKidney injuryGenetic lociAssociation studiesExploratory genome-wide association studyAcute kidney injury casesHospital acute kidney injuryCommon genetic variantsIndependent lociGene TBX1Chromosome 4Novel pathwayCritical illnessCardiac surgerySevere complicationsLociPatient populationTherapeutic advancesGenetic variantsGenotype imputationInjury casesExpedite recoveryInjuryFine-Scale Mapping at 9p22.2 Identifies Candidate Causal Variants That Modify Ovarian Cancer Risk in BRCA1 and BRCA2 Mutation Carriers
Vigorito E, Kuchenbaecker K, Beesley J, Adlard J, Agnarsson B, Andrulis I, Arun B, Barjhoux L, Belotti M, Benitez J, Berger A, Bojesen A, Bonanni B, Brewer C, Caldes T, Caligo M, Campbell I, Chan S, Claes K, Cohn D, Cook J, Daly M, Damiola F, Davidson R, de Pauw A, Delnatte C, Diez O, Domchek S, Dumont M, Durda K, Dworniczak B, Easton D, Eccles D, Ardnor C, Eeles R, Ejlertsen B, Ellis S, Evans D, Feliubadalo L, Fostira F, Foulkes W, Friedman E, Frost D, Gaddam P, Ganz P, Garber J, Garcia-Barberan V, Gauthier-Villars M, Gehrig A, Gerdes A, Giraud S, Godwin A, Goldgar D, Hake C, Hansen T, Healey S, Hodgson S, Hogervorst F, Houdayer C, Hulick P, Imyanitov E, Isaacs C, Izatt L, Izquierdo A, Jacobs L, Jakubowska A, Janavicius R, Jaworska-Bieniek K, Jensen U, John E, Vijai J, Karlan B, Kast K, Khan S, Kwong A, Laitman Y, Lester J, Lesueur F, Liljegren A, Lubinski J, L. P, Manoukian S, Mazoyer S, Meindl A, Mensenkamp A, Montagna M, Nathanson K, Neuhausen S, Nevanlinna H, Niederacher D, Olah E, Olopade O, Ong K, Osorio A, Park S, Paulsson-Karlsson Y, Pedersen I, Peissel B, Peterlongo P, Pfeiler G, Phelan C, Piedmonte M, Poppe B, Pujana M, Radice P, Rennert G, Rodriguez G, Rookus M, Ross E, Schmutzler R, Simard J, Singer C, Slavin T, Soucy P, Southey M, Steinemann D, Stoppa-Lyonnet D, Sukiennicki G, Sutter C, Szabo C, Tea M, Teixeira M, Teo S, Terry M, Thomassen M, Tibiletti M, Tihomirova L, Tognazzo S, van Rensburg E, Varesco L, Varon-Mateeva R, Vratimos A, Weitzel J, McGuffog L, Kirk J, Toland A, Hamann U, Lindor N, Ramus S, Greene M, Couch F, Offit K, Pharoah P, Chenevix-Trench G, Antoniou A. Fine-Scale Mapping at 9p22.2 Identifies Candidate Causal Variants That Modify Ovarian Cancer Risk in BRCA1 and BRCA2 Mutation Carriers. PLOS ONE 2016, 11: e0158801. PMID: 27463617, PMCID: PMC4963094, DOI: 10.1371/journal.pone.0158801.Peer-Reviewed Original ResearchConceptsOvarian cancer riskBRCA2 mutation carriersModify ovarian cancer riskBRCA1 mutation carriersCancer riskOvarian cancer associationMutation carriersCausal variantsFine-scale mappingGeneral populationBRCA-2 mutation carriersCancer associationCancer risk modificationGenome wide association studiesPotential causal variantsTranscription start siteCorrelated SNPsGenotype imputationRisk modificationStart siteAssociation studiesGenotype dataBRCA1BRCA2BNC2
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