2022
New Insight into the human genetic diversity in North African populations by genotyping of SNPs in DRD3, CSMD1 and NRG1 genes
Mestiri S, Boussetta S, Pakstis AJ, Kamel S, Gaaied A, Kidd KK, Cherni L. New Insight into the human genetic diversity in North African populations by genotyping of SNPs in DRD3, CSMD1 and NRG1 genes. Molecular Genetics & Genomic Medicine 2022, 10: e1871. PMID: 35128830, PMCID: PMC8922960, DOI: 10.1002/mgg3.1871.Peer-Reviewed Original ResearchConceptsNorth African populationsSingle nucleotide polymorphismsGenetic diversityGenetic variabilitySignificant gene flowHuman genetic diversityLowest average heterozygosityAfrican populationsGene flowEvolutionary forcesGenetic structureAverage heterozygosityAdmixed AmericansChromosome 3NRG1 geneChromosome 8Genetic relationshipsGenesDomain 1Nucleotide polymorphismsSushi multiple domains 1CSMD1 geneHaplotypic analysisWorldwide populationNew insights
2021
STAT3 polymorphisms in North Africa and its implication in breast cancer
Ziadi W, Boussetta S, Elkamel S, Pakstis AJ, Kidd KK, Medimegh I, Elgaaied A, Cherni L. STAT3 polymorphisms in North Africa and its implication in breast cancer. Molecular Genetics & Genomic Medicine 2021, 9: e1744. PMID: 34251094, PMCID: PMC8404238, DOI: 10.1002/mgg3.1744.Peer-Reviewed Original ResearchConceptsNorth African populationsAfrican populationsSTAT3 regionSingle nucleotide polymorphismsRare haplotypesHsa-mirMiR databaseMajor haplotypesGenesNucleotide polymorphismsHaplotypesSNPsSTAT3Allele frequenciesRs7211777Tunisian populationPolymorphismPopulationDiversityNorth AfricaAllelesSignificant frequencyRecombinationAssaysCancerA Distinctive Pattern of Diversity for the TAS2R38 Gene in North Africa
Mourali-Chebil S, Elkamel S, Boussetta S, Pakstis A, Kidd K, Benammar-Elgaaied A, Cherni L. A Distinctive Pattern of Diversity for the TAS2R38 Gene in North Africa. Human Biology 2021, 93: 163-177. PMID: 37733614, DOI: 10.1353/hub.2021.0009.Peer-Reviewed Original ResearchGenetic diversity of the North African population revealed by the typing of SNPs in the DRD2/ANKK1 genomic region
Mestiri S, Boussetta S, Pakstis AJ, Elkamel S, Elgaaied ABA, Kidd KK, Cherni L. Genetic diversity of the North African population revealed by the typing of SNPs in the DRD2/ANKK1 genomic region. Gene 2021, 777: 145466. PMID: 33524518, DOI: 10.1016/j.gene.2021.145466.Peer-Reviewed Original ResearchMeSH KeywordsAdultAfrica, NorthernAllelesBlack PeopleEthnicityFemaleGene FrequencyGenetic Predisposition to DiseaseGenetic VariationGenomicsGenotypeGenotyping TechniquesHaplotypesHeterozygoteHuman MigrationHumansLinkage DisequilibriumMaleMiddle AgedPolymorphism, Single NucleotideProtein Serine-Threonine KinasesReceptors, Dopamine D2ConceptsNorth African populationsGenetic diversitySingle nucleotide polymorphismsGenetic structureAncestral gene poolPeculiar genetic structureLowest average heterozygosityNorth African onesAfrican populationsHigh linkage disequilibriumGenetic driftGenomic regionsAverage heterozygosityGene poolSame locusLinkage disequilibriumDisequilibrium analysisGenetic componentGenesNucleotide polymorphismsLociReceptor geneDiversityHuman populationEuropean populations
2020
The distinctive geographic patterns of common pigmentation variants at the OCA2 gene
Kidd KK, Pakstis AJ, Donnelly MP, Bulbul O, Cherni L, Gurkan C, Kang L, Li H, Yun L, Paschou P, Meiklejohn KA, Haigh E, Speed WC. The distinctive geographic patterns of common pigmentation variants at the OCA2 gene. Scientific Reports 2020, 10: 15433. PMID: 32963319, PMCID: PMC7508881, DOI: 10.1038/s41598-020-72262-6.Peer-Reviewed Original ResearchConceptsOculocutaneous albinism type 2Genetic variationOCA2 genePopulation genetic variationGeographic patternsNormal pigmentation variationPigmentation variationSingle nucleotide polymorphismsPositive selectionHypomorphic proteinEnhancer variantsPigmentation variantsGenesNucleotide polymorphismsDistinctive geographic patternsEye colorStrong selection effectsVariant frequencyPigmentationVariantsProteinAllelesVariationDifferent patternsPolymorphism
2016
Proposed nomenclature for microhaplotypes
Kidd KK. Proposed nomenclature for microhaplotypes. Human Genomics 2016, 10: 16. PMID: 27316555, PMCID: PMC4912715, DOI: 10.1186/s40246-016-0078-y.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsHUGO Gene Nomenclature CommitteeGene Nomenclature CommitteeGroup of genesGene familyPopulation geneticsChromosome numberChromosome 1Related genesGenetic markersNucleotide polymorphismsNomenclature CommitteeGenesMicrohaplotypesRootsChromosomesFamilyLociUnique characterStandardized nomenclatureGeneticsNomenclatureSequencePolymorphism
2014
Maritime route of colonization of Europe
Paschou P, Drineas P, Yannaki E, Razou A, Kanaki K, Tsetsos F, Padmanabhuni SS, Michalodimitrakis M, Renda MC, Pavlovic S, Anagnostopoulos A, Stamatoyannopoulos JA, Kidd KK, Stamatoyannopoulos G. Maritime route of colonization of Europe. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 9211-9216. PMID: 24927591, PMCID: PMC4078858, DOI: 10.1073/pnas.1320811111.Peer-Reviewed Original ResearchConceptsSouthern European coastsGene flowGenome-wide DNA polymorphismsEuropean coastsWest clineDNA polymorphismsNeolithic farmersCoastal routeMediterranean SeaNetwork analysisMediterranean coastMainland EuropeNeolithic populationsCentral EuropeClineCoastGenesColonizationNear EastStriking structurePolymorphismPopulationAnatoliaHypothesisIslandsA Form of the Metabolic Syndrome Associated with Mutations in DYRK1B
Keramati AR, Fathzadeh M, Go GW, Singh R, Choi M, Faramarzi S, Mane S, Kasaei M, Sarajzadeh-Fard K, Hwa J, Kidd KK, Babaee Bigi MA, Malekzadeh R, Hosseinian A, Babaei M, Lifton RP, Mani A. A Form of the Metabolic Syndrome Associated with Mutations in DYRK1B. New England Journal Of Medicine 2014, 370: 1909-1919. PMID: 24827035, PMCID: PMC4069260, DOI: 10.1056/nejmoa1301824.Peer-Reviewed Original ResearchConceptsKinase-like domainMapping susceptibility genesHistidine 90Disease-causing genesFunctional characterizationDisease genesDYRK1BKey gluconeogenic enzymesGenetic analysisCardiovascular risk traitsWhole-exome sequencingDistinct familiesLinkage analysisSecond mutationPosition 102Susceptibility genesFamily membersLarge familyGenesCausative mutationsUnaffected family membersMutationsFunction activityAffected family membersGluconeogenic enzymesExtensive sequence variation in the 3′ untranslated region of the KRAS gene in lung and ovarian cancer cases
Kim M, Chen X, Chin L, Paranjape T, Speed W, Kidd K, Zhao H, Weidhaas J, Slack FJ. Extensive sequence variation in the 3′ untranslated region of the KRAS gene in lung and ovarian cancer cases. Cell Cycle 2014, 13: 1030-1040. PMID: 24552817, PMCID: PMC3984301, DOI: 10.4161/cc.27941.Peer-Reviewed Original ResearchMeSH Keywords3' Untranslated RegionsCarcinoma, Non-Small-Cell LungCarcinoma, Ovarian EpithelialCase-Control StudiesFemaleHumansLung NeoplasmsMicroRNAsNeoplasms, Glandular and EpithelialOvarian NeoplasmsPolymorphism, Single NucleotideProto-Oncogene ProteinsProto-Oncogene Proteins p21(ras)Ras ProteinsConceptsMiRNA complementary sitesSequence variationComplementary sitesSingle nucleotide polymorphismsUntranslated regionRegulation of genesHigh-throughput sequencingExtensive sequence variationRegulation of KRASParticular single nucleotide polymorphismsOvarian cancer casesCapture enrichmentHuman diseasesSequence variantsImportant regulatorFunctional roleMiR-181Additional sequence variantsGenetic biomarkersCellular proliferationGenesNucleotide polymorphismsKRAS geneCancer casesUTR
2013
An historical perspective on “The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus”
Kidd KK, Pakstis AJ, Yun L. An historical perspective on “The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus”. Human Genetics 2013, 133: 431-433. PMID: 24162668, DOI: 10.1007/s00439-013-1386-0.Peer-Reviewed Original ResearchConceptsThousands of lociGene frequency patternsPatterns of divergenceRandom genetic driftHuman population geneticsLow-frequency allelesDopamine D4 receptor locusGenetic driftPopulation geneticsImportant genesPopulation variationWorld-wide distributionReceptor locusFrequency allelesDifferent allelesLociDistinct populationsNative American populationsEast Asian populationsAllelesAllele frequenciesSame populationAmerican populationGenesGenetics
2012
High diversity and no significant selection signal of human ADH1B gene in Tibet
Lu Y, Kang L, Hu K, Wang C, Sun X, Chen F, Kidd JR, Kidd KK, Li H. High diversity and no significant selection signal of human ADH1B gene in Tibet. Investigative Genetics 2012, 3: 23. PMID: 23176670, PMCID: PMC3528464, DOI: 10.1186/2041-2223-3-23.Peer-Reviewed Original ResearchSingle nucleotide polymorphismsSelection signalsPositive selectionSignificant positive selectionMicro-evolutionary studiesPositive selection signalsLong-range haplotypesSino-Tibetan populationsDiversification historyADH1B geneGene diversityHaplotype diversityCommon ancestorHuman genesHigh diversityTibetan populationHaplogroupsGenesPolymorphic sitesNucleotide polymorphismsSmall populationDiversityAncestorSouthwest AsiaAllelesGenome-wide association study of Tourette's syndrome
Scharf JM, Yu D, Mathews CA, Neale BM, Stewart SE, Fagerness JA, Evans P, Gamazon E, Edlund CK, Service SK, Tikhomirov A, Osiecki L, Illmann C, Pluzhnikov A, Konkashbaev A, Davis LK, Han B, Crane J, Moorjani P, Crenshaw AT, Parkin MA, Reus VI, Lowe TL, Rangel-Lugo M, Chouinard S, Dion Y, Girard S, Cath DC, Smit JH, King RA, Fernandez TV, Leckman JF, Kidd KK, Kidd JR, Pakstis AJ, State MW, Herrera LD, Romero R, Fournier E, Sandor P, Barr CL, Phan N, Gross-Tsur V, Benarroch F, Pollak Y, Budman CL, Bruun RD, Erenberg G, Naarden AL, Lee PC, Weiss N, Kremeyer B, Berrío GB, Campbell DD, Cardona Silgado JC, Ochoa WC, Mesa Restrepo SC, Muller H, Valencia Duarte AV, Lyon GJ, Leppert M, Morgan J, Weiss R, Grados MA, Anderson K, Davarya S, Singer H, Walkup J, Jankovic J, Tischfield JA, Heiman GA, Gilbert DL, Hoekstra PJ, Robertson MM, Kurlan R, Liu C, Gibbs JR, Singleton A, Hardy J, Strengman E, Ophoff R, Wagner M, Moessner R, Mirel D, Posthuma D, Sabatti C, Eskin E, Conti D, Knowles J, Ruiz-Linares A, Rouleau G, Purcell S, Heutink P, Oostra B, McMahon W, Freimer N, Cox N, Pauls D. Genome-wide association study of Tourette's syndrome. Molecular Psychiatry 2012, 18: 721-728. PMID: 22889924, PMCID: PMC3605224, DOI: 10.1038/mp.2012.69.Peer-Reviewed Original ResearchMeSH KeywordsAdolescentAdultAttention Deficit Disorder with HyperactivityCase-Control StudiesChromosomes, Human, Pair 9FemaleFibrillar CollagensGenetic Predisposition to DiseaseGenome-Wide Association StudyGenotypeHumansInternational CooperationMaleMeta-Analysis as TopicObsessive-Compulsive DisorderPolymorphism, Single NucleotideTourette SyndromeWhite PeopleYoung AdultConceptsGenome-wide association studiesFirst genome-wide association studyAssociation studiesTop signalsFull genetic architectureAncestry-matched controlsEuropean ancestry samplesGenetic architectureGWAS dataComplex inheritanceEuropean-derived populationsSusceptibility variantsSusceptibility genesEventual identificationEuropean ancestryCosta RicaChromosome 9q32Familial recurrence rateNorth AmericaComplete understandingAmerican populationCentral ValleyNeuropsychiatric diseasesDevelopmental disordersGenes
2011
Duplicated Gene Evolution of the Primate Alcohol Dehydrogenase Family
Oota H, Oota H, Kidd K. Duplicated Gene Evolution of the Primate Alcohol Dehydrogenase Family. Primatology Monographs 2011, 149-161. DOI: 10.1007/978-4-431-54011-3_9.Peer-Reviewed Original ResearchSequence similarityCopy number variationsSame speciesAmino acid sequence similarityNumber variationsADH gene familySouthern hybridization dataAlcohol dehydrogenase familyClass I genesGene evolutionGene familyGenome databaseGene conversionShares 60Old World monkeysMultiple duplicationsDehydrogenase familyEnzyme familyI geneHybridization dataHigh similarityGenesBiochemical propertiesWorld monkeysAlcohol dehydrogenase enzymeDiversification of the ADH1B Gene during Expansion of Modern Humans
Li H, Gu S, Han Y, Xu Z, Pakstis AJ, Jin L, Kidd JR, Kidd KK. Diversification of the ADH1B Gene during Expansion of Modern Humans. Annals Of Human Genetics 2011, 75: 497-507. PMID: 21592108, PMCID: PMC3722864, DOI: 10.1111/j.1469-1809.2011.00651.x.Peer-Reviewed Original ResearchConceptsShort tandem repeat polymorphismsSingle nucleotide polymorphismsGeographic patternsAncient DNA samplesADH1B geneSelective forcesRegulatory region variantsUnusual geographic distributionMigration eventsCommon haplogroupsDistinct geographic patternsGeographic distributionGenesNucleotide polymorphismsEast Asian populationsTandem repeat polymorphismDNA samplesHaplogroupsWorldwide setAllelesModern humansRegion variantsRepeat polymorphismPolymorphismEast AsiaAn Application of the Elastic Net for an Endophenotype Analysis
Palejev D, Hwang W, Landi N, Eastman M, Frost SJ, Fulbright RK, Kidd JR, Kidd KK, Mason GF, Mencl WE, Yrigollen C, Pugh KR, Grigorenko EL. An Application of the Elastic Net for an Endophenotype Analysis. Behavior Genetics 2011, 41: 120-124. PMID: 21229297, PMCID: PMC3613288, DOI: 10.1007/s10519-011-9443-8.Peer-Reviewed Original Research
2010
Using a Pharmacokinetic Model to Relate an Individual’s Susceptibility to Alcohol Dependence to Genotypes
Mustavich LF, Miller P, Kidd KK, Zhao H. Using a Pharmacokinetic Model to Relate an Individual’s Susceptibility to Alcohol Dependence to Genotypes. Human Heredity 2010, 70: 177-193. PMID: 20714161, PMCID: PMC3164201, DOI: 10.1159/000317056.Peer-Reviewed Original ResearchConceptsMolecular levelStatistical gene-gene interactionsTissues of individualsGenetic variationGene-gene interactionsMolecular mechanismsGenesParticular genotypeHaplotype frequenciesPopulation levelGenotype effectsDisease riskIndividual susceptibilityMechanistic modelGenotypesADH7SusceptibilityCommon diseaseMechanistic modelingInteractionADH1CALDH2ADH1BStatistical interactionTAS2R38
2008
Global patterns of variation in allele and haplotype frequencies and linkage disequilibrium across the CYP2E1 gene
Lee M, Mukherjee N, Pakstis A, Khaliq S, Mohyuddin A, Mehdi S, Speed W, Kidd J, Kidd K. Global patterns of variation in allele and haplotype frequencies and linkage disequilibrium across the CYP2E1 gene. The Pharmacogenomics Journal 2008, 8: 349-356. PMID: 18663376, PMCID: PMC2782390, DOI: 10.1038/tpj.2008.9.Peer-Reviewed Original ResearchConceptsGenetic variationGene expressionAssociation studiesFamily of enzymesDifferent human populationsHaplotype variationHuman population samplesMajor geographical regionsTandem repeatsPolymorphism haplotypesGenesMultiple populationsHaplotypesSusceptibility mutationsGlobal patternsHuman populationAdditional polymorphismsHaplotype frequenciesCentral roleDifferent populationsDiverse patternsEndogenous compoundsDisequilibriumLD dataPolymorphismThe complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase
Mukherjee N, Kidd K, Pakstis A, Speed W, Li H, Tarnok Z, Barta C, Kajuna S, Kidd J. The complex global pattern of genetic variation and linkage disequilibrium at catechol-O-methyltransferase. Molecular Psychiatry 2008, 15: 216-225. PMID: 18574484, PMCID: PMC2811226, DOI: 10.1038/mp.2008.64.Peer-Reviewed Original ResearchConceptsNon-synonymous single nucleotide polymorphismsSingle nucleotide polymorphismsGenetic variationDiverse evolutionary lineagesFuture association studiesEvolutionary lineagesPromoter regionAssociation studiesGenesLinkage disequilibriumFunctional consequencesUndetected variantsNucleotide polymorphismsCommon haplotypeComplex global patternsGlobal patternsDNA samplesHaplotypesLineagesExonsHaplotypic combinationsKbDNACOMT geneOnly variation
2006
Sub‐Saharan African coding sequence variation and haplotype diversity at the NAT2 gene
Patin E, Harmant C, Kidd K, Kidd J, Froment A, Mehdi S, Sica L, Heyer E, Quintana‐Murci L. Sub‐Saharan African coding sequence variation and haplotype diversity at the NAT2 gene. Human Mutation 2006, 27: 720-720. PMID: 16786516, DOI: 10.1002/humu.9438.Peer-Reviewed Original ResearchConceptsNon-synonymous mutationsNovel non-synonymous mutationsEvolutionary conservationDetailed genetic characterizationIndividuals/populationsHaplotype diversityAgriculturalist populationsSequence variationProtein activityAfrican populationsWestern PygmiesAfrican haplotypesGenetic characterizationUnknown functional effectsGenesFunctional effectsNAT2 geneHaplotype frequenciesSub-Saharan African populationsMutationsChromosomesDamaging effectsLociPopulationProtein
2004
Indications of Linkage and Association of Gilles de la Tourette Syndrome in Two Independent Family Samples: 17q25 Is a Putative Susceptibility Region
Paschou P, Feng Y, Pakstis A, Speed W, DeMille M, Kidd J, Jaghori B, Kurlan R, Pauls D, Sandor P, Barr C, Kidd K. Indications of Linkage and Association of Gilles de la Tourette Syndrome in Two Independent Family Samples: 17q25 Is a Putative Susceptibility Region. American Journal Of Human Genetics 2004, 75: 545-560. PMID: 15303240, PMCID: PMC1182043, DOI: 10.1086/424389.Peer-Reviewed Original ResearchMeSH KeywordsC-Reactive ProteinChromosome MappingChromosomes, Human, Pair 17Gene FrequencyGenetic LinkageGenetic Predisposition to DiseaseGenotypeHaplotypesHumansLinkage DisequilibriumLod ScoreMicrosatellite RepeatsMicrotubule-Associated ProteinsNerve Tissue ProteinsPedigreePolymorphism, Single NucleotideTourette SyndromeWhite PeopleConceptsSingle nucleotide polymorphismsLinkage disequilibriumSusceptibility regionsThree-site haplotypesPutative susceptibility regionsBackground linkage disequilibriumSignificant association resultsIndication of linkageNonparametric LOD scoreGenomic regionsThree-marker haplotypeComplex genetic backgroundAdditional microsatellite markersFine mappingGenetic basisHigher LD valuesMicrosatellite markersExpression profilesAssociation resultsTransmission/disequilibrium testChromosome 17Genetic componentGenetic backgroundGenesLOD score