2021
Genetic 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
2019
Usefulness of COMT gene polymorphisms in North African populations
Boussetta S, Cherni L, Pakstis AJ, Ben Salem N, Elkamel S, Khodjet-El-Khil H, Kidd KK, Elgaaied ABA. Usefulness of COMT gene polymorphisms in North African populations. Gene 2019, 696: 186-196. PMID: 30790653, DOI: 10.1016/j.gene.2019.02.021.Peer-Reviewed Original Research
2013
Haplotype structure and positive selection at TLR1
Heffelfinger C, Pakstis AJ, Speed WC, Clark AP, Haigh E, Fang R, Furtado MR, Kidd KK, Snyder MP. Haplotype structure and positive selection at TLR1. European Journal Of Human Genetics 2013, 22: 551-557. PMID: 24002163, PMCID: PMC3953919, DOI: 10.1038/ejhg.2013.194.Peer-Reviewed Original ResearchConceptsToll-like receptor 2Toll-like receptor 1Missense variantsInnate immune systemReduced riskMedical conditionsReceptor 2Immune systemReceptor 1Cell surface receptorsSepsisSubsequent activationTLR1Surface receptorsBacterial lipoproteinsLeprosySurface traffickingDiseaseHuman healthRiskHealthMultiple functional allelesRs5743618TuberculosisLipoproteinWorldwide Population Variation and Haplotype Analysis at the Serotonin Transporter Gene SLC6A4 and Implications for Association Studies
Murdoch JD, Speed WC, Pakstis AJ, Heffelfinger CE, Kidd KK. Worldwide Population Variation and Haplotype Analysis at the Serotonin Transporter Gene SLC6A4 and Implications for Association Studies. Biological Psychiatry 2013, 74: 879-889. PMID: 23510579, DOI: 10.1016/j.biopsych.2013.02.006.Peer-Reviewed Original ResearchConceptsVariable number tandem repeatSingle nucleotide polymorphismsFunctional single nucleotide polymorphismsPromoter variable number tandem repeatRestricted distributionAssociation studiesRare allelesPutative functional single nucleotide polymorphismsPossible functional variationPopulation-specific distributionWide geographic distributionAlleles of interestHealth-related phenotypesAdditional single nucleotide polymorphismsPopulation variationSerotonin transporter gene SLC6A4Transporter geneFunctional variationTandem repeatsNumber tandem repeatSNP rs25531Extent of variationGeographic distributionNucleotide polymorphismsHaplotype background
2012
Structural diversity and African origin of the 17q21.31 inversion polymorphism
Steinberg KM, Antonacci F, Sudmant PH, Kidd JM, Campbell CD, Vives L, Malig M, Scheinfeldt L, Beggs W, Ibrahim M, Lema G, Nyambo TB, Omar SA, Bodo JM, Froment A, Donnelly MP, Kidd KK, Tishkoff SA, Eichler EE. Structural diversity and African origin of the 17q21.31 inversion polymorphism. Nature Genetics 2012, 44: 872-880. PMID: 22751100, PMCID: PMC3408829, DOI: 10.1038/ng.2335.Peer-Reviewed Original ResearchMini-haplotypes as lineage informative SNPs and ancestry inference SNPs
Pakstis AJ, Fang R, Furtado MR, Kidd JR, Kidd KK. Mini-haplotypes as lineage informative SNPs and ancestry inference SNPs. European Journal Of Human Genetics 2012, 20: 1148-1154. PMID: 22535184, PMCID: PMC3476707, DOI: 10.1038/ejhg.2012.69.Peer-Reviewed Original Research
2011
A global view of the OCA2-HERC2 region and pigmentation
Donnelly MP, Paschou P, Grigorenko E, Gurwitz D, Barta C, Lu RB, Zhukova OV, Kim JJ, Siniscalco M, New M, Li H, Kajuna SL, Manolopoulos VG, Speed WC, Pakstis AJ, Kidd JR, Kidd KK. A global view of the OCA2-HERC2 region and pigmentation. Human Genetics 2011, 131: 683-696. PMID: 22065085, PMCID: PMC3325407, DOI: 10.1007/s00439-011-1110-x.Peer-Reviewed Original ResearchHunter-gatherer genomic diversity suggests a southern African origin for modern humans
Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodríguez-Botigué L, Ramachandran S, Hon L, Brisbin A, Lin AA, Underhill PA, Comas D, Kidd KK, Norman PJ, Parham P, Bustamante CD, Mountain JL, Feldman MW. Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 5154-5162. PMID: 21383195, PMCID: PMC3069156, DOI: 10.1073/pnas.1017511108.Peer-Reviewed Original ResearchConceptsHunter-gatherer populationsAfrican hunter-gatherer populationsModern humansGenome-wide linkage disequilibriumModern human populationsSex-biased migrationSevere population bottleneckLinkage disequilibriumSouthern African originHuman prehistoryAfrican populationsComplex historyPopulation differentiationPopulation bottlenecksGenetic diversityGenomic diversityEastern AfricaGenetic variationAfrican originPopulation todaySouthern AfricaGeographic patternsContinent of originAfricaSouth Africa
2009
Genetic Landscape of Eurasia and “Admixture” in Uyghurs
Li H, Cho K, Kidd JR, Kidd KK. Genetic Landscape of Eurasia and “Admixture” in Uyghurs. American Journal Of Human Genetics 2009, 85: 934-937. PMID: 20004770, PMCID: PMC2790568, DOI: 10.1016/j.ajhg.2009.10.024.Peer-Reviewed Original Research
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 ResearchMeSH KeywordsAllelesBiological EvolutionCytochrome P-450 CYP2E1Genetic DriftHaplotypesHumansLinkage DisequilibriumConceptsGenetic 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
2007
Motoneuron-specific NR3B gene: No association with ALS and evidence for a common null alleleSYMBOL
Niemann S, Landers J, Churchill M, Hosler B, Sapp P, Speed W, Lahn B, Kidd K, Brown R, Hayashi Y. Motoneuron-specific NR3B gene: No association with ALS and evidence for a common null alleleSYMBOL. Neurology 2007, 70: 666-676. PMID: 17687115, DOI: 10.1212/01.wnl.0000271078.51280.17.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCase-Control StudiesDNA Mutational AnalysisGene FrequencyGenetic Predisposition to DiseaseGenetics, PopulationGenotypeHaplotypesHumansLinkage DisequilibriumMotor Neuron DiseaseMotor NeuronsPolymorphism, Single NucleotideReceptors, N-Methyl-D-AspartateSuperoxide DismutaseSuperoxide Dismutase-1ConceptsSporadic amyotrophic lateral sclerosisAmyotrophic lateral sclerosisSingle nucleotide polymorphismsGRIN3B geneGlutamate-mediated excitotoxicityCase-control studyFamilial amyotrophic lateral sclerosisIonotropic glutamate receptorsNervous system-related genesTag single nucleotide polymorphismsPolymorphic CAG repeatNMDA typeGlutamate receptorsLateral sclerosisReceptor responsesAllele frequenciesCommon polymorphismsUnreported single nucleotide polymorphismsNR3BCAG repeatsGenetic dysfunctionGRIN3BNucleotide polymorphismsNull allelesIndividuals
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 KeywordsChromosome MappingChromosomes, Human, Pair 17C-Reactive ProteinGene 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 scoreThe Genetic Architecture of Selection at the Human Dopamine Receptor D4 (DRD4) Gene Locus
Wang E, Ding Y, Flodman P, Kidd J, Kidd K, Grady D, Ryder O, Spence M, Swanson J, Moyzis R. The Genetic Architecture of Selection at the Human Dopamine Receptor D4 (DRD4) Gene Locus. American Journal Of Human Genetics 2004, 74: 931-944. PMID: 15077199, PMCID: PMC1181986, DOI: 10.1086/420854.Peer-Reviewed Original ResearchConceptsLittle linkage disequilibriumHuman dopamine receptor D4 genePolymorphic sitesDNA sequence organizationMost polymorphic sitesPatterns of recombinationObserved LD patternRare mutational eventsDRD4 locusGenetic architectureHaplotype diversityPositive selectionMore polymorphismsSequence organizationGene locusTandem repeatsMutational eventsLD patternsLinkage disequilibriumDopamine receptor D4 geneLociPhysiological differencesSame alleleReceptor variantsAllelesCOMT haplotypes suggest P2 promoter region relevance for schizophrenia
Palmatier M, Pakstis A, Speed W, Paschou P, Goldman D, Odunsi A, Okonofua F, Kajuna S, Karoma N, Kungulilo S, Grigorenko E, Zhukova O, Bonne-Tamir B, Lu R, Parnas J, Kidd J, DeMille M, Kidd K. COMT haplotypes suggest P2 promoter region relevance for schizophrenia. Molecular Psychiatry 2004, 9: 859-870. PMID: 15098000, DOI: 10.1038/sj.mp.4001496.Peer-Reviewed Original Research
2000
Worldwide Genetic Analysis of the CFTR Region
Mateu E, Calafell F, Lao O, Bonné-Tamir B, Kidd J, Pakstis A, Kidd K, Bertranpetit J. Worldwide Genetic Analysis of the CFTR Region. American Journal Of Human Genetics 2000, 68: 103-117. PMID: 11104661, PMCID: PMC1234903, DOI: 10.1086/316940.Peer-Reviewed Original ResearchConceptsCystic fibrosis transmembrane conductance regulator (CFTR) geneShort tandem repeat polymorphismsSingle nucleotide polymorphismsLinkage disequilibriumHaplotype backgroundTransmembrane conductance regulator geneWorldwide population samplesModern human populationsHaplotype variationHigh heterozygosityCFTR regionOut of AfricaRegulator geneSevere genetic disorderGenetic analysisMutation rateDifferent haplotypesAncestral haplotypeAllele sizeOutcome of differencesSNP haplotypesLD analysisNon-AfricansHaplotypesLD measuresHaplotype Evolution and Linkage Disequilibrium: A Simulation Study
Calafell F, Grigorenko E, Chikanian A, Kidd K. Haplotype Evolution and Linkage Disequilibrium: A Simulation Study. Human Heredity 2000, 51: 85-96. PMID: 11096275, DOI: 10.1159/000022963.Peer-Reviewed Original ResearchShort Tandem-Repeat Polymorphism/Alu Haplotype Variation at the PLAT Locus: Implications for Modern Human Origins
Tishkoff S, Pakstis A, Stoneking M, Kidd J, Destro-Bisol G, Sanjantila A, Lu R, Deinard A, Sirugo G, Jenkins T, Kidd K, Clark A. Short Tandem-Repeat Polymorphism/Alu Haplotype Variation at the PLAT Locus: Implications for Modern Human Origins. American Journal Of Human Genetics 2000, 67: 901-925. PMID: 10986042, PMCID: PMC1287905, DOI: 10.1086/303068.Peer-Reviewed Original ResearchMeSH KeywordsAfrica South of the SaharaAllelesAlu ElementsAnimalsChromosomes, Human, Pair 8Dinucleotide RepeatsEvolution, MolecularGene FrequencyGenetic VariationHaplotypesHominidaeHumansLinkage DisequilibriumMicronesiaPapua New GuineaPhylogenyPolymorphism, GeneticSequence DeletionTandem Repeat SequencesConceptsNon-African populationsHaplotype variationGene flowLinkage disequilibriumShort tandem repeat polymorphismsHaplotype diversityPLAT locusLarge effective population sizesAncient gene flowEffective population sizeDinucleotide short tandem repeat polymorphismsRecent common ancestryAlu insertion/deletion polymorphismHuman evolutionary historyDiverse human populationsModern human originsEvolutionary historyCommon ancestryAfrican populationsPopulation substructureAlu elementsPolymorphic Alu elementsPopulation sizeRare haplotypesDinucleotide repeatsTransmission/Disequilibrium Tests Using Multiple Tightly Linked Markers
Zhao H, Zhang S, Merikangas K, Trixler M, Wildenauer D, Sun F, Kidd K. Transmission/Disequilibrium Tests Using Multiple Tightly Linked Markers. American Journal Of Human Genetics 2000, 67: 936-946. PMID: 10968775, PMCID: PMC1287895, DOI: 10.1086/303073.Peer-Reviewed Original ResearchThe Accuracy of Statistical Methods for Estimation of Haplotype Frequencies: An Example from the CD4 Locus
Tishkoff S, Pakstis A, Ruano G, Kidd K. The Accuracy of Statistical Methods for Estimation of Haplotype Frequencies: An Example from the CD4 Locus. American Journal Of Human Genetics 2000, 67: 518-522. PMID: 10859209, PMCID: PMC1287198, DOI: 10.1086/303000.Peer-Reviewed Original Research