2022
A multipurpose panel of microhaplotypes for use with STR markers in casework
Kidd KK, Pakstis AJ, Gandotra N, Scharfe C, Podini D. A multipurpose panel of microhaplotypes for use with STR markers in casework. Forensic Science International Genetics 2022, 60: 102729. PMID: 35696960, PMCID: PMC11071123, DOI: 10.1016/j.fsigen.2022.102729.Peer-Reviewed Original Research
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
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
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 ResearchMixture deconvolution by massively parallel sequencing of microhaplotypes
Bennett L, Oldoni F, Long K, Cisana S, Madella K, Wootton S, Chang J, Hasegawa R, Lagacé R, Kidd KK, Podini D. Mixture deconvolution by massively parallel sequencing of microhaplotypes. International Journal Of Legal Medicine 2019, 133: 719-729. PMID: 30758713, DOI: 10.1007/s00414-019-02010-7.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 allelesRs5743618TuberculosisLipoprotein
2012
Mini-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
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 dataPolymorphism
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
The 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 variantsAlleles
2001
Comparisons of Two Methods for Haplotype Reconstruction and Haplotype Frequency Estimation from Population Data
Zhang S, Pakstis A, Kidd K, Zhao H. Comparisons of Two Methods for Haplotype Reconstruction and Haplotype Frequency Estimation from Population Data. American Journal Of Human Genetics 2001, 69: 906-912. PMID: 11536083, PMCID: PMC1226079, DOI: 10.1086/323622.Peer-Reviewed Original ResearchInsertional polymorphisms of full-length endogenous retroviruses in humans
Turner G, Barbulescu M, Su M, Jensen-Seaman M, Kidd K, Lenz J. Insertional polymorphisms of full-length endogenous retroviruses in humans. Current Biology 2001, 11: 1531-1535. PMID: 11591322, DOI: 10.1016/s0960-9822(01)00455-9.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 repeatsHaplotypes and Linkage Disequilibrium at the Phenylalanine Hydroxylase Locus, PAH, in a Global Representation of Populations
Kidd J, Pakstis A, Zhao H, Lu R, Okonofua F, Odunsi A, Grigorenko E, Tamir B, Friedlaender J, Schulz L, Parnas J, Kidd K. Haplotypes and Linkage Disequilibrium at the Phenylalanine Hydroxylase Locus, PAH, in a Global Representation of Populations. American Journal Of Human Genetics 2000, 66: 1882-1899. PMID: 10788337, PMCID: PMC1378054, DOI: 10.1086/302952.Peer-Reviewed Original Research
1999
Tandem duplication polymorphism upstream of the dopamine D4 receptor gene (DRD4)
Seaman M, Fisher J, Chang F, Kidd K. Tandem duplication polymorphism upstream of the dopamine D4 receptor gene (DRD4). American Journal Of Medical Genetics 1999, 88: 705-709. PMID: 10581493, DOI: 10.1002/(sici)1096-8628(19991215)88:6<705::aid-ajmg22>3.0.co;2-f.Peer-Reviewed Original ResearchAllelesAnimalsCodon, InitiatorConsensus SequenceDatabases, FactualEvolution, MolecularGene FrequencyGenetic VariationGorilla gorillaHumansPan troglodytesPolymorphism, GeneticPongo pygmaeusReceptors, Dopamine D2Receptors, Dopamine D4Response ElementsSequence Homology, Nucleic AcidTandem Repeat SequencesTranscription FactorsGlobal variation in the frequencies of functionally different catechol-O-methyltransferase alleles
Palmatier M, Kang A, Kidd K. Global variation in the frequencies of functionally different catechol-O-methyltransferase alleles. Biological Psychiatry 1999, 46: 557-567. PMID: 10459407, DOI: 10.1016/s0006-3223(99)00098-0.Peer-Reviewed Original ResearchConceptsRestriction site polymorphismsSingle nucleotide polymorphismsAllele frequenciesDifferent population frequenciesControl allele frequenciesEnzyme activity levelsAncestral alleleCandidate genesPopulation-based association studyAssociation studiesSite polymorphismFirst global surveyNucleotide polymorphismsAllelesEnzyme activityPopulation frequencyPolymorphismDifferent populationsCOMT enzyme activityActivity alleleLow-activity alleleGenesProteinGlobal variationPopulationA paradigm for finding genes for a complex human trait: Polycystic ovary syndrome and follistatin
Odunsi K, Kidd K. A paradigm for finding genes for a complex human trait: Polycystic ovary syndrome and follistatin. Proceedings Of The National Academy Of Sciences Of The United States Of America 1999, 96: 8315-8317. PMID: 10411866, PMCID: PMC33617, DOI: 10.1073/pnas.96.15.8315.Peer-Reviewed Original Research