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 frequencyRecombinationAssaysCancer
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
2015
Genetic markers for massively parallel sequencing in forensics
Kidd K, Speed W, Wootton S, Lagace R, Langit R, Haigh E, Chang J, Pakstis A. Genetic markers for massively parallel sequencing in forensics. Forensic Science International Genetics Supplement Series 2015, 5: e677-e679. DOI: 10.1016/j.fsigss.2015.12.004.Peer-Reviewed Original ResearchShort tandem repeat polymorphismsSingle nucleotide polymorphismsParallel sequencingSingle single-nucleotide polymorphismSequence readsMore haplotypesSNP panelGenetic markersMultiple allelesAncestry inferenceNucleotide polymorphismsCodominant systemsTandem repeat polymorphismMicrohaplotypesLociSequencingIndividual identificationRepeat polymorphismPolymorphismField of forensicsDNAHaplotypesReadsPhenotypeAlleles
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 structurePolymorphismPopulationAnatoliaHypothesisIslands
2011
Single nucleotide polymorphisms and haplotypes in Native American populations
Kidd JR, Friedlaender F, Pakstis AJ, Furtado M, Fang R, Wang X, Nievergelt CM, Kidd KK. Single nucleotide polymorphisms and haplotypes in Native American populations. American Journal Of Biological Anthropology 2011, 146: 495-502. PMID: 21913176, PMCID: PMC3658315, DOI: 10.1002/ajpa.21560.Peer-Reviewed Original ResearchConceptsSingle nucleotide polymorphismsNative American populationsAutosomal markersModern Native American populationsNucleotide polymorphismsOld World populationsEvolutionary relationshipsAmerican populationDifferent small setsDNA polymorphismsEurasian originAncestry inferenceMultiple populationsPolymorphismLarge comprehensive datasetAscertainment biasesNew WorldSmall independent setsMarkersComprehensive datasetClose relationshipPopulationHaplotypesNew informationDiversification 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 AsiaAnalyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples
Kidd JR, Friedlaender FR, Speed WC, Pakstis AJ, De La Vega FM, Kidd KK. Analyses of a set of 128 ancestry informative single-nucleotide polymorphisms in a global set of 119 population samples. Investigative Genetics 2011, 2: 1. PMID: 21208434, PMCID: PMC3025953, DOI: 10.1186/2041-2223-2-1.Peer-Reviewed Original ResearchAncestry informative single nucleotide polymorphismsInformative single nucleotide polymorphismsSingle nucleotide polymorphismsTrait association studiesAncestry informative markersForensic ancestry inferencePopulation structureEurasian populationsAdmixture mappingAssociation studiesAncestry inferenceAncestry assignmentInformative markersAdmixture studiesIndividual ancestryHuman populationNumber of individualsAncestryAllele frequenciesMarker panelOriginal selectionPopulation sampleSpecific setStructure programPolymorphismRare BRCA1 haplotypes including 3’UTR SNPs associated with breast cancer risk
Pelletier C, Speed WC, Paranjape T, Keane K, Blitzblau R, Hollestelle A, Safavi K, van den Ouweland A, Zelterman D, Slack FJ, Kidd KK, Weidhaas JB. Rare BRCA1 haplotypes including 3’UTR SNPs associated with breast cancer risk. Cell Cycle 2011, 10: 90-99. PMID: 21191178, PMCID: PMC3048078, DOI: 10.4161/cc.10.1.14359.Peer-Reviewed Original ResearchConceptsGenetic markersRare haplotypesNew genetic markersBRCA1 3'UTRSequence mutationsMicroRNA bindingFunctional variantsSuch polymorphismsHaplotypesMutationsBRCA1Haplotype analysisPolymorphismSNPsRegion polymorphismsVariantsFunctional polymorphismsBreast cancer subtypesCancer subtypesMarkersBRCA1 haplotypeMiRNALarge populationBRCA1 mutationsBinding
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
1999
Global 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 variationPopulationLinkage Disequilibrium at the ADH2 and ADH3 Loci and Risk of Alcoholism
Osier M, Pakstis A, Kidd J, Lee J, Yin S, Ko H, Edenberg H, Lu R, Kidd K. Linkage Disequilibrium at the ADH2 and ADH3 Loci and Risk of Alcoholism. American Journal Of Human Genetics 1999, 64: 1147-1157. PMID: 10090900, PMCID: PMC1377839, DOI: 10.1086/302317.Peer-Reviewed Original ResearchMeSH KeywordsAlcohol DehydrogenaseAlcoholismAllelesBase SequenceChinaChromosomes, Human, Pair 4Cloning, MolecularGene FrequencyGenetic Predisposition to DiseaseGenetic VariationHaplotypesHumansIndians, Central AmericanLinkage DisequilibriumMexicoMolecular Sequence DataMultigene FamilyNative Hawaiian or Other Pacific IslanderPolymorphism, Single NucleotideRacial GroupsTaiwanConceptsProportion of chromosomesAlcohol dehydrogenase geneDehydrogenase geneChromosome 4Functional variantsChromosomesLinkage disequilibriumADH2Functional polymorphismsADH3Allele frequenciesPairwise disequilibriumGenesIntronic polymorphismDisequilibriumPolymorphismDifferent efficienciesRisk of alcoholismHigher VmaxClass I alcohol dehydrogenase (ADH) genesVariantsLociKbHaplotypesPopulationY‐chromosome specific YCAII, DYS19 and YAP polymorphisms in human populations: a comparative study
QUINTANA‐MURCI L, SEMINO O, POLONI E, LIU A, VAN GIJN M, PASSARINO G, BREGA A, NASIDZE I, MACCIONI L, COSSU G, AL‐ZAHERY N, KIDD J, KIDD K, SANTACHIARA‐BENERECETTI A. Y‐chromosome specific YCAII, DYS19 and YAP polymorphisms in human populations: a comparative study. Annals Of Human Genetics 1999, 63: 153-166. PMID: 10738527, DOI: 10.1046/j.1469-1809.1999.6320153.x.Peer-Reviewed Original ResearchConceptsY Alu PolymorphismGenetic structureGenetic affinityStrong genetic structurePopulation genetic structureAlu polymorphismsY markersHuman populationYCAIIDifferent populationsRelated groupsPolymorphismSpecific markersPopulationMarkersDYS19Geographic locationDifferent statistical analysesFrequency distributionSTRAffinityAllele Frequencies in a Worldwide Survey of a CA Repeat in the First Intron of the CFTR Gene
Mateu E, Calafell F, Bonné-Tamir B, Kidd J, Casals T, Kidd K, Bertranpetit J. Allele Frequencies in a Worldwide Survey of a CA Repeat in the First Intron of the CFTR Gene. Human Heredity 1999, 49: 15-20. PMID: 9858852, DOI: 10.1159/000022834.Peer-Reviewed Original ResearchConceptsCFTR geneIntron 1Allele frequenciesMolecular varianceGenetic varianceFirst intronDinucleotide CACA repeatsGenesCF mutationsHaplotypic analysisMutationsMajor geographical areasAfrican populationsUnknown mutationsAllele distributionPolymorphismCystic fibrosisIntronsChromosomesRepeatsGeographical regionsLociHeterozygosityPopulation
1998
Genetic Structure of the Ancestral Population of Modern Humans
Ziętkiewicz E, Yotova V, Jarnik M, Korab-Laskowska M, Kidd K, Modiano D, Scozzari R, Stoneking M, Tishkoff S, Batzer M, Labuda D. Genetic Structure of the Ancestral Population of Modern Humans. Journal Of Molecular Evolution 1998, 47: 146-155. PMID: 9694663, DOI: 10.1007/pl00006371.Peer-Reviewed Original ResearchConceptsNucleotide diversityAncestral populationsNeutral DNA polymorphismsOverall nucleotide diversityPopulation-specific variantsOld polymorphismsGenetic structureAncestral stateHuman divergenceOrthologous sitesGenetic variabilityDNA polymorphismsNew allelesHuman variantsPolymorphic sitesNon-AfricansWorldwide sampleGreat apesEffective sizeModern humansHuman groupsDiversityPolymorphismDivergenceNew GuineaShort tandem repeat polymorphism evolution in humans
Calafell F, Shuster A, Speed W, Kidd J, Kidd K. Short tandem repeat polymorphism evolution in humans. European Journal Of Human Genetics 1998, 6: 38-49. PMID: 9781013, DOI: 10.1038/sj.ejhg.5200151.Peer-Reviewed Original ResearchConceptsDinucleotide short tandem repeat polymorphismsStepwise mutation modelSet of populationsPrivate allelesShort tandem repeat polymorphismsGenetic distanceHigh heterozygosityGenetic variationLinkage analysisMutation modelPolymorphism evolutionTandem repeat polymorphismEuropean populationsModern humansHeterozygosityAllelesRepeat polymorphismAfrican sampleReplacement hypothesisEast AsiansDifferentiationHumansPolymorphismPopulationTrees
1997
Concerted evolution of the tandemly repeated genes encoding human U2 snRNA (the RNU2 locus) involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion
Liao D, Pavelitz T, Kidd J, Kidd K, Weiner A. Concerted evolution of the tandemly repeated genes encoding human U2 snRNA (the RNU2 locus) involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion. The EMBO Journal 1997, 16: 588-598. PMID: 9034341, PMCID: PMC1169662, DOI: 10.1093/emboj/16.3.588.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceChromosomesCloning, MolecularDNA, SatelliteElectrophoresis, Agar GelEvolution, MolecularGenetic MarkersHaplotypesHumansLinkage DisequilibriumMolecular Sequence DataPedigreePolymorphism, GeneticPolymorphism, Restriction Fragment LengthPrimatesRecombination, GeneticRepetitive Sequences, Nucleic AcidRNA, Small NuclearSequence AnalysisConceptsU2 tandem arrayTandem arraysConcerted evolutionIntrachromosomal homogenizationU2 snRNAInterchromosomal gene conversionHuman U2 snRNARepeat unitsGenetic exchangeU2 genesGene conversionChromosome lineagesIndependent assortmentFlanking markersDiverse panelGenesMicrosatellite polymorphismSnRNACT alleleSacISacI polymorphismPolymorphismAllelesChromatid exchangesPrimary driving force
1996
DRD2 Haplotypes Containing the TaqI A1 Allele: Implications for Alcoholism Research
Kidd K, Pakstis A, Castiglione C, Kidd J, Speed W, Goldman D, Knowler W, Lu R, Bonne‐Tamir B. DRD2 Haplotypes Containing the TaqI A1 Allele: Implications for Alcoholism Research. Alcohol Clinical And Experimental Research 1996, 20: 697-705. PMID: 8800387, DOI: 10.1111/j.1530-0277.1996.tb01674.x.Peer-Reviewed Original ResearchMeSH KeywordsAlcoholismAllelesAnimalsChromosome MappingDeoxyribonucleases, Type II Site-SpecificEthnicityGene FrequencyGenetics, PopulationHaplotypesHumansPolymerase Chain ReactionPolymorphism, GeneticPolymorphism, Restriction Fragment LengthReceptors, Dopamine D2Repetitive Sequences, Nucleic AcidResearchConceptsGenetic variationAssociation studiesUnrelated control samplesDopamine D2 receptor locusDiversity of haplotypesShort tandem repeat polymorphismsDRD2 locusEvolutionary historyRestriction fragment length polymorphismPopulation geneticsPhylogenetic originFragment length polymorphismAncestral originReceptor locusHomologous regionsIntron 2LociAllelic systemHigher primatesHaplotypesTandem repeat polymorphismAllelesConsiderable diversityDRD2 haplotypesPolymorphismThe world-wide distribution of allele frequencies at the human dopamine D4 receptor locus
Chang F, Kidd J, Livak K, Pakstis A, Kidd K. The world-wide distribution of allele frequencies at the human dopamine D4 receptor locus. Human Genetics 1996, 98: 91-101. PMID: 8682515, DOI: 10.1007/s004390050166.Peer-Reviewed Original ResearchConceptsImperfect tandem repeatsAllele frequenciesDifferent populationsActual allele frequenciesDopamine D4 receptor locusSelective forcesEvolutionary significanceWorld-wide distributionAssociation studiesReceptor locusTandem repeatsThird exonBase pairsAmino acidsFunctional relevanceRepeatsReceptor geneAllelesLociModern humansPolymorphismD4 receptor geneDopamine D4 receptor geneRepeat polymorphismExons
1995
Apparent monomorphism of ALDH2 in seven American Indian populations
Novoradovsky A, Kidd J, Kidd K, Goldman D. Apparent monomorphism of ALDH2 in seven American Indian populations. Alcohol 1995, 12: 163-167. PMID: 7772269, DOI: 10.1016/0741-8329(94)00086-7.Peer-Reviewed Original ResearchConceptsNew World populationsSouth American Indian populationsALDH2 geneMitochondrial aldehyde dehydrogenaseNorth American populationsALDH2 cDNAALDH2 functionRestriction endonucleasesAldehyde dehydrogenaseConformation polymorphism techniqueSouth American IndiansGenesAllele-specific amplificationAllelesStudied individualsPolymorphism techniquePolymorphismAmerican populationFragmentsAmerican Indian populationsCDNAALDH2EndonucleaseVariantsPopulation