2014
Inferring population structure and demographic history using Y-STR data from worldwide populations
Xu H, Wang CC, Shrestha R, Wang LX, Zhang M, He Y, Kidd JR, Kidd KK, Jin L, Li H. Inferring population structure and demographic history using Y-STR data from worldwide populations. Molecular Genetics And Genomics 2014, 290: 141-150. PMID: 25159112, DOI: 10.1007/s00438-014-0903-8.Peer-Reviewed Original ResearchMeSH KeywordsChromosomes, Human, YDemographyGenealogy and HeraldryGenetics, PopulationHumansMaleMicrosatellite RepeatsMolecular Sequence DataPopulation DensityTime FactorsConceptsEffective population sizeLarge genetic distancePopulation structureDemographic historyGenetic distanceLarge effective population sizesSmall effective population sizePopulation sizeLow genetic diversitySmall geographical rangesWorldwide population structureOrigin of populationsPopulation genetic studiesClose genetic affinityRecent common ancestorNon-African populationsSerial founder modelGood genetic materialClear geographic patternWorldwide populationEvolutionary historyGenetic diversityCommon ancestorEurasian populationsFuture forensic applications
2011
The Molecular Origin and Consequences of Escape from miRNA Regulation by HLA-C Alleles
O'hUigin C, Kulkarni S, Xu Y, Deng Z, Kidd J, Kidd K, Gao X, Carrington M. The Molecular Origin and Consequences of Escape from miRNA Regulation by HLA-C Alleles. American Journal Of Human Genetics 2011, 89: 424-431. PMID: 21907013, PMCID: PMC3169826, DOI: 10.1016/j.ajhg.2011.07.024.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 measuresHaplotypes 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 ResearchIdentifying conservation units within captive chimpanzee populations
Deinard A, Kidd K. Identifying conservation units within captive chimpanzee populations. American Journal Of Biological Anthropology 2000, 111: 25-44. PMID: 10618587, DOI: 10.1002/(sici)1096-8644(200001)111:1<25::aid-ajpa3>3.0.co;2-r.Peer-Reviewed Original ResearchConceptsGenetic diversityNuclear lociCaptive management programsGene poolGenetic dataPygmy chimpanzeesWild gene poolDNA sequence dataCommon chimpanzee subspeciesConservation unitsMitochondrial D-loopCaptive managementCaptive populationsChimpanzee populationsCaptive chimpanzee populationEvolutionary relationshipsDiversitySequence dataPolymorphic microsatellitesD-loopChimpanzee subspeciesMicrosatellite allelesManagement programCommon chimpanzeesLoci
1999
Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans
Barbulescu M, Turner G, Seaman M, Deinard A, Kidd K, Lenz J. Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans. Current Biology 1999, 9: 861-s1. PMID: 10469592, DOI: 10.1016/s0960-9822(99)80390-x.Peer-Reviewed Original ResearchConceptsOpen reading frameFull-length open reading frameHuman genome todayReading frameFull length HERVGenome todayGenomes of humansCis-acting sequencesHERV-K provirusesViral open reading framesGorilla genomeHuman genomePrimate evolutionMouse mammary tumor virusComplete sequencingHost genomePreintegration siteHuman endogenous retrovirus KGenomeHERV-K proteinsEndogenous retrovirusesMammary tumor virusTumor virusProvirusMultiple provirusesLinkage 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) genesVariantsLociKbHaplotypesPopulation
1998
A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus
Kidd K, Morar B, Castiglione C, Zhao H, Pakstis A, Speed W, Bonne-Tamir B, Lu R, Goldman D, Lee C, Nam Y, Grandy D, Jenkins T, Kidd J. A global survey of haplotype frequencies and linkage disequilibrium at the DRD2 locus. Human Genetics 1998, 103: 211-227. PMID: 9760208, DOI: 10.1007/s004390050809.Peer-Reviewed Original ResearchEvolution of a D2 Dopamine Receptor Intron Within the Great Apes and Humans
Deinard A, Kidd K. Evolution of a D2 Dopamine Receptor Intron Within the Great Apes and Humans. Mitochondrial DNA Part A 1998, 8: 289-301. PMID: 10993600, DOI: 10.3109/10425179809034074.Peer-Reviewed Original ResearchConceptsDenaturing Gradient Gel ElectrophoresisGenetic variationComparative phylogenetic analysisDNA sequence variationSequence comparative analysisCross-species comparisonsGreat apesEvolutionary relationshipsGradient gel electrophoresisPhylogenetic analysisGeographical rangeSequence variationPygmy chimpanzeesCommon chimpanzeesDNA sequencingDirect DNA sequencingIntronsGel electrophoresisSpeciesChimpanzeesApesSequencingComparative analysisHumansVariation
1997
A Novel, Heritable, Expanding CTG Repeat in an Intron of the SEF2-1 Gene on Chromosome 18q21.1
Breschel T, McInnis M, Margolis R, Sirugo G, Corneliussen B, Simpson S, McMahon F, MacKinnon D, Xu J, Pleasant N, Huo Y, Ashworth R, Grundstrom C, Grundstrom T, Kidd K, DePaulo J, Ross C. A Novel, Heritable, Expanding CTG Repeat in an Intron of the SEF2-1 Gene on Chromosome 18q21.1. Human Molecular Genetics 1997, 6: 1855-1863. PMID: 9302263, DOI: 10.1093/hmg/6.11.1855.Peer-Reviewed Original ResearchMeSH KeywordsAllelesBase SequenceBasic Helix-Loop-Helix Leucine Zipper Transcription FactorsBipolar DisorderBlotting, SouthernCell LineChromosomes, Human, Pair 18Cloning, MolecularDNA-Binding ProteinsFemaleGene FrequencyHelix-Loop-Helix MotifsHumansIntronsMaleMolecular Sequence DataPedigreeSequence AnalysisTCF Transcription FactorsTrans-ActivatorsTranscription Factor 4Transcription Factor 7-Like 2 ProteinTranscription FactorsTrinucleotide RepeatsConceptsCEPH reference pedigreesSouthern blot analysisReference pedigreesUnstable alleleDNA binding proteinTriplet repeat mutationBlot analysisCTG repeatsTranscriptional regulationGenomic digestsHuman chromosomesKb cloneStable allelesCandidate genesAbnormal phenotypeBinding proteinRepeatsRepeat lociBipolar pedigreesGenesChromosome 18q21.1Repeat mutationsSomatic mutationsIntronsAllelesRapid molecular haplotyping of the first exon of the human dopamine D4 receptor gene by heteroduplex analysis
Chang F, Kidd K. Rapid molecular haplotyping of the first exon of the human dopamine D4 receptor gene by heteroduplex analysis. American Journal Of Medical Genetics 1997, 74: 91-94. PMID: 9034013, DOI: 10.1002/(sici)1096-8628(19970221)74:1<91::aid-ajmg18>3.0.co;2-m.Peer-Reviewed Original ResearchConcerted 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
Distribution and frequency of a polymorphicAlu insertion at the plasminogen activator locus in humans
Tishkoff S, Ruano G, Kidd J, Kidd K. Distribution and frequency of a polymorphicAlu insertion at the plasminogen activator locus in humans. Human Genetics 1996, 97: 759-764. PMID: 8641693, DOI: 10.1007/bf02346186.Peer-Reviewed Original ResearchConceptsPlasminogen activator geneHuman populationTissue plasminogen activator geneRestriction fragment length polymorphismActivator geneActivator locusInsertion eventsFragment length polymorphismPLAT locusHuman evolutionPolymerase chain reaction analysisChain reaction analysisLength polymorphismPresence/absenceAllele frequenciesAllelesLociModern humansMinisatellite diversity supports a recent African origin for modern humans
Armour J, Anttinen T, May C, Vega E, Sajantila A, Kidd J, Kidd K, Bertranpetit J, Pääbo S, Jeffreys A. Minisatellite diversity supports a recent African origin for modern humans. Nature Genetics 1996, 13: 154-160. PMID: 8640220, DOI: 10.1038/ng0696-154.Peer-Reviewed Original ResearchConceptsRecent African originNon-African populationsModern human diversityAllelic diversityMinisatellite diversityVariable lociAncestral relationshipsHuman chromosomesAllelic structureAfrican originGreat diversityDiversityHuman diversityAfrican chromosomesChromosomesAllele familiesLociModern humansDifferent populationsGlobal Patterns of Linkage Disequilibrium at the CD4 Locus and Modern Human Origins
Tishkoff S, Dietzsch E, Speed W, Pakstis A, Kidd J, Cheung K, Bonné-Tamir B, Santachiara-Benerecetti A, Moral P, Krings M, Pääbo S, Watson E, Risch N, Jenkins T, Kidd K. Global Patterns of Linkage Disequilibrium at the CD4 Locus and Modern Human Origins. Science 1996, 271: 1380-1387. PMID: 8596909, DOI: 10.1126/science.271.5254.1380.Peer-Reviewed Original ResearchChromosomal localization of long trinucleotide repeats in the human genome by fluorescence in situ hybridization
Haaf T, Sirugo G, Kidd K, Ward D. Chromosomal localization of long trinucleotide repeats in the human genome by fluorescence in situ hybridization. Nature Genetics 1996, 12: 183-185. PMID: 8563757, DOI: 10.1038/ng0296-183.Peer-Reviewed Original ResearchConceptsLong trinucleotide repeatsChromosomal localizationTrinucleotide repeatsHuman genomeNormal human genomeSitu hybridizationDifferent genetic diseasesUnstable trinucleotide repeatsChromosomal distributionTrinucleotide microsatellitesLarge repeatsAGG repeatsCCG repeatsRepeatsGenetic diseasesRepeat lociLarge CTG expansionsGenomeCTG expansionHybridizationPathological significanceMyotonic dystrophyMicrosatellitesLocalizationLociConserved regulatory element involved in the early onset of Hoxb6 gene expression
Becker D, Jiang Z, Knödler P, Deinard A, Eid R, Kidd K, Shashikant C, Ruddle F, Schughart K. Conserved regulatory element involved in the early onset of Hoxb6 gene expression. Developmental Dynamics 1996, 205: 73-81. PMID: 8770553, DOI: 10.1002/(sici)1097-0177(199601)205:1<73::aid-aja7>3.0.co;2-2.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceConserved SequenceDNADNA PrimersEmbryonic and Fetal DevelopmentEnhancer Elements, GeneticGene Expression Regulation, DevelopmentalGenes, HomeoboxGenes, RegulatorGenes, ReporterHomeodomain ProteinsHumansIn Situ HybridizationMesodermMiceMice, TransgenicMolecular Sequence DataSequence Homology, Nucleic AcidConceptsGene expressionPosterior lateral plate mesodermConserved regulatory elementsLateral plate mesodermReporter gene analysisSimilar enhancer activityHuman DNA sequencesBp DNA fragmentMammalian embryosMouse developmentPlate mesodermRegulatory elementsDNA sequencesEnhancer activityExpression patternsDNA fragmentsGene analysisEnhancerTransgenic miceExpressionInitial activationEarly stagesMesodermEmbryosTransgene
1995
Evidence for inter-generational instability in the CAG repeat in the MJD1 gene and for conserved haplotypes at flanking markers amongst Japanese and Caucasian subjects with Machado-Joseph disease
Takiyama Y, Igasrashi S, Rogaeva E, Endo K, Rogaev E, Tanaka H, Sherrington R, Sanpei K, Liang Y, Saito M, Tsuda T, Takano H, Ikeda M, Lin C, Chi H, Kennedy J, Lang A, Wherrett J, Segawa M, Nomura Y, Yuasa T, Weissenbach J, Yoshida M, Nishizawa M, Kidd K, Tsuji S, St George-Hyslop P. Evidence for inter-generational instability in the CAG repeat in the MJD1 gene and for conserved haplotypes at flanking markers amongst Japanese and Caucasian subjects with Machado-Joseph disease. Human Molecular Genetics 1995, 4: 1137-1146. PMID: 8528200, DOI: 10.1093/hmg/4.7.1137.Peer-Reviewed Original ResearchAge of OnsetAllelesAsian PeopleAtaxin-3Base SequenceConserved SequenceFemaleGenetics, PopulationHaplotypesHomozygoteHumansJapanMachado-Joseph DiseaseMaleMeiosisMolecular Sequence DataNerve Tissue ProteinsNuclear ProteinsPedigreePhenotypePolymorphism, GeneticProteinsRepetitive Sequences, Nucleic AcidRepressor ProteinsWhite PeopleApparent 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 populationsCDNAALDH2EndonucleaseVariantsPopulationThe CEPH consortium linkage map of human chromosome 16
Kozman H, Keith T, Donis-keller H, White R, Weissenbach J, Dean M, Vergnaud G, Kidd K, Gusella J, Royle N, Sutherland G, Mulley J. The CEPH consortium linkage map of human chromosome 16. Genomics 1995, 25: 44-58. PMID: 7774955, DOI: 10.1016/0888-7543(95)80108-x.Peer-Reviewed Original ResearchConceptsHuman chromosome 16Genetic mapLinkage mapMap lengthSomatic cell hybrid panelFemale map lengthsChromosome 16Male map lengthFramework genetic mapCell hybrid panelMean genetic distanceSex-averaged mapRestriction enzyme combinationsGenetic distanceAverage heterozygosityEntire chromosomesHybrid panelPhysical mapCEPH consortium linkage mapFamily DNACEPH family DNAsPrimer pairsMarker genotypesLociEnzyme combinations