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
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 patternsPolymorphismFrogAncestryCalc: A standalone batch likelihood computation tool for ancestry inference panels catalogued in FROG-kb
Rajeevan H, Soundararajan U, Pakstis AJ, Kidd KK. FrogAncestryCalc: A standalone batch likelihood computation tool for ancestry inference panels catalogued in FROG-kb. Forensic Science International Genetics 2020, 46: 102237. PMID: 31991337, DOI: 10.1016/j.fsigen.2020.102237.Peer-Reviewed Original Research
2019
Population relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels
Pakstis AJ, Speed WC, Soundararajan U, Rajeevan H, Kidd JR, Li H, Kidd KK. Population relationships based on 170 ancestry SNPs from the combined Kidd and Seldin panels. Scientific Reports 2019, 9: 18874. PMID: 31827153, PMCID: PMC6906462, DOI: 10.1038/s41598-019-55175-x.Peer-Reviewed Original ResearchConceptsGenetic diversityPopulation relationshipsHuman populationAncestry informative SNP panelsInformative SNP panelsMajor continental regionsHuman reference populationsSNP panelIndividual populationsGenotype dataReference populationNative American populationsDiverse collectionAISNPsAllele frequency databasesWorldwide populationDiversityFrequency databaseAmerican populationReference population dataPopulationSNPsPrincipal component analysisCombined panelCluster patternsGenetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs
Pakstis AJ, Gurkan C, Dogan M, Balkaya HE, Dogan S, Neophytou PI, Cherni L, Boussetta S, Khodjet-El-Khil H, Ben Ammar ElGaaied A, Salvo NM, Janssen K, Olsen GH, Hadi S, Almohammed EK, Pereira V, Truelsen DM, Bulbul O, Soundararajan U, Rajeevan H, Kidd JR, Kidd KK. Genetic relationships of European, Mediterranean, and SW Asian populations using a panel of 55 AISNPs. European Journal Of Human Genetics 2019, 27: 1885-1893. PMID: 31285530, PMCID: PMC6871633, DOI: 10.1038/s41431-019-0466-6.Peer-Reviewed Original ResearchGenetic history of the population of Crete
Drineas P, Tsetsos F, Plantinga A, Lazaridis I, Yannaki E, Razou A, Kanaki K, Michalodimitrakis M, Perez‐Jimenez F, De Silvestro G, Renda MC, Stamatoyannopoulos JA, Kidd KK, Browning BL, Paschou P, Stamatoyannopoulos G. Genetic history of the population of Crete. Annals Of Human Genetics 2019, 83: 373-388. PMID: 31192450, PMCID: PMC6851683, DOI: 10.1111/ahg.12328.Peer-Reviewed Original ResearchConceptsHistorical recordsCretan populationMedieval historyMedieval periodArab occupationMultiple warsSmall genetic contributionContemporary recordsMiddle AgesGenetic historyIsland of CreteEastern EuropeansPopulation of CreteHistoriansCreteVenetiansOccupationCretanBiased interpretationLocal populationHistoryGenetic perspectiveRecordsIslandsConquerorsMixture 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
2017
Increasing the reference populations for the 55 AISNP panel: the need and benefits
Pakstis AJ, Kang L, Liu L, Zhang Z, Jin T, Grigorenko EL, Wendt FR, Budowle B, Hadi S, Al Qahtani MS, Morling N, Mogensen HS, Themudo GE, Soundararajan U, Rajeevan H, Kidd JR, Kidd KK. Increasing the reference populations for the 55 AISNP panel: the need and benefits. International Journal Of Legal Medicine 2017, 131: 913-917. PMID: 28070634, PMCID: PMC5491587, DOI: 10.1007/s00414-016-1524-z.Peer-Reviewed Original Research
2014
Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations
Yun L, Gu Y, Rajeevan H, Kidd KK. Application of six IrisPlex SNPs and comparison of two eye color prediction systems in diverse Eurasia populations. International Journal Of Legal Medicine 2014, 128: 447-453. PMID: 24395150, DOI: 10.1007/s00414-013-0953-1.Peer-Reviewed Original Research
2013
Worldwide 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
Genome-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
Selecting SNPs to Identify Ancestry
Sampson JN, Kidd KK, Kidd JR, Zhao H. Selecting SNPs to Identify Ancestry. Annals Of Human Genetics 2011, 75: 539-553. PMID: 21668909, PMCID: PMC3141729, DOI: 10.1111/j.1469-1809.2011.00656.x.Peer-Reviewed Original ResearchAn 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
A variant of the endothelial nitric oxide synthase gene (NOS3) associated with AMS susceptibility is less common in the Quechua, a high altitude Native population.
Wang P, Ha AY, Kidd KK, Koehle MS, Rupert JL. A variant of the endothelial nitric oxide synthase gene (NOS3) associated with AMS susceptibility is less common in the Quechua, a high altitude Native population. High Altitude Medicine & Biology 2010, 11: 27-30. PMID: 20367485, DOI: 10.1089/ham.2009.1054.Peer-Reviewed Original ResearchConceptsHigh-altitude pulmonary edemaEndothelial nitric oxide synthaseAcute mountain sicknessNitric oxideG alleleEndothelial nitric oxide synthase geneAltitude-related illnessesG894T polymorphismNitric oxide synthase geneNitric oxide synthaseAltitude pulmonary edemaOxide synthase geneNOS3 genotypesPulmonary edemaOxide synthaseVascular enzymeMountain sicknessT polymorphismBlood flowAltitude toleranceNOS3AMS susceptibilityHypoxic environmentHigh-altitude native populationsEnvironmental hypoxia
2008
The 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 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
2003
Selective Pressure has not Acted Against Hypercoagulability Alleles in High‐Altitude Amerindians
Rupert J, Monsalve M, Kidd K, Tan C, Hochachka P, Devine D. Selective Pressure has not Acted Against Hypercoagulability Alleles in High‐Altitude Amerindians. Annals Of Human Genetics 2003, 67: 426-432. PMID: 12940916, DOI: 10.1046/j.1469-1809.2003.00043.x.Peer-Reviewed Original ResearchMeSH KeywordsAltitudeGene FrequencyGenotypeHumansIndians, South AmericanSelection, GeneticThrombophiliaGenetic Polymorphisms in the Renin‐Angiotensin System in High‐Altitude and Low‐Altitude Native American Populations
Rupert J, Kidd K, Norman L, Monsalve M, Hochachka P, Devine D. Genetic Polymorphisms in the Renin‐Angiotensin System in High‐Altitude and Low‐Altitude Native American Populations. Annals Of Human Genetics 2003, 67: 17-25. PMID: 12556231, DOI: 10.1046/j.1469-1809.2003.00004.x.Peer-Reviewed Original Research