Search results for "Haplotype estimation"

showing 3 items of 3 documents

Accounting for haplotype phase uncertainty in linkage disequilibrium estimation

2007

The characterization of linkage disequilibrium (LD) is applied in a variety of studies including the identification of molecular determinants of the local recombination rate, the migration and population history of populations, and the role of positive selection in adaptation. LD suffers from the phase uncertainty of the haplotypes used in its calculation, which reflects limitations of the algorithms used for haplotype estimation. We introduce a LD calculation method, which deals with phase uncertainty by weighting all possible haplotype pairs according to their estimated probabilities as evaluated by PHASE. In contrast to the expectation-maximization (EM) algorithm as implemented in the HA…

Linkage disequilibriumGenotypeEpidemiologyPopulationValidation Studies as TopicPolymorphism Single NucleotideLinkage DisequilibriumGene FrequencyExpectation–maximization algorithmHumansComputer SimulationeducationGenetics (clinical)Genetic associationMathematicsGeneticseducation.field_of_studyModels GeneticHaplotypeComputational BiologyContrast (statistics)WeightingHaplotypesHaplotype estimationAlgorithmSoftwareGenetic Epidemiology
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Comparison of HapMap and 1000 genomes reference panels in a large-scale genome-wide association study

2017

An increasing number of genome-wide association (GWA) studies are now using the higher resolution 1000 Genomes Project reference panel (1000G) for imputation, with the expectation that 1000G imputation will lead to the discovery of additional associated loci when compared to HapMap imputation. In order to assess the improvement of 1000G over HapMap imputation in identifying associated loci, we compared the results of GWA studies of circulating fibrinogen based on the two reference panels. Using both HapMap and 1000G imputation we performed a meta-analysis of 22 studies comprising the same 91,953 individuals. We identified six additional signals using 1000G imputation, while 29 loci were ass…

Netherlands Twin Register (NTR)0301 basic medicineGlycobiologySocial Scienceslcsh:MedicineGenome-wide association study030105 genetics & heredityBiochemistryMathematical and Statistical TechniquesSociologyCell SignalingConsortiaGENETIC-VARIANTSMedicine and Health SciencesIMPUTATIONInternational HapMap Projectlcsh:ScienceGeneticsMultidisciplinaryCOMMON VARIANTSGenomicsMultidisciplinary SciencesINSIGHTSCARDIOVASCULAR-DISEASEPhysical SciencessymbolsScience & Technology - Other TopicsHealth Services ResearchGenomic Signal ProcessingStatistics (Mathematics)Research ArticleSignal TransductionGenotypingSUSCEPTIBILITY LOCIGeneral Science & TechnologyBIOLOGYSingle-nucleotide polymorphismGenomicsHapMap ProjectComputational biologyPRESSUREBiologyResearch and Analysis Methods03 medical and health sciencessymbols.namesakeMD MultidisciplinaryGenome-Wide Association StudiesGeneticsJournal Article/dk/atira/pure/keywords/cohort_studies/netherlands_twin_register_ntr_HumansStatistical Methods1000 Genomes ProjectMolecular Biology TechniquesMolecular BiologyMETAANALYSISGlycoproteinsScience & Technologylcsh:RHuman GenomeCONSORTIUMBiology and Life SciencesComputational BiologyFibrinogenHuman GeneticsCell BiologyComparative GenomicsGenome AnalysisHealth Care030104 developmental biologyBonferroni correctionlcsh:QHaplotype estimationMathematicsImputation (genetics)Meta-AnalysisGenome-Wide Association Study
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Development of an Italian RM Y-STR haplotype database: Results of the 2013 GEFI collaborative exercise.

2015

Recently introduced rapidly mutating Y-chromosomal short tandem repeat (RM Y-STR) loci, displaying a multiple-fold higher mutation rate relative to any other Y-STRs, including those conventionally used in forensic casework, have been demonstrated to improve the resolution of male lineage differentiation and to allow male relative separation usually impossible with standard Y-STRs. However, large and geographically-detailed frequency haplotype databases are required to estimate the statistical weight of RM Y-STR haplotype matches if observed in forensic casework. With this in mind, the Italian Working Group (GEFI) of the International Society for Forensic Genetics launched a collaborative ex…

Quality ControlMutation rateRegional ItalianLineage differentiationDNA PrimerY-chromosome; Rapidly mutating Y-STRs (RM Y-STRs); Haplotype; Lineage differentiation; Relative differentiation; Italy2734Biologycomputer.software_genrePathology and Forensic MedicineGeneticDatabases GeneticGeneticsHaplotype Italy Lineage differentiation Rapidly mutating Y-STRs (RM Y-STRs) Relative differentiation Y-chromosomeHaplotypeHumansY-STRCooperative BehaviorY-chromosomeDNA PrimersChromosomes Human YDatabaseBase SequenceMedicine (all)HaplotypeRelative differentiationhumanitiesForensic scienceHaplotypesItalyLineage differentiationMicrosatelliteRapidly mutating Y-STRs (RM Y-STRs)Haplotype estimationcomputerHumanForensic science international. Genetics
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