We separated an Aw10 allele by allele-specific sequencing in two Aw10/B101 samples that had the AweakB phenotype. Two samples with the A102/B101 genotype were also tested as a control. The reverse primers using position 930 at exon7 were designed for allele-specific sequencing. The differential positions were a total of 52 points for distinguishing the A-allele from the B-allele. Although overlaps with another haplotype allele that showed a minor chromatographic peak were observed in almost all the points, the specific allele-separation rate was 100% (52/52) by assessing the dominance in the chromatographic peak height. Based on the separation rate in the two cases with Aw10/B101 and the two AB controls, allele-specific sequencing is a convenient and reliable method for the separating the A-allele and B-allele in a clinical laboratory.
Alleles ; Genotype ; Haplotypes ; Phenotype

Y-STR haplotyping is a powerful forensic and anthropological tool for identifying male lineages. We used high-resolution Y-STR haplotyping to evaluate the possibility of an ancestral relationship between two individuals with the different surname. Of the 17 Y-STRs genotyped, 16 had identical alleles in two individuals, except for an unambiguously sporadic mutation (one-step mutation) at DYS385 locus. The common allele 11.1 (U3Ains) at DYS439 locus was also observed in these two individuals. Sequencing analysis of these alleles of two samples demonstrated an A insertion at base 3 upstream from the repeat region's first GATA motif. These findings suggested that two individuals were paternally related, even if male individuals live with different surname.
Alleles ; Haplotypes ; Humans ; Male

OBJECTIVE: The aim of this study was to investigate the genetic association of the FAT gene with schizophrenia in the Korean population, as well as analyzing the association of FAT gene with clinical variables. METHODS: Four variants within the FAT gene were investigated in 189 patients with schizophrenia and 119 healthy controls (rs2306987 A/C, rs2306990 T/C, rs2637777 G/T, and rs2304865 G/C). RESULTS: Significant association at the rs273777 with schizophrenia was observed; however, rs2306987, rs2306990, and rs2304865 were not associated with schizophrenia. Haplotype analyses revealed that the haplotype A/T/T/G was associated with a significantly protective effect. Sliding window analysis (rs2637777 G/T and rs2304865 G/C) revealed the more common T/G haplotype, included in the A/T/T/G protective combination, showed a small protective effect, in particular the effect was due to the rs273777 T variant (minor allele). CONCLUSION: The present finding suggests that FAT polymorphism may play a putative role in the susceptibility to schizophrenia in the Korean population. Further studies using a larger number of subjects should be performed to determine whether the FAT gene polymorphism may be truly involved in the development of schizophrenia.
Cadherins ; Haplotypes ; Humans ; Schizophrenia

The thirteen DRB1, 6 DQA1, and 5 DQB1 alleles were defined in 362 healthy Korean controls using reverse dot blot hybridization method. The twenty-four immobilized SSOs for DRB1, 8 for DQA1, and 6 for DQB1 were used for this study. The frequencies of genotypes were DRB104 (17.1'Yo), '09 (13.1%), and '13 (11.6%); DQA1'01 (46.7%), 03 (30.8%), and '05 (11.7%); DQB1*03 (39.5%), '06 '(29.8%), and 05 (16.0%). ...continue...
Alleles* ; Genotype ; Haplotypes* ; HLA-DRB1 Chains

Recently, studies on mitochondrial DNA (mtDNA) have increased rapidly. Conventional parameters, such as diversity index, pairwise comparison, are used to interpret and validate data on autosomal DNA; however, the use of these parameters to validate data from mitochondrial DNA databases (mtDNA DBs) needs to be verified because of the different transmission patterns of mtDNA. This study was done to verify the use of these conventional parameters and to test the "coverage concept" for a new parameter. The mtDNA DB is not very big; however, it is necessary to check how the change in parameters corresponds to the DB size. For this, we artificially rearranged a Korean DB into several small sub-DBs of variable sizes. The results show that the diversity in nucleotide variations and the different haplotype numbers do not vary as the size of DB increases. However, the "coverage" changed a lot. The coverage increased from 0.113 in a DB of 100 people to 0.260 in a DB of 653 people. Additionally, using the "coverage concept", we predicted how the total number of haplotypes changed with variations in the sub-DB size and compared the predicted result with final result. In conclusion, "coverage", in addition to conventional statistical parameters, can be used to check the usability of an mtDNA DB. Finally, we tried to predict the size of the whole mtDNA number in Korea using "saturation concept".
DNA ; DNA, Mitochondrial* ; Haplotypes ; Korea ; Phylogeny

There is increasing interest in the application of personalized therapy to healthcare to increase the effectiveness of and reduce the adverse reactions to treatment. Pharmacogenomics is a core element in personalized therapy and pharmacogenomic research is a growing field. Understanding pharmacogenomic research tools enables better design, conduct, and analysis of pharmacogenomic studies, as well as interpretation of pharmacogenomic results. This review provides a general and brief introduction to pharmacogenomics research tools, including genotyping technology, web-based genome browsers, and software for haplotype analysis.
Delivery of Health Care ; Genome ; Haplotypes ; Humans ; Pharmacogenetics*

In this study the population data at seven STR loci on the Y chromosome, DYS19, DYS388, DYS389, DYS390, DYS391, DYS392 and DYS393 are described for 1054 Koreans. In each locus, 6-22 alleles were noted, and allelic distribution patterns were found to be different from those of other populations. The PD was 0.28-0.886 and no interallele was noted. In 388 father-son pairs, 9 cases of mutation, one in DYS19 locus, one in DYS388, two in DYS389, three in DYS391, one in DYS392 and one in DYS393 locus were noted. In total 563 different haplotypes were noted. 630 cases shared the same haplotype with someone among 1054 object studied. Even in case which showed different haplotypes, many cases showed differences only in one locus and genotypes in the remaining seven loci were the same. The discrimination between mutation and different haplotypes seems to be problematic in these situations. Experiences for the large scale haplotype data base in Koreans were described.
Alleles ; Discrimination (Psychology) ; Genotype ; Haplotypes* ; Y Chromosome*

In this study the population data at seven STR loci on the Y chromosome, DYS19, DYS388, DYS389, DYS390, DYS391, DYS392 and DYS393 are described for 1054 Koreans. In each locus, 6-22 alleles were noted, and allelic distribution patterns were found to be different from those of other populations. The PD was 0.28-0.886 and no interallele was noted. In 388 father-son pairs, 9 cases of mutation, one in DYS19 locus, one in DYS388, two in DYS389, three in DYS391, one in DYS392 and one in DYS393 locus were noted. In total 563 different haplotypes were noted. 630 cases shared the same haplotype with someone among 1054 object studied. Even in case which showed different haplotypes, many cases showed differences only in one locus and genotypes in the remaining seven loci were the same. The discrimination between mutation and different haplotypes seems to be problematic in these situations. Experiences for the large scale haplotype data base in Koreans were described.
Alleles ; Discrimination (Psychology) ; Genotype ; Haplotypes* ; Y Chromosome*

SUMMARY: HapAnalyzer is an analysis system that provides minimum analysis methods for the SNP-based association studies. It consists of Hardy-Weinberg equilibrium (HWE) test, linkage disequilibrium (LD) computation, haplotype reconstruction, and SNP (or haplotype)-phenotype association assessment. It is well suited to a case-control association study for the unrelated population.
Case-Control Studies ; Haplotypes* ; Linkage Disequilibrium

In this paper, we provide an overview of statistical models for haplotype-based association studies, and summarize their features based on the design matrix. We classify the design matrix into the two types: direct and indirect. For these two kinds of matrices, we present and compare characteristics using a simple hypothetical example, and a real data set. The motivation behind this study was to provide practitioners with an improved understanding, to facilitate the informed selection of the appropriate haplotype-based model and to improve the interpretability of the models.
Case-Control Studies ; Dataset ; Haplotypes ; Models, Statistical ; Motivation