Characterization of publicly available SNPs in the Korean population

Lee, Seong-Gene; Hong, Sunghee; Yoon, Yongsook; Yang, Insil; Song, Kyuyoung

doi:10.1002/humu.24

Cited by 14 publications

(12 citation statements)

References 14 publications

(18 reference statements)

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“…This result indicates that SNPs available at the public SNP database have very limited numbers of allele frequency data in a particular population. Furthermore, this result, together with previous available data showing only limited SNP characterization using the Korean population (Lee et al 2001), suggests that, using the Korean population, an extensive characterization of publicly available SNPs should be undertaken prior to use of those candidate SNPs for disease association studies.…”

Section: Ethnic Differences In Snp Allele Frequencymentioning

confidence: 79%

Characterization of 458 single nucleotide polymorphisms of disease candidate genes in the Korean population

et al. 2003

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Single nucleotide polymorphisms (SNPs) are considered as very promising genetic markers for complex disease gene hunting. However, it has been demonstrated that there are significant ethnic differences in genetic variations. In order to investigate the genetic variations in the Korean population and their ethnic differences, a large number of SNPs of 161 disease candidate genes were collected from a publicly available SNP database and then tested for the distribution of allele frequency in the Korean population. Of all 458 SNPs tested, approximately 43.9% were polymorphic in the Korean population, whereas 44.5% were monomorphic. The remaining 11.6% were failed in the test. Significant differences have been observed when SNP allele frequency pattern of Koreans was compared with those of Caucasians and Africans, whereas this pattern was highly similar between Korean and Japanese populations. Our data indicate that although many of the SNPs available in publicly available database, especially coding-region SNPs (cSNPs), can be used as informative genetic markers for disease association studies, an extensive verification of public SNPs in a particular population studied should be undertaken prior to their association studies.

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Section: Ethnic Differences In Snp Allele Frequencymentioning

confidence: 79%

Characterization of 458 single nucleotide polymorphisms of disease candidate genes in the Korean population

et al. 2003

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“…Genomic DNA was isolated from peripheral blood samples following standard procedures (Lee et al, 2001). Signed informed consent was obtained from all study subjects or their tutors according to the institutional review board policies.…”

Section: Genotypingmentioning

confidence: 99%

Lamin A/C mutations associated with familial and sporadic cases of dilated cardiomyopathy in Koreans

Song

Dubé²,

Lim³

et al. 2007

Exp Mol Med

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Dilated cardiomyopathy (DCM) is characterized by cardiac dilation and systolic dysfunction. So far sixteen genes have been shown to cause autosomal dominant familial dilated cardiomyopathy (FDC). We identified a large Korean family from the Jeju island showing a clear Mendelian inheritance of FDC. A genomewide linkage scan at 9 cM marker density identified a peak multipoint LOD score of 2.82 at D1S195. Haplotyping of the region with 15 additional markers defined a candidate interval that included a known candidate gene encoding the lamin A/C (LMNA). Sequencing of the LMNA exons revealed one missense mutation at C568T (Arg190Trp) in the -helical rod domain of the LMNA gene cosegregating with FDC with conduction-system disease. The same mutation was found in patients of another Korean family with FDC without conduction-system disease. Upon screening 14 sporadic DCM cases, we found three LMNA mutations including a case having a previously described (Glu161Lys) mutation and two having novel mutations (Glu53Val and Glu186Lys). Our results suggest that variable genotypes of laminopathy are implicated in not only familial but also considerable proportion of sporadic DCM.

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“…Although a pooled DNA sequencing approach is not highly accurate for detecting SNPs with a minor allele frequency of less than 10%, it still is a useful approach for identifying informative SNP markers and estimating their allele frequencies in a cost-effective way. 13,14 We have shown that the accuracy of a pooled DNA sequencing approach is within 9% of that determined by sequencing each individual in the pool. 14 The markers were considered to be monomorphic only when the peak patterns in both directions were clear, without the background signal of a minor allele.…”

Section: Resultsmentioning

confidence: 95%

“…13,14 We have shown that the accuracy of a pooled DNA sequencing approach is within 9% of that determined by sequencing each individual in the pool. 14 The markers were considered to be monomorphic only when the peak patterns in both directions were clear, without the background signal of a minor allele. When a weak signal of a minor allele was present in the pool, those markers were categorized to have minor allele frequencies of less than 10%, as shown on previous analyses.…”

Section: Resultsmentioning

confidence: 95%

“…14 In this report, we present allele frequencies of 406 publicly available cSNPs in 24 Koreans. Although a pooled DNA sequencing approach is not highly accurate for detecting SNPs with a minor allele frequency of less than 10%, it still is a useful approach for identifying informative SNP markers and estimating their allele frequencies in a cost-effective way.…”

Section: Resultsmentioning

confidence: 99%

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Allele frequency determination of publicly available cSNPs in the Korean population

Lee

Yoon

Hong

et al. 2002

Genetics in Medicine

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Purpose: As a first step toward the construction of a single-nucleotide polymorphism (SNP) database of the Korean population, the authors determined the allele frequencies of 406 cSNPs selected from the public database.Methods: A pooled DNA sequencing approach was used to determine the allele frequencies of 406 cSNPs selected from 120 genes in 24 individuals. Results: Of 406 cSNPs, 53% were monomorphic in the Korean samples. Among tested SNPs, 292 SNPs (72%) were uncommon (minor allele Ͻ20%) and 114 SNPs (28%) were common (minor allele Ն20%) in our population. Conclusion: An extensive SNP characterization would be necessary, and the ethnic and population-based differences should be considered in the selection of SNPs for the study of complex diseases with association mapping methods. Genet Med 2002:4(6, Supplement):49S-51S. The central aim of genetics is to correlate specific molecular variation with particular phenotype changes. Since the human genome draft sequence was announced in June 2000, it has become possible to understand the spectrum of genetic variation in the human gene pool and its relation to diseases, individual responses to environmental factors, and biological processes such as development and aging. Geneticists have so far used familial linkage methods for studying simple single-gene diseases. 1 However, complex, high-incidence, multigene diseases are thought to require a different approach, that is, an association study, for which single-nucleotide polymorphisms (SNPs) can play a key role. [1][2][3] SNPs consist of the most abundant form of genetic variation and have great potential for mapping complex genetic traits. 4 -7 Because of their potential as genetic markers, scientists in the public and private sectors have begun to focus their attention on searching for SNPs throughout the human genome. 3,8 -12 For whole-genome association studies, it is estimated that approximately 100,000 to 500,000 SNPs would be required. 5,6 Currently, a great deal of effort is being invested in the identification of SNPs. As of June 14, 2002, 4,275,093 SNPs had been deposited into public databases (http://www.ncbi.nlm.nih. gov/SNP) compared with 7,000 SNPs in April 1999. As the SNP identification process accelerates, it becomes necessary to characterize a large number of publicly available SNPs in a population. For an association mapping study, SNP allele frequencies in the population would be critical.We decided to characterize publicly available cSNPs in the Korean population because (1) many SNPs are publicly available already, (2) those SNPs were discovered using rather limited samples, (3) some SNPs may not be common in a given population, and (4) SNP allele frequencies in the population would be critical for an association mapping study. Here, we present the allele frequencies of 406 publicly available cSNPs in 24 Koreans. MATERIALS AND METHODS Collection of candidate cSNPsCandidate cSNPs were identified in the Whitehead Institute for Genome Research (http://www.genome.wi.mit.edu) databases. We picke...

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Characterization of publicly available SNPs in the Korean population

Cited by 14 publications

References 14 publications

Characterization of 458 single nucleotide polymorphisms of disease candidate genes in the Korean population

Characterization of 458 single nucleotide polymorphisms of disease candidate genes in the Korean population

Lamin A/C mutations associated with familial and sporadic cases of dilated cardiomyopathy in Koreans

Allele frequency determination of publicly available cSNPs in the Korean population

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