• Genomics & Informatics
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• v.7 no.1
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• pp.13-19
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• 2009

Osteoporosis is characterized by impaired osteogenesis. BMD is a major determinant of bone strength. The role of the VDR gene in predisposition to primary osteoporosis has been recognized. However, population-based case-control studies have been reported controversial results for known candidate genes in an ethnically distinct group. To determine the genetic effects of VDR variants on osteoporosis and BMD, we directly sequenced the VDR gene in 24 unrelated Korean individuals and identified eighteen sequence variants. We investigated the potential involvement of eight SNPs in osteoporosis in postmenopausal women (n = 729). Two SNPs (LD) in intron 2, -5294G>C (rs2238135) and -4817G>A (rs17882443) showed the evidence of association with enhanced BMD of the femoral neck ($p_{additive}$=0.031 for rs2238135; $p_{additive}$=0.017 and $p_{dominant}$= 0.019 for 17882443). Moreover, VDR -4817G>A was significantly associated with protective effect on all fracture risk ($p_{recessive}$=0.035, OR=0.2, 95% CI=$0.05{\sim}0.89$), and tended to be higher BMD values at various proximal femur sites. Therefore, we suggest that the -4817G>A may be useful genetic marker for vitamin D-related metabolism and may have an important role in the increased BMD of the proximal femur in postmenopausal Korean women.

• Korean Journal of Clinical Laboratory Science
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• v.44 no.1
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• pp.24-30
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• 2012

In this study, we have examined the effects of the storage time and temperature on DNA quality and have also studied the effects of the hydration buffer in which DNA is dissolved. This study was performed using 160 human blood samples collected with informed consent from 2007 to 2008 in the hospital where this cohort study was performed. The DNA extracted was dissolved using distilled water (DW) or Tris-EDTA (TE) buffer, and stored in the deep freezer or refrigerator for up to 10 weeks at $-70^{\circ}C$, $-20^{\circ}C$, $4^{\circ}C$, and $25^{\circ}C$, respectively. DNA integrity was determined by the degree of smearing of DNA on the gel. After four weeks, all of the 20 DNA samples dissolved in DW and stored at $25^{\circ}C$ were entirely degraded. After 10 weeks, 6 of the 20 DNA samples dissolved in TE buffer and stored at $25^{\circ}C$ were fairly degraded, and 4 of the 20 DNA samples dissolved in DW and stored at $4^{\circ}C$ were fairly degraded. The 20 DNA samples dissolved in TE buffer and stored at $4^{\circ}C$ were stable for 10 weeks. DNA samples stored at $-20^{\circ}C$ and $-70^{\circ}C$ did not appear to degrade in either DW or TE buffer, even at the 10-week point. We suggest that TE buffer should use for DNA elution, in order to protect against degradation and to preserve DNA for a long period of time, and the samples should be stored at $-20^{\circ}C$ or $-70^{\circ}C$.

• Genomics & Informatics
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• v.3 no.3
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• pp.74-79
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• 2005

The H19 gene, located at human chromosome 11p15.5, is imprinted in most normal human tissues. However, imprinting is often lost in tumors suggesting H19 is a putative tumor suppressor. We analyzed the single nucleotide polymorphisms (SNPs) of a 16 kb region that includes the H19 gene and its imprinting control region (ICR) in the Korean population. To identify SNPs, we directly sequenced this region in 18 Korean subjects. We identified 64 SNPs, of which 7 were in the exons of H19, 2 were in the introns, 14 were in the 3' intergenic region and 41 were in the 5' intergenic region. Of the 64 SNPs, 21 had not previously been reported and thus appear to be unique to the Korean population. The identified SNPs of H19 in the Korean population may eventually be useful as genetic markers associated with various diseases. In this study, 7 of the 64 identified SNPs were at CTCF binding sites in the ICR and may affect regulation of H19 gene imprinting. Thus, several genetic variations of the H19 gene may be important markers in human diseases that involve genomic imprinting, including cancer.

• Genomics & Informatics
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• v.10 no.1
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• pp.65-67
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• 2012

We have discovered copy number variations (CNVs) in 3,578 Korean individuals with the Affymetrix Genome-Wide SNP array 5.0, and 4,003 copy number variation regions (CNVRs) were defined in a previous study. To explore the details of the variants easily in related studies, we built a database, cataloging the CNVs and related information. This system helps researchers browsing these variants with gene and structure variant annotations. Users can easily find specific regions with search options and verify them from system-integrated genome browsers with annotations.

• Proceedings of the Microbiological Society of Korea Conference
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• 2000.05a
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• pp.52-57
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• 2000

• Journal of Animal Science and Technology
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• v.62 no.6
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• pp.952-955
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• 2020

Bacteroides sp. CACC 737 was isolated from a feline, and its potential probiotic properties were characterized using functional genome analysis. Whole-genome sequencing was performed using the PacBio RSII and Illumina HiSeq platforms. The complete genome of strain CACC 737 contained 4.6 Mb, with a guanine (G) + cytosine (C) content of 45.8%, six cryptic plasmids, and extracellular polysaccharide gene as unique features. The strain was beneficial to animal health when consumed as feed, for example, for ameliorating immunological dysfunctions and metabolic disorders. The genome information adds to the comprehensive understanding of Bacteroides sp. and suggests potential animal-related industrial applications for this strain.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.100-100
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• 2005

• The Korea Genome Conference
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• 2003.09a
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• pp.53.2-53.2
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• 2003

• Biotechnology and Bioprocess Engineering:BBE
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• v.5 no.5
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• pp.307-312
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• 2000

As the first assembly of the human genome was announced on June 26, 2000, we have entered post genome era. The genome sequence represents a new starting point for science and medicine with possible impact on research across the life sciences. In this review I tried to offer brief summaries of history and progress of the Human Genome Project and two major challenges ahead, functional genomics and DNA sequence variation research.

• Genomics & Informatics
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• v.6 no.4
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• pp.231-234
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• 2008

Precise and reliable identification of CNV is still important to fully understand the effect of CNV on genetic diversity and background of complex diseases. SNP marker has been used frequently to detect CNVs, but the analysis of SNP chip data for identifying CNV has not been well established. We compared various normalization methods for CNV analysis and suggest optimal normalization procedure for reliable CNV call. Four normal Koreans and NA10851 HapMap male samples were genotyped using Affymetrix Genome-Wide Human SNP array 5.0. We evaluated the effect of median and quantile normalization to find the optimal normalization for CNV detection based on SNP array data. We also explored the effect of Robust Multichip Average (RMA) background correction for each normalization process. In total, the following 4 combinations of normalization were tried: 1) Median normalization without RMA background correction, 2) Quantile normalization without RMA background correction, 3) Median normalization with RMA background correction, and 4) Quantile normalization with RMA background correction. CNV was called using SW-ARRAY algorithm. We applied 4 different combinations of normalization and compared the effect using intensity ratio profile, box plot, and MA plot. When we applied median and quantile normalizations without RMA background correction, both methods showed similar normalization effect and the final CNV calls were also similar in terms of number and size. In both median and quantile normalizations, RMA backgroundcorrection resulted in widening the range of intensity ratio distribution, which may suggest that RMA background correction may help to detect more CNVs compared to no correction.