• Journal of Genetic Medicine
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• 제13권1호
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• pp.20-25
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• 2016

Purpose: Xeroderma pigmentosum (XP) is rare autosomal recessive genetic disorder of DNA repair in which the ability to repair damage caused by ultraviolet light is deficient. We reported the first molecularly confirmed Korean patient of XP by targeted exome sequencing. The prevalence of XP included all subtype and carrier frequency of XP-A the using public data were estimated for the first time in South Korea. Materials and Methods: We described a 4-year-old Korean girl with clinical diagnosis of XP. We performed targeted exome sequencing in the patient for genetic confirmation considering disease genetic heterogeneity and for differential diagnosis. We verified a carrier frequency of c.390-1G>C in XPA gene known as mutational hot spot using Korean Reference Genome Data Base. We estimated the period prevalence of all subtypes of XP based on claims data of the Health Insurance Review and Assessment Service in South Korea. Results: We identified homozygous splicing mutation of XPA (c.390-1G>C) in the patient. The carrier frequency of risk for XPA (c.390-1G>C) was relatively high 1.608 e-03 (allele count 2/1244). The prevalence of XP in South Korea was 0.3 per million people. Conclusion: We expect that c.390-1G>C is hot spot for the mutation of XPA and possible founder variant in South Korea. However, the prevalence in South Korea was extremely low compared with Western countries and Japan.

• Genomics & Informatics
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• 제13권2호
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• pp.31-39
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• 2015

Sequencing depth, which is directly related to the cost and time required for the generation, processing, and maintenance of next-generation sequencing data, is an important factor in the practical utilization of such data in clinical fields. Unfortunately, identifying an exome sequencing depth adequate for clinical use is a challenge that has not been addressed extensively. Here, we investigate the effect of exome sequencing depth on the discovery of sequence variants for clinical use. Toward this, we sequenced ten germ-line blood samples from breast cancer patients on the Illumina platform GAII(x) at a high depth of ${\sim}200{\times}$. We observed that most function-related diverse variants in the human exonic regions could be detected at a sequencing depth of $120{\times}$. Furthermore, investigation using a diagnostic gene set showed that the number of clinical variants identified using exome sequencing reached a plateau at an average sequencing depth of about $120{\times}$. Moreover, the phenomena were consistent across the breast cancer samples.

• Journal of Genetic Medicine
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• 제6권2호
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• pp.146-154
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• 2009

Multiplex ligation dependent probe amplification (MLPA)은 탐침자를 표적지에 교잡시킨 후, ligation 시키고, 그 산물을 중합효소연쇄반응으로 증폭시킴으로써 표적지의 존재여부 또는 농도를 확인할 수 있는 방법으로, 그 원리가 소개된 이래로 여러 유전자들에 대한 거대결실 및 중복돌연변이에 대한 탐색에 이용되었다. 유전자진단은 질환에 관련된 유전자에 대한 돌연변이를 탐색함으로써 질환을 진단하는 방법으로, 단일유전자 결핍 질환에 대한 유전자진단은 주로 중합효소연쇄반응과 염기서열 분석 방법을 통한 점돌연변이의 탐색에 집중되어 있다. 거대결실 또는 중복돌연변이의 경우, 특히 이형접합자를 형성하게 되는 경우는 중합효소 연쇄반응을 통하여 결실 또는 중복돌연변이 여부의 확인이 힘들다. PCR 방법에 기초하여 유전자의 농도(gene dosage)를 알 수 있는 방법으로 MLPA 방법이 소개되면서 거대결실 또는중복돌연변이를 포함하고 있던 질병 관련돌연변이들의 규명이 한층 쉬워졌다. MLPA의 원리를 응용하여 단순한 유전자의 농도 측정뿐 아니라 유전자내의 메칠화양상의 차이를 확인하거나, 염색체의 배수체 이상 등 염색체이상의 돌연변이 규명과, 전체 유전자의 크기가 비교적 커서 거대결실 돌연변이를 많이 동반하는, 주로 우성유전의 암 관련 유전자 돌연변이의 규명에 유용하게 이용된다. MLPA는 상용적인 중합효소연쇄반응으로 확인할 수 없는 유전자의 농도를 효과적으로 규명할 수 있는 방법으로, 적은 양의 주형 DNA만을 사용하고, 한가지의 실험원리로 다양한 응용이 가능하며 high-throughput이 가능한 장점을 가지는 반면, 주형 DNA의 질에 결과의 의존도가 높고, 민족 또는 개인간의 차이를 보일 수 있는 표적 DNA 염기서열 내의 single nucleotide polymorphism (SNP) 등으로 인해 분석의 오류가 생길 수 있으며, 양적 차이를 규명하는 것이므로 수 차례의 대조군 검사가 함께 진행되어야 하는 단점이 있다. 여기서는 MLPA를 이용하여 질병유전자의 돌연변이를 밝힌 사례를 바탕으로 MLPA의 원리와 탐색할 수 있는 돌연변이의 종류, 그리고 이 방법의 장단점에 대해 고찰해 보고자 한다.

• KSBB Journal
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• 제24권4호
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• pp.410-414
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• 2009

단염기 다양성 (Single-Nucleotide Polymorphisms, SNPs)은 핵산수준에서의 개개인의 유전 서열간의 차이를 나타내는 말로 최근 맞춤의약 분야에서 각광 받고 있다. 일반적으로 SNPs존재 유무를 확인하는데 주로 사용되는 방법은 ABI automated DNA sequencer와 같은 대용량 염기서열 결정 기계에서 산출되는 결과물 파일로부터 DNA서열을 추출하여 BLAST와 같은 상동성 검색을 수행하는 것이다. 본 논문에서는 사용자로부터 참조서열, AB1파일, SNPs 존재 가능성을 가진 염기의 위치 정보를 입력 값으로 받아 해당 위치에 존재하는 염기의 SNPs 치환 및 heterozygosity 여부를 확인 할 수 있는 프로그램인 SNPchaser를 개발하였다. 특정 유전자 서열 내에서 SNPs를 보이는 염기의 위치에 대한 정보를 사용자가 알고 있는 경우, 전체 유전자 서열에 대해 SNPs유무를 조사할 필요 없이 SNPs를 보인다고 보고된 위치의 염기를 조사하여 SNPs유무를 판단하고, 해당지역의 염기의 chromatogram정보를 사용자에게 제공하는 기능을 가지고 있다. 또한 SNPchaser는 사람과 같은 2배체의 염색체를 가진 생명체에 존재 하는 SNPs지역의 염기에 대한 heterozygosity여부를 사용자가 손쉽게 판별할 수 있도록 하였다. 본 논문에서 개발한 SNPchaser는 http://www.bioinformatics.ac.kr/SNPchaser에서 사용 가능하다.

• Journal of Genetic Medicine
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• 제12권2호
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• pp.118-122
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• 2015

Noninvasive prenatal test (NIPT) is a novel screening method for the diagnosis of fetal chromosomal aneuploidies. NIPT is based on technology that detects cell-free fetal DNA in maternal plasma and analyzes it with massively parallel sequencing technology to determine whether the fetus is at risk of trisomy 21, trisomy 18, trisomy 13 or sex chromosome abnormalities (SCAs). NIPT has been reported to have sensitivity of 99% and a false positive rate of less than 1% for detecting trisomy 21 and trisomy 18. Although extension of the application of NIPT to other SCAs has been attempted, there are concerns in extending NIPT to SCAs because of maternal or fetal mosaicism, undetected maternal SCAs, and multiple pregnancies. Recently, we assessed a pregnancy with the rare Turner syndrome mosaicism 45, X/47, XXX, which was reported as 45, X with NIPT. We present the case here and briefly review the current literatures on NIPT in testing for fetal monosomy X. To the best of our knowledge, this is the first report of the 45, X/47, XXX mosaicism in Korea to be reported as 45, X by NIPT with whole genome sequencing. This case report will provide valuable information for counseling women who want to undergo NIPT.

• Journal of Genetic Medicine
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• 제12권2호
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• pp.109-117
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• 2015

Purpose: Mitochondrial diseases are clinically and genetically heterogeneous disorders, which make their exact diagnosis and classification difficult. The purpose of this study was to identify pathogenic mitochondrial DNA (mtDNA) mutations in 2 Korean families with myoclonic epilepsy with ragged-red fibers (MERRF) and Leigh syndrome, respectively. Materials and Methods: Whole mtDNAs were sequenced by the method of mtDNA-targeted next-generation sequencing (NGS). Results: Two causative mtDNA mutations were identified from the NGS data. An m.8344A>G mutation in the tRNA-Lys gene (MT-TK) was detected in a MERRF patient (family ID: MT132), and an m.9176T>C (p.Leu217Pro) mutation in the mitochondrial ATP6 gene (MT-ATP6) was detected in a Leigh syndrome patient (family ID: MT130). Both mutations, which have been reported several times before in affected individuals, were not found in the control samples. Conclusion: This study suggests that mtDNA-targeted NGS will be helpful for the molecular diagnosis of genetically heterogeneous mitochondrial diseases with complex phenotypes.

• Journal of Genetic Medicine
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• 제12권2호
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• pp.79-84
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• 2015

Purpose: We developed and validated a fetal trisomy detection method for use as a noninvasive prenatal test (NIPT) including a Clinical Laboratory Improvement Amendments (CLIA)-certified bioinformatics pipeline on a cloud-based computing system using both Illumina and Life Technology sequencing platforms for 221 Korean clinical samples. We determined the necessary proportions of the fetal fraction in the cell-free DNA (cfDNA) sample for NIPT of trisomies 13, 18, and 21 through a limit of quantification (LOQ) test. Materials and Methods: Next-generation sequencing libraries from 221 clinical samples and three positive controls were generated using Illumina and Life Technology chemistries. Sequencing results were uploaded to a cloud and mapped on the human reference genome (GRCh37/hg19) using bioinformatics tools. Based on Z-scores calculated by normalization of the mapped read counts, final aneuploidy reports were automatically generated for fetal aneuploidy determination. Results: We identified in total 29 aneuploid samples, and additional analytical methods performed to confirm the results showed that one of these was a false-positive. The LOQ test showed that the proportion of fetal fraction in the cfDNA sample would affect the interpretation of the aneuploidy results. Conclusion: Noninvasive chromosome examination (NICE), a CLIA-certified NIPT with a cloud-based bioinformatics platform, showed unambiguous success in fetus aneuploidy detection.

• BMB Reports
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• 제45권1호
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• pp.44-46
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• 2012

Recent advances in high-throughput genotyping technologies have enabled us to conduct a genome-wide association study (GWAS) on a large cohort. However, analyzing millions of single nucleotide polymorphisms (SNPs) is still a difficult task for researchers conducting a GWAS. Several difficulties such as compatibilities and dependencies are often encountered by researchers using analytical tools, during the installation of software. This is a huge obstacle to any research institute without computing facilities and specialists. Therefore, a proper research environment is an urgent need for researchers working on GWAS. We developed BioSMACK to provide a research environment for GWAS that requires no configuration and is easy to use. BioSMACK is based on the Ubuntu Live CD that offers a complete Linux-based operating system environment without installation. Moreover, we provide users with a GWAS manual consisting of a series of guidelines for GWAS and useful examples. BioSMACK is freely available at http://ksnp.cdc.go.kr/biosmack.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제20권2호
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• pp.114-123
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• 2017

Purpose: The goal of this study was the early diagnosis of ABCB11 spectrum liver disorders, especially those focused on benign recurrent intrahepatic cholestasis and progressive familial intrahepatic cholestasis. Methods: Fifty patients presenting neonatal cholestasis were evaluated to identify underlying etiologies. Genetic analysis was performed on patients suspected to have syndromic diseases or ABCB11 spectrum liver disorders. Two families with proven ABCB11 spectrum liver disorders were subjected to genetic analyses to confirm the diagnosis and were provided genetic counseling. Whole exome sequencing and Sanger sequencing were performed on the patients and the family members. Results: Idiopathic or viral hepatitis was diagnosed in 34%, metabolic disease in 20%, total parenteral nutrition induced cholestasis in 16%, extrahepatic biliary atresia in 14%, genetic disease in 10%, neonatal lupus in 2%, congenital syphilis in 2%, and choledochal cyst in 2% of the patients. The patient with progressive familial intrahepatic cholestasis had novel heterozygous mutations of ABCB11 c.11C>G (p.Ser4*) and c.1543A>G (p.Asn515Asp). The patient with benign recurrent intrahepatic cholestasis had homozygous mutations of ABCB11 c.1331T>C (p.Val444Ala) and heterozygous, c.3084A>G (p.Ala1028Ala). Genetic confirmation of ABCB11 spectrum liver disorder led to early liver transplantation in the progressive familial intrahepatic cholestasis patient. In addition, the atypically severe benign recurrent intrahepatic cholestasis patient was able to avoid unnecessary liver transplantation after genetic analysis. Conclusion: ABCB11 spectrum liver disorders can be clinically indistinguishable as they share similar characteristics related to acute episodes. A comprehensive genetic analysis will facilitate optimal diagnosis and treatment.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.123-123
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• 2017

In spite of the potential medicinal significance and a wide range of pharmacologic properties of Platycodon grandiflorum, the molecular mechanism of its roots is still unknown. The present study was conducted to profile proteins from 3, 4 and 5 months aged diploid and tetraploid roots of Platycodon grandiflorum using high throughput proteome approach. Two-dimensional gels stained with CBB, a total of 68 differential expressed proteins were identified from the diploid root out of 767 protein spots using image analysis by Progenesis SameSpot software. Out of total differential expressed spots, 29 differential expressed protein spots (${\geq}2-fold$) were analyzed using LTQ-FTICR MS whereas a total of 24 protein spots were up-regulated and 5 protein spots were down-regulated. On the contrary, in the case of tetraploid root, a total of 86 differential expressed proteins were identified from tetraploid root out of 1033 protein spots of which a total of 39 differential expressed protein spots (${\geq}2-fold$) were analyzed using LTQ-FTICR MS whereas a total of 21 protein spots were up-regulated and a total of 18 protein spots were down-regulated. It was revealed that the identified proteins from the explants were mainly associated with the nucleotide binding, oxidoreductase activity, transferase activity. Taken together, the identified proteins may be helpful to identify key candidate proteins for genetic improvement of plants.