• Journal of KIISE:Databases
• /
• v.41 no.4
• /
• pp.249-255
• /
• 2014

Copy number variations(CNVs) are a recently recognized class of human structural variations and are associated with a variety of human diseases, including cancer. To find important cancer genes, researchers identify novel CNVs in patients with a particular cancer and analyze large amounts of genomic and clinical data. We present a tool called CNVDAT which is able to detect CNVs from NGS data and systematically analyze the genomic and clinical data associated with variations. CNVDAT consists of two modules, CNV Detection Engine and Sequence Analyser. CNV Detection Engine extracts CNVs by using the multi-resolution system of scale-space filtering, enabling the detection of the types and the exact locations of CNVs of all sizes even when the coverage level of read data is low. Sequence Analyser is a user-friendly program to view and compare variation regions between tumor and matched normal samples. It also provides a complete analysis function of refGene and OMIM data and makes it possible to discover CNV-gene-phenotype relationships. CNVDAT source code is freely available from http://dblab.hallym.ac.kr/CNVDAT/.

• Proceedings of the Korea Information Processing Society Conference
• /
• 2008.11a
• /
• pp.356-359
• /
• 2008

최근 생물정보학 분야에서 인간 유전체에 존재하는 CNV(copy number variation)에 관한 연구가 주목 받고 있다. CNV 영역은 1kbp-3Mbp 사리의 서열이 반복되거나 결실되는 변이 영역으로 정의된다. 우리는 선행연구에서 기가 시퀀싱(giga sequencing)의 결과 산출되는 DNA 서열조각인 리드(read)를 레퍼런스 시퀀스에 서열 정렬하여 CNV 영역을 찾아내는 새로운 CNV 검색 방식을 제안하였다. 후속 연구로서 본 논문에서는 DNA 서열에 존재하는 repeat 영역 문제를 해결하기 위한 새로운 방안을 제안하고, 리드의 출현 빈도 정보를 분석하여 CNV 영역을 찾아내는 CNV 영역 검색 알고리즘을 보인다. 제안된 알고리즘 Gaussian 분포를 갖는 출현 빈도 정보로부터 통계적 유의성을 갖는 영역을 추출하여 CNV 영역후보로 하고, 다음 경제 과정을 거쳐 최종의 CNV 영역을 추출한다. 성능 평가를 위하여 프로토타임 시스템을 개발하였으며, 시뮬레이션 실험을 수행하였다. 실험 결과에 의하여 제안된 방식은 반복되거나 결실되는 형태의 CNV 영역을 효율적으로 검출하며, 또한 다양한 크기의 CNV 영역을 효율적으로 검출할 수 있음을 입증한다.

• The KIPS Transactions:PartD
• /
• v.18D no.2
• /
• pp.89-100
• /
• 2011

The CNV (Copy Number Variation) which is one of the genetic structural variations in human genome is closely related with the function of gene. In particular, the genome-wide association studies for genetic diseased persons have been researched. However, there have been few studies which infer the genetic function of CNV with normal human. In this paper, we propose the analysis method to reveal the functional relationship between common CNV and genes without considering their genomic loci. To achieve that, we propose the data integration method for heterogeneity biological data and novel measurement which can calculate the correlation between common CNV and genes. To verify the significance of proposed method, we has experimented several verification tests with GO database. The result showed that the novel measurement had enough significance compared with random test and the proposed method could systematically produce the candidates of genetic function which have strong correlation with common CNV.

• The KIPS Transactions:PartD
• /
• v.16D no.5
• /
• pp.661-672
• /
• 2009

Recently it was found that various genetic structural variations such as CNV(copy number variation) exist in the human genome, and these variations are closely related with disease susceptibility, reaction to treatment, and genetic characteristics. In this paper we propose a new CNV detection algorithm using millions of short DNA sequences generated by giga-sequencing technology. Our method maps the DNA sequences onto the reference sequence, and obtains the occurrence frequency of each read in the reference sequence. And then it detects the statistically significant regions which are longer than 1Kbp as the candidate CNV regions by analyzing the distribution of the occurrence frequency. To select a proper read alignment method, several methods are employed in our algorithm, and the performances are compared. To verify the superiority of our approach, we performed extensive experiments. The result of simulation experiments (using a reference sequence, build 35 of NCBI) revealed that our approach successfully finds all the CNV regions that have various shapes and arbitrary length (small, intermediate, or large size).

• Proceedings of the Korea Information Processing Society Conference
• /
• 2011.04a
• /
• pp.1264-1267
• /
• 2011

시퀀싱 기술의 발달로 최근에는 비교적 저렴한 비용으로 개인의 유전체 시퀀싱 데이터를 산출할 수 있게 되었다. 하지만 이를 기반으로 하는 기존의 분석 방법은 매우 고가의 컴퓨팅 환경을 요구하기 때문에 분석을 위한 비용이 매우 높은 문제가 있다. 본 논문에서 클라우드 컴퓨팅 환경의 병렬 CNV 검출알고리즘을 제안한다. 제안하는 방법은 모양 기반의 CNV 검출 알고리즘인 CNV_shape을 MapReduce 기법으로 개발한 것으로 시퀀싱 데이터를 레퍼런스 서열에 매핑한 결과로부터 리드 커버리지 (read coverage)를 계산하여 커버리지가 감소하거나 증가하는 일정 길이 이상의 영역을 검출하는 방법이다. 클라우드 컴퓨팅 환경에 적용하고 노드의 밸런싱 유지를 위한 방법으로 파티셔닝 기법을 사용하였다. 또한 실 데이터를 이용한 실험을 통해 제안하는 방법의 효율적 데이터 처리를 보인다.

• Proceedings of the Korean Society for Emotion and Sensibility Conference
• /
• 2001.05a
• /
• pp.308-312
• /
• 2001

본 연구에서는 사상관련전위인 수반음성변동(CNV)을 이용하여 쾌/불쾌 향의 영향을 평가하고자 하였다. 즉, 건강한 20대 성인을 대상으로 쾌한 향(레몬)과 불쾌한 향(E3) 자극에 따른 CNV의 전기성분 및 후기성분의 변화를 대뇌부위별, 가산횟수별로 비교 분석하였고, 쾌/불쾌 향의 자극 반복에 따른 주관적 평가도 부가하여 검토하였다. 그 결과, 쾌/불쾌 향은 CNV 후기성분의 중심엽 부위에서 10∼15회 가산평균의 경우 정량적으로 구별될 수 있는 가능성을 보였고, 주관적인 평가에서는 반복 자극횟수가 증가함에 따라 쾌/불쾌감이 저하하는 것을 알 수 있었다.

• Proceedings of the Korean Information Science Society Conference
• /
• 2012.06c
• /
• pp.19-21
• /
• 2012

모든 암 세포는 체세포 변이를 동반한다. 따라서 암 유전체 변이 분석에 의하여 암을 발생시키는 유전자 및 진단/치료법을 찾아낼 수 있다. 본 연구에서는 차세대 시퀀싱 데이터를 이용하여 암 특이적 단이 반복 변이(copy number variation, CNV) 유형을 밝히는 새로운 알고리즘을 제안한다. 제안하는 방식은 암 환자의 정상 세포와 암세포로부터 얻어진 정상 유전체와 암 유전체를 동시 분석하여 각각 CNV 후보 영역을 추출하며, 통계적 유의성 분석을 통하여 암 특이적 CNV 후보 영역을 선별하고, 다음 후처리 과정에서 참조 표준 서열(reference sequence)에 존재하는 오류 영역 보정 작업을 수행하여 정확한 암 특이적 CNV 영역을 추출해 낸다. 또한 다수의 대용량 유전체 데이터 동시 분석을 위하여 맵리듀스(MapReduce) 기법을 기반으로 하는 병렬 수행 알고리즘을 제안한다.

• Journal of Life Science
• /
• v.20 no.5
• /
• pp.703-709
• /
• 2010

Glucuronidation is a major pathway for NNAL [4-(methylnitrosamno)-1-(3-pyridyl)-1-butanol] and UGT2B17 (UGT, uridine diphospho-glucuronosyltransferase) is from the UGT2B family that glucuronidates carcinogens. UGT2B17 deletion was associated with decreased levels of NNAL and with increased risk of some cancers. The UGT2B17 gene varies in copy number from zero to two per individual in humans. To examine whether UGT2B17 gene deletion is associated with the risk of lung cancer, we investigated copy number variants (CNV) in 271 cancer-free controls and 176 cases of lung cancer in Koreans by a PCR-based method. The frequency of the UGT2B17 deleted alleles was much higher than in other Caucasian and African-American groups which have already been reported. While only up to 10% of Caucasians have zero copies of the gene, up to 74% of Koreans in this study showed that both copies of the gene were deleted. Furthermore, the overall frequency of this dual deletion in female groups was higher than in male groups. However, there was no association between CNV in UGT2B17 and lung cancer. This result suggested that the UGT2B17 deletion allele was not associated with the susceptibility of lung cancers in the Korean group. However, this UGT2B17 CNV polymorphism may be a useful marker for evolutionary analysis among races.

• Korean Journal of Poultry Science
• /
• v.41 no.4
• /
• pp.305-311
• /
• 2014

Copy number variation (CNV) is a form of structural variation that shows various numbers of copies in segments of the DNA. It has been shown to account for phenotypic variations in human diseases and agricultural production traits. Currently, most of chicken breeds in the poultry industry are based on European-origin breeds that have been mostly provided from several international breeding companies. Therefore, National Institute of Animal Science, RDA has been trying to restore and improve Korean native chicken breeds (12 lines of 5 breeds) for about 20 years. Thanks to the recent advance of sequencing technologies, genome-wide CNV can be accessed in the higher resolution throughout the genome of species of interest. However, there is no systematic study available to dissect the CNV in the native chicken breed in Korea. Here, we report genome-wide copy number variations identified from a genome of Korean native chicken (Line L) by comparing between the chicken reference sequence assembly (Gallus gallus) and a de novo sequencing assembly of the Korean native chicken (Line L). Throughout all twenty eight chicken autosomes, we identified a total of 501 CNVs; defined as gain and loss of duplication and deletion respectively. Furthermore, we performed gene ontology (GO) analysis for the putative CNVs using DAVID, leading to 68 GO terms clustered independently. Of the clustered GO terms, genes related to transcription and gene regulation were mainly detected. This study provides useful genomic resource to investigate potential biological implications of CNVs with traits of interest in the Korean native chicken.

• Maxillofacial Plastic and Reconstructive Surgery
• /
• v.30 no.2
• /
• pp.205-212
• /
• 2008

Genetic variation in the human genome occurs on various levels; from the single nucleotide polymorphism to large, microscopically visible chromosome anomalies. It can be present in many forms, including variable number of tandem repeat (VNTRs; e.g., mini- and microsatellites), presence/absence of transposable elements (e.g., Alu elements), single nucleotide polymorphisms, and structural alterations (e.g., copy number variation, segmental duplication, inversion, translocation). Until recently SNPs were thought to be the main source of genetic and phenotypic human variation. However, the use of methods such as array comparative genomic hybridization (array CGH) and fluorescence in situ hybridization (FISH) have revealed the presence of copy number variations(CNVs) ranging from kilobases (kb) to megabases (Mb) in the human genome. There is great interest in the possibility that CNVs playa role in the etiology of common disease such as HIV-1/AIDS, diabetes, autoimmune disease, heart disease and cancer. The discovery of widespread copy number variation in human provides insights into genetic variability among populations and provides a foundation for studies of the contribution of CNVs to evolution and disease.