• 제목/요약/키워드: oligonucleotide array-CGH

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Comparison of Non-amplified and Amplified DNA Preparation Methods for Array-comparative Gnomic Hybridization Analysis

  • Joo, Hong-Jin;Jung, Seung-Hyun;Yim, Seon-Hee;Kim, Tae-Min;Xu, Hai-Dong;Shin, Seung-Hun;Kim, Mi-Young;Kang, Hyun-Mi;Chung, Yeun-Jun
    • Molecular & Cellular Toxicology
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    • 제4권3호
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    • pp.246-252
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    • 2008
  • Tumor tissue is usually contaminated by normal tissue components, which reduces the sensitivity of analysis for exploring genetic alterations. Although microdissection has been adopted to minimize the contamination of tumor DNA with normal cell components, there is a concern over the amount of microdissected DNA not enough to be applied to array-CGH reaction. To amplify the extracted DNA, several whole genome amplification (WGA) methods have been developed, but objective comparison of the array-CGH outputs using different types of WGA methods is still scarce. In this study, we compared the performance of non-amplified microdissected DNA and DNA amplified in 2 WGA methods such as degenerative oligonucleotide primed (DOP)-PCR, and multiple strand displacement amplification (MDA) using Phi 29 DNA polymerase. Genomic DNA was also used to make a comparison. We applied those 4 DNAs to whole genome BAC array to compare the false positive detection rate (FPDR) and sensitivity in detecting copy number alterations under the same hybridization condition. As a result microdissected DNA method showed the lowest FPDR and the highest sensitivity. Among WGA methods, DOP-PCR amplified DNA showed better sensitivity but similar FPDR to MDA-amplified method. These results demonstrate the advantage and applicability of microdissection for array-CGH analysis, and provide useful information for choosing amplification methods to study copy number alterations, especially based on precancerous and microscopically invaded lesions.

High-Resolution Microarrays for Mapping Promoter Binding sites and Copy Number Variation in the Human Genome

  • Albert Thomas
    • 한국생물정보학회:학술대회논문집
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    • 한국생물정보시스템생물학회 2006년도 Principles and Practice of Microarray for Biomedical Researchers
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    • pp.125-126
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    • 2006
  • NimbleGen has developed strategies to use its high-density oligonucleotide microarray platform (385,000 probes per array) to map both promoter binding sites and copy number variation at very high-resolution in the human genome. Here we describe a genome-wide map of active promoters determined by experimentally locating the sites of transcription imitation complex binding throughout the human genome using microarrays combined with chromatin immunoprecipitation. This map defines 10,567 active promoters corresponding to 6,763 known genes and at least 1,196 un-annotated transcriptional units. Microarray-based comparative genomic hybridisation (CGH) is animportant research tool for investigating chromosomal aberrations frequently associated with complex diseases such as cancer, neuropsychiatric disorders, and congenital developmental disorders. NimbleGen array CGH is an ultra-high resolution (0.5-50 Kb) oligo array platform that can be used to detect amplifications and deletions and map the associated breakpoints on the whole-genome level or with custom fine-tiling arrays. For whole-genome array CGH, probes are tiled through genic and intergenic regions with a median probe spacing of 6 Kb, which provides a comprehensive, unbiased analysis of the genome.

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고집적어레이 기반의 비교유전체보합법(CGH)을 통한 신경아세포종 Neuro2a 세포의 유전체이상 분석 (High Resolution Genomic Profile of Neuro2a Murine Neuroblastoma Cell Line by Array-based Comparative Genomic Hybridization)

  • 도진환;김인수;고현명;최동국
    • 생명과학회지
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    • 제19권4호
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    • pp.449-456
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    • 2009
  • 신경아세포종은 미분화된 신경외배엽 세포로부터 유래한 신경능세포에 의해 형성된 소아기에 보는 가장 많이 발생하는 악성 종양 중 하나이다. 신경아세포종인 Neuro-2a 세포는 신경세포의 분화, 세포사 억제 효능, 세포독성 검정 등에 활용되고 있다. Neuro-2a 역시 다른 신경아세종과 같이 염색체 변이를 가지고 있지만, 이에 대해 고밀도의 게놈수준에서 염색체 변이에 대해 보고된 바가 없다. 본 연구에서는 고집적 마이크로어레이(최소 43,000 개의 코딩, non-코딩 유전자 서열이 집적된 마이크로어레이)기반의 비교유전체보합법을 활용하여, 고해상도의 Neuro-2a 유전체 이상을 분석하였다. 마이크로 어레이 데이터는 Hidden Markov Model을 활용하여, 유전체 변이를 double loss, single loss, normal, single gain 그리고 amplification으로 나누어 분석하였다. Neuro2a는 MYCN 유전자의 증폭은 관찰되지 않았고, GDNF, BDNF, NENF등의 neurotrophic factor 가운데 NENF의 gain 현상이 관찰 되었다. 염색체의 이상은 4,8,10,11,15번에서 발견되었으며, 염색체 3,17,18,19에서는 전부 20개 미만의 염색체 이상이 발견되었다. 염색체 이상이 연속적으로 일어난 부위 중 gain으로서 가장 긴 부분은 Chr8:8,427,841-35,162,415의 약 26.7 Mb이며, single loss로서 가장 긴 곳은 Chr4:73,265,785-88,374,165의 약 15.1 Mb였다. 염색체의 위치는 UCSC 데이터베이스 (UCSC mm8, NCBI Build 36)에 근거하였다.

Genomic Alteration of Bisphenol A Treatment in the Testis of Mice

  • Kim, Seung-Jun;Park, Hye-Won;Youn, Jong-Pil;Ha, Jung-Mi;An, Yu-Ri;Lee, Chang-Hyeon;Oh, Moon-Ju;Oh, Jung-Hwa;Yoon, Seok-Joo;Hwang, Seung-Yong
    • Molecular & Cellular Toxicology
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    • 제5권3호
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    • pp.216-221
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    • 2009
  • Bisphenol A (BPA) is commonly used in the production of pharmaceutical, industrial, and housing epoxy, as well as polycarbonate plastics. Owing to its extensive use, BPA can contaminate the environment either directly or through derivatives of these products. BPA has been classified as an endocrine disruptor chemicals (EDCs), and the primary toxicity of these EDCs in males involves the induction of reproductive system abnormality. First, in order to evaluate the direct effects on the Y chromosome associated with reproduction, we evaluated Y chromosome abnormalities using a Y chromosome microdeletion detection kit. However, we detected no Yq abnormality as the result of BPA exposure. Secondly, we performed high-density oligonucleotide array-based comparative genome hybridization (CGH) to assess genomic alteration as a component of our toxicity assessment. The results of our data analysis revealed some changes in copy number. Seven observed features were gains or losses in chromosomal DNA (P-value<1.0e-5, average log2 ratio>0.2). Interestingly, 21 probes of chr7:7312289-10272836 (qA1-qA2 in cytoband) were a commonly observed amplification (P-value 3.69e-10). Another region, chr14:4551029-10397399, was also commonly amplified (P-value 2.93e-12, average of log2 ratios in segment>0.3786). These regions include many genes associated with pheromone response, transcription, and signal transduction using ArrayToKegg software. These results help us to understand the molecular mechanisms underlying the reproductive effects induced by BPA.

염색체 마이크로어레이를 이용한 표지염색체의 분자세포유전학적 특성 (Molecular Cytogenetic Characterization of Supernumerary Marker Chromosomes by Chromosomal Microarray)

  • 배미현;유한욱;이진옥;홍마리아;서을주
    • Journal of Genetic Medicine
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    • 제8권2호
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    • pp.119-124
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    • 2011
  • 목적: 표지염색체(supernumerary marker chromosome, SMC)는 유래한 염색체에 따라서 임상 증상이 다양하다. 본 연구는 염색체 마이크로어레이를 이용하여 SMC의 기원을 밝히고 각 증례마다 분자세포유전학적 특성과 임상 표현형을 분석하고자 하였다. 대상 및 방법: 염색체 검사에서 SMC가 검출된 환자들 중에서 15번 염색체 유래를 제외한 4명의 환자에서 CGH 기법의 올리고 뉴클레오티드 염색체 마이크로어레이를 시행하였다. 결과: 3명의 환자에서 유래된 염색체 부위를 확인할 수 있었다. 증례1은 1q21.1-q23.3에서 16.1 Mb의 SMC를 가졌고, 증례2는 19p13.11-q13.12에서 21 Mb, 증례3은 22q11.1-q11.21과 22q11.22-q11.23의 두 구간에서 각각 2.5Mb와 2.0Mb로 재배열된 4.5 Mb의 SMC를 나타내었다. 결론: 증례1은 1q21.1 중복증후군을 포함하여 광범위한 임상표 현형을 나타내었다. 증례2는 아스퍼거 증후군과 유사한 정신행동 이상 소견은 19p12-q13.11, 청력장애와 사시는 19p13.11, 그 외 증상은 19q13.12의 유전자와 연관 가능성이 높다. 증례3은 묘안 증후군 type I 및 22q11.2 미세중복증후군과 비교했을 때 항문폐쇄는 22q11.1-q11.21, 그 외 증상들은 22q11.22-q11.23과 연관성을 시사하였다. 고해상도 염색체 마이크로어레이 분석은 SMC의 유래를 확인할 수 있고 유전형-표현형 상관성을 이해함으로써 유전상담에 도움이 된다.