'Nucleic Acids Research'에 해당되는 글 2건
2010. 12. 2. 11:48
이전 TIARA 논문을 쓰기 이전에 co-author로 참여했던 논문 비록 주요 알고리즘 부분보다는 시스템 구현쪽에 참여했던 논문이다. 이 논문에 사용된 engine 기술을 바탕으로 TIARA를 만들게 된것이다.
이 논문은 우리끼리 CARA라 명명한 논문이다.
이 논문은 우리끼리 CARA라 명명한 논문이다.
Comparative genomic hybridization (CGH) microarrays have been used to determine copy number variations (CNVs) and their effects on complex diseases. Detection of absolute CNVs independent of genomic variants of an arbitrary reference sample has been a critical issue in CGH array experiments. Whole genome analysis using massively parallel sequencing with multiple ultra-high resolution CGH arrays provides an opportunity to catalog highly accurate genomic variants of the reference DNA (NA10851). Using information on variants, we developed a new method, the CGH array reference-free algorithm (CARA), which can determine reference-unbiased absolute CNVs from any CGH array platform. The algorithm enables the removal and rescue of false positive and false negative CNVs, respectively, which appear due to the effects of genomic variants of the reference sample in raw CGH array experiments. We found that the CARA remarkably enhanced the accuracy of CGH array in determining absolute CNVs. Our method thus provides a new approach to interpret CGH array data for personalized medicine.
PMID : 20802225
CARA Web Site : http://cara.gmi.ac.kr
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2010. 12. 2. 11:40
연구소 와선 첫 First 논문! 기능이 많이 있고 기술적인 거보다는 만들어서 논문으로 제출했다는 의미가 더 큰 논문!! 다음에 더 좋은 논문으로!!
High-throughput genomic technologies have been used to explore personal human genomes for the past few years. Although the integration of technologies is important for high-accuracy detection of personal genomic variations, no databases have been prepared to systematically archive genomes and to facilitate the comparison of personal genomic data sets prepared using a variety of experimental platforms. We describe here the Total Integrated Archive of Short-Read and Array (TIARA; http://tiara.gmi.ac.kr) database, which contains personal genomic information obtained from next generation sequencing (NGS) techniques and ultra-high-resolution comparative genomic hybridization (CGH) arrays. This database improves the accuracy of detecting personal genomic variations, such as SNPs, short indels and structural variants (SVs). At present, 36 individual genomes have been archived and may be displayed in the database. TIARA supports a user-friendly genome browser, which retrieves read-depths (RDs) and log2 ratios from NGS and CGH arrays, respectively. In addition, this database provides information on all genomic variants and the raw data, including short reads and feature-level CGH data, through anonymous file transfer protocol. More personal genomes will be archived as more individuals are analyzed by NGS or CGH array. TIARA provides a new approach to the accurate interpretation of personal genomes for genome research.
PMID : 21051338
TIARA Web Site : http://tiara.gmi.ac.kr
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