location : yonsei severance
- Identification of disease-causing mutations by high throughput Targeted Resequencing [Luke Danneberg(Roche NimbleGen)]
Although recently sequencing technology achieve incredible development, sequencing of a higher organism such as human demand a considerable sum of money. On the top of this, till now, because of lack of knowledge, the clue in non-coding DNA sequence could not be helpful for discover the disease-causing mutations. The speaker in this talk introduced two sequence capture technology for solving these problem. One of the tech is exon capturing and the another is supervised targeted capturing. Exon capturing literally focus on exon sequence of genome, and the other targeted capturing tech is regardless of whether the region is exon or not, just concentrate on the region in which investigators are interested. Maybe, the difference is not clear in my classification, but I accept that difference as the size of targeted capturing regions are longer than exon. Anyway the importance of this technology is financial efficiency. With same amount of money for one whole genome sequencing, dozens of patients can be interrogated. The speaker recommend using solexa for captured exons sequencing and FLX for targeted region sequencing, because sometime targeted region contain repeat sequences. I think this technology is just temporary solution or being useless in the near future. To find out the disease-causing mutation, I think unsupervised approach is needed, and as many news say (http://www.technologyreview.com/biomedicine/25481/?a=f) sequencing price is gonna be very chip.
- Studying Gene Structure, Expression and Regulation Using the Illumina HiSeq 2000 System[Gary P.Schroth(Illumina, Inc.)]
This talk focused on performance of HiSeq 2000 which was developed in Illumina, as we can surmise from speaker's affiliation. The big difference of HiSeq with GA is that there are two flow cell in device. This result in production of larger amount of reads. As well as this quantitative advance, a change in scanning image of spot make improvement in efficiency, HiSeq produce 200Gb per run and 25Gb per day. The speaker also introduced methodology which they developed for selecting mRNA from RNA's pool. In general, the amount of mRNA is too small to interrogate without selecting mRNA. Usually poly-A selection is used for selecting mRNA, but this lead to degradation of mRNA. Normalization using DSN(duplex-specific nuclease), which utilize the fact that more amount RNA can make duplex easily during annealing from denaturation. This method affect little on mRNA quantity and have additional effect that capture non-coding RNA like lincRNA, smRNA.
- Transcriptome analysis for identification Fusion Genes[Sang-hyuk,Lee(KOBIC)]
In this talk, the speaker introduced fusion gene database (http://ercsb.ewha.ac.kr:8080/FusionGene/index.jsp) which use EST(from UniGene) and NGS(from SRA) data. A phenomenon of fusion of gene was found in some case of cancer patient, and this leaded researcher's attempt to discover the other cases. The speaker also retry to build database in the same context(according to speaker, he already prepare this kind of website 5 years ago).
- Transcriptome analysis for identification Fusion Genes[Sang-hyuk,Lee(KOBIC)]
In this talk, the speaker introduced fusion gene database (http://ercsb.ewha.ac.kr:8080/FusionGene/index.jsp) which use EST(from UniGene) and NGS(from SRA) data. A phenomenon of fusion of gene was found in some case of cancer patient, and this leaded researcher's attempt to discover the other cases. The speaker also retry to build database in the same context(according to speaker, he already prepare this kind of website 5 years ago).
- Metagenome analysis[Jong-sik Chun(Seoul National University)]
This is the most interesting talk. Through this talk I realize that microorganism area is so huge and has enormous potential. In brief, metagenome analysis is genome sequencing of mixed microbes in specific location. According to speaker, only about 6000 species of microbes are revealed while insects are found more than tens of thousands, because a lots of microbes cannot be cultured in artificial condition. The speaker anticipate that the number of microbes should be more than insects and he believe that investigation of the role of extraordinary microbe have great effect. To illustrate, one article which in published in nature compared the microbes in overweight patient's stomach with normal's. They found that the ratio of microbes in the obesity are significantly different with the normal. And the Craig Venter, the celebrity in biological field, who are introduced by speaker as freak (The speaker said that when the sequencing price is not that cheap, Venter was the first who sequenced the microbes living in sea water.) have been focusing on microbe and finally he made it that creation of microbe as if he was being God in recent time. Anyhow, many country invest a lot in metagenome field. Because the most novel microbe cannot be cloned and besides, maybe group of microbes living together can be considered as one organism, that means each of microbe has his own role in the domain, usually investigator don't try to assembly the genome, they just align each read to known organisms. Aligning reads using BLAST mean need endless time for searching every sequence, the speaker emphasize classification of microbe and he indeed made the website for classification of microbe and boast of his achievement(http://eztaxon-e.org/).
