Changes
From Biolecture.org
no edit summary
In 2009, genome sequencing technologies will achieve one person's whole genome per day in terms of DNA fragments sequenced. Personal genomics is a new term that utilizes such fast sequencers. In 2008, the cost for one personal genome is less than $350,000 USD. If the cost goes down below $1,000 USD, the impact of personal genomics is predicted to be the largest ever in biology on common people's life. Reflecting this technological advancement to the society is the PGP (Personal Genome Project), a project to sequence as many people as possible with lowest possible costs </span><span style="FONT-SIZE: 9pt">(Church 2005)</span><span style="FONT-SIZE: 9pt">. At present, Google Inc. and Church group are working together to sequence 100,000 people's genetic regions of DNA. In Saudi Arabia, the government is planning to sequence 100 Arabic people. In Europe, there are various groups of people and nations who have been genotyping the populations. Especially, Iceland has been successful in that effort by utilizing their well-kept genealogical data encompassing 100,000s people. In Asia, Jeongsun Seo of Seoul National University has been working on East Asia Genome Project in the past years. His group collected thousands of samples from Mongolian tribes with a gigantic genealogical tree among them </span><span style="FONT-SIZE: 9pt">(Park et al. 2008; Sung et al. 2008)</span><span style="FONT-SIZE: 9pt">. Seo is said to be sequencing at least 100 Korean genomes in collaboration with Church and Green Cross Inc. of Korea. The aim of Seo's genome project is to produce a resource for the East Asians as well as Koreans. He is presently sequencing at least two Korean people. In China, Beijing Genome Institute has been successful in terms of sequencing. Their first achievement came from a plant genome, rice. After rice, they launched a 100 Han Chinese genome sequencing project. In Nov. 2008, they published their first Chinese genome in a joural, Nature. In Dec. 2008, another Korean group, Lee Gilyeo Cancer and Diabetes Institute (LCDI) and Korean Bioinformation Center (KOBIC) made a Korean genome sequence public. The genome was sequenced by Solexa paired-end sequencer and comparative genomics analyses and SNP data were uploaded as a public resource for everyone. The time taken to analyze the 7.8x Korean genome took only one week using 150 computer CPUs to produce mapping DNA fragments to a reference genome, generate new SNP information, compare with other individual genomes, and map it with 1600 already known phehotype information from the public literature.<br />
<br />
</span><strong><span style="FONT-SIZE: 9pt">Genome revolutionRevolution </span></strong><strong><span style="FONT-SIZE: 9pt"><br />
</span></strong><span style="FONT-SIZE: 9pt">These public genome data alongside previously known Craig Venter's and James Watson's mark that full genome sequences are not in academic domain anymore. Anyone who has money and will can sequence human genomes. This 'genomic revolution' will eventually lead to the 'BioRevolution' in terms of making the most essential human information completely mapped and publically available. These are revolutionary because humans can now engineer themselves with a map or a blue print not directly relying on trial and error style conventional evolutionary methods. This indicates that evolution went into a conscious level of driving evolution. It is almost designing the evolution using computers. <br />
<br />
</span><strong><span style="FONT-SIZE: 9pt">Genomes and personalized medicinePersonalized Medicine</span></strong><span style="FONT-SIZE: 9pt"><br />
The consequences of 'BioRevolution' where genomic information is utilized by scientists to engineers all kinds of biological processes including evolution itself will bring us the personalized medicine. The essence of personalized medicine is that enzymes in our tissues such as cytochrome P450 have distinct differences among individuals and populations. Certain drugs produce different responses in individuals. <br />
<br />
Alongside and with the associations of eIMBL, A-IMBN, and HVP, a variome project that tries to map Asian population variome was launched in 2008. This was a group effort of Korean researchers who have been interested in genome sequences, SNPs, and CNVs. They have formed a Korean Variome Consortium (KOVAC: <a href="http://variome.kr/"><font color="#0000ff">http://variome.kr</font></a>) and supported AVP as one of the first projects. eIMBL that is the virtual laboratory network of Asia linking key biology groups modeled after EMBL has acquired $80,000 USD in 2008 to support AVP. eIMBL aims to establish a virtual bioinformatics center in Asia Pacific region that links many bioinformation processing scientists in Asia.<br />
<br />
<span style="FONT-SIZE: 9pt"><strong>Construction of Reference Genomes for the world.<br /></strong></span><span style="FONT-SIZE: 9pt">Sanger center, EBI, NCBI and the genome center of the University of Washington have formed a consortium to produce a reference genome (<a href="http://referencegenome.org/"><font color="#000080">http://referencegenome.org</font></a>). Reference standard is the most important standard among all the standards. Providing an accurate reference genome to biologists is an important task. The first reference genome by the above consortium is based on Caucasian genomes. Due to the extent of SNPs and CNVs, it is necessary to construct reference genomes for diverse ethnic groups. In Korea, since 2006, the reference standard genome project has begun and produced the first draft for Koreans in Nov. 2008 using a male doner. Through the analysis, the Korean researchers in LDCI and KOBIC found that there is a strong justification for any nation to launch large scale genome projects to map population diversities. Even such close populations, the Korean and the Chinese, seemed to show a large quantity of SNP difference.</span><br /><br /></span><strong><span style="FONT-SIZE: 9pt">Bioinformatics for personal genomes Personal Genomes and variomesVariomes</span></strong><span style="FONT-SIZE: 9pt"><br />
Bioinformatics is the key in personal genome projects and variome projects. Bioinformatics is not a set of tools but it is a proper scientific discipline. It regards life as a gigantic information processing phenomenon and tries to map its components and to model the emerging networks of the components. Bioinformatics in 2008 is driving biology into an information science. Most biology researches are now with massive amount of data that cannot be processed by hand. Nearly all the biological research outcomes in the next five years will have some form of high throughput data such as genome sequences, microarray data, proteome analyses, SNPs, epigenome chips, and large scale phenotype mapping. Bioinformatics tools in genomics and variomics can be found from various internet resources. There are various bioinformatics hubs such as NCBI (National Center for Biotechnology Information), EBI (European Bioinformatics Institute), DDBJ (Databank of Japan), and KOBIC. Some others are: Bioinformatics Organization (<a href="http://bioinformatics.org/"><font color="#0000ff">http://Bioinformatics.Org</font></a>), EMBnet (<a href="http://www.embnet.org/"><font color="#0000ff">http://www.embnet.org/</font></a>), and The International Society for Computational Biology (<a href="http://iscb.org/"><font color="#0000ff">http://iscb.org</font></a>). The following are major bioinformatics journals:<br />
<br />
<br />
</span><strong><span style="FONT-SIZE: 9pt">Mapping expression using DNA sequencing</span></strong><span style="FONT-SIZE: 9pt"><br />
DNA sequencing technology used to be for mapping genotypes. However, they are now used to map expression levels in cells. Cells produce various RNAs. mRNA is the most abundant and important. In the past, microarray and DNA chips were used for measuring expression levels. They are not accurate and it takes many bioinformatic adjustments before it becomes reliable expression data. New sequencing technologies can measure expression levels much more accurately. By sequencing the RNAs, we can now quantify the mRNA levels by precisely knowing the RNA sequences. Sequencing technologies will restructure the expression analyses in the future.</span><p> <br /p><pspan style="FONT-SIZE: 9pt"> <br /p><divbr /><strong><font size="2">Conclusion</font>Linking Genome information On-line</strong><br /><font size="2">In 2009 Sequencing a genome is one thing but analyzing the whole genome is another thing. Therefore, a worldwide effort is required to link all the genome information for proper management and onwards, personal utilization. The internet is the best infrastructure for genome projects will produce unprecedented amount of biological datainformation exchange. New bioinformatics technologies will Bioinformatics resources should be required to handle themavailable as freely as possible for underdeveloped and developing nations. New Genome sequencing technologies will drive and associated analysese should be done freely in certain instances by the next decades support of biology local governments and transform international organizations. For maximum efficient, an adequote data and information license is also required. Some researchers propose an openfree sharing of bioinformatics analysis tools as well as the medical practices in hospitals within the next decadesgenome sequences (under proper permission). Fast sequencing unexpectedly brought us interesting applications One of such as metagenomics and ecogenomics. movement is Free Genomics (</font><font sizea href="2http://freegenomics.org">We have examined the current trends in genomics and variomicshttp://freegenomics.org</fonta>). <br />
<br />
</span>
<div><font size="2"><br />
<strong>Conclusion</strong></font><br />
<font size="2">In 2009 and onwards, personal genome projects will produce unprecedented amount of biological data. New bioinformatics technologies will be required to handle them. New sequencing technologies will drive the next decades of biology and transform the medical practices in hospitals. Fast sequencing unexpectedly brought us interesting applications such as metagenomics and ecogenomics. </font><font size="2">We have examined the current trends in genomics and variomics. </font><br />
</div>
<div><strong><font size="2">Acknowledgements</font></strong><br />
<font size="2">SK was supported by Soongsil University Reserach Fund.</font><br />
<br />
</div>
