View source for Week8-How many novel SNPs are in Human

<p style="margin-left:40.0pt"><strong>How many novel SNPs are in Human?&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</strong></p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 20141215</p>

<p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Jihoon moon</p>

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<p><strong>Abstract</strong></p>

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<p>SNP is a variation in a single&nbsp;nucleotide&nbsp;that occurs at a specific position in the&nbsp;genome, that each variation is present to some appreciable degree within a population (&gt;&nbsp;1%). One SNP appears each 1000 bases, and In these slightly difference, the genetic function become different and determine race, hair color, height, probability of disease. And also SNP roles how the genetic variances are similar. Using these, we can make ordered medicine.</p>

<p>The novel SNPs is SNP that haven&#39;t been previously discovered. We say above, slightly difference between individuals. Then How many novel SNPs are in human? Can we calculate each person&rsquo;s number of novel SNP with using probability in thinking?</p>

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<p><strong>Introduction</strong></p>

<p>An important group of SNPs are those that corresponds to&nbsp;missense mutations&nbsp;causing amino acid change on protein level.&nbsp;Point mutation&nbsp;of particular amino acid residue can have different effect on protein function. Even disrupt completely or no effect on protein. Usually, change in amino acids with similar size like leucine to valin, has mild effect. &nbsp;Similarly, if SNP disrupts&nbsp;secondary structure elements for example substitution to proline in&nbsp;alpha helix region, such mutation usually may affect whole protein structure and function</p>

<p><img alt="http://koreagenome.kobic.re.kr/en/img/sub/ven_fig.png" src="file:///C:\Users\문지훈\AppData\Local\Temp\msohtmlclip1\01\clip_image002.png" style="float:left; height:247px; width:255px" />&nbsp;So we can sequencing the DNA and comparing with other DNA, we can find our novel SNP. In my opinion, without comparing we can&rsquo;t find out our own novel SNP. Because novel SNPs are only exist in only our own genome. I don&rsquo;t know exactly about individual&rsquo;s novel SNP&rsquo;s number, But If we want to know, the sequencing and comparing is essential things.</p>

<p>In KOREF project they compare korean&rsquo;s sequence with Chinese and western people and find the number of novel SNP of Korean.&nbsp;3,439,107 SNPs were found from the KOREF as defined by MAQ software. 3,019,024 SNPs were matched in dbSNP (2,592,113 as validated and 426,911 as non-validated SNPs) and the remaining 420,083 SNPs were novel. The SNPs of KOREF genome were compared with the two available individual genomes of Venter&rsquo;s (HuRef) and YH. Approximately 60% of KOREF SNPs were overlapped with the YH genome and 50% were overlapped with the HuRef genome, while the YH genome shared 52% with HuRef genome.</p>

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<p><strong>Result</strong></p>

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<p>&nbsp;We don&rsquo;t calculate each people&rsquo;s number of SNP using with statics about probability of SNPs in whole genome. Because we don&rsquo;t know the each SNP&rsquo;s location and how much they are exist.</p>

<p>&nbsp;So we must do sequencing and comparing. First we earn DNA that contain SNP. Second, using PCR assay for amplify the STS that DNA parts contain SNP. Third, using Sequencing, find SNP.</p>

<p>Forth, Mapping the SNP in unique position of genome. Fifth, calculate the frequency of SNP at each alle and comparing with other people&rsquo;s SNP for finding novel(the only)SNP. Then we can find the number of novel SNPs and find there own characters with genome. Not limited in phenotypes (Darwin&rsquo;s theory is limited in phenotypes)</p>

<p>Then we can say the novel SNP improves differential survivability and mortality of each races and individual.</p>

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<p><strong>Reference</strong></p>

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<p><a href="http://koreagenome.kobic.re.kr/en/sub_2.html">http://koreagenome.kobic.re.kr/en/sub_2.html</a></p>

<p>Single nucleotide polymorphism libraries: why and how are we building them? Molecular medicine today 5, 538-543.</p>

<p><a href="http://genome.sph.umich.edu/wiki/SNP_Call_Set_Properties">http://genome.sph.umich.edu/wiki/SNP_Call_Set_Properties</a></p>

<p><strong>http://www.nature.com/scitable/definition/single-nucleotide-polymorphism-snp-295</strong></p>