MolCellEng_Notes9

MolCellEng_Notes9 - A.i....

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A.i. SNP Genotyping by MALDI-TOF MS and SBE (single base extension) A.i.1. Have SNPs at diff locations A.i.2. Must already know where SNPs are and what their  genotypes are A.i.3. Not true discovery of SNPs, it is rather a Screening of  known SNPs for large number of samples to guess frequency of  SNP in population or to verify epidemic changes in genotype A.i.4. Design primer that sits right next to each SNP and primers  get extended at SNP position A.i.5. extension A.i.6. After extension reaction, will have unextended primer  (always add excess, so have some left over) and extension products  – then, purify sample (salt will interfere with mass analysis) A.i.7. Read genotype by looking at peaks; primers will have peaks A.i.8. Limitations A.i.8.a. Unwanted measurement of unextended primers with  the extension products   limits the scope of multiplexing A.i.8.a.i. If have 2 SNPs looking at, no issue b/c will have 6  peaks maximum – not too complicated spectrum A.i.8.a.ii. If have 20 SNPs, have max of 3 peaks for each SNP  – 60 peaks in spectrum, makes spectrum  complicated as seen in this slide’s picture.  A.i.8.b. Really don't need primer peaks, they bring down the  intensity of other extension products and lowers the 
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This note was uploaded on 04/06/2012 for the course BIO 436 taught by Professor Kim during the Spring '12 term at Rutgers.

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MolCellEng_Notes9 - A.i....

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