BME100 f2014:Group5 L5
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LAB 5 WRITE-UP
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Representative Images of Negative and Positive Samples
PCR Results Summary
SNP Information & Primer Design
Background: About the Disease SNP
Polymorphism is when there is genetic variation within a population. This can occur through natural selection. Nucleotides are the basic structural units of DNA, when the bases are switched this causes genetic variations or mutations. The SNP rs16991654 is only found in humans (Homo sapiens) and occurs on the 21st chromosome. The clinical significance of this SNP is that it is a pathogenic allele. The gene affected by this SNP is KCNE2, which stands for potassium voltage-gated channel, Isk-related family, member 2. KCNE2 gene has a variety of functions these include: regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. An allele is two or more alternative forms of a gene that are created through mutations and are located on the same place on a chromosome. When this gene contains the disease-associated allele sequence is CTC.
Primer Design and Testing
The primers we created worked as expected. The primers were created by isolating where the disease SNP is located in the genome. With that location, 20 base pairs were matched on either side of the disease coding sequence so that primers could be created at that specific location. In layman's terms, the primers hold the coordinates to the corresponding location on the human genome. The Non-Disease Primers (Forward and Reverse) worked and created the 220bp long sequence where the disease would be. The Disease Primers (Forward and Reverse) contained no matches. This is because the primers are trying to match onto DNA that does not contain the disease. The forward primer cannot attach because of the difference in base pairs between the forward non-disease primer (CATGGTGATGATTGGAATGT) and the forward disease primer (CATGGTGATGATTGGAATGC). The only difference is the T changes to a C in the disease primer. The reverse primers for disease and non-disease are the same. The following pictures are from the test to tell if the primers will work.