Allele Synthesis Lab Report

Determining Allele Frequencies of the PV92 Alu Element using DNA Isolated from Human Cheek Cells and PCR Amplification

Background
Alu elements are the most abundant repetitive elements in the human genome that have mobilized throughout primate genomes by retrotransposition over the past 65 million years ago from a 5’ to 3’ fusion of the 7SL RNA gene, to reach the present number of more than one million copies. Over the last few years, several lines of evidence demonstrated that these elements modulate gene expression at the post-transcriptional level in at least independent manners. They have been shown to be involved in alternating splicing, RNA editing and translation regulation (1). These elements have also been proposed to have
Fifty milliliters of 1.5% agarose solution was swirled and inserted into the microwave for 1 to 2 minutes until the agarose solution was clear. The solution was put into a cooling bath of 60 °C for 15 minutes. After cooled, the agarose was poured into the prepared gel-casting tray for 30 minutes until it became solid. The well-forming comb was then removed and 1X TBE buffer was added to fill in wells, to create a smooth buffer surface. Using a micropipette 25 µL of my dye sample mix was added to the well. The gel was run at 130 V for 30 minutes. The gel was stained for 10 to 15 minutes using ethidium bromide. The gel was viewed using UV transillumination and a photograph was taken of the gel.
Analysis of Genotype and Allele Frequency In Whole-Class Data
Each student’s genotype of +/+, +/-, and -/- were counted and put into a genotype frequency equation of to get a percentage. The Hardy-Weinberg equation was then used to determine the genotypes frequencies that were expected in a population at equilibrium. The class data was entered into the Allele Server database (http://www.bioservers.org) where a chi-square test was used to compare observed genotype frequencies with those predicted by the Hardy-Weinberg equation. The data was then compared to genotype frequencies in world populations, where the data were compared in pie charts and several comparisons were
Chi-square test whole-class data vs. Chinese

Chi-square: 50.46
P-value: 0.0000 Chinese
Alongi Cell-Molecular 2013 Total samples: 50
+ Alleles: 86
- Alleles: 14
Total samples: 26
+ Alleles: 8
- Alleles: 44
+/+
0.74;
0.00
+/-
0.24;
0.31
-/-
0.02;
0.69

Conclusions
Amplification of DNA by PCR and gel electrophoresis of PCR amplification products was successful for the individual data collected. The null hypothesis matched the observed data that was received using the allele sever. The class data showed that for 26 participants no one had the genotype of homozygous +/+, 31% was heterozygous, and 69% were homozygous -/-. The Chi square value was 0.86, which was close to expected considering the p-value of 0.3526. The whole-class data compared to the German was similar in genotypes, but almost opposite genotypes to the Chinese.
References
1. Hasler J, Strub K: Alu Elements as Regulators of Gene Expression. Nucleic Acid Res. 2006, 19:5491-5497
2. Deininger P, Batzer M: Alu Repeats and Human Disease. Molecular Genetics and Metabolism. 1999,