The Distribution of Alu Genotypes
DNA is mostly found in the nucleus of nearly every cell in the human body, it contains the biological instructions that make us unique. Located on the genome at different locations are short, identifiable sequences known as Alu insertion polymorphisms. The application of Alu elements has recently become used in forensic identification and paternity testing. Alu elements are found in nearly one million copies per haploid gene which approximately 5 – 10% of the human genome. The Alu elements can be found bordering genes or gathered with other interspersed repeated sequences (Primrose 1998).
Alu elements are repeated short DNA sequences that are found on the chromosomes of humans. They are useful polymorphic genetic markers, and are either present or absent, they are often referred to as Alu dimorphisms.
In forensic work there are two polymorphic Alu elements that are commonly used, ACE and TPA-25. TPA-25 insertion site can be found on chromosome 8 in the tissue type plasminogen activator gene. This particular insertion is dimorphic; it is present in some individuals and not in other individuals. The ACE insertion site can be found on chromosome 17 in the Angiotensin-converting enzyme gene, again this insertion is dimorphic, so it will either be present or absent.
The presence of an insertion is signified as a (+); the absence is signified as a (-). There are three possible genotype outcomes, they are (+/+), (+/-) and (-/-). The (+/+) indicates that both parents contributed an Alu insertion; the (+/-) indicates that one parent contributed an Alu insertion and finally the (-/-) indicates that neither parent contributed an Alu insertion.
The aim of the experiment is to isolate purified genomic DNA from cheek cells, prepare the sample for PCR reaction, place prepared sample in agarose gel through a procedure called electrophoresis. From this I hope to establish the distribution of ACE and TPA-25 Alu genotypes in the group. Hardy Weinberg test and the Chi squared test can then be used to establish as to whether the group results are in Hardy Weinberg Equilibrium.
If the designed primers accurately identified and distinguished the ACE and TPA-25 loci through PCR amplification, the electrophoresis gel from the amplified DNA will reflect the presence or absence of insertions at the ACE and TPA-25 loci, the individual’s genotypes can then be established. The group results can then be put through two statistical tests, Hardy-Weinberg and Chi Squared analysis to establish whether the results meet Hardy-Weinberg equilibrium.
Materials & Method
As per handbook.
ACE + 490bp, ACE – 190bp TPA-25 + 400bp, TPA-25 – 100bp
Figure 1: Group Results showing ACE and TPA-25 insertions in DNA | ACE| | TPA|
+ -| 9,4,18,15,21,27,2019,31,16,24,25,23,22| + -| 8,6,7,9,5,1,12,31,25,22,29| + +| 2,28| + +| 17,18,15,21,27,20,24,26,30|
- -| 11,10,8,6,7,14,3,5,1,12,13,17,26,29,30| - -| 11,10,14,3,4,13,2,19,16,23,28|
Figure 2: Genotype by number of students for ACE and TPA-25
| ACE| | TPA|
+ +| 2| + +| 9|
+ -| 14| + -| 11|
- -| 15| - -| 11|
Figure 3: Genotype by number of students, ACE and TPA-25 considered together Genotype| Student Code| Total number of students ineach genotype class| ACE ++TPA-25 ++| | 0|
ACE + -TPA-25 ++| 18, 15, 21, 27, 20, 24| 6|
ACE - -TPA-25 ++| 17, 26, 30| 3|
ACE ++TPA-25 + -| | 0|
ACE ++TPA-25 --| 2, 28| 2|
ACE +-TPA-25 +-| 9, 31, 25, 22| 4|
ACE - -TPA-25 - -| 11, 10, 14, 3, 13| 5|
ACE +-TPA-25 - -| 4, 19, 16, 23| 4|
ACE - -TPA-25 + -| 8, 6, 7, 5, 1, 12, 29| 7|
Figure 4: Photograph of agarose gel containing the PCR products of ACE and TPA-25
Hardy Weinberg Distribution
From the allele frequencies that I have...