Editing Final Report/Thesis 2019 (section)

==Task 1: Testing with Somerton Man’s DNA reference file==
===Aims===
The aim of this task is to have a basic understanding of the DNA reference file and DNA analysis techniques. The project provides a DNA reference file of the Somerton Man which is a corrupted DNA data. A screenshot of the file is shown in figure 6.
[[File:sm_dna.png|thumb|center|300px|Figure 6: Screenshot of Somerton Man's DNA reference file]]
The first goal of this task is to evaluate the quality of the file including counting the total amount of SNPs and the amount of available (non-empty) SNPs. The second goal is to conduct some DNA analysis on the DNA reference file.

===Methods===
To approach the first goal of this project, the team developed a program which provide functions for counting total amount of SNPs, amount of available SNPs (SNPs that do not have genotype of “--”), and determine the percentages of available SNPs for chromosome 1 to 22 of the Somerton Man’s DNA raw data. The program was developed using C++ language.
A website called GEDmatch was used for conducting DNA analysis. GEDmatch is a website that has an open data personal genomics database and provide tools for DNA and genealogy research. The site become well known after law enforcement in California use it for the Golden State Killer case and are commonly used by all law enforcement in United States. The Somerton Man’s DNA reference file was uploaded to the website and several DNA analysis tools provided on the website was used.

===Results and discussion===
The counting outputs of Somerton man's DNA data is presented in figure 7. As the figure shown, there are more than 0.6 million SNPs in the files, but only about 2% of them have determined base pairs. In DNA analysis, only the SNPs with available base pairs can be used and most genetic analysis technique would require a certain amount of available SNPs.
[[File:SM_Counting.png|thumb|center|300px|Figure 7: SNPs counting results of Somerton man DNA file]]
Then the Somerton Man's DNA reference file was uploaded to GEDmatch to be used on the one-to-many tool. One-to-many tool is the main service provided by GEDmatch. When a DNA raw data reference file is updated, it will be stored as a kit in GEDmatch database, and be compared with other kits in the public database. After the matching process has finished, the one-to-many tool can show how many kits in database match with the kit that the user has uploaded. Unfortunately the website rejects to process the Somerton Man's data to use the one-to-many tool since the file did not meet the minimum requirements of 2000 SNPs for each chromosome. 
[[File:SNP_low.png|thumb|600px|center|Figure 8: DNA kit not accepted due to low amount of SNPs]]

===Conclusion===
The quality of Somerton Man's DNA reference file is lower than expected. Only about 2% of 613905 SNPs in the files are available for use. Such low quality DNA file is not accepted by GEDmatch to conduct DNA match examination. In order to satisfy the minimum requirements of GEDmatch, a data recovery work would be required which will be introduced in the next task.