Editing Final Report/Thesis 2019 (section)

==Task 2: Artificially recover DNA file==

===Aims===
In this task, the project group aims to artificially recover Somerton Man's DNA file to satisfy the basic SNPs amount requirements (2000 SNPs for each chromosome) of GEDmatch's one-to-many tool and find out how many people is related to Somerton Man's DNA kit.

===Methods===
The recovery works was done by developing multiple programs using C++. In general, the recovery work is to replace a fixed amount of empty SNPs which is 2000 SNPs for each chromosome with available SNPs. Several simple recovery algorithms were implemented. The first algorithm is called random algorithm which is to replace empty SNPs with random base pairs in genotype. The second algorithm used was by replacing empty genotype with homozygous pairs (AA, GG, TT, CC) which resulted in 4 new algorithms.
In addition, if there was no DNA kit that matches with Somerton Man' DNA in the database, recovering more empty SNP's of the Somerton Man's DNA could be a back up plan. With the recovery algorithm introduced before, the project team can recover more SNPs in Somerton Man's DNA reference file and try to use the one-to-many tool on those kits.

===Results and discussion===
With the developed program, multiple artificial DNA kits which have 2000 SNPs in each chromosome were created. Unfortunately, all of these DNA kits have 0 matches with other DNA in the public database which means these artificial DNA kits do not relate to any kit in the GEDmatch database.
[[File:zero_match.png|thumb|600px|center|Figure 9: match results of artificial DNA(replace empty SNPs with random pairs to 2000 SNPs in each choromosone)]]
Then kits with more amount of empty SNPs were replaced with homozygous pairs or random pairs were created, but none of these files could find relative DNA kits in the database. Even the DNA kits with all empty SNPs recovered could find a matched DNA result. It is important to note that all 5 recovery strategies were all implemented.
As GEDmatch is the most commonly used DNA database in public, it contains a huge amount of DNA kits in its database. As the website shown, the total number of kits managed by GEDmatch database is 1363427157376. Therefore, the chance that no DNA kit in the database is related to Somerton Man is nearly impossible. This means that the quality of Somerton Man's DNA file is too low to be used on the one-to-many tool and implementing simple recovery algorithms are pointless.

===Conclusion===
It is obvious that there is too many empty SNPs in Somerton Man's DNA reference file. The recovery algorithms introduced were too simple and cannot help to increase the chance of finding Somerton Man's relatives in the GEDmatch database. With DNA data that only contains approximate 2% available SNPs, it is nearly impossible to find any possible related DNA kits to Somerton Man.