Final Report/Thesis 2019 - Revision history

A1722261: /* Conclusions */

2019-11-07T00:30:13Z

Conclusions

← Older revision		Revision as of 10:00, 7 November 2019
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	==Conclusions==		==Conclusions==
	The Somerton Man's DNA reference file provided to the project contain 613905 SNPs, but only 2.08% of SNPs ~~are~~ not empty and ~~be able~~ for DNA analysis. With such low ~~proportion~~ of available ~~SNPs~~, limited DNA analysis techniques can be conducted on the file.		The Somerton Man's DNA reference file provided to the project contain 613905 SNPs, but only 2.08% of SNPs that were not empty and were available for DNA analysis. With such low portion of available SNP, limited DNA analysis techniques can be conducted on the file.
	Unfortunately, there is no DNA ~~kits~~ that matched with Somerton Man's DNA kit ~~were~~ found in GEDmatch database. According to the result of task 2 and task 4, the degradation process would have huge effect on the match results of a human DNA data. And it is impossible to recover Somerton Man's DNA by implementing simple recovery methods such as replacing empty SNPs with random base pairs or homozygous pairs. But if some reliable recovery strategies were introduced which have not been determined yet and allow Somerton Man's DNA to be recovered to more than 60% SNPs, then his relatives may be discovered.		Unfortunately, there was no DNA kit that matched with Somerton Man's DNA kit found in GEDmatch database. According to the result of task 2 and task 4, the degradation process would have huge effect on the match results of a human DNA data. And it is impossible to recover Somerton Man's DNA by implementing simple recovery methods such as replacing empty SNPs with random base pairs or homozygous pairs. But if some reliable recovery strategies were introduced which have not been determined yet and allow Somerton Man's DNA to be recovered to more than 60% SNPs, then his relatives may be discovered.
	Moreover, it shows that Somerton Man ~~comes~~ from Europe. To be specific, his ethnicity is about 36.21% North Atlantic and 20.44% Baltic.		Moreover, the result from task 4 shows that the Somerton Man originated from Europe. To be specific, his ethnicity is about 36.21% North Atlantic and 20.44% Baltic.
	As for the genetic disease, 574 diseases were found, but there is no disease ~~was~~ found that ~~related~~ to his known appearance.		As for the genetic disease, 574 diseases were found, but there was no disease found that relates to his known appearance.
	So far, that is what the project can ~~found with~~ Somerton Man's DNA data. There is no clear clue that can lead to his identity. Who the Somerton Man is will still be ~~an unsolved~~ mystery.		So far, that is what the project can find in regards to the Somerton Man's DNA data. There was no clear clue that can lead to his identity. Who the Somerton Man is will still be a mystery.

	==Future Work==		==Future Work==

A1722261: /* Reference */

2019-11-07T00:24:59Z

Reference

A1722261: /* Result and discussion */

2019-11-07T00:22:57Z

Result and discussion

← Older revision		Revision as of 09:52, 7 November 2019
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	===Result and discussion===		===Result and discussion===
	With the support of data mining program, 613905 SNPs were searched in the database and 574 diseases were found. Figure 19 shows part of the genetic diseases outputs. As the figure shown, the program recorded the rsid of SNP that the disease belonged to in rsid column. ~~The column alleles presents the change of nucleotide change of the SNPs. Moreover,~~ dbSNP only ~~provide~~ a brief description of the clinical effects. More details are linked to another database called ClinVar which is a freely accessible, public database that provide medical reports of the relationships among human variants and phenotypes [12]. Therefore ClinVar Accession column is introduced to collect the ID of the recorded disease. This ID linked to the Clinvar database and allow the user to find a detailed medical report about the disease. ~~Last but not least, the~~ diseases names are recorded in disease name column. It is necessary to indicate that there are multiple diseases named with 'not specified' or 'not provided' which ~~would require~~ the user to find a detailed description of the disease in Clinvar. Unfortunately, none of diseases in the results relates or corresponds to Somerton Man's known ~~appearance~~.		With the support of data mining program, 613905 SNPs were searched in the database and 574 diseases were found. Figure 19 shows part of the genetic diseases outputs. As the figure shown, the program recorded the rsid of SNP that the disease belonged to in rsid column. dbSNP provides only a brief description of the clinical effects. More details are linked to another database called ClinVar which is a freely accessible, public database that provide medical reports of the relationships among human variants and phenotypes [12]. Therefore ClinVar Accession column is introduced to collect the ID of the recorded disease. This ID linked to the Clinvar database and allow the user to find a detailed medical report about the disease. The diseases names are recorded in disease name column. It is necessary to indicate that there are multiple diseases named with 'not specified' or 'not provided' which requires the user to find a detailed description of the disease in Clinvar. Unfortunately, none of diseases in the results relates or corresponds to Somerton Man's known characteristics.
	[[File:disease_list.png\|thumb\|600px\|center\|Figure 19: Outputs of data mining program]]		[[File:disease_list.png\|thumb\|600px\|center\|Figure 19: Outputs of data mining program]]

A1722261: /* Genetic diseases search */

2019-11-07T00:19:44Z

Genetic diseases search

← Older revision		Revision as of 09:49, 7 November 2019
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	==Genetic diseases search==		==Genetic diseases search==
	===Aims===		===Aims===
	During this task, the team ~~would focus~~ on searching clinical effects of each available SNP and identify any possible genetic disease or physical characteristics that Somerton Man could have.		During this task, the team focused on searching clinical effects of each available SNP and identify any possible genetic disease or physical characteristics that Somerton Man could have.

	===Methods===		===Methods===
	To search the clinical effects of SNPs, the team ~~would develop~~ a data mining program that ~~collecting~~ information in SNP database. Python language ~~would be~~ used for development since it is convenient for web development. The SNP database the project selected to use is dbSNP which is the largest database for nucleotide variations in the world, and is managed by the National Center for Biotechnology Information (NCBI) ~~[11]~~. Figure 6.1 shows the information provided by dbSNP. The team ~~would collect~~ the clinical significance ~~refers~~ to each rsid in Somerton Man's file.		To search the clinical effects of SNPs, the team developed a data mining program that collects information in SNP database. Python language was used for development since it is convenient for web development. The SNP database the project selected to use was dbSNP which is the largest database for nucleotide variations in the world, and is managed by the National Center for Biotechnology Information (NCBI). Figure 6.1 shows the information provided by dbSNP. The project team collected the clinical significance related to each rsid in Somerton Man's file.

	[[File:dbSNP.png\|thumb\|600px\|center\|Figure 19:information of SNP rs12913832]]		[[File:dbSNP.png\|thumb\|600px\|center\|Figure 19:information of SNP rs12913832]]
	The program ~~should be able to extract each~~ non-empty SNP in Somerton Man's DNA reference file. With the API provided by dbSNP, connection to dbSNP ~~should be~~ established and each rsid of the extracted SNP ~~should be~~ sent. If the connection is successfully set up, dbSNP ~~will send~~ back the information of corresponding SNP in JSON format. ~~Then the~~ data sent back ~~will be read~~ and clinical information such as genetic disease name associated with the ~~SNP will be~~ recorded.
			The program extracted every non-empty SNP in Somerton Man's DNA reference file. With the API provided by dbSNP, connection to dbSNP was established and each rsid of the extracted SNP was sent. When the connection was successfully set up, dbSNP sent back the information of corresponding SNP in JSON format. The data sent back was analysed and clinical information such as genetic disease name associated with the SNPs was recorded.

	===Result and discussion===		===Result and discussion===
	With the support of data mining program, 613905 SNPs were searched in the database and 574 diseases were found. Figure 19 shows part of the genetic diseases outputs. As the figure shown, the program ~~would record~~ the rsid of SNP that the disease belonged to in rsid column. ~~And~~ column alleles ~~present~~ the change of nucleotide change of the SNPs. Moreover, dbSNP only provide a brief description of the clinical effects. More details are linked to another database called ClinVar which is a freely accessible, public database that provide medical reports of the relationships among human variants and phenotypes [12]. Therefore ClinVar Accession column is introduced to collect the ID of the recorded disease. This ID linked to the Clinvar database and allow the user to find a detailed medical report about the disease. Last but not least, the diseases names are recorded in disease name column. It is necessary to indicate that there are multiple diseases named with 'not specified' or 'not provided' which would require the user to find a detailed description of the disease in Clinvar. Unfortunately, none of diseases in the results relates or corresponds to Somerton Man's known appearance.		With the support of data mining program, 613905 SNPs were searched in the database and 574 diseases were found. Figure 19 shows part of the genetic diseases outputs. As the figure shown, the program recorded the rsid of SNP that the disease belonged to in rsid column. The column alleles presents the change of nucleotide change of the SNPs. Moreover, dbSNP only provide a brief description of the clinical effects. More details are linked to another database called ClinVar which is a freely accessible, public database that provide medical reports of the relationships among human variants and phenotypes [12]. Therefore ClinVar Accession column is introduced to collect the ID of the recorded disease. This ID linked to the Clinvar database and allow the user to find a detailed medical report about the disease. Last but not least, the diseases names are recorded in disease name column. It is necessary to indicate that there are multiple diseases named with 'not specified' or 'not provided' which would require the user to find a detailed description of the disease in Clinvar. Unfortunately, none of diseases in the results relates or corresponds to Somerton Man's known appearance.
	[[File:disease_list.png\|thumb\|600px\|center\|Figure 19: Outputs of data mining program]]		[[File:disease_list.png\|thumb\|600px\|center\|Figure 19: Outputs of data mining program]]

A1722261: /* Task 3: Investigation on ethnicity */

2019-11-07T00:11:42Z

Task 3: Investigation on ethnicity

← Older revision		Revision as of 09:41, 7 November 2019
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	===Methods===		===Methods===
	An ethnicity tool called Eurogenes Ad-Mix Utilities was used. This tool was provided by GEDmatch and can generate a report of ethnicity proportions to the given DNA kit. Eurogenes K13 model is selected as the 'calculator' model. This model calculates and gives results of the ethnicity proportion in 13 different global regions as shown in ~~figure~~ 10, and this mode is ~~primary~~ for European background ~~persons~~ since it ~~provide~~ more sub-continental regions for Europe. The Somerton Man's DNA ~~would be~~ selected as input kit of the utility and the ethnicity report ~~will be~~ generated ~~and evaluated~~.		An ethnicity tool called Eurogenes Ad-Mix Utilities was used. This tool was provided by GEDmatch and can generate a report of ethnicity proportions to the given DNA kit. Eurogenes K13 model is selected as the 'calculator' model. This model calculates and gives results of the ethnicity proportion in 13 different global regions as shown in Figure 10, and this mode is primarily for European background people since it provides more sub-continental regions for Europe. The Somerton Man's DNA was selected as input kit of the utility and the ethnicity report was generated.

	[[File:ethnicity_sample.png\|thumb\|300px\|center\|Figure 10: A sample report of Eurogenes Ad-Mix Utilities]]		[[File:ethnicity_sample.png\|thumb\|300px\|center\|Figure 10: A sample report of Eurogenes Ad-Mix Utilities]]
	In addition, to investigate the reliability of a low quality DNA data file's ethnicity report, several complete DNA samples ~~would be required~~. The project ~~will order~~ 2 sets of complete DNA reference data from 23andMe which provide same format as Somerton Man's file. A program ~~will be~~ developed that ~~allow~~ the user to degrade the selected DNA file ~~to be degraded~~ into different levels of DNA data. This program ~~will be~~ also developed in C++. The project team ~~will degrade~~ each complete DNA sample files into 9 files by removing 10% SNPs, 20% SNPs and then step by step to 90% SNPs. An extra file which ~~would~~ only ~~contained~~ the SNPs with same rsids in Somerton Man's DNA file and be named as degraded_DNA ~~will be generated~~ for each set of complete DNA sample data ~~as well~~. ~~Then these~~ files ~~will be~~ uploaded to GEDmatch and ~~conduct~~ the same ethnicity research as what has been done on Somerton man's DNA raw data. All ethnicity reports ~~are going to be~~ recorded, and the change of how the ethnicity proportion changes ~~will be~~ observed.
	In order to provide stronger evidence to prove whether the low quality DNA file's ethnicity report is reliable or not, different degradation algorithms ~~are~~ introduced ~~to be performed~~. The first strategy is that for every 10 SNPs, ~~remove~~ first n% SNPs where n% is the percentage of SNPs we like to remove. The next algorithm ~~perform~~ opposite ~~way~~ of the first algorithm. This algorithm ~~require~~ the ~~program to remove~~ last n% SNPs for every 10 SNPs, where n% is the percentage of SNPs we like to remove. The third and fourth methods ~~are~~ remove the first and last n% of SNPs for each chromosome, where n% is the percentage of SNPs we like to remove.		In addition, to investigate the reliability of a low quality DNA data file's ethnicity report, several complete DNA samples was analysed. The project ordered 2 sets of complete DNA reference data from 23andMe which provide same format as Somerton Man's file. A program was developed that allows the user to degrade the selected DNA file into different levels of DNA data. This program was also developed using C++. The project team degraded each complete DNA sample files into 9 files by removing 10% SNPs, 20% SNPs and then step by step to 90% SNPs. An extra file which contains only the SNPs with same rsids in Somerton Man's DNA file was created and was named as degraded_DNA for each set of complete DNA sample data. These files were then uploaded to GEDmatch and the same ethnicity research was conducted as what has been done on Somerton man's DNA raw data. All ethnicity reports were recorded, and the change of how the ethnicity proportion changes was also observed.

			In order to provide stronger evidence to prove whether the low quality DNA file's ethnicity report is reliable or not, different degradation algorithms were introduced. The first strategy was that for every 10 SNPs, the first n% SNPs were removed where n% is the percentage of SNPs we would like to remove. The next algorithm performed was the opposite of the first algorithm. This algorithm removed the last n% SNPs for every 10 SNPs, where n% is the percentage of SNPs we would like to remove. The third and fourth methods were to remove the first and last n% of SNPs for each chromosome, where n% is the percentage of SNPs we would like to remove.

	===Results and discussion===		===Results and discussion===
	The ethnicity report of Somerton Man's DNA are shown in ~~figure~~ 11. As the pie chart ~~shown~~, the first 2 major regions are North Atlantic region which ~~has~~ 36.21% ~~proportion~~ and Baltic region which ~~has~~ 20.44% ~~proportion~~.		The ethnicity report of Somerton Man's DNA are shown in Figure 11. As the shown in the pie chart, the first 2 major regions are North Atlantic region which contributes up to 36.21% of the chart, and Baltic region which is 20.44%.
	[[File:ethnicity_SM.png\|thumb\|400px\|center\|Figure 11: Ethnicity report of Somerton Man's DNA]]		[[File:ethnicity_SM.png\|thumb\|400px\|center\|Figure 11: Ethnicity report of Somerton Man's DNA]]

	According to the population averages table[15] for Eurogenes K13 model provided by the developer Davidski (Polako), both Baltic and North Atlantic regions are in Europe. ~~the figure~~ 12 is a map that ~~indicate~~ the areas of Baltic region and ~~figure~~ 13 shows ~~the~~ North Atlantic region.		According to the population averages table[15] for Eurogenes K13 model provided by the developer Davidski (Polako), both Baltic and North Atlantic regions are in Europe. Figure 12 is a map that indicates the areas of Baltic region and Figure 13 shows North Atlantic region.
	<div style="text-align:center;"><ul>		<div style="text-align:center;"><ul>
	<li style="display: inline-block;"> [[File:Baltic.png\|right\|thumb\|300px\|Figure 12: Map of Baltic region]] </li>		<li style="display: inline-block;"> [[File:Baltic.png\|right\|thumb\|300px\|Figure 12: Map of Baltic region]] </li>
	<li style="display: inline-block;"> [[File:North_atlantic.png\|right\|thumb\|323px\|Figure 13: Map of North Atlantic region]] </li>		<li style="display: inline-block;"> [[File:North_atlantic.png\|right\|thumb\|323px\|Figure 13: Map of North Atlantic region]] </li>
	</ul></div>		</ul></div>
	To prove the ethnicity report created is reliable, 2 complete DNA files were gained and be degraded to the same level of Somerton Man's DNA which is 2% SNPs remaining in the file. Sample DNA reference file 1 contained 613967 SNPs and 96.41% of them ~~are~~ not empty, and DNA reference file 2 has 614009 SNPs and 97.68% of them ~~are~~ available for use. The ethnicity reports of 2 complete sample DNA files are presented in figure 16 and 17. Also, ethnicity reports of degraded_DNA files for each complete DNA are shown in figure 14 and 15. According to the ethnicity reports shown in figures, the proportion of largest and second largest ethnicity regions of sample DNA file 1 have changed to 83.13% to 78.66% and 14.82% to 18.14% after degradation process. The first major region proportion has reduced 4.64% and the second region proportion has increased for 3.32%. The degradation process ~~effect~~ the proportion of each ethnicity region for DNA sample 1, but the change is not much and the first and second regions are still the largest 2 regions in the pie chart. Similar phenomenon can be discovered when comparing ethnicity reports of DNA sample 2. The largest ethnicity regions has grown for 2.33% from 81.44% to 83.77%, and the second largest region increased 0.28% from 7.12% to 7.40%. These changes shows that the proportion of major ethnicity regions would not ~~have great~~ change ~~which could be within 5%~~ when a complete human DNA file is degraded to a level of 2% SNPs remaining.		To prove the ethnicity report created was reliable, 2 complete DNA files were gained and were degraded to the same level of Somerton Man's DNA which is 2% SNPs remaining in the file. Sample DNA reference file 1 contained 613967 SNPs and 96.41% of them were not empty, and DNA reference file 2 has 614009 SNPs and 97.68% of them were available for use. The ethnicity reports of 2 complete sample DNA files are presented in figure 16 and 17. Also, ethnicity reports of degraded_DNA files for each complete DNA are shown in figure 14 and 15. According to the ethnicity reports shown in those figures, the proportion of the largest and second largest ethnicity regions of sample DNA file 1 have changed to 83.13% to 78.66% and 14.82% to 18.14% after degradation process. The first major region proportion has reduced 4.64% and the second region proportion has increased for 3.32%. The degradation process affected the proportion of each ethnicity region for DNA sample 1, but the change is not much and the first and second regions are still the largest 2 regions in the pie chart. Similar phenomenon can be discovered when comparing ethnicity reports of DNA sample 2. The largest ethnicity regions has grown for 2.33% from 81.44% to 83.77%, and the second largest region increased 0.28% from 7.12% to 7.40%. These changes shows that the proportion of major ethnicity regions would not change greatly when a complete human DNA file is degraded to a level of 2% SNPs remaining.
	<div style="text-align:center;"><ul>		<div style="text-align:center;"><ul>
	<li style="display: inline-block;"> [[File:s1_eth.png\|right\|thumb\|410px\|Figure 14: Ethnicity reports of sample DNA file 1]] </li>		<li style="display: inline-block;"> [[File:s1_eth.png\|right\|thumb\|410px\|Figure 14: Ethnicity reports of sample DNA file 1]] </li>
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	<li style="display: inline-block;"> [[File:degrade_s2_eth.png\|right\|thumb\|425px\|Figure 17: Ethnicity reports of sample DNA file 2 after degradation]] </li>		<li style="display: inline-block;"> [[File:degrade_s2_eth.png\|right\|thumb\|425px\|Figure 17: Ethnicity reports of sample DNA file 2 after degradation]] </li>
	</ul></div>		</ul></div>
	To provide more ~~evidences~~ to prove this theory, several degradation algorithms introduced in section 5.2 have been applied and changes of ethnicity proportions during different degradation processes have been observed and recorded. 2 sample DNA reference files ~~are~~ degraded into 9 files at different levels from 90% to 10% SNPs remaining. The proportion of first 2 largest ethnicity regions of each degraded files have been plotted on line graphs. Figure 18 is the line graph that ~~show~~ how the means of ethnicity proportions change via the degradation process with standard error provided. As the graph shown, each region proportion fluctuate at a certain level. For instance the percentage of first region of sample 1 fluctuate at around 83% which is a close value to the original proportion 81.44%. However, error bars or standard errors of each region become larger, as more SNPs are removed, which indicate that as more SNPs being removed, the proportions presented in ethnicity reports become less ~~accuracy~~. But in another case, the highest standard error for first and second region proportions of sample 1 and 2 are 1.32%, 1.41%, 1.33% and 1.03%. None of these standard errors exceed 1.5% which can be seen as an acceptable errors. Therefore the project ~~conclude~~ that when a large amount of SNPs are removed from a set of DNA data, the ethnicity report generated from the DNA data would be influenced, but the results are still acceptable ~~for identifying~~ owner's ethnicity.		To provide more evidence to prove this theory, several degradation algorithms introduced in section 5.2 have been applied and changes of ethnicity proportions during different degradation processes have been observed and recorded. 2 sample DNA reference files were degraded into 9 files at different levels from 90% to 10% SNPs remaining. The proportion of first 2 largest ethnicity regions of each degraded files have been plotted on line graphs. Figure 18 is the line graph that shows how the means of ethnicity proportions change via the degradation process with standard error provided. As the graph shown, each region proportion fluctuate at a certain level. For instance the percentage of first region of sample 1 fluctuate at around 83% which is a close value to the original proportion 81.44%. However, error bars or standard errors of each region become larger, as more SNPs are removed, which indicate that as more SNPs being removed, the proportions presented in ethnicity reports become less accurate. But in another case, the highest standard error for first and second region proportions of sample 1 and 2 are 1.32%, 1.41%, 1.33% and 1.03%. None of these standard errors exceed 1.5% which can be seen as an acceptable errors. Therefore the project concludes that when a large amount of SNPs are removed from a set of DNA data, the ethnicity report generated from the DNA data would be influenced, but the results are still acceptable to identify the owner's ethnicity.
	[[File:eth_line_graph.png\|thumb\|600px\|center\|Figure 18: Line graph of means of ethnicity proportions vs degradation level]]		[[File:eth_line_graph.png\|thumb\|600px\|center\|Figure 18: Line graph of means of ethnicity proportions vs degradation level]]

	===Conclusion===		===Conclusion===
	According to the observation of ethnicity change during the degradation process, as more amount of SNPs are removed from a complete human DNA reference file, the result of ethnicity report would be less ~~accuracy. But for~~ the largest and second largest ethnicity regions in the report are still reliable. Therefore the major ethnicity of Somerton Man is North Atlantic and Baltic.		According to the observation of ethnicity change during the degradation process, as more amount of SNPs are removed from a complete human DNA reference file, the result of ethnicity report would be less accurate but the largest and second largest ethnicity regions in the report are still reliable. Therefore the top two major ethnicity of the Somerton Man are North Atlantic and Baltic, where these two regions are mostly around Europe.

	==Genetic diseases search==		==Genetic diseases search==

A1722261: /* Task 3: Investigation on ethnicity */

2019-11-06T22:50:10Z

Task 3: Investigation on ethnicity

← Older revision		Revision as of 08:20, 7 November 2019
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	==Task 3: Investigation on ethnicity==		==Task 3: Investigation on ethnicity==

	===Aims===		===Aims===
	The first aim of this task is ~~investigating~~ the ethnicity of Somerton Man~~'s DNA~~. As described in previous section, the quality of Somerton Man's DNA is low, therefore the second aim is to study the reliability of low quality DNA's ethnicity examination results.		The first aim of this task is to investigate the ethnicity of the Somerton Man. As described in previous section, the quality of Somerton Man's DNA is low, therefore the second aim is to study the reliability of low quality DNA's ethnicity examination results.

	===Methods===		===Methods===
	~~Firstly, an~~ ethnicity tool called Eurogenes Ad-Mix Utilities ~~will be~~ used. This tool is provided on GEDmatch and can generate a report of ethnicity proportions ~~with~~ given DNA kit. Eurogenes K13 model is selected as the 'calculator' model. This model ~~allow the utility calculate~~ the ethnicity proportion ~~into~~ 13 different global regions as figure 10 ~~shown~~, and this mode is primary for European background persons since it provide more sub-continental regions for Europe ~~[13]~~. The Somerton Man's DNA would be selected as input kit of the utility and the ethnicity report will be generated and evaluated.		An ethnicity tool called Eurogenes Ad-Mix Utilities was used. This tool was provided by GEDmatch and can generate a report of ethnicity proportions to the given DNA kit. Eurogenes K13 model is selected as the 'calculator' model. This model calculates and gives results of the ethnicity proportion in 13 different global regions as shown in figure 10, and this mode is primary for European background persons since it provide more sub-continental regions for Europe. The Somerton Man's DNA would be selected as input kit of the utility and the ethnicity report will be generated and evaluated.
	[[File:ethnicity_sample.png\|thumb\|300px\|center\|Figure 10: A sample report of Eurogenes Ad-Mix Utilities]]		[[File:ethnicity_sample.png\|thumb\|300px\|center\|Figure 10: A sample report of Eurogenes Ad-Mix Utilities]]
	In addition, to investigate the reliability of a low quality DNA data file's ethnicity report, several complete DNA samples would be required. The project will order 2 sets of complete DNA reference data from 23andMe which provide same format as Somerton Man's file. A program will be developed that allow the user to degrade the selected DNA file to be degraded into different levels of DNA data. This program will be also developed in C++. The project team will degrade each complete DNA sample files into 9 files by removing 10% SNPs, 20% SNPs and then step by step to 90% SNPs. An extra file which would only contained the SNPs with same rsids in Somerton Man's DNA file and be named as degraded_DNA will be generated for each set of complete DNA sample data as well. Then these files will be uploaded to GEDmatch and conduct the same ethnicity research as what has been done on Somerton man's DNA raw data. All ethnicity reports are going to be recorded, and the change of how the ethnicity proportion changes will be observed.		In addition, to investigate the reliability of a low quality DNA data file's ethnicity report, several complete DNA samples would be required. The project will order 2 sets of complete DNA reference data from 23andMe which provide same format as Somerton Man's file. A program will be developed that allow the user to degrade the selected DNA file to be degraded into different levels of DNA data. This program will be also developed in C++. The project team will degrade each complete DNA sample files into 9 files by removing 10% SNPs, 20% SNPs and then step by step to 90% SNPs. An extra file which would only contained the SNPs with same rsids in Somerton Man's DNA file and be named as degraded_DNA will be generated for each set of complete DNA sample data as well. Then these files will be uploaded to GEDmatch and conduct the same ethnicity research as what has been done on Somerton man's DNA raw data. All ethnicity reports are going to be recorded, and the change of how the ethnicity proportion changes will be observed.

A1722261: /* Task 2: Artificially recover DNA file */

2019-11-06T22:43:46Z

Task 2: Artificially recover DNA file

← Older revision		Revision as of 08:13, 7 November 2019
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	==Task 2: Artificially recover DNA file==		==Task 2: Artificially recover DNA file==

	===Aims===		===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 ~~relative with~~ Somerton Man's DNA kit.		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===		===Methods===
	The recovery works ~~would be~~ done by developing multiple programs ~~with~~ C++. In general, the recovery work is to replace fixed amount of empty SNPs which is 2000 SNPs for each chromosome with available SNPs. Several simple recovery algorithms ~~will be introduced and~~ implemented. ~~First~~ algorithm called random algorithm is to replace empty SNPs with random base pairs in genotype. ~~Replacing~~ empty genotype with homozygous pairs (AA, GG, TT, CC) ~~can be considered~~ which ~~provide~~ 4 new algorithms ~~to use~~.		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 is no DNA kit ~~matched~~ with Somerton Man' DNA in the database, ~~trying to recover~~ Somerton Man's DNA ~~more empty SNPs can~~ 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 the ~~recovered DNA kits with~~ one-to-many tool.		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===		===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 ~~have no relative can be found~~ in the GEDmatch database.		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)]]		[[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.		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 ~~contained~~ 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. ~~Which~~ means that the quality of Somerton Man's DNA file is too low ~~for using~~ one-to-many tool and implementing simple recovery algorithms ~~introduced~~ are ~~useless~~.		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===		===Conclusion===
	It is obvious that there is too many empty SNPs in Somerton Man's DNA reference file. ~~And the~~ recovery algorithms introduced ~~in section 4.1 are~~ too simple and ~~can not~~ 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 ~~with~~ Somerton Man.		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.

	==Task 3: Investigation on ethnicity==		==Task 3: Investigation on ethnicity==

A1722261: /* Conclusion */

2019-11-06T22:32:51Z

Conclusion

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	===Conclusion===		===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 ~~would~~ be introduced in next task.		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.

	==Task 2: Artificially recover DNA file==		==Task 2: Artificially recover DNA file==

A1722261: /* Results and discussion */

2019-11-06T22:32:16Z

Results and discussion

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	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.		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]]		[[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 ~~for using~~ one-to-many tool. ~~The one~~-to-many tool is the main service provided by GEDmatch. When a DNA raw data reference file ~~was~~ updated, it ~~would~~ be stored as a kit in GEDmatch database, and be compared with other kits in the public database. After the ~~match~~ process finished, the one-to-many tool ~~could~~ show how many kits in database ~~are matched~~ with the kit that the user has uploaded. Unfortunately the website ~~reject~~ to process the Somerton Man's data ~~for using~~ one-to-many tool since the file did not meet the minimum requirements of 2000 SNPs for each chromosome.		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]]		[[File:SNP_low.png\|thumb\|600px\|center\|Figure 8: DNA kit not accepted due to low amount of SNPs]]

	===Conclusion===		===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 would be introduced in next task.		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 would be introduced in next task.

A1722261: /* Methods */

2019-11-06T22:27:43Z

Methods

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	===Methods===		===Methods===
	To approach the first goal of this ~~task~~, the team ~~will develop~~ 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 1 to 22 ~~chromosones~~ of Somerton Man’s DNA raw data. ~~Program~~ was developed by C++ language.		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.
	~~Then a~~ website called GEDmatch ~~will be~~ 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 to the Golden State Killer case and are commonly used by all law enforcement in United ~~State [10]~~. Somerton Man’s DNA reference file ~~will be~~ uploaded to the website and ~~tried to conduct~~ several DNA analysis provided on the website.		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===		===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.		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.

← Older revision		Revision as of 09:54, 7 November 2019
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	==Reference==		==Reference==
	[1]Bineth, J, "Somerton Man: One of Australia's most baffling cold cases could be a step closer to being solved" This Is About, 13 December 2017. [online] Available at: https://www.abc.net.au/news/2017-12-14/somerton-man-cold-case-could-be- one-step-closer-to-solved/9245512 [Accessed 1 Jun. 2019].		[1] Bineth, J, "Somerton Man: One of Australia's most baffling cold cases could be a step closer to being solved" This Is About, 13 December 2017. [online] Available at: https://www.abc.net.au/news/2017-12-14/somerton-man-cold-case-could-be- one-step-closer-to-solved/9245512 [Accessed 1 Jun. 2019].

	[2]U.S. National Library of Medicine, "What is DNA?",U.S. National Library of Medicine, May. 28, 2019. [online] Available at: https://ghr.nlm.nih.gov/primer/basics/dna [Accessed 2 Jun. 2019].		[2] U.S. National Library of Medicine, "What is DNA?",U.S. National Library of Medicine, May. 28, 2019. [online] Available at: https://ghr.nlm.nih.gov/primer/basics/dna [Accessed 2 Jun. 2019].

	[3]U.S. National Library of Medicine, "What is a chromosome?",U.S. National Library of Medicine, May. 28, 2019. [online] Available at: https://ghr.nlm.nih.gov/primer/basics/chromosome [Accessed 2 Jun. 2019].		[3] U.S. National Library of Medicine, "What is a chromosome?",U.S. National Library of Medicine, May. 28, 2019. [online] Available at: https://ghr.nlm.nih.gov/primer/basics/chromosome [Accessed 2 Jun. 2019].

	[4]U.S. National Library of Medicine, "How many chromosomes do people have?",U.S. National Library of Medicine, May. 28, 2019. [Online]. Available: https://ghr.nlm.nih.gov/primer/basics/howmanychromosomes. [Accessed: 02- Jun- 2019].		[4] U.S. National Library of Medicine, "How many chromosomes do people have?",U.S. National Library of Medicine, May. 28, 2019. [Online]. Available: https://ghr.nlm.nih.gov/primer/basics/howmanychromosomes. [Accessed: 02- Jun- 2019].

	[5]U.S. National Library of Medicine, "What are single nucleotide polymorphisms (SNPs)?",U.S. National Library of Medicine, May. 28, 2019. [Online]. Available: https://ghr.nlm.nih.gov/primer/genomicresearch/snp. [Accessed: 02- Jun- 2019].		[5] U.S. National Library of Medicine, "What are single nucleotide polymorphisms (SNPs)?",U.S. National Library of Medicine, May. 28, 2019. [Online]. Available: https://ghr.nlm.nih.gov/primer/genomicresearch/snp. [Accessed: 02- Jun- 2019].

	[6]G. Shaw. “Polymorphism and Single nucleotide polymorphisms (SNPs)” Science Made Simple, Vol. 112, pp.664-665 2013.		[6] G. Shaw. “Polymorphism and Single nucleotide polymorphisms (SNPs)” Science Made Simple, Vol. 112, pp.664-665 2013.

	[7]“DEAD MAN FOUND LYING ON SOMERTON BEACH” The News, December 1, 1948, p. 1 [online]. Available: https://trove.nla.gov.au/newspaper/article/129897161. [Accessed: 03- Jun- 2019].		[7] “DEAD MAN FOUND LYING ON SOMERTON BEACH” The News, December 1, 1948, p. 1 [online]. Available: https://trove.nla.gov.au/newspaper/article/129897161. [Accessed: 03- Jun- 2019].

	[8]“Cryptic Note On Body” The News, June 6, 1949, p. 1 [online]. Available: https://trove.nla.gov.au/newspaper/article/36371152. [Accessed: 03- Jun- 2019].		[8] “Cryptic Note On Body” The News, June 6, 1949, p. 1 [online]. Available: https://trove.nla.gov.au/newspaper/article/36371152. [Accessed: 03- Jun- 2019].

	[9]"Raw Data Technical Details", 23andMe, 2019. [Online]. Available: https://customercare.23andme.com/hc/en-us/articles/115004459928-Raw-Data- Technical-Details. [Accessed: 04- Jun- 2019].		[9] "Raw Data Technical Details", 23andMe, 2019. [Online]. Available: https://customercare.23andme.com/hc/en-us/articles/115004459928-Raw-Data- Technical-Details. [Accessed: 04- Jun- 2019].

	~~[10]~~[10]S. Zhang, "The Coming Wave of Murders Solved by Genealogy", The Atlantic, 2019. [Online]. Available: https://www.theatlantic.com/science/archive/2018/05/the-coming-wave-of- murders-solved-by-genealogy/560750/. [Accessed: 04- Jun- 2019].		[10] S. Zhang, "The Coming Wave of Murders Solved by Genealogy", The Atlantic, 2019. [Online]. Available: https://www.theatlantic.com/science/archive/2018/05/the-coming-wave-of- murders-solved-by-genealogy/560750/. [Accessed: 04- Jun- 2019].

	[11]"General Information about dbSNP as a Database Resource", Center for Biotechnology Information (US), 2005. [Online]. Available: https://www.ncbi.nlm.nih.gov/books/NBK44469/. [Accessed: 06- Jun- 2019].		[11] "General Information about dbSNP as a Database Resource", Center for Biotechnology Information (US), 2005. [Online]. Available: https://www.ncbi.nlm.nih.gov/books/NBK44469/. [Accessed: 06- Jun- 2019].

	[12]Landrum, M., Lee, J., Riley, G., Jang, W., Rubinstein, W., Church, D. and Maglott, D. (2013). ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research, 42(D1), pp.D980-D985.		[12] Landrum, M., Lee, J., Riley, G., Jang, W., Rubinstein, W., Church, D. and Maglott, D. (2013). ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Research, 42(D1), pp.D980-D985.

	[13]Chick, H. (2017). Finally! A Gedmatch Admixture Guide!. [Blog] genealogical musings. Available at: https://genealogical-musings.blogspot.com/2017/04/finally-gedmatch-admixture-guide.html [Accessed 29- Oct- 2019].		[13] Chick, H. (2017). Finally! A Gedmatch Admixture Guide!. [Blog] genealogical musings. Available at: https://genealogical-musings.blogspot.com/2017/04/finally-gedmatch-admixture-guide.html [Accessed 29- Oct- 2019].

	[14]Chen, J. and Seroka, A. (2018). Cipher cracking Final Report/Thesis 2018. [online] Eleceng.adelaide.edu.au. Available at: https://www.eleceng.adelaide.edu.au/personal/dabbott/wiki/index.php/Final_Report/Thesis_2018 [Accessed 1 Nov. 2019].		[14] Chen, J. and Seroka, A. (2018). Cipher cracking Final Report/Thesis 2018. [online] Eleceng.adelaide.edu.au. Available at: https://www.eleceng.adelaide.edu.au/personal/dabbott/wiki/index.php/Final_Report/Thesis_2018 [Accessed 1 Nov. 2019].

	[15]Davidski. (2019). K13_population_averages. [online] Available at: https://docs.google.com/spreadsheets/d/1Oz6P5-SVEJciPX1TciGe-zoqA5JtOGIMG7nh-rCOj0c/edit#gid=804264822 [Accessed 1 Nov. 2019].		[15] Davidski. (2019). K13_population_averages. [online] Available at: https://docs.google.com/spreadsheets/d/1Oz6P5-SVEJciPX1TciGe-zoqA5JtOGIMG7nh-rCOj0c/edit#gid=804264822 [Accessed 1 Nov. 2019].

			[16] Inside Story, presented by Stuart Littlemore, ABC TV, screened at 8 pm, Thursday, 24th August, 1978

	~~[16]Inside Story, presented by Stuart Littlemore, ABC TV, screened at 8 pm, Thursday, 24th August, 1978~~
	==Appendix A: Codes and tables used in the project==		==Appendix A: Codes and tables used in the project==
	*[https://github.com/ratherto/Who-killed-the-Somerton-Man-2019 Code and tables used for the project]		*[https://github.com/ratherto/Who-killed-the-Somerton-Man-2019 Code and tables used for the project]