ABSTRACT loci is particularly useful in population genetics,

ABSTRACT
The allele frequencies and statistical forensic parameters were determined based on the 21 STR loci contained in the Globalfiler PCR amplification kit. Presented population genetic data of 21 STRs (D3S135, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, SE33, D10S1248, D1S1656, D12S391, D2S1338) obtained from a sample of 500 unrelated individuals from Middle Eastern country. The P-values of exact test for Hardy–Weinberg equilibrium probabilities, observed and expected heterozygosity, matching probability, power of discrimination and exclusion, polymorphic information content, paternity index and the other population-genetic indices were calculated.
INTRODUCTION
Short tandem repeat (STR) typing has become the state-of-the-art technique for forensic identification and paternity testing (Shimada I; Klintschar M). In the human genome, there are repeated sequenced and generally non-functional series with a certain base index with a length of 2–7 base pair. These series are termed microsatellites or STR (short tandem repeat). As STR loci have a high heterozygosity, the variability in these loci is particularly useful in population genetics, chromosome mapping and forensic studies (Butler 2005). The biological basis of contemporary forensic DNA profiling is linked to the processes of cell and human reproduction. From the many variations that subsequently exist on the human genome, short tandem repeats (STRs) have emerged as the most suitable markers for current forensic identification. The variation of short tandem repeats or microsatellites dispersed through the whole human genome, is actively investigated in forensic labs for personal identification and determination of genetic relationships between individuals. Population genetics and forensic biology are inextricably linked disciplines. The relationships among groups of populations and intra-population characteristics complement each other in phylogenetic and forensic studies. In order to perform a reliable statistical analysis, forensic population database should be established (P.J. Collins) (S. Rand). Short tandem repeat (STR) typing is the standard analysis for human identification. To provide significance in cases where there is a failure to exclude an individual(s) as the source of DNA evidence population data are needed (Population genetic analyses of 15 STR loci from seven forensically-relevant populations residing in the state of Kuwait , Mohammad Al-enizi, Jianye Ge, 2012 FSI: Genetics). This work shows the allele frequency distributions and statistical parameters (matching probability, power of discrimination, polymorphism information content, power of exclusion, typical paternity index, observed heterozygosity, expected heterozygosity, Hardy–Weinberg equilibrium exact test) for forensic testing based on the 21 STR loci for Middle Eastern country.

RESULTS AND DISCUSSION
Allele frequencies and statistic parameters for the 21 STR loci of the population of a Middle Eastern country were calculated by using a webbased tool FORSTAT (Forensic Statistic Analysis Toolbox). GENEPOP 4.2. (F. RoussetGenepop’007: a complete re-implementation of the genepop software for Windows and Linux Mol Ecol Resour, 8 (2008), pp. 103-106) a population genetics software was used to assess the Hardy-Weinberg Exact test. Allele frequencies and statistic parameters for the 21 STR loci of the population of a Middle Eastern Country are shown in Table 1 and Table 2 respectively. All loci analyzed but CSF1PO, D10S1248, D12S391, D13S317, D18S51, D19S433, D21S11, D22S1045, D2S441, D3S135, D5S818, D8S1179, FGA, SE33, TH01, TPOX were in Hardy–Weinberg (HWE) equilibrium in the studied population (p ;0.05). The exact test p-values for some loci remained significant even after Bonferroni’s correction. Possible explanations for HWE departure are population substructure and admixture. However, after Bonferroni correction with 21 comparisons (?= 0.05/21 = 0.00238095 for HWE test), the significant deviations from HWE were observed on loci: CSF1PO, D10S1248, D12S391, D13S317, D19S433, D21S11, D22S1045, D2S441, D3S135, D5S818, D8S1179, SE33, TH01, TPOX. The observed heterozygosity and expected heterozygosity ranged from 0.8580000 (D18S51, SE33) to 0.5700000 (TPOX), 0.947530 (SE33) to 0.646680 (TPOX), respectively. Minimum allele frequency is 5/2N (0.005). Combined power of discrimination and the power of exclusion for the 21 STRs studied were 1.00000000000000000000 and 0.999999976211 respectively, which indicated that these loci are highly polymorphic and could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. SE33 was considered as the most informative locus (PIC=0,94498281513) with 52 alleles and TPOX was the lowest (PIC=0,607327938552) with 12 alleles. Minimum allele frequencies were set at 5/2N. All tested loci were polymorphic; the most discriminating are D18S51, SE33 while the least is TPOX. Through the analysis of allele frequency data, allele 8 of TPOX was found to exhibit the highest allele frequency with 53.8% in the total samples analyzed for the population. The forensic parameter averages calculated for the STRs were: polymorphism information content (PIC) 78%; power of discrimination (PD) is %; power of exclusion is (PE) is %; observed heterozygosity (Ho) %. D18S51 and SE33 showed the highest level of Ho (0.8580000), SE33 showed the highest PD (0.992208) and PIC (0,94510603249). TPOX had the lowest Ho (0.5700000), PD (0.828832) and PIC (0,607327938552). The SE33 locus showed the largest number of different alleles (51 alleles) and D2S441 and D7S820 loci showed the smallest number of different alleles (9 alleles). The combined MP value is 1 in 1.0816×10-26. In the forensic application field, CPE and CPD values are common indicators to estimate the forensic efficiency. The combined power of discrimination and the power of exclusion for the 21 STRs studied were 1.00000000000000000000 and 0.999999976211 respectively, which indicated that these 21 loci could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. SE33 was considered as the most informative locus (PIC= 0,94510603249) with 52 alleles and TPOX was the lowest (PIC= 0,607327938552) with 12 alleles. The high CPD value clarified that these 21 STR loci could be used as efficient genetic markers in forensic identification cases, while the relatively lower CPE value indicated that the 21 STR loci could be used as complementary genetic markers for paternity testing. According to Barni et al. (2006) data from Iraq indicate that standardized multilocus STR panels may be a useful forensic tool which can be applied for identification purposes, but the comparison among this population and other population from the middle-eastern region demonstrated a remarkable and statistically significant genetic differentiation across this area. Their results further suggest that proper DNA databases should be generated and employed for forensic genetics calculations, especially in populations where interpopulation genetic exchange is extremely reduced both due to ethnoreligious and geographical reasons. (Filippo Barni et al. 2006, Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region). According to Nazir M. et al (2016) the data support that there is high diversity in the UAE population, and the data are consistent with the geographic distance among the populations. This information is useful for human identification. (A genetic overview of 23Y-STR markers in UAE population, Muhammad Nazir College of Biotechnology, University of Modern Sciences, Dubai, United Arab Emirates Hasan Alhaddad, 2016).
CONCLUSION
In conclusion, allele frequencies for 21 STR loci were estimated and analyzed in 500 unrelated individuals from the Middle Eastern Country using the GlobalFiler. Significant departure from Hardy–Weinberg equilibrium was detected after Bonferroni correction for multiple tests. Possible explanations for HWE departure are population substructure and admixture. The combined power of discrimination and the power of exclusion for the 21 STRs indicated that these loci could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. The high CPD value clarified that these 21 STR loci could be used as efficient genetic markers in forensic identification cases, while the relatively lower CPE value indicated that the 21 STR loci could be used as complementary genetic markers for paternity testing.
REFERENCES
Raymond, M. and Rousset, F. GENEPOP (Version 3.4). ; 2003
F. Rousset Genepop’007: a complete re-implementation of the genepop software for Windows and Linux Mol Ecol Resour, 8 (2008), pp. 103-106
Shimada I, Rand S, Brinkmann B, Hohoff C. Kurdish population data for 11 STR loci (ACTBP2, CSF1P0, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D13S317 and D21S11). Int J Legal Med 2002;116:301–303.

We Will Write a Custom Essay Specifically
For You For Only $13.90/page!


order now

Excoffier, L.G. Laval, S. Schneider, Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1 (2005), 47–50.

P.J. Collins, L.K. Hennessy, C.S. Leibelt, R.K. Roby, D.J. Reeder, P.A. FoxhallDevelopmental validation of a singletube amplification of the 13 CODIS STR loci, D2S1338, D19S433 and amelogenin: the AmpFISTR Identifiler PCR Amlification kit J. Forensic Sci., 49 (6) (2004), pp. 1265-1277
S. Rand, M. Schurenkamp, C. Hohoff, B. BrinkmannThe GEDNAP blind trial concept. Part II. Trends and developments Int. J. Legal Med., 118 (2) (2004), pp. 83-89
J.M. Butler Forensic DNA typing: biology, technology, and genetics of STR markers
(second ed.), Elsevier Academic Press, London (2005) p.464.
B.S. Weir, Multiple tests, in: Genetic Data Analysis, Sinauer Associates, Inc., Sunderland, MA, 1990, pp. 109–110.) (p-value = 0.05/21 = 0.00238095 for HWE test
Population genetic analyses of 15 STR loci from seven forensically-relevant populations residing in the state of Kuwait , Mohammad Al-enizi, Jianye Ge, 2012 FSI: Genetics
Filippo Barni et al. 2006, Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region.
ACTBP2, CSF1P0, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D13S317 and D21S11). Int J Legal Med 2002;116:301–303.
Klintschar M, Al-Hammadi N, Reichenpfader B. Significant differences between Yemenite and Egyptian STR profiles and the influence on frequency estimations in Arabs. Int J Legal Med 2001;114:211–214.

The high combined forensic statistical parameters of these loci, and collectively as haplotypes, illustrate that they are informative and discriminatory. (A.O. Tillmar, D. Kling, J.M. Butler, W. Parson, M. Prinz, P.M. Schneider, T. Egeland,L. Gusmão, DNA Commission of the International Society for Forensic Genetics(ISFG): Guidelines on the use of X-STRs in kinship analysis, Forensic Sci. Int. Genet.29 (2017) 269–275.)
he differentiation between the data obtained in this study and the data from the Yemeni, Omani 5, Kuwaiti, Egyptian, Iraqi,Iranian, Indian 6, Qatari 13 and UAE populations 14 varies, with a general trend of more significant differences being detected as the populations become more geographically separated. (Hussain M. Alsafiah, William H. Goodwin, Sibte Hadi, Population genetic data for 21 autosomal STR loci for the Saudi Arabian population using the GlobalFiler® PCR amplification kit, 2017).

ABSTRACT
The allele frequencies and statistical forensic parameters were determined based on the 21 STR loci contained in the Globalfiler PCR amplification kit. Presented population genetic data of 21 STRs (D3S135, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, SE33, D10S1248, D1S1656, D12S391, D2S1338) obtained from a sample of 500 unrelated individuals from Middle Eastern country. The P-values of exact test for Hardy–Weinberg equilibrium probabilities, observed and expected heterozygosity, matching probability, power of discrimination and exclusion, polymorphic information content, paternity index and the other population-genetic indices were calculated.
INTRODUCTION
Short tandem repeat (STR) typing has become the state-of-the-art technique for forensic identification and paternity testing (Shimada I; Klintschar M). In the human genome, there are repeated sequenced and generally non-functional series with a certain base index with a length of 2–7 base pair. These series are termed microsatellites or STR (short tandem repeat). As STR loci have a high heterozygosity, the variability in these loci is particularly useful in population genetics, chromosome mapping and forensic studies (Butler 2005). The biological basis of contemporary forensic DNA profiling is linked to the processes of cell and human reproduction. From the many variations that subsequently exist on the human genome, short tandem repeats (STRs) have emerged as the most suitable markers for current forensic identification. The variation of short tandem repeats or microsatellites dispersed through the whole human genome, is actively investigated in forensic labs for personal identification and determination of genetic relationships between individuals. Population genetics and forensic biology are inextricably linked disciplines. The relationships among groups of populations and intra-population characteristics complement each other in phylogenetic and forensic studies. In order to perform a reliable statistical analysis, forensic population database should be established (P.J. Collins) (S. Rand). Short tandem repeat (STR) typing is the standard analysis for human identification. To provide significance in cases where there is a failure to exclude an individual(s) as the source of DNA evidence population data are needed (Population genetic analyses of 15 STR loci from seven forensically-relevant populations residing in the state of Kuwait , Mohammad Al-enizi, Jianye Ge, 2012 FSI: Genetics). This work shows the allele frequency distributions and statistical parameters (matching probability, power of discrimination, polymorphism information content, power of exclusion, typical paternity index, observed heterozygosity, expected heterozygosity, Hardy–Weinberg equilibrium exact test) for forensic testing based on the 21 STR loci for Middle Eastern country.

RESULTS AND DISCUSSION
Allele frequencies and statistic parameters for the 21 STR loci of the population of a Middle Eastern country were calculated by using a webbased tool FORSTAT (Forensic Statistic Analysis Toolbox). GENEPOP 4.2. (F. RoussetGenepop’007: a complete re-implementation of the genepop software for Windows and Linux Mol Ecol Resour, 8 (2008), pp. 103-106) a population genetics software was used to assess the Hardy-Weinberg Exact test. Allele frequencies and statistic parameters for the 21 STR loci of the population of a Middle Eastern Country are shown in Table 1 and Table 2 respectively. All loci analyzed but CSF1PO, D10S1248, D12S391, D13S317, D18S51, D19S433, D21S11, D22S1045, D2S441, D3S135, D5S818, D8S1179, FGA, SE33, TH01, TPOX were in Hardy–Weinberg (HWE) equilibrium in the studied population (p ;0.05). The exact test p-values for some loci remained significant even after Bonferroni’s correction. Possible explanations for HWE departure are population substructure and admixture. However, after Bonferroni correction with 21 comparisons (?= 0.05/21 = 0.00238095 for HWE test), the significant deviations from HWE were observed on loci: CSF1PO, D10S1248, D12S391, D13S317, D19S433, D21S11, D22S1045, D2S441, D3S135, D5S818, D8S1179, SE33, TH01, TPOX. The observed heterozygosity and expected heterozygosity ranged from 0.8580000 (D18S51, SE33) to 0.5700000 (TPOX), 0.947530 (SE33) to 0.646680 (TPOX), respectively. Minimum allele frequency is 5/2N (0.005). Combined power of discrimination and the power of exclusion for the 21 STRs studied were 1.00000000000000000000 and 0.999999976211 respectively, which indicated that these loci are highly polymorphic and could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. SE33 was considered as the most informative locus (PIC=0,94498281513) with 52 alleles and TPOX was the lowest (PIC=0,607327938552) with 12 alleles. Minimum allele frequencies were set at 5/2N. All tested loci were polymorphic; the most discriminating are D18S51, SE33 while the least is TPOX. Through the analysis of allele frequency data, allele 8 of TPOX was found to exhibit the highest allele frequency with 53.8% in the total samples analyzed for the population. The forensic parameter averages calculated for the STRs were: polymorphism information content (PIC) 78%; power of discrimination (PD) is %; power of exclusion is (PE) is %; observed heterozygosity (Ho) %. D18S51 and SE33 showed the highest level of Ho (0.8580000), SE33 showed the highest PD (0.992208) and PIC (0,94510603249). TPOX had the lowest Ho (0.5700000), PD (0.828832) and PIC (0,607327938552). The SE33 locus showed the largest number of different alleles (51 alleles) and D2S441 and D7S820 loci showed the smallest number of different alleles (9 alleles). The combined MP value is 1 in 1.0816×10-26. In the forensic application field, CPE and CPD values are common indicators to estimate the forensic efficiency. The combined power of discrimination and the power of exclusion for the 21 STRs studied were 1.00000000000000000000 and 0.999999976211 respectively, which indicated that these 21 loci could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. SE33 was considered as the most informative locus (PIC= 0,94510603249) with 52 alleles and TPOX was the lowest (PIC= 0,607327938552) with 12 alleles. The high CPD value clarified that these 21 STR loci could be used as efficient genetic markers in forensic identification cases, while the relatively lower CPE value indicated that the 21 STR loci could be used as complementary genetic markers for paternity testing. According to Barni et al. (2006) data from Iraq indicate that standardized multilocus STR panels may be a useful forensic tool which can be applied for identification purposes, but the comparison among this population and other population from the middle-eastern region demonstrated a remarkable and statistically significant genetic differentiation across this area. Their results further suggest that proper DNA databases should be generated and employed for forensic genetics calculations, especially in populations where interpopulation genetic exchange is extremely reduced both due to ethnoreligious and geographical reasons. (Filippo Barni et al. 2006, Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region). According to Nazir M. et al (2016) the data support that there is high diversity in the UAE population, and the data are consistent with the geographic distance among the populations. This information is useful for human identification. (A genetic overview of 23Y-STR markers in UAE population, Muhammad Nazir College of Biotechnology, University of Modern Sciences, Dubai, United Arab Emirates Hasan Alhaddad, 2016).
CONCLUSION
In conclusion, allele frequencies for 21 STR loci were estimated and analyzed in 500 unrelated individuals from the Middle Eastern Country using the GlobalFiler. Significant departure from Hardy–Weinberg equilibrium was detected after Bonferroni correction for multiple tests. Possible explanations for HWE departure are population substructure and admixture. The combined power of discrimination and the power of exclusion for the 21 STRs indicated that these loci could be qualified for personal identification and used as complementary genetic markers for paternity tests in forensic cases. The high CPD value clarified that these 21 STR loci could be used as efficient genetic markers in forensic identification cases, while the relatively lower CPE value indicated that the 21 STR loci could be used as complementary genetic markers for paternity testing.
REFERENCES
Raymond, M. and Rousset, F. GENEPOP (Version 3.4). ; 2003
F. Rousset Genepop’007: a complete re-implementation of the genepop software for Windows and Linux Mol Ecol Resour, 8 (2008), pp. 103-106
Shimada I, Rand S, Brinkmann B, Hohoff C. Kurdish population data for 11 STR loci (ACTBP2, CSF1P0, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D13S317 and D21S11). Int J Legal Med 2002;116:301–303.

We Will Write a Custom Essay Specifically
For You For Only $13.90/page!


order now

Excoffier, L.G. Laval, S. Schneider, Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1 (2005), 47–50.

P.J. Collins, L.K. Hennessy, C.S. Leibelt, R.K. Roby, D.J. Reeder, P.A. FoxhallDevelopmental validation of a singletube amplification of the 13 CODIS STR loci, D2S1338, D19S433 and amelogenin: the AmpFISTR Identifiler PCR Amlification kit J. Forensic Sci., 49 (6) (2004), pp. 1265-1277
S. Rand, M. Schurenkamp, C. Hohoff, B. BrinkmannThe GEDNAP blind trial concept. Part II. Trends and developments Int. J. Legal Med., 118 (2) (2004), pp. 83-89
J.M. Butler Forensic DNA typing: biology, technology, and genetics of STR markers
(second ed.), Elsevier Academic Press, London (2005) p.464.
B.S. Weir, Multiple tests, in: Genetic Data Analysis, Sinauer Associates, Inc., Sunderland, MA, 1990, pp. 109–110.) (p-value = 0.05/21 = 0.00238095 for HWE test
Population genetic analyses of 15 STR loci from seven forensically-relevant populations residing in the state of Kuwait , Mohammad Al-enizi, Jianye Ge, 2012 FSI: Genetics
Filippo Barni et al. 2006, Allele frequencies of 15 autosomal STR loci in the Iraq population with comparisons to other populations from the middle-eastern region.
ACTBP2, CSF1P0, FGA, TH01, TPOX, vWA, D3S1358, D5S818, D7S820, D13S317 and D21S11). Int J Legal Med 2002;116:301–303.
Klintschar M, Al-Hammadi N, Reichenpfader B. Significant differences between Yemenite and Egyptian STR profiles and the influence on frequency estimations in Arabs. Int J Legal Med 2001;114:211–214.

The high combined forensic statistical parameters of these loci, and collectively as haplotypes, illustrate that they are informative and discriminatory. (A.O. Tillmar, D. Kling, J.M. Butler, W. Parson, M. Prinz, P.M. Schneider, T. Egeland,L. Gusmão, DNA Commission of the International Society for Forensic Genetics(ISFG): Guidelines on the use of X-STRs in kinship analysis, Forensic Sci. Int. Genet.29 (2017) 269–275.)
he differentiation between the data obtained in this study and the data from the Yemeni, Omani 5, Kuwaiti, Egyptian, Iraqi,Iranian, Indian 6, Qatari 13 and UAE populations 14 varies, with a general trend of more significant differences being detected as the populations become more geographically separated. (Hussain M. Alsafiah, William H. Goodwin, Sibte Hadi, Population genetic data for 21 autosomal STR loci for the Saudi Arabian population using the GlobalFiler® PCR amplification kit, 2017).

x

Hi!
I'm Mary!

Would you like to get a custom essay? How about receiving a customized one?

Check it out