Population Genetics Data - Research Paper Example

Evaluation to population genetics data College: Human identification database typically has 12 to 15 STR loci together with their associated frequencies (Lischer 2010). The Genotypes of 200 unrelated individuals as indicated in the excel file (Tereba 1995) was analyzed using the Arlequin Application by providing genetics with large set of statistical tests (Excoffier and Lischer, 2010). The graphical interface illustrated show different data set with different perspectives. The genetic data is represented in the form of haplotypes from the haploid genomes analysis. Polymorphism information and gene match probability was analyzed using the Powestat software (Ehnholm1992). The genetic variants identified accounted for small part of heritability. The genome wide association of the wider sample was used to determine the remaining data set. The small part of the unrelated gene shows the proportion of the total variance in the polymorphism. Allele frequency was calculated by power stats v 12 application. Hardy Weinberg equilibrium was analyzed using the Chi square x2. Significance level was 0.05 in all the 15 Loci. The sampled population was compared to Turkey, Iraq Iranian, Pakistan and Russian populations. The Fst values were calculated and Bonferroni correction test done in order to confirm the significant differences in the analysis. The estimated haplotypes frequencies from the data show there is 56 haplotypes and estimated 107 with no missing genotypes. The estimated result show haplotype frequencies are identical. Implementation of Stephen Al’s Bayesian method is used since the haplotype frequencies is not to be included in the reporting phase.(Czarny 2005). The analyzed genotype showed that data sets with 200 subjects and 132 STRs contained in one gene. Allelic diversity which provides unbiased estimates of the expected heterozygote frequency was computed. The genotype data was used to estimate the power of discrimination (Pakstis&Castiglione 1997).Allele frequencies distribution for 15 PCR based Loci D8S1179, D21S11, D7S820, CSFIPO, D3S1358, TH01, D13S137, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA) for a sample of 200 unrelated individuals as it shows in the table below. Table 1: Allele frequencies and associated statistical parameters of Identifiler® PCR Amplification Kit loci in n=200 The observed allele frequencies and statistical parameters based on the 15STR as summarized in the above table show allelic frequencies ranging from 0.0021 to 0.4077 with number of alleles ranging from 6 (THO1, TPOX and D5S818) to 17 (D21S11, D18S51 and FGA). The 15 STR are highly polymorphic. The new allele is underlined while most common alleles are indicated in bold(0.0021). Afteremploying Bonferroni correction method for the number of analyzed Loci was not significant. TPOX was more variable with expected heterozygosity greater than 0.7 Comparing the alleles in the 200 individuals and the size of alleles in the same loci in order to determine STR genotyping 15 different alleles are seen from the table with PCR amplification of the locus and high electrophoresis’ (ELMRGHNI, S 2012). With 18 and 24 having the most common alleles with frequency of 0.188 and 0.408 respectively while the rest having a value less than 0.10. The most common genotypes is 24 with frequency of 0.160 and 18 to 24 with frequency of 0.145, the rest have a frequency no more than 10. In order for the data given to be utilized in forensic science, it should have Hardy-Weinberg assumption(Gogos JA, 1998). Due to the large number of genotypes in the sample, deviations from Hardy Weinberg would be impossible. From the chi- square analysis the result is, there is no deviation from the Hardy- Weinberg. With pie= 6.28. p> 0.25 and df=8. With a power of discrimination as 0.94, the heterozygosity is 0.80 of 0.781 + -0.029 which proves that the sample follows Hardy- Weinberg expectations. The sampled database was compared to other populations and the results shown as below According to the table 3, European populations emphasize that Fst value=0.01 is conservative for forensic applications. Allele TH01 and D3S1358 are the most different Loci. After comparing the 200 sample database between the 200 samples and Duzce populations’ results show differences DS138, D21S11 using Fst> 0.01. When comparing with Istanbul the results show different Loci CSF1P0, D7S820, TPOX and THO1. Turkey and Greece population have a p value of 0.326, p=0.642 and p=0.887 respectively. The results indicate that the AnpFlstr identfiler kit, Except the TPOX locus is suitable for paternity test for the population. The result show the importance of population studies with sufficient number of individuals in areas where random migration takes place. Social factors like, marriage between people of different social groups has an effect on the genetic data. Analysis of molecular variance AMOVA was conducted in order to detect the mutational differences between the Loci in the different populations. Fst value generated using the Arlequin software was used as the genetic distance to estimate the phylogenetic relationship. AMOVA results for different populations. As seen from the results, all the variation was due within location variation. Variation attribute in the different locations was non-significant at 0.11 with Fst 0.0011. The pairwise comparison in the different locations failed to show significant differences. The results show deep contrast between in the values higher than 0.06 recorded in other geographically closely locate populations. The AMOVA results showed that Pakistan populations were more closely related to the 15 loci sample than the Turkey population. Turkey had 0.55% genetic variation while Pakistan 0.98%. From the above analysis, we can conclude that the database consist of Pakistan population. The AMOVA in Pakistan revealed 9% of generic variation was related to the database. The corrected Fst for Pakistan analysis was 0.022 whereas that of database was 0.028. This may have resulted due to increased levels of genetic drift. Comparing the Pakistan results to allele distribution in Russia, there was a sharp contrast with Loci with allele higher than 0.02 which also may have resulted due to geographically close relations. The Amova and the distance analyses results indicated Pakistan population was closely similar to the allele distribution in the database. The results from the Pakistan population where 15 STRS were typed were similar to the 15 STRS in the database. Same Haplotypes and almost similar allele frequency distribution show proportional gene flow among the populations. A Caucasian Male DNA profile generated shows Loci D8 D21 D7 CSF1PO D3 THO1 D13 D16 Alleles 8, 17 34, 34,2 9, 9 8, 14 14, 14 8, 10 9, 10 14, 15 Loci D2 D19 vWA TPOX D18 D5 FGA Alleles 19, 19 11, 14.2 18, 18 10, 10 11, 19 8, 9 18.2, 19.2 The previous database is signifacntly related to the pakistan database. They had problem maatching the suspect because the above did not match caucasian allele frequencies as shown in the figure Allele frequencies in North America populations. The above populated databasse was generated by collecting different sets of biological samples from unrelated individuals. After the samples were genotyped, allele frequencies were determined for a paticular locus. the allele copies present were divided by the total number of alleles present in the same locus. The expected Hardy – Weinberg as shown in the diagram below was calculated by binomial expansion (Lischer 2010). From the tables allele number 10 was more frequent in both the three populations. Differences between the the observed genotype frequencies from the north American population were not significant(p>0.05) to the database which may be attributed to sampling error in the 200 sample population. Population parameters in the three American populations. The graph illustrate the exact test of p- values in the Hispanic, Black and Caucasian population selected following the criteria of heteroxygosity. The distribution of the observed genotypes was in agreement with the Hardy-Weinberg equilibrium prediction. The observed heterozygosity for the population sample was 0.80 with the a diversity of 0.684 0.039 and the power of discrimination 0.93.RMPs. Observed and the expected heterozygosity are in agreement for only 5 of the 15 loci especially in the Caucasian population. This may have resulted due to intermarriage and migration; some Caucasian population may be living in Asia. If the dataset was analyzed with the Caucasian database in Pakistan, the genotype and frequency distribution would be 50 times more frequent than if analyzed with the America Caucasian Database. (Elmrghni 2012). Due to the high significant disagreement between the expected genotypes frequencies and the frequency database, we can assume the database cannot be used to estimate the frequency of a genetic population in a given population. A white Caucasian male was arested and his DNA profile was obtained, but the defense team argued that the Arab database is unsiutable to obtain of the profile as the offender is not Arab origin, therefore it is more sensible to Caucasian database in order to obtain allele frequencies and the match probability of his profile. Several studies were revealed that the Caucasian database is significantly different to the Arab database as P< 0.001. There are many Caucasian populations living in various Arab states, the table below displays the P values using exact test between Dubai Arab database and Dubai Caucasian populations (Israel and Polish) in order to compare the differences against Arab database. Table 5: Displays the differences of P values using exact test between Arab database against Polish and Israel populations living in Dubai. Populations Loci Dubai Polish Israel D8S1179 0.02467 0.00 0.00068 D21S11 0.00273 0.00 0.29138 D7S820 0.10845 0.0305 - CSF1PO 0.1886 0.0005 0.1211 D3S1358 0.3894 0.0447 0.0129 THO1 0.1309 0.00 0.0005 D13S317 0.0240 0.0086 0.00 D16S539 0.5203 0.00 0.17996 D2S1338 0.0079 0.00 0.0050 D19S433 0.0039 0.00 0.1636 vWA 0.0257 0.00 0.0337 TPOX 0.0258 0.00046 - D18S51 0.4302 0.00 0.7936 D5S818 0.2297 0.0001 - FGA 0.0005 0.00 0.0182 Notice: The most common alleles are indicated in italic bold and new allele is undelined. The figure illustrate the exact test of p- values in the Arabic and American Caucasian. Te loci are all either located on the chromosomes that differed from the 13 locis. The loci were selected following the criteria of heteroxygosity. The distribution of the observed genotypes was in agreement with the Hardy-Weinberg equilibrium prediction. The observed heterozygosity for the population sample was 0.80 with the a diversity of 0.684 0.039 and the power of discrimination 0.93.RMPs quantitative are calculated using a variety of databases and the most conservative value which support the case is used in courts (Brandt and Casadevall 200). The defence team may have raised the issue because the culprit STR alleles do not match with the 200 sample Database. Comparing the different allele in the police sample and the database, using the Hardy- Weinberg Calculation, Hardy-Weinberg in the police sample is p>0.05 while in the database is p Read More