Allele and genotype frequencies for D1S80 locus in a Brazilian population sample

Gene and genotype frequencies in relation to the D1S80 locus were determined in a sample of 197 unrelated individuals (144 Caucasians and 53 Mulattoes), living in the city of S?o Paulo, Brazil. The Mulatto group was composed by mixed individuals who presented at least one negroid physical characteristic or declared themselves to be of mixed (Black-White) ancestry. Nineteen different alleles were detected in the Caucasian sample and 15 among Mulattoes. Alleles 18 and 24 were found to be the most common ones in the Caucasian population with frequencies of 0.173 and 0.357 respectively; the sample heterozygote frequency was estimated in 0.824. Alleles 18, 24, and 28 were found to be the most common alleles among Mulattoes with respective frequencies of 0.150, 0.349, and 0.113; the sample heterozygote frequency was 0.759. Fifty-five different genotypes were detected among Brazilian Caucasians whereas the respective figure among Mulattoes was 31. No significant deviations from Hardy-Weinberg equilibrium were found in both population samples.     

World population data for the HLA-DQA1, PM and D1S80 loci with least and most common profile frequencies for combinations of loci estimated following NRC II guidelines

All published and unpublished gene frequency data for the PCR-based loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80 that could be located are presented in summary tables. These gene frequencies provide the data necessary for estimating probabilities of chance match according to NRC II guidelines for any DNA profile that includes any combination of these loci for any of the populations. To illustrate the range of polymorphism for combined locus profiles, least and most common profile frequencies were estimated following NRC II guidelines for: the PM loci for all populations for which PM data were available; and for combinations of HLA-DQA1/PM, HLA-DQA1/D1S80, PM/D1S80, and HLA-DQA1/ PM/D1S80 for populations for which data were available for the relevant combinations. The profile frequencies were calculated at theta values of zero and 0.01. Minimum allele frequencies (MAF) were calculated, and are shown, for each data set for which the MAF was greater than the lowest observed allele frequency. Least common profile frequencies were calculated using MAF in those cases to illustrate a conservative estimate. The effect of using MAF versus lowest observed allele frequency in estimating least common profile frequencies is briefly illustrated as well. We finally show that aggregate U.S. gene frequency data for the classical MN and GC polymorphisms for both Caucasian and African-American populations is fully in accord with the DNA-based gene frequency data obtained from PM reverse dot-blot strips for GYPA and GC, respectively.     

STR data for the AmPFlSTR SGM plus from a regional population of Austria.

Allele frequencies for 10 microsatellite loci--D3S1358, vWA, D16S539, D2S1338, D19S433, THO1, FGA, D8S1179, D21S11 and D18S51--were determined in an Austrian Caucasian population sample from Vienna using the AmpFlSTR SGM plus amplification kit (Applied Biosystems). This study was done on a population sample of 609 unrelated individuals from the city of Vienna.     

The analysis of three short tandem repeat (STR) loci in the Slovene population by multiplex PCR

Allele frequencies for three tetrameric short tandem repeat (STR) loci D3S1358, HUMVWA, and HUMFGA were determined in a Slovene Caucasian population sample. DNA samples from a total of 221 Slovenes were amplified by multiplex PCR using the commercial kit AmpFISTR Blue (Perkin-Elmer). Separation and detection of the amplified STR fragments were carried out using a 377 automated genetic analyzer (Applied Biosystem Division/Perkin Elmer). Seven alleles at the D3S1358 locus, 8 alleles at the HUMVWA31A locus, and 13 alleles at the HUMFGA locus were observed. A deviation from Hardy-Weinberg equilibrium was observed, only at the HUMVWA31A locus (p = 0.045, exact test). The departure at this locus was not significant after Bonferroni correction. There were no detectable departures between pairwise comparisons of the loci. The combined power of discrimination for all three loci is 0.9998, and the power of exclusion is 0.9526. The observed allele frequencies for the loci D3S1358, HUMVWA31A, and HUMFGA are similar to those in European and U.S. Caucasian populations.     

Analysis of eight polymorphic human genetic markers in a well-defined Greek population

The use of DNA in forensic science has become a basic tool for person identification or parentage testing. The use of polymorphic markers permits the formation of a unique profile for each individual. The knowledge of allele frequencies in a given population allows the scientist to estimate the probability of a particular allele combination. For this task, allele databanks are essential. In this report, the authors estimate the frequencies of eight polymorphic markers (namely, HumFES, HumF13A1, HumTHO1, HumVWA, HumFABP2, HumLIPOL, D1S80, and D17S5) in a randomly selected sample from Crete, Greece. The allele profile of all markers, with the exception of D17S5 and HumFABP2, concurs with previous reports and international data.     

Data on the PCR Turkish population based loci: LDLR, GYPA, HBGG, D7S8, and Gc

Allele and genotype frequencies for the five PCR-based loci were analyzed in 157 unrelated Turkish individuals. The five PCR-based loci included LDLR, GYPA, HBGG, D7S8, and Gc. The results of the chi-square and exact tests showed that the genotype distribution at the LDLR, GYPA, D7S8, and Gc loci did not significantly differ from the Hardy-Weinberg Expectation (HWE). However, the genotype distribution at the HBGG locus did not conform to HWE. Moreover, the genotype frequencies calculated in this study were compared with the published genotype frequencies of US African American and US Caucasian populations. The Turkish population was significantly different at the HBGG locus from the US Caucasian population. However, there were highly significant differences at the LDLR, HBGG, and Gc loci between the Turkish and African American populations.     

Genetic polymorphisms of 20 STR loci in Chinese Han population in Tianjin,North China

The PowerPlex^® 21 System PCR Amplification Kit was a new PCR Amplification Kit developed for forensic laboratories, but there was a lack of data about this kit in Chinese people in Tianjin, North China. This kit contained 20 STR loci, D3S1358, D1S1656, D6S1043, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433 and FGA. In order to evaluate this kit and to get basic population data for its use in forensic practice in Chinese Han population, 360 unrelated Chinese Han individuals from Tianjin were typed using the Kit. Allele frequencies of the 20 STR loci and further population forensic genetic parameters were obtained. The observed genotype frequencies and expected genotype frequencies were evaluated by χ² test. No significant deviation from the Hardy–Weinberg equilibrium was observed in the population sample for the 20 STR loci. The population data in the present study can be used for routine forensic practice in Tianjin, North China.     

Portuguese population data on the six short tandem repeat loci — CSF1PO,TPOX, THO1, D3S1358, VWA and FGA

Allele frequencies for six tetrameric short tandem repeat (STR) loci CSF1PO, TPOX, THO1, D3S1358, VWA and FGA were determined in a Caucasian population sample from Portugal. All loci are highly polymorphic and meet Hardy-Weinberg expectations. There is little evidence for association of alleles among the six loci. The three loci D3S1358, VWA and FGA are more polymorphic and, hence, are more informative than the loci CSF1PO, TPOX, and THO1. However, all six loci would be useful for human identification applications. The STR allelic frequency data are similar to other Caucasian data.     

Allele frequencies for nine STR loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) in the Italian population

Genotype and allele frequencies for STR loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820 were investigated in 289 unrelated Italian Caucasian individuals from the North and South regions. After co-amplification by polymerase chain reaction, automatic DNA profiling of these nine STR loci was performed by ABI PRISM((R)) 310 DNA Genetic Analyzer. For each locus, statistical parameters for forensic and paternity purposes were then calculated; the combined power of discrimination and the combined power of exclusion of all nine loci were 0.9999999999917 and 0.99992 for the Northern population and 0.9999999999921 and 0.99991 for the Southern population.     

Polymorphism of LDLR, GYPA, HBGG, D7S8, GC, HLA-DQA1, Ig-JH, D17S30, ApoB and D1S80 loci in northwestern Russians

Allele frequencies for polymarker, HLA-DQA1, Ig-JH, D17S30, ApoB and D1S80 loci and population genetic parameters were obtained from a sample of 501 unrelated individuals born in the northwestern Federal Region of Russia.     

Swiss Caucasian population data for 13 STR loci using AmpFISTR profiler plus and cofiler PCR amplification kits.

Allele and genotype frequencies for the 13 core STR loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, THO1, TPOX, CSF1PO, and D16S539) were determined in a Swiss Caucasian population sample (n = 206) using two commercially available multiplex PCR kits (AmpFISTR Profiler Plus and AmpFISTR Cofiler) and subsequent electrophoresis on an ABI PRISM CE 310 Genetic Analyzer instrument. All loci meet Hardy-Weinberg expectations. In addition, there is little evidence for association of alleles among the 13 loci. The allelic frequency data can be used in forensic analyses and paternity tests to estimate the frequency of a multiple STR locus DNA profile in the Swiss population.     

Swiss Caucasian population data for the STR loci D2S1338 and D19S433 using the AmpFISTR SGM plus PCR amplification kit

Allele and genotype frequencies for the ten STR loci D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01, FGA were determined in a Swiss Caucasian population sample (n=206) using the AmpFISTR SGM Plus Amplification kit. Electrophoresis was carried out on an ABI PRISM CE 310 Genetic Analyzer instrument. Previously, allele frequencies were published for the 13 STR loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, THO1, TPOX, CSF1PO and D16S539 for the same samples (n=206) amplified with the AmpFISTR Profiler Plus and Cofiler PCR Amplification kits. Since the results for the eight loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, THO1, D16S539 shared between the AmpFISTR SGM Plus, Profiler Plus and Cofiler PCR Amplification kits already are published, only the allele frequencies for the two STR loci D2S1338 and D19S433 are reported in this paper. The two loci meet Hardy-Weinberg expectations. In addition, there is little evidence for association of alleles among the 15 loci (amplified with the Profiler, Cofiler, and SGM Plus amplification kits). The allelic frequency data can be used in forensic analyses to estimate the frequency of a multiple STR locus DNA profile in the Swiss population.     

Iranian STR variation at the fringes of biogeographical demarcation

The integrative relationship between population genetics and forensic biology allows for a thorough genetic characterization of extant human populations. This study aimed to genetically characterize 150 unrelated healthy donors from a general population in Iran both forensically and phylogenetically. The allelic frequencies of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were generated. This constitutes the core of polymerase chain reaction (PCR)-based DNA genetic markers in the US Combined DNA Index System (CODIS) plus two additional loci (D2S1338 and D19S433) that together are consistent with several other worldwide database requirements. There were no deviations from Hardy-Weinberg expectations. Based upon the allelic frequencies, several important forensic parameters were calculated including: gene diversity (GD) index, power of discrimination (PD), polymorphic information content (PIC) and power of exclusion (PE). G-tests indicate the allelic frequencies of the Iranians are statistically non-significant compared to two Turkish populations yet, statistically different from the remaining 18 groups obtained from the literature and examined in this study. This suggests that the Iranian dataset may be forensically equivalent to the dataset from the Turkish region of Eastern Anatolia and the general population from Turkey. Phylogenetic analysis of our population with the full set of 15 loci indicate the Iranians occupy an intermediate position relative to the major Caucasian and East Asian clades on a global level. A regional phylogenetic analysis using 13 of the 15 loci indicate the Iranians segregate in a more compact association with groups from southeastern Spain, Arabs from Morocco and Syria, and especially with the general population from Turkey and those from Eastern Anatolia. These groups are flanked by highly differentiated populations from northern India and a Berber group from Tunisia on opposing ends of the regional phylogram. This report also demonstrates the necessity to thoroughly characterize the genetic composition of populations located in geographic intersections in order to choose the appropriate dataset on which to base forensic calculations, not only at an intra-population level, but also at an inter-population level as well.     

The Slovenian population data on the PCR based loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80

Allele frequencies for the loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8, GC, and D1S80 were determined for a sample population of unrelated individuals from Slovenia. All loci meet Hardy-Weinberg expectations, except the loci GYPA (p = 0.041) and D1S80 (p = 0.009). There is little evidence for association of alleles among the seven loci. Only one out of 21 pairwise comparisons demonstrated departures from independence (HLA-DQA1/HBGG, p = 0.008). The allelic frequency data generally are similar to that of U.S. Caucasians.     

The use of capillary electrophoresis for the study of D13S317 and D7S820 microsatellites in Caucasian population of the Ural region of Russia

A method for the simultaneous amplification and typing of microsatellites D13S17 and D7S820 by using monocomplex sets GenePrint Fluorescent STR Systems ("Promega Corp.", USA) was worked out. The offered method is accurate, reproductive, sensitive and needs a short time for analysis. Allele frequencies D13S17 and D7S820 for the above mentioned Caucasians were determined on the population sample of 120 persons who were not relatives and who resided in the Ural region of Russia. The genotype frequencies of both locuses in this population sample did not differ statistically from Hardy-Weinberg equilibrium. The aggregate discrimination factor for both locuses amounted to 0.995. The null hypothesis of independence among locuses D13S17 and D7S820 was checked by using an accurate test. No relation was found between alleles of the 2 tested locuses in the population sample of Ural Caucasians. The testing of the null hypothesis of the population homogeneity of allele frequencies of the examined locuses showed, among 5 Caucasian population samples, a reliable difference only for locus D7S802 in case of a couple of an Ural and Polish population sample. Allele frequencies for other couples were homogeneous.     

Allelic frequencies of the 15 STR loci included in the AmpFlSTR Identifiler PCR Amplification Kit in an autochthonous sample from Spain

The aim of this study was to estimate the allelic frequencies of the 15 STR loci included in the AmpFlSTR Identifiler PCR Amplification Kit in a sample of 342 unrelated Caucasian individuals autochthonous from Spain to be used for forensic purposes and population studies. The combined power of discrimination and the combined power of exclusion for all of the 15 loci were 5.68x10(-18) and 0.9999964, respectively. According to the obtained data, the D18S51 locus may be considered the most informative among the tested loci.     

Validation of the PowerPlex 1.1 loci for use in human identification

STR typing is now the favored method of DNA analysis for the purposes of human identification in the forensic community. The Forensic Services Division of the Detroit Police Department has completed its validation of the PowerPlex 1.1 loci (CSF1PO, TPOX, THO1, vWA, D16S539, D7S820, D13S317, and D5S818) for use in forensic casework. Detroit Metro Area Red Cross samples were typed from each of five racial/ethnic groups--the Hispanic, Caucasian, African American, Asian, and American Indian populations--and allele and genotype frequencies were calculated. A rare off-ladder variant (9.1 allele at D7S820) was identified among the database samples. A number of validation studies were performed. DNA was extracted from different substrates and typed as expected, except for the DNA extracted from leather (signal absent from the D16S539, D7S820, D13S317, CSF1PO, and TPOX loci) and from dirt (no PCR product generated). The minor contributor in the mixture study (250 pg input DNA) was facile to discern. The Concordance study, the variety of fluids from the same individual, and NIST standards studies all produced the expected results. Finally, STR data confirmed previous DNA typing results from adjudicated casework samples.     

Practical applications of genotypic surveys for forensic STR testing

Legitimate genotype frequency estimation for multiallelic loci relies on component allele frequencies, as population surveys represent only a fraction of possible DNA profiles. Multilocus genotypes from two ethnic human populations, African American (n=195) and U.S. Caucasian (n=200), were compiled at 13 STR loci that are used worldwide in forensic investigation (D3S1358, vWA, FGA, D16S539, TH01, TPOX, CSF1PO, D8S1179, D21S11, D18S51, D5S818, D13S317, and D7S820). Sex-specific AmpFlSTR multiplexes provided stringent PCR-based STR typing specifically optimized for multicolor fluorescence detection. Heterozygosity at each STR locus ranged from 0.57 to 0.89 and encompassed from seven (TH01) to twenty-one (D21S11) alleles. Homozygosity tests, tests based on the distinct numbers of observed homozygous and heterozygous classes, log likelihood ratio tests, and exact tests assessed that the degree of divergence from theoretical Hardy-Weinberg proportions for all 13 STRs does not have practical consequence in genotype frequency estimation. Departures from linkage equilibrium, between loci, that imposed significance to forensic calculations were not indicated by observed variance of the number of heterozygous loci or Karlin interclass correlation tests. For forensic casework, reliable multilocus profile estimates may be obtained from the product of component genotype frequencies, each calculated through application of the Hardy-Weinberg equation to population database allele frequency estimates reported here. The average probability that two randomly selected, unrelated individuals possess an identical thirteen-locus DNA profile was one in 1.8x10(15) African Americans and one in 3.8x10(14) U.S. Caucasians.     

Allele frequencies for 15 autosomal STR loci and admixture estimates in Puerto Rican Americans

Allelic frequencies of 15 short tandem repeats (STR) markers (CSF1PO, FGA, THO1, TPOX, VWA, D3S11358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D19S433 and D2S1338) were determined using the AmpFl STR Identifiler PCR Amplification Kit in Puerto Rican American individuals (N=205) from Massachusetts. The FGA, D18S51 and D2S1338 loci had a high power of discrimination (PD) with values of 0.967, 0.965 and 0.961, respectively. Significant deviations from the Hardy-Weinberg (HW) equilibrium were not detected. An important genetic contribution of Caucasian European (76.4%) was detected in Puerto Rican Americans. However, comparative analysis between Puerto Rican American and other neighboring populations from United States mainly with African and Caucasian Americans, revealed significant differences in the distribution of STR markers. Our results are important for future comparative genetic studies of different American ethnic groups, in particular a cultural group called Hispanic-Americans and should be helpful for forensic and paternity testing.     

Gene and genotype frequencies for HLA-DQA1 in Caucasians and Mulattoes in Brazil.

Gene and genotype frequencies of the HLA-DQA1 locus were determined in a sample of 197 unrelated individuals (144 Caucasians and 53 Mulattoes), living in the city of S?o Paulo, Brazil. The Mulatto group consisted of mixed individuals who presented at least one negroid physical characteristic or declared themselves to be of mixed ancestry. A total of six different alleles were identified with frequencies ranging from 0.087 to 0.316 in the Caucasian population and from 0.066 to 0.330 in the Mulatto population. We observed an increased frequency of allele 1.2 among Mulattoes in relation to Caucasians. The sample heterozygote frequency was 0.722 among Caucasians and 0.736 among Mullatoes. No significant deviations from Hardy-Weinberg equilibrium were found either in the Caucasian or in the Brazilian Mullato population samples.