Genetic admixture and diversity estimations in the Mexican Mestizo population from Mexico City using 15 STR polymorphic markers

The 15 AmpFlSTR Identifiler loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA were analyzed in a sample of 378 unrelated individuals from Mexico City, Mexico. Significant deviations from HW equilibrium in 14/15 STR loci alleles were not detected. The D18S51 locus had the highest power of discrimination (0.970). Genetic admixture estimations revealed a 69% of Amerindian, 26% of European and 5% of African contribution. Comparative analyses between Mexicans and other neighboring populations reveal significant differences in genetic diversity. Our results are important for future comparative genetic studies in different Latin American ethnic groups, particularly Mexican Mestizos and Amerindians. They should also be helpful in genetics, population evolution, forensic and paternity testing.     

Allele frequencies for 70 autosomal SNP loci with U.S. Caucasian, African-American, and Hispanic samples

189 samples from 3 different U.S. sample groups Caucasian (74), African American (71) and Hispanic (44) were typed for 70 autosomal genetic markers. These 70 markers are bi-allelic (C/T) short nucleotide polymorphisms (SNPs). For each sample, the 70 SNP markers were typed in 11 unique 6-plexes and a single 4-plex PCR. A total of 10 of the 210 tests (70 loci x 3 populations) for Hardy-Weinberg equilibrium indicated a statistically significant result. In order to evaluate the minimum number of SNP loci needed to distinguish all 189 samples from one another, we ranked the loci according to their levels of observed heterozygosity and p-values obtained upon testing for Hardy-Weinberg equilibrium. The top 12 loci according to these ranking criteria were tabulated along with the number of unique genotypes observed when combining subsequent SNP markers. The 12 selected SNPs possessed an observed heterozygosity of >0.45 in all three populations examined and thus would be expected to exhibit more differences between samples. All of the 189 samples in this study were individualized with a subset of 12 SNP loci. However, it is likely that the addition of more than 12 SNP loci will be required to resolve larger sets of unrelated individuals from one another. By way of comparison, in these same 189 individuals all but one pair is resolved from one another with three of the traditional short tandem repeat (STR) loci possessing the highest heterozygosity values (D2S1338, D18S51, and FGA) run with the Identifiler kit. The final pair of unrelated samples could be resolved with the combination of 4 STR loci: D2S1338, D18S51, FGA, and VWA.     

Concordance study between the AmpFlSTR MiniFiler PCR amplification kit and conventional STR typing kits

The AmpFlSTR MiniFiler polymerase chain reaction amplification kit developed by Applied Biosystems enables size reduction on eight of the larger STR loci amplified in the Identifiler kit, which will aid recovery of information from highly degraded DNA samples. The MiniFiler Kit amplifies CSF1PO, FGA, D2S1338, D7S820, D13S317, D16S539, D18S51, and D21S11 as well as the sex-typing locus amelogenin. A total of 1308 samples were evaluated with both the MiniFiler and Identifiler STR kits: 449 African American, 445 Caucasian, 207 Hispanic, and 207 Asian individuals. Full concordance between Identifiler and MiniFiler Kits was observed in 99.7% (10,437 out of 10,464) STR allele calls compared. The 27 differences seen are listed in Table 1 and encompass the loci D13S317 (n = 14) and D16S539 (n = 10) as well as D18S51 (n = 1), D7S820 (n = 1), and CSF1PO (n = 1). Genotyping discrepancies between the Identifiler and MiniFiler kits were confirmed by reamplification of the samples and further testing using the PowerPlex 16 kit in many cases. DNA sequence analysis was also performed in order to understand the nature of the genetic variations causing the allele dropout or apparent repeat unit shift.     

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.     

Allele frequencies of 15 STR loci using AmpF/STR Identifiler kit in a Korean population

The genetic variations for 15 short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA were performed on 231 unrelated Korean population using commercially available AmpF/STR Identifiler kit.     

Thai population data on 15 tetrameric STR loci-D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA

The genetic variations for 15 short tandem repeat (STR) loci-D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA, were performed on a population of 210 unrelated Thai individuals using the commercially available AmpF/STR Identifiler kit.     

Genetic polymorphisms of 15 STR loci in Han population from Shaanxi (NW China)

The genetic polymorphisms of 15 STR loci, namely D3S1358, D5S818, D7S820, D13S317, vWA, FGA, TH01, TPOX, CSF1PO, D16S539, D8S1179, D21S11, D18S51, D19S433 and D2S1338, were studied in 203 unrelated Han population from Shaanxi province using AmpF/STR Identifiler kit.     

Data for 10 autosomal STR markers in South Tunisian population

Allele frequencies, together with some parameters of forensic interest for 10 STRs (D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA) were estimated from 201 unrelated individuals originating from southern Tunisia. Significant deviation from Hardy-Weinberg equilibrium was observed for only one marker. Comparative analyses between our population data and other populations showed that only markers D3S158, vWA and FGA were homogenous among populations. The combination of these 10 STR loci provide a powerful tool for forensic identification in Tunisian population.     

Mini-SGM multiplex in degraded samples

A five Mini-SGM multiplex which encompasses TH01, FGA, D18S51, D16S539 and D2S1338, common STR markers in human identity testing, have been performed. Two cases with different biological tissues were selected to illustrate the usefulness of this technique in forensic casework. The use of routine methodology can sometimes give only a partial genetic profile or no profile at all. However, using the Mini-STR technique, a full profile was obtained for the majority of the degraded samples. We conclude that the Mini-SGM methodology is more sensible than routine methodology for degraded samples, although a full genetic profile is not obtained in all cases as results are still very much sample-dependent. This Mini-SGM multiplex can be considered a useful tool to complement conventional STR analysis in degraded samples.     

Allele frequencies of 13 short tandem repeat (STR) loci in the Romanian population

A population study on 13 tetra- and pentameric STR loci (D3S1358, VWA, D8S1179, D21S11, D18S51, D16S539, D2S1338, D19S433, THO1, FGA, ACTBP2 (SE33), Penta D and Penta E) was performed with Romanians from the Bucharest area.     

Development and validation of the AmpFlSTR MiniFiler PCR Amplification Kit: a MiniSTR multiplex for the analysis of degraded and/or PCR inhibited DNA

DNA typing of degraded DNA samples can be a challenging task when using the current commercially available multiplex short tandem repeat (STR) analysis kits. However, the ability to type degraded DNA specimens improves by redesigning current STR marker amplicons such that smaller sized polymerase chain reaction (PCR) products are generated. In an effort to increase the amount of information derived from these types of DNA samples, the AmpFlSTR MiniFiler PCR Amplification Kit has been developed. The kit contains reagents for the amplification of eight miniSTRs which are the largest sized loci in the AmpFlSTR Identifiler PCR Amplification Kit (D7S820, D13S317, D16S539, D21S11, D2S1338, D18S51, CSF1PO, and FGA). Five of these STR loci (D16S539, D21S11, D2S1338, D18S51, and FGA) also are some of the largest loci in the AmpFlSTR SGM Plus kit. This informative nine-locus multiplex, which includes the gender-identification locus Amelogenin, has been validated according to the FBI/National Standards and SWGDAM guidelines. Our results demonstrate significant performance improvements in models of DNA degradation, PCR inhibition, and nonprobative samples when compared to the AmpFlSTR Identifiler and SGM Plus kits. These data support that the MiniFiler kit will increase the likelihood of obtaining additional STR information from forensic samples in situations in which standard STR chemistries fail to produce complete profiles.     

单亲鉴定案例STR选择探讨和PI值计算方法评价

作者对STR位点的个体识别能力(DP)、杂合度(H)、非父排除率(PE)、多态信息含量(PIC)等进行统计学分析,探寻了适合中国人群单亲子鉴定、且有利于国内外DNA实验室数据交流的STR位点,并对现行的PI值计算方法进行了评价。     

Genetic diversity at 15 STR loci in two tribal populations in Southern China

In this research, the allelic distribution of 15 tetrameric short tandem repeats (STR) loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA) were obtained from 167 Mulao and 108 Maonan unrelated individuals. The Genepop v3.4 and the PowerStats v1.2 were used to perform statistical tests and to calculate the forensic parameters. All loci of the two populations showed no significant deviation from Hardy-Weinberg equilibrium. The results showed the 15 STR loci of the two populations have a high degree of genetic polymorphism.     

Genetic diversity and forensic evaluation of 10 STR loci in Lodz region of Poland

Allele frequency data and forensic efficiency parameters for 10 STR loci: D3S1358, vWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA, were estimated from a sample of 207 unrelated individuals in Lodz region of Poland.     

16 STR data of a Greek population

Allele frequencies for 16 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, and SE33) were calculated for a sample of 300 unrelated individuals from Greece. No deviations from Hardy–Weinberg equilibrium were observed for all loci. The combined power of discrimination (PD) and the combined power of exclusion (PE) for the 16 tested STR loci were 0.999999999 and 0.999999816, respectively. Population comparisons were carried out and low genetic distances were found between our data and those previously published for other neighbouring European populations.     

Population genetic data for 18 STR loci in Costa Rica

Allele frequencies for 18 STR autosomal loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, TH01, TPOX, CSF1PO, Penta D, Penta E, D19S433, D2S1338 and SE33) were obtained from a sample of 191-500 unrelated individuals from Costa Rica, Central America.     

Population data on the AmpF/STR Identifiler loci in Africans and Europeans from South Africa

Allele frequencies of 15 short tandem repeat (STR) loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA, were determined for 98 unrelated Africans from South Africa and 98 unrelated Europeans from South Africa using the AmpFlSTR Identifiler PCR amplification kit. The genotype frequency distributions of the 15 STR loci were in the Hardy-Weinberg equilibrium for both populations.     

DNATyper^TM15基因座的研究与选择

目的为研发复合扩增荧光检测试剂盒,对现有的STR基因座进行分析研究并优选新的高鉴别力基因座。方法收集汉族、锡泊族、畲族、壮族、藏族等5个民族群体血样共1200份,提取DNA,应用复合扩增方法检测1200名5个民族群体无关个体的24个基因座的等位基因分布。结果TPOX和TH01基因座的等位基因在5个民族群体中分布不平衡;D2S1338、D6S1043和Penta E等3个STR基因座在5个民族群体中均具有高度遗传多态性,等位基因频率分布均匀,在各群体间无显著差异,而且等位基因传递遵循孟德尔遗传规律。结论确定出DNATyperTM15试剂盒中的14个适合中国人群体遗传学特征和法医学应用的STR基因座。     

Genetic data of 15 STR forensic loci in eastern Chinese population

Allele frequencies for the 15 short tandem repeats (STR) loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, CSF1PO, TH01, D16S539, D2S1338, TPOX D19S433 (AmpFLSTR Identifiler) were determined in a population sample of unrelated individuals living in eastern China.     

Allelic frequencies of 13 STR loci in autochthonous Basques from the province of Vizcaya (Spain)

Allelic frequencies of 13 STR loci (D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D16S539, TH01, TPOX, CSF1PO, and D7S820) were estimated from a sample of 73 unrelated healthy donors natives of the Spanish Basque province of Vizcaya. These STR loci constitute the core of polymerase chain reaction (PCR)-based DNA genetic markers in the US Combined DNA Index System (CODIS). All STR loci analysed met Hardy-Weinberg expectations. Based upon the allelic frequencies, forensically important parameters including gene diversity (GD), polymorphism information content (PIC) and power of discrimination (PD) were calculated.