Combined Mean Exclusion Chance Research Articles

Forensic efficiency and genetic polymorphisms of 12 X-chromosomal STR loci in Northeastern Thai populations.

Northeastern Thailand comprises one-third of the country and is home to various populations, with Lao Isan constituting the majority, while others are considered minority groups. Previous studies on forensic short tandem repeats (STRs) in Thailand predominantly focused on autosomal STRs but there was a paucity of X-STRs, exclusively reported from the North and Central regions of the country. In this study, we have newly established a 12 X-STRs from a total of 896 samples from Northeastern Thailand, encompassing Lao Isan as the major group in the region, alongside nine minor populations (Khmer, Mon, Nyahkur, Bru, Kuy, Phutai, Kalueang, Nyaw, and Saek). Across all ten populations, the combined powers of discrimination in both genders were high and the combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were also high (> 0.99999). DXS10148 emerged as the most informative marker, while DXS7423 was identified as the least informative. Genetic comparison based on X-STRs frequency supported genetic distinction of cerain minor groups such as Kuy, Saek and Nyahkur from other northeastern Thai groups as well as genetic differences according to the geographic region of Thai groups (Northeast, North and Central). In sum, the overall results on population genetics are in agreement with earlier reports on other genetic systems, indicating the informativeness of X-STRs for use in anthropological genetics studies. From a forensic perspective, despite the limitations of small sample sizes for minority groups, the present results contribute to filling the gap in the reference X-STRs database of the major group Lao Isan, providing valuable frequency data for forensic applications in Thailand and neighboring countries.

Development and validation of a custom panel including 114 InDels using massively parallel sequencing for forensic application.

Insertion/deletion polymorphisms (InDels) have particular characteristics, such as a relatively low mutation rate, small amplicon size, and no stutter artifacts when genotyped via the capillary electrophoresisplatform. It would be an important complementary tool for individual identification and certain kinship analyses. At present, massively parallel sequencing (MPS) has shown excellent application value in forensic studies. Therefore, in this study, we developed a custom MPS InDel panel that contains 114 InDels [77 autosomal InDels (A-InDels), 32 X-chromosomal InDels (X-InDels), and 5 Y-chromosomal InDels) based on previous studies. To assess this panel's performance, several validation experiments were performed, including sensitivity, inhibitor, degraded DNA testing, species specificity, concordance, repeatability, case-type samples, and population studies. The results showed that the lowest DNA input was 0.25ng. All genotypes were obtained in the presence of 80ng/µL humic acid, 2000µmol/L calcium, 3000µmol/L EDTA and indigo. In degraded DNA testing, 90% of loci could be detected for 16-day-old formalin-fixed hearts. In addition, this panel has good species specificity. The values of combined power of discrimination and the combined power of exclusion for 77 A-InDels were 1-3.9951×10-32 and 1-4.2956×10-7 , respectively. The combined mean exclusion chance for 32 X-InDels was 0.99999 in trios and 0.99904 in duos. The validation results indicate that this newly developed MPS multiplex system is a robust tool for forensic applications.

High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System

Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|Hexp – Hobs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.

Genetic features and phylogenetic relationship analyses of Guizhou Han population residing in Southwest China via 38 X-InDels.

The insertion/deletion polymorphism (InDel), an ideal forensic genetic marker with a low spontaneous mutation rate and small amplification product fragments, is widely distributed in the genome, combining the advantages of STR and SNP genetic markers. The X-chromosome has high application value in complex paternity testing, and it is an excellent system for evaluating population admixture and studying evolutionary anthropology. However, further research is needed on the population genetics of X-chromosome InDels (X-InDels). In this article, a system composed of 38 X-InDel loci was utilized to analyse and evaluate the forensic parameters of the Guizhou Han population in order to explore its forensic application efficiency. The results showed that expected heterozygosities spanned from 0.0189 to 0.5715, and the cumulative power of discrimination of the 32 X-InDels and three linkage blocks was 0.9999999954 and 0.999999999999741 for males and females, respectively. The combined mean exclusion chance of these loci for trios and duos is 0.999999 and 0.999747, respectively. Multiple methods like principal component analysis, Fst genetic distance, and phylogenetic reconstruction were employed for dissecting the genetic structure of the Guizhou Han population by comparing it with previously reported populations. As expected, the studied Han population displayed relatively close genetic affinities with the East Asian populations. At the same time, there were obvious genetic differentiations between the Guizhou Han population and other continental populations that were discerned, especially for the African populations. This study further verified the applicability of 38 X-InDels for human personal identification and kinship analyses of Han Chinese, and also showed the application potential of X-InDels in population genetics.

Development and validation of a multiplex 19 X-chromosomal short tandem repeats typing system for forensic purposes

X-chromosome short tandem repeat (X-STR) markers are a powerful complementary system used for paternity and forensic casework. This study presents the development and validation of a new highly efficient multiplex-fluorescent-labeled 19 X-STR typing system, including DXS10079, DXS101, DXS10135, DXS10162, DXS6795, DXS6800, DXS6803, DXS6807, DXS6809, DXS6810, DXS7133, DXS7423, DXS981, DXS9902, DXS9907, GATA165B12, GATA172D05, GATA31E08 and HPRTB along with sex-typing locus, amelogenin. The system was validated according to guidelines issued by the Scientific Working Group on DNA Analysis Methods. Allele frequency and forensic parameters were investigated from 1085 (494 males and 591 females) unrelated Beijing Han individuals, the combined power of discrimination by the 19 X-STR loci in females and males, as well as the combined mean exclusion chance in trios and duos, were 0.999999999999999995, 0.99999999995, 0.9999999995, and 0.9999996, respectively. The results demonstrate that this multiplex system is robust and reliable, and considered to be a powerful tool for forensic application.

Development of a 16 X-STR multiplex PCR system for kinship analysis and its applicability for the Sinhalese population in Sri Lanka.

The study describes the development of a new multiplex PCR system that simultaneously amplifies 16 X chromosome short tandem repeats (X-STRs) loci in a single PCR reaction and its applicability on a sample of 200 from the Sinhalese population in Sri Lanka. 13 X-STR loci located in four clusters are selected for the assay (DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074-DXS10075, DXS6801-DXS6809-DXS6789 and DXS7424-DXS101-DXS7133). In addition, three single loci were also selected (DXS9902, HPRTB and DXS7423). Genomic DNA extracted using the Chelex-100 method was amplified with modified published primers and subjected to capillary gel electrophoresis. Complete DNA profiles were obtained with 0.20 ng 9947A DNA and the band sizes ranged between 100 and 320 bp with 10 loci having sizes below 237 bp. A total of 160 alleles were observed among the sample with 5-23 alleles for each locus. The forensic efficiency evaluation showed high values for the combined power of discrimination in males (1 in 1 × 1010) and females (1 in 1 × 1017). Combined mean exclusion chance (MEC) indices calculated for deficiency, normal trio and duo cases were equally high (> 0.99999). Application of the new multiplex system to two actual kinship cases of full sibling and deficient paternity suggested that these 16 short tandem repeat loci are highly appropriate for forensic and kinship testing among the Sinhalese population.

Development and validation of a multiplex insertion/deletion marker panel, SifaInDel 45plex system

In addition to commonly used short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs), insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because they combine desirable characteristics of both STRs and SNPs. In the present study, the SifaInDel 45plex system was designed to amplify 45 InDel markers, including 27 autosomal InDels (A-InDels), 16 X chromosome InDels (X-InDels) and two Y chromosome InDels (Y-InDels), simultaneously in a single PCR procedure and then detect products by capillary electrophoresis (CE). We also optimized the PCR conditions for the novel panel and performed several validation studies including repeatability/reproducibility, concordance, accuracy, sensitivity, stability, species specificity and population genetics.The results confirmed that full profiles could be obtained from ≥62.5 pg of input DNA and from a series of challenging samples encountered in routine casework. The SifaInDel 45plex panel could tolerate different concentrations of inhibitors, such as ≤50 μM hematin, ≤20 ng/μL nigrosine and ≤8000 ng/μL urea. In a population investigation, for the 27 A-InDels, the combined power of discrimination (CPD) exceeded 0.999999, and the combined power of exclusion in duos (CPED) and trios (CPET) was 0.955118 and 0.997754, respectively. For the 16 X-InDels, the combined PDMale and PDFemale was computed as 0.999845 and 0.999998, respectively, and the combined mean exclusion chance in father/daughter or mother/son duos (MECDuo) and mean exclusion chance in standard trios involving daughters (MECTrio) was 0.976220 and 0.998163, respectively. In addition, the two Y-InDels could play a role in correctly determining gender. Overall, the established SifaInDel 45plex panel is a well-performing, reliable and robust multiplex system that stands out for combining a considerable number of A-indels, X-indels and Y-indels based on a CE platform. The population study results also demonstrated that the SifaInDel 45plex panel could be a valid complementary approach for human identification and complex kinship analysis.

Genetic Polymorphism of 30 InDel Loci in Han Population from Jiangsu Province

To investigate the genetic information of 30 insertion/deletion （InDel） loci in Han population from Jiangsu Province, and to explore the application values of Investigator® DIPplex kit for guiding the forensic analysis in Han population from Jiangsu Province. The autosomal InDel loci of 305 unrelated healthy Han individuals from Jiangsu Province were genotyped and analysed by Investigator® DIPplex kit, and the allelic frequencies and forensic parameters of 30 InDel loci were statistically analysed. The distribution of 30 InDel loci in Han population from Jiangsu Province conformed to Hardy-Weinberg equilibrium. The minor allele frequencies of 21 InDel loci were above 0.3. The polymorphism information content ranged from 0.089 to 0.375, while the discrimination power distributed from 0.093 to 0.500. The paternity exclusion in duo cases and trio cases were 0.047-0.250 and 0.046-0.219, respectively. The linkage disequilibrium analysis of 30 InDel loci showed that all loci were independent from each other. The combined discrimination power was 1-7.369×10⁻⁸, whereas the combined mean exclusion chance in duo cases was 0.998 933 978, in trio cases was 0.997 806 392. The Fst values were all less than 0.06 except HLD118 and other four loci, which showed small differences between groups. The InDel loci of Investigator® DIPplex kit can be used as complementary genetic markers for the cases associated with forensic genetics.

Genetic characterization of four Colombian populations using Investigator® Argus X-12 kit

X-STR markers have been shown to be a powerful tool for solving complex cases of biological relations; their use increases the probability of solving difficult cases in contrast to using only A-STR markers. The objective of this study was to analyze 806 men from four Colombian populations (Department of Antioquia (n=202), Department of Cauca (n=200), Department of Santander (n=204) and Cundiboyacense Region (n=200)) with the Investigator® Argus X-12 kit. Allelic and haplotype frequencies were calculated, and some basic parameters of forensic interest were established for each population. High combined discrimination power was obtained in all populations, both in men (>99.99999%) and in women (>99.99999999999), as well as a high combined mean exclusion chance in father/daughter pairs (>99, 99%) and in father/mother/daughter trios (>99.9999). This work is contributing to increasing the knowledge about the 12 X-STRs included in the Investigator® Argus X-12 kit and the genetic composition of the Colombian populations studied.

Genetic analysis of 12 X-STR loci in the Serbian population from Vojvodina Province.

The analysis of 12 X-STR loci included in the Investigator® Argus X-12 kit was performed on a sample of 325 unrelated persons from Vojvodina Province, Republic of Serbia. No significant differences were observed in the allele frequencies in males and females. Heterozygosity values among the studied loci ranged from 67.62 to 94.28%. All loci in female individuals were consistent with the Hardy-Weinberg equilibrium test. The combined power of discrimination values in male and female individuals was 0.9999999994 and 0.999999999999999, respectively. The combined mean exclusion chance was 0.999998 in deficiency cases, 0.9999999977 in normal trio cases, and 0.9999994 in duo cases. Loci DXS10135 and DXS10101 were found to be most polymorphic. The haplotype diversity was found to be greater than 0.993 for all linkage groups. The exact test for pairwise linkage disequilibrium for the 12 loci in the male samples showed significant linkage disequilibrium for the DXS10103-DXS10101 and DXS10134-DXS10146 pairs of loci. The results from the current study confirmed that the panel of 12 X-STR loci is highly polymorphic and informative and can be implemented as a powerful tool in deficient paternity testing and kinship analysis, as well as a useful complement tool of autosomal short tandem repeats (STRs) in forensic investigation. Population differentiation analyses indicated significant differences in genetic structure between the Serbian population and the geographically and ethno-linguistically distant populations, while genetic homogeneity was present in populations with similar geographic origin.

Genetic diversity study on 12 X-STR loci of investigator® Argus X STR kit in Bangladeshi population

The X-chromosome short tandem repeat (STR) loci are of particular interest for solving complex kinship and paternity cases. Here, we report the genetic data from 209 unrelated Bangladeshi individuals (102 males and 107 females) that were genotyped using the 12 X-chromosomal STR markers included in the Investigator® Argus X-12 kit (Qiagen). The 12 X-STR markers are located in four linkage groups (linkage group I: DXS10135, DXS10148, and DXS8378; linkage group II: DXS7132, DXS10079, and DXS10074; linkage group III: DXS10103, HPRTB, and DXS10101; and linkage group IV: DXS10146, DXS10134, and DXS7423). Allelic frequencies of the 12 X-STR loci and haplotype frequencies of the four linkage groups were investigated. No significant difference was observed in the allele frequencies of males and females. Distributions of heterozygosity were observed from 64.5 to 92.5% among the studied 12 X STR loci. DXS10135 and DXS10101 loci were found to be most polymorphic. For all the four linkage groups, the haplotype diversity was found to be greater than 0.986. A total of 95, 73, 66, and 74 haplotypes were observed in linkage groups I, II, III, and IV, respectively. Hardy-Weinberg equilibrium tests showed no significant deviation from expected values for all 12 loci (p>0.05). The exact test for pairwise linkage disequilibrium for the 12 loci in the male samples did not show any significant linkage disequilibrium except the DXS10103 and DXS10101 loci after the p values were corrected by Bonferroni's correction for multiple testing (p>0.05/66). A combined power of discrimination in male and female individuals were 0.999999998159791 and 0.999999999999993, respectively. The combined mean exclusion chance were 0.999997635 in deficiency cases, 0.999999996 in normal trio cases, and 0.999999178 in duo cases. The currently investigated Bangladeshi population showed significant differences when compared with previously reported X-STR data from other 12 populations. The results of the data analysis indicated that all the loci in the Investigator® Argus X 12 kit were fairly informative and might be useful in forensic application and kinship analysis in Bangladeshi population.

Diversity study of 12 X-chromosomal STR loci in Hui ethnic from China.

X-chromosomal STRs (X-STRs) have been used as complements of autosomal STR application in recent years. In this work, we present population genetic data of 12 X-STRs including DXS101, DXS10159, DXS10162, DXS10164, DXS6789, DXS7133, DXS7423, DXS7424, DXS8378, DXS981, GATA165B12, and GATA31E08 loci in a sample of 231 unrelated healthy individuals from the Hui ethnic group in Ningxia Hui Autonomous Region, China. Allelic frequencies of the 12 X-STR loci and haplotypic frequencies of the reported linkage groups (DXS7424-DXS101 and DXS10159-DXS10164-DXS10162) were investigated in the group, respectively. No STR loci showed significant deviations from the Hardy-Weinberg equilibriums and no linkage disequilibriums of pairwise loci were found after Bonferroni correction, respectively. A combined power of discrimination in female individuals was 0.999999999985 and that in male individuals was 0.99999967, respectively. The combined mean exclusion chance in deficiency cases, normal trios and duo cases were 0.999934, 0.995754, and 0.999796, respectively. Significant differences were observed from 0 to 8 loci, when making comparisons between the data of Hui ethnic group and previously reported data from other 16 populations. The results indicated the new panel of 12 X-STR loci might be useful for forensic science application.

Genetic polymorphisms of 12 X‐chromosomal STR loci in Taiwanese individuals and likelihood ratio calculations applied to case studies of blood relationships

Allele frequencies for the 12 short tandem repeat loci of the Investigator Argus X-12 kit were obtained from 514 unrelated Taiwanese individuals (327 males and 187 females). Hardy-Weinberg equilibrium tests with samples demonstrated no significant deviation from expected values for all 12 loci (p > 0.05). The linkage disequilibrium for the 12 loci in the female samples was identical to what was observed in other Han Chinese populations, with only the DXS10103 and DXS10101 loci showing significant linkage disequilibrium after corrected by Bonferroni's correction for multiple testing (p < 0.05/66). No significant differences were observed by population pairwise genetic distance analysis between Taiwanese and other Han Chinese populations. When compared with other Asian, European, and African populations, however, significant differences were observed at more than one locus. The combined mean exclusion chance was 0.99999 in duo cases and 0.99999999 in trio cases. This study used mathematical logic inferred likelihood ratio calculation formulas for full-sister, half-sister from the same father, and paternal grandmother-granddaughter relationships. The results for these three real familial cases suggest that these 12 short tandem repeat loci may appropriate for forensic relationship testing.

Genetic polymorphisms in 12 autosomal STRs in a Shanghai Han population from China

In this study, a total of 484 unrelated healthy individuals and 359 two-generation families in the Han population in Shanghai, China were successfully analyzed with the Investigator HDplex Kit (Qiagen, Hilden, Germany). Hardy-Weinberg equilibrium tests demonstrated no significant deviation from expected values (p > 0.05) for the 12 autosomal STRs included in this kit. A total of 173 alleles were detected in 12 autosomal STR loci; the largest number of alleles (32) was detected for the SE33 locus. The combined power of discrimination was 0.99999999992. The combined mean exclusion chance in duo cases was 0.99982, whereas the combined mean exclusion chance in trio cases was 0.9999986. The average mutation rate across all loci was 0.0023 (95% confidence intervals: 0.0013-0.0039). These results suggest that the 12 autosomal STR loci can provide highly informative polymorphic data for paternity testing and forensic identification in the Han population in Shanghai, China.

The polymorphisms of 12 X-STR loci in six ethnic populations in China

To explore the genetic polymorphisms of 12 X-STR loci for Guangdong Han population and other five minor ethnic populations (Tibetan, Mongolian, Korean, Uighur and Hui) in China, 1298 samples from unrelated individuals of these 6 ethnic populations were amplified with Investigator™ Argus X-12 multiplex PCR system. 238 alleles were observed totally, which included 66 off-ladder alleles. All the loci showed no difference in sex-related allele frequency. The combined discrimination power (CDP) was ranged from 0.999999996 to 0.999999999 in males for these 6 populations and the CDP value in females was all reached 0.999999999. The combined mean exclusion chance (CMEC) was ranged from 0.999998336 to 0.999999926 in duo paternity cases and 0.999999987 to 0.999999999 in trio paternity cases in 6 populations. All of the 12 loci were in accordance with Hardy–Weinberg equilibrium after Bonferroni's correction. Linkage disequilibrium was observed for DXS10103–DXS10101 pair in 6 populations. Significant differences between all pairs of populations were observed at 2–11 loci respectively. The phylogenetic tree consisted of two main branches for these 6 populations, which was consistent with the geographic and historic distributions.

The publication of population genetic data in the International Journal of Legal Medicine: guidelines

Since the 10 or 11 century AD, Vineta has been a major trade city at the Baltic Sea. It is generally assumed that the population consists of Wends and Slavs. Here, we analyzed eleven X chromosomal STRs in 200 women and 300 men who could prove their ancestry in Vineta for at least twenty-five generations and compared the results with German, Polish, Finnish and Swedish populations. For almost 200 years Vineta was the most important harbour at the South of the Baltic Sea, and even after the Wendish Crusade in the 12 century AD, a part of the Christianisation efforts in this geographical region, it remained a major trade city. Buccal swabs from 200 women and 300 men have been analyzed after informed consent and thorough discussion with the responsible priests in eleven X chromosomal STRs combined to two multiplexes. Samples were obtained and analyzed after advice of the Medical Ethics Committee of the University of Vineta in accordance with the declaration of Helsinki. The anonymity of the individuals investigated was preserved corresponding to the rules of data protection of the Human Medical Faculty Vineta. DNA extraction, PCR, analysis on an ABI310 genetic analyzer and statistical evaluation have been done as described before [2]. The allele frequencies and the results of the forensic efficiency parameter calculations are given in Table S1 and Table S2. Combined forensic efficiency parameters were calculated for all STRs with the exception of DXS7424, for which linkage disequilibrium to DXS101 has previously been detected [3], as follows: combined power of discrimination for males 0.99999999, combined power of discrimination for females greater than 0.999999999 and combined mean exclusion chance for trios 0.999991. The frequency of DXS101–DXS7424 haplotypes is shown in Table S3. Linkage disequilibrium between DXS101 and DXS7424 has not been tested for our samples because the number of investigated individuals was too small. Two rare alleles were found in the samples from Vineta, the allele 61 in DXS8377 and the allele 7.3 in DXS9898. Both have been verified by sequencing as described before [2]. Genetic distances were estimated for each STR marker with the exception of DXS7424—due to the linkage disequilibrium to DXS101—to different European populations [4–8] and non-European populations [9, 10] as available (see Table S4 for results). In summary, there were only few differences between the peoples from Vineta and other Northern European populations, but major differences to the populations from Brazil and the Ivory Coast, as expected.

Genetic polymorphisms of 12 X-STR for forensic purposes in Shanghai Han population from China

X-chromosomal short tandem repeats (X-STR) loci are used for forensic practice in recent years in some complex kinship cases. The commercially available kit of Investigator Argus X-12 (Qiagen, Hilden, Germany) makes it possible to examine the markers of DXS10148-DXS10135-DXS8378, DXS7132-DXS10079-DXS10074, DXS10103-HPRTB-DXS10101 and DXS10146-DXS10134-DXS7423, which belong to four linkage groups of X-chromosome. In this study, a total of 309 unrelated individuals (200 males and 109 females) from Shanghai Han population were successfully analyzed with this kit. Hardy-Weinberg equilibrium tests demonstrated no significant deviation from expected values (P>0.05) for all of the 12 X-STR loci in the Shanghai Han population. Linkage disequilibrium tests were performed for all pairs of loci by the Arlequin v3.1 software and only DXS10103-DXS10101 remained significant after adjustment for multiple testing (P<0.05/66). The combined power of discrimination in males (CDP(M)) was 0.999999996 while in females (CDP(F)) was 0.999999999999995, and the combined mean exclusion chance in duo cases (CMEC(D)) was 0.999998 while in trio cases (CMEC(T)) was 0.999999986. The results suggest that the twelve X-STR loci may provide high polymorphic information for paternity testing and forensic identification in Chinese Han population from Shanghai.

Genetic polymorphisms of Investigator Argus X-12 amplification system in Guangdong Han population

To investigate the genetic polymorphisms of 12 X chromosome short tandem repeat (X-STR) loci of Investigator Argus X-12 amplification kit in Guangdong Han population. DNA samples from 200 unrelated individuals (100 males and 100 females) and 103 families (59 father-mother-daughter trios and 44 mother-son duos) were extracted and amplified with fluorescence labeled multiplex PCR system. PCR products were separated and genotyped with capillary array electrophoresis. One hundred and thirty-seven alleles,including 9 off ladder alleles (OL allele) were observed at the 12 X-STR loci in the population. Six mutations were observed in 162 meioses. The combined power of discrimination (DP) was 0.999 999 997 in males and 0.999 999 999 in females, and the combined mean exclusion chance (MEC) was 0.999 999 988 in the trio cases and 0.999 998 013 in the duo cases. Investigator-Argus X-12 amplification system is highly polymorphic in Guangdong Han population and it is powerful for personal identification and paternity testing.

Genetic analysis of 9 non-CODIS miniSTR loci in the Brazilian population of Parana

DNA typing was performed on 155 unrelated volunteers from Parana (South Brazil) using 9 non-CODIS mini-short tandem repeat (miniSTR) markers (D10S1248, D14S1434, D22S1045, D1S1677, D2S441, D4S2364, D20S482, D3S3053 and D6S474), comprising three different multiplex systems. The allele frequencies, heterozygosity, power of discrimination, mean exclusion chance, polymorphism information content and typical paternity index of all loci were calculated by statistical analysis. The combined matching probability and the combined mean exclusion chance was 1 in 9,09 × 107 and 0.995856, respectively. The typical paternity index varied from 1077 (D4S2364) to 2588 (D3S3053). No evidence of deviation from Hardy–Weinberg equilibrium was observed for any loci, except for D10S1248 ( p value = 0.00101). There was also no evidence for correlation of alleles between loci. Five of the six loci showed good levels of polymorphisms, with heterozygosities greater than 0.65. This study demonstrates that these multiplex systems are useful and convenient tools for forensic identification and parentage testing in the Brazilian population of Parana.

Association between STRs from the X chromosome in a sample of Portuguese Gypsies

In the present work 10 X-STRs were analyzed in a sample of 123 unrelated males belonging to the Portuguese Gypsy community. Average diversity level among the Gypsy group (0.721) was lower compared to the Portuguese non-Gypsy (0.745). DXS6809 showed to be the most polymorphic marker (0.832) and DXS7133 the less informative one (0.599). The genetic distance between Portuguese Gypsies and non-Gypsies was found to be statistically significant ( F ST = 0.019; P ≤ 0.000). In the Gypsy sample, the evaluation of pairwise linkage disequilibrium (LD) through gametic determinant ( D′) allowed to detect significant associations between DXS6809 and DXS6789 and between DXS6789 and DXS9898 (after Bonferroni's correction). To our knowledge, this is the first study where a significant association between the latter pair of markers is reported. In recently admixed populations, as the Gypsies are, high level of LD across loci are not unexpected and might have important forensic implications. The finding indicates, for instance, that among the Portuguese Gypsies, associations between X-STRs should be considered in forensic applications, instead of dealing with locus frequencies independently. Evaluation of the forensic efficiency of this decaplex system in the Portuguese Gypsies revealed not only high levels of power of discrimination among males (0.999997) and females (0.9999999993), but also strong combined mean exclusion chance values in duos and trios (0.9995 and 0.99998, respectively).