Comparisons between Japanese and Han Chinese populations for 261 autosomal STR loci

In this study, Japanese and Han Chinese individuals (n = 32, each) were genotyped for 261 autosomal STRs, and allele frequencies were calculated for each locus in each population. The average number of alleles for all loci in Japanese and Han Chinese populations was 6.65 and 6.56, respectively. The tests for deviations from HWE performed using an exact test showed that the number of STRs (P > 0.05) in Japanese and Han Chinese populations was 236 and 241, respectively. Calculation of forensic parameters showed heterozygosity, and the exclusion means in the Japanese population were 0.7185 and 4813 and those in the Han Chinese population were 0.7308 and 0.5008. In addition, population genetic analyses, such as principal component analysis and factorial correspondence analysis, were performed and a differential formula with likelihood ratios was applied for various number of STR loci based on the effectiveness of differentiation between the two populations. Accordingly, this study suggests that statistical differentiation between genetically close populations, such as the Japanese and Han Chinese populations, is possible if approximately 40–50 effective STR loci are analyzed.     

STR等位基因频率对父权指数的影响

目的观察中国汉族不同人群STR等位基因频率对联合父权指数(CPI)的影响。方法随机取108例13个CODIS基因座分型结果不排除父权关系的三联体案和二联体案,用5个不同地区人群的等位基因频率计算CPI值。结果三联体案的CPI值在2077.63～50897711626.46之间,同一案例的最大CPI与最小值CPI之比大于100者有20例(19.52%);二联体案的CPI值在25.12～2998685141之间,同一案例的最大CPI与最小值CPI之比大于100者有13例(12.04%)。结论不同人群等位基因频率计算CODIS基因座所得的CPI值在部分亲权鉴定案中有很大的差异。为了防止等位基因频率不确定性带来的误差,建议在亲权鉴定中用保守法计算CPI值。     

Analysis of forensically used autosomal short tandem repeat markers in Polish and neighboring populations

The purpose of this study was to evaluate the homogeneity of Polish populations with respect to STRs chosen as core markers of the Polish Forensic National DNA Intelligence Database, and to provide reference allele frequencies and to explore the genetic interrelationship between Poland and neighboring countries. The allele frequency distribution of 10 STRs included in the SGMplus kit was analyzed among 2176 unrelated individuals from 6 regional Polish populations and among 4321 individuals from Germany (three samples), Austria, The Netherlands, Sweden, Czech Republic, Slovakia, Belarus, Ukraine and the Russian Federation (six samples). The statistical approach consisted of AMOVA, calculation of pairwise Rst values and analysis by multidimensional scaling. We found homogeneity of present day Poland and consistent differences between Polish and German populations which contrasted with relative similarities between Russian and German populations. These discrepancies between genetic and geographic distances were confirmed by analysis of an independent data set on Y chromosome STRs. Migrations of Goths, Viking influences, German settlements in the region of Volga river and/or forced population resettlements and other events related to World War II are the historic events which might have caused these finding.     

Genetic variation of high-altitude Ecuadorian population using autosomal STR markers

Fifteen autosomal STRs were analyze in order to elucidate the differences between low and high land Ecuadorian population. Seven Ecuadorian geographic areas (Tisaleo-Mocha, Cañar, Quito, Rocafuerte, Santa Rosa, Guayaquil and Lago Agrio) from different altitude were selected for the study. After the analysis, little genetic distances were observed between all cities, the more distant cities (F_ST = 0.02354) were Rocafuerte at an elevation of 17 m.a.s.l. and Quito at 2850 m.a.s.l. and the similar cities (F_ST = 0.00033) were Rocafuerte (17 m.a.s.l.) and Santa Rosa (10 m.a.s.l). In conclusion, there is not a great genetic distance in the 15 STRs reported in high and low land Ecuadorian population, therefore previously reported frequencies could been used in identification and paternity cases under analysis.     

ISFG: Recommendations on biostatistics in paternity testing

The Paternity Testing Commission (PTC) of the International Society for Forensic Genetics has taken up the task of establishing the biostatistical recommendations in accordance with the ISO 17025 standards and a previous set of ISFG recommendations specific to the genetic investigations in paternity cases. In the initial set, the PTC recommended that biostatistical evaluations of paternity are based on a likelihood ratio principle – yielding the paternity index, PI. Here, we have made five supplementary biostatistical recommendations. The first recommendation clarifies and defines basic concepts of genetic hypotheses and calculation concerns needed to produce valid PIs. The second and third recommendations address issues associated with population genetics (allele probabilities, Y-chromosome markers, mtDNA, and population substructuring) and special circumstances (deficiency/reconstruction and immigration cases), respectively. The fourth recommendation considers strategies regarding genetic evidence against paternity. The fifth recommendation covers necessary documentation, reporting details and assumptions underlying calculations. The PTC strongly suggests that these recommendations should be adopted by all laboratories involved in paternity testing as the basis for their biostatistical analysis.     

Allelic frequencies and statistical data obtained from 48 AIM INDEL loci in an admixed population from the Brazilian Amazon

Allelic frequencies of 48 informative insert-delete (INDEL) loci were obtained from a sample set of 130 unrelated individuals living in Macapá, a city located in the northern Amazon region, in Brazil. The values of heterozygosity (H), polymorphic information content (PIC), power of discrimination (PD), power of exclusion (PE), matching probability (MP) and typical paternity index (TPI) were calculated and showed the forensic efficiency of these genetic markers. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 50%, 21% and 29%. Comparing these allele frequencies with those of other Brazilian populations and the parental populations, statistically significant distances were found. The interpopulation genetic distance (F_ST coefficients) to the present database ranged from F_ST = 0.0431 (p < 0.00001) between Macapá and Belém to F_ST = 0.266 (p < 0.00001) between Macapá and the Native American group.     

STR data for the AmpFℓSTR Identifiler loci from Swedish population in comparison to European, as well as with non-European population

The modern Swedish population is a mixture of people that originate from different parts of the world. This is also the truth for the clients participating in the paternity cases investigated at the department. Calculations based on a Swedish frequency database only, could give us overestimated figures of probability and power of exclusion in cases including clients with a genetic background other than Swedish. Here, we describe allele frequencies regarding the markers in the Identifiler-kit. We have compared three sets of population samples; Swedish, European and non-European to investigate how these three groups of population samples differ. Also, all three population sets were compared to data reported from other European and non-European populations.Swedish allele frequencies for the 15 autosomal STRs included in the Identifiler kit were obtained from unrelated blood donors with Swedish names. The European and non-European frequencies were based on DNA-profiles of alleged fathers from our paternity cases in 2005 and 2006.     

Y-chromosome STR haplotypes in males from Greenland

A total of 272 males from Greenland were typed for 11 Y-chromosome STRs DYS19, DYS385a/b, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 with the PowerPlex^® Y System (Promega). A total of 146 different haplotypes were observed and the haplotype diversity was 0.9887. The number of haplotypes seen once was 108 and the most common haplotype was observed in 12 males. A significant F_ST value was observed (F_ST = 0.012, P < 0.00001) when comparing the population of 15 locations in Greenland assigned to 7 groups. The significance could mainly be attributed to the subpopulation of males from Tasiilaq (East of Greenland). The R_ST value was not statistically significant (R_ST = 0.016, P = 0.15).     

Results of the 2009 Paternity Testing Workshop of the English Speaking Working Group of the International Society for Forensic Genetics

Here we present the results of the 2009 Paternity Testing Workshop of the English Speaking Working Group of the International Society for Forensic Genetics. The exercise included paternity testing of blood samples from a mother, a child and two alleged fathers. The laboratories were encouraged to answer questions concerning their laboratory routines and a paper challenge was distributed in order to compare statistical calculations. A total of 62 laboratories participated. The laboratories used a total of 49 autosomal STRs and PCR-investigated VNTRs, 19 Y-chromosomal STRs, 8 X-chromosomal STRs, 7 VNTR systems investigated with RFLP, 49 autosomal SNPs and 11 mtDNA SNPs. The rate of typing and reporting errors was 0.1%.     

Genetic profile of the Madeira Archipelago population using the new PowerPlex16 System kit

Allele and haplotype frequencies of 17 chromosome STR loci, 15 of them included in the kit PowerPlex 16 System from Promega, were determined in a sample of unrelated males from Madeira and Porto Santo Islands. PowerPlex 16 includes STRs not studied before in the Madeira population. The-kit includes two new allele markers (Penta D and Penta E), which proved to be extremely useful for paternity testing (PD = 0.952 and 0.977, respectively). The study revealed that the Madeira population does not differ from that of the north Portugal. Nevertheless, some loci presented alleles found in sub-Saharan and North European populations which were not reported so far in Portugal.     

A comprehensive GlobalFiler™ autosomal STR reference dataset for Southern Africa

In this study a total of n = 832 autosomal DNA profiles from Southern Africa are analysed using the GlobalFiler™ STR panel. The dataset includes South Africa (SA) profiles (n = 541) produced by Ristow et al. 2016 and includes newly generated data for SA Sepedi (n = 96) and Lesotho populations (n = 195). For the newly generated (n = 291) genotypes, we report a large degree of rare and novel variation. This included (n = 7) off-ladder allele variants and (n = 7) TPOX tri-alleles. We report forensic summary statistics and genetic diversity parameters. Expected heterozygosity and observed heterozygosity ranged between (0.7– 0.9) with SE33 as the most polymorphic and TH01 the least. For SA and Lesotho genotypes the combined match probability was (1.13 ×10^-24 and 6.035 ×10^-24) and the combined paternity index (1.4 ×10⁹ and 2.44 ×10⁸) respectively. The power of exclusion (0.9999) was similar for each dataset and no significant departures from Hardy-Weinberg equilibrium (HWE) were observed after Bonferroni correction. Population comparisons were performed by MDS and neighbour-joining and population structure inferred by STRUCTURE and DAPC unsupervised clustering.     

The problem of single parent/child paternity analysis--practical results involving 336 children and 348 unrelated men

In a certain amount of paternity investigations, only DNA from child and alleged father is analyzed, thus increasing the possibility of false paternity inclusions. The aim of this study was to determine how many wrong paternity inclusions could be detected in a rather small geographical area comparing empirical results from 336 children and 348 men (13-15 STRs were investigated per person). This comparison between each child and all unrelated men (i.e. all putative fathers from the other cases) with an especially designed computer program resulted in 116,004 man/child pairs. Less than three excluding STRs were found in 1666 child/unrelated man pairs (1.44% of the comparisons). At least one unrelated man with only two or less STR mismatches could be determined for 322 children (95.8% of all investigated children). In 26 comparisons no STR mismatches between a child and an unrelated man were detected, thus at least one and up to three "second father(s)" under 350 men could be found for 23 children, if the mother is excluded. Paternity probabilities between 95.475% and 99.996% were calculated. Our results underline the difficulties in motherless paternity cases using only STR analysis and advise great precaution in assigning verbal predicates such as "paternity proven" in those investigations.     

Y-chromosome STR haplotype diversity in three ethnic populations in Singapore

In this study, 12 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438 and DYS439) were genotyped in the three major ethnic populations in Singapore, namely the Chinese, Malay and Indian. Allele frequency distribution, locus diversity, haplotype diversity and discrimination capacity were estimated. Analysis of molecular variance between the three ethnic populations indicated that 87.71% of the haplotypic variation is found within population and 12.29% is between populations (Fixation Index FST=0.123, p=0.000). Population pairwise comparisons showed significant Phist values between all population pairs, with the lowest (RST=0.05) for Chinese-Malay and the highest (RST=0.19) for Chinese-Indian.     

Choice of population database for forensic DNA profile analysis

When evaluating the weight of evidence (WoE) for an individual to be a contributor to a DNA sample, an allele frequency database is required. The allele frequencies are needed to inform about genotype probabilities for unknown contributors of DNA to the sample. Typically databases are available from several populations, and a common practice is to evaluate the WoE using each available database for each unknown contributor. Often the most conservative WoE (most favourable to the defence) is the one reported to the court. However the number of human populations that could be considered is essentially unlimited and the number of contributors to a sample can be large, making it impractical to perform every possible WoE calculation, particularly for complex crime scene profiles. We propose instead the use of only the database that best matches the ancestry of the queried contributor, together with a substantial F_ST adjustment. To investigate the degree of conservativeness of this approach, we performed extensive simulations of one- and two-contributor crime scene profiles, in the latter case with, and without, the profile of the second contributor available for the analysis. The genotypes were simulated using five population databases, which were also available for the analysis, and evaluations of WoE using our heuristic rule were compared with several alternative calculations using different databases. Using F_ST = 0.03, we found that our heuristic gave WoE more favourable to the defence than alternative calculations in well over 99% of the comparisons we considered; on average the difference in WoE was just under 0.2 bans (orders of magnitude) per locus. The degree of conservativeness of the heuristic rule can be adjusted through the F_ST value. We propose the use of this heuristic for DNA profile WoE calculations, due to its ease of implementation, and efficient use of the evidence while allowing a flexible degree of conservativeness.     

Investigation of 74 microhaplotypes for kinship testing in US populations

Microhaplotypes are markers that consist of haplotype blocks of SNPs, which can be analyzed by massively parallel sequencing technologies. These allow determining the haplotype phase at every locus by clonal sequencing each DNA strand. MHs are polymorphic loci with same size alleles, no stutter, and lower mutation rate than STRs. They can provide the same power of discrimination of STR-kits, thus useful for mixture deconvolution, but more accurate ancestry prediction than STRs. In this study we investigated the potential of a recently developed 74plex-MH panel for kinship testing using the Familias software.Samples from families of four major US population groups were collected and genotyped using the 74plex-MH panel. MH allele frequency data from 347 individuals were imported into Familias software along with STR allele frequency data of 29 loci (NIST dataset) from 1036 individuals. Different family scenarios were tested and these included unrelated vs parent-child, unrelated vs full siblings, unrelated vs half siblings, unrelated vs cousin pairs. The prediction of the kinship relation for the four populations of interest was reported as Log10 of the likelihood ratio (LR).Overall, the panel of 74MHs and 29STRs showed similar performance in predicting the correct kinship scenarios tested. Correct prediction was reported for parent-child, full siblings, and half sibling scenarios, but not for the cousin pairs scenario. The panel of 74 MHs showed larger Log10LR values than the 29 STR-assay, thus demonstrating the effectiveness of this biomarker as a tool for kinship testing in addition to mixture deconvolution and ancestry prediction.     

Analysis of global variability in 15 established and 5 new European Standard Set (ESS) STRs using the CEPH human genome diversity panel

The CEPH human genome diversity cell line panel (CEPH-HGDP) of 51 globally distributed populations was used to analyze patterns of variability in 20 core human identification STRs. The markers typed comprised the 15 STRs of Identifiler, one of the most widely used forensic STR multiplexes, plus five recently introduced European Standard Set (ESS) STRs: D1S1656, D2S441, D10S1248, D12S391 and D22S1045. From the genotypes obtained for the ESS STRs we identified rare, intermediate or off-ladder alleles that had not been previously reported for these loci. Examples of novel ESS STR alleles found were characterized by sequence analysis. This revealed extensive repeat structure variation in three ESS STRs, with D12S391 showing particularly high variability for tandem runs of AGAT and AGAC repeat units. The global geographic distribution of the CEPH panel samples gave an opportunity to study in detail the extent of substructure shown by the 20 STRs amongst populations and between their parent population groups. An assessment was made of the forensic informativeness of the new ESS STRs compared to the loci they will replace: CSF1PO, D5S818, D7S820, D13S317 and TPOX, with results showing a clear enhancement of discrimination power using multiplexes that genotype the new ESS loci. We also measured the ability of Identifiler and ESS STRs to infer the ancestry of the CEPH-HGDP samples and demonstrate that forensic STRs in large multiplexes have the potential to differentiate the major population groups but only with sufficient reliability when used with other ancestry-informative markers such as single nucleotide polymorphisms. Finally we checked for possible association by linkage between the two ESS multiplex STRs closely positioned on chromosome-12: vWA and D12S391 by examining paired genotypes from the complete CEPH data set.     

我国未来民法典中亲子关系否认制度的建构

亲子关系否认制度是亲子法领域确立父母与子女法律身份一项非常重要的制度,父母子女关系的调整离不开法律这一手段。我国现行《婚姻法》对此尚未明文规定,致使亲子法的立法结构及内容有严重缺陷。学界对这一问题缺乏更加深入的探讨,也使之成为立法中一个较为薄弱的环节。立足于我国国情及社会需要,从制度完善的层面探讨我国现有的法律规定。同时,对该制度的否认权人、否认之诉的相对人、否认的前提、否认的客观事实、否认请求权的期间、否认的法律效力等问题作出基本的设想。     

DNA human identification for the family rights: One year of agreement between UNESP/Laboratory of Paternity and Public Defender Service in São Paulo State

The universities have realized the importance of extending their knowledge to the population through the provision of services. Thus, this paper presents the data obtained in an agreement between UNESP/Laboratory of Paternity and Public Defender Service in São Paulo State to make DNA paternity tests.     

SNPs in paternity investigation: The simple future

Based on the 52 SNP-plex developed by the SNPforID Consortium, we designed two 10-plex to study single nucleotide polymorphisms (SNPs) for human identification and to establish its usefulness in paternity casework. This 20 autosomal SNP set was studied in 56 paternity investigation cases from South Portuguese resident population, also analyzed with 17 Short Tandem Repeats (STRs). Results obtained with both methodologies were consistent with each other, except for one case where the alleged father could not be excluded by SNPs. No mutation was found in the SNP loci, whereas a mismatch in STRs was detected. The use of SNPs as a complement to the analysis of autosomal STRs in paternity casework can result in paternity index and paternity probability values equivalent or higher than those obtained with more STR loci, but with lower costs. This study shows that instead of using additional STR loci, the analysis of 20 autosomal SNPs, as a complement technique to standard methodologies, is an appealing alternative in paternity investigation cases.     

Four X-chromosomal STRs and their allele frequencies in a Chinese population

X-chromosomal markers are particularly useful for solving complex problems relating to kinship and deficiency paternity analysis. In the present study, population genetics data of four X-chromosomal short tandem repeats (STRs) DXS8378, HPRTB, DXS7423 and DXS7132 were obtained by analyzing 500 unrelated Chinese individuals (250 males and 250 females). Population genetics data obtained from the Chinese were compared with those of the Asian and European population. Mutations in X-chromosomal markers were analyzed based on a total of 61 proven father-child and 45 proven mother-child pairs.