Population genetics of the STRs vWA, D3S1358 and FGA in the Pomerania-Kujawy region of Poland

This paper presents the results of a Polish population study (n = 210) for the three STR loci vWA, D3S1358 and FGA analysed using the multiplex PCR system AmpflSTR Blue. The allele distributions were in accordance with Hardy-Weinberg expectations. The combined mean exclusion chance, mean paternity index and power of discrimination for the three loci were MEC = 0.96055, MPI = 127.1295 and PD = 0.99986. This demonstrates that these systems are valuable tools for forensic identification and paternity testing. Received: 24 August 1998 / Received in revised form: 19 January 1999     

Forensic parameters of 19 X-STR polymorphisms in two Chinese populations

Application of X-STRs as complements of autosomal STR application in the forensic genetics has become a tendency for kinship testing, especially in deficiency paternity cases. Recently, a novel kit of 19 X-STR loci was developed, which permitted the analysis of 19 STR in the same PCR reaction, and these markers can be clustered into seven groups for the physical linkage. The objective of this study was to evaluate the allele and haplotype diversity of 19 X-STR loci in the Uygur (n = 220) and Tibetan nationality (n = 270) and to estimate the usefulness for complex kinship analysis. In the Tibetan and Uygur populations, a total of alleles of all loci were 188 and 212, with the allele frequencies ranged from 0.0037 to 0.5593 and from 0.0045 to 0.5409, respectively. Compared with previous studies, DXS10135 was the most polymorphic locus in the two population groups, whereas the least variant locus was DXS10164 in the Uygur population and DXS7423 in the Tibetan nationality. Haplotype diversity obtained in this investigation was greater than 0.9 across all LGs. This study indicated the new kit could be used as a supplementary tool in kinship testing in China. In addition, the data sets can be used as supplementary national X-STR references to enlarge the database.

     

Assessment of application value of 19 autosomal short tandem repeat loci of GoldenEyeTM 20A kit in forensic paternity testing

This study was carried out to assess the application value of 19 autosomal short tandem repeat (STR) loci of GoldenEye^TM 20A kit, in which 13 combined DNA index system core STR loci and PentaE, PentaD, D2S1338, D19S433, D12S391, and D6S1043 of six STR loci could be used in forensic paternity testing in Chinese population. We amplified the genomic DNA from blood samples on FTA paper of 289 paternity testing cases by using the GoldenEye^TM 20A kit. The amplified products were detected by capillary electrophoresis, and then the genotypes of 20 genetic markers including 19 STR loci as well as Amelogenin for sex determination were analyzed by GeneMapper v3.2 and GeneMarker HID Software. The results of genotypes were compared to the three commonly used commercial kits including AmpF?STR Identifiler^TM, PowerPlex^TM16, and AmpF?STR Sinofiler^TM kits. Compared to the three other common commercial kits, the GoldenEye^TM 20A kit had higher value of combined paternity index in certainty of paternity or non-exclusion paternity cases, and more numbers of STR loci were excluded in exclusionary paternity cases. Our data in this study showed that the GoldenEye^TM 20A kit has a higher application value in forensic paternity testing and will be of help for kinship analysis.     

Isoelectric focusing studies on the PGM1 subtypes in the northern Japanese population

Summary The distribution of the human red cell phosphoglucomutase (PGM₁) subtypes in samples from Japanese population (n=277) living in the Miyagi Prefecture, the northern part of Japan, was investigated by applying the thinlayer polyacrylamide gel isoelectric focusing. In our population sample all the ten common phenotypes were demonstrated, and the estimated allele frequencies for the genes PGM ₁ ¹⁺ , PGM ₁ ^1– , PGM ₁ ²⁺ , and PGM ₁ ^2– were 0.671, 0.107, 0.161, and 0.061, respectively. Family studies (n=40) indicated an autosomal codominant inheritance and confirmed the four alleles. The new system will increase the probability of exclusion in paternity cases among Japanese to 29.4% compared with 14.3% if the two allele system is used.     

The examination of the ITI system in disputed paternities

Summary 106 paternity cases with a total of 114 putative fathers were examined in the inter--trypsin inhibitor (ITI) system. Analysis was performed by isoelectric focusing (IEF) of untreated sera on polyacrylamide gels. From 39 paternity exlusions, determined in other genetic systems, 7 were confirmed in the ITI system. In 75 expertises the alleged man was not excluded from fatherhood; in 68 cases the probability of paternity was W > 99.73%. The practical exclusion rate in the ITI system was therefore calculated to be 10.45%. The theoretical exclusion rate was determined to be 19.3%. In one paternity case the alleged father and the child showed inverse homozygosity in the ITI system, while the man was not excluded from fatherhood in 28 additional marker systems. The calculated probability of his paternity was 99.99%. The assumption of an incomplete expression of the ITI phenotypes in infants is supported by a significant deviation between the observed and expected ITI distributions at population equilibrium.     

Population structure of Han nationality in Central-Southern China

Knowledge of population structure is very important for forensic genetics. However, the population substructure in Central-Southern China Han nationality has still not been fully described. In this study, we investigated the genetic diversity of 15 forensic autosomal STR loci from 6879 individuals in 12 Han populations subdivided by administrative provinces in Central-Southern China. The statistical analysis of genetic variation showed that genetic differentiation among these populations was very small with a F_st value of 0.0009. The Discriminant Analysis of Principal Components (DAPC) showed that there were no obvious population clusters in Central-Southern China Han population. In practice, the population structure effect in Central-Southern China Han population can be negligible in forensic identification and paternity testing.     

Distribution of Likelihood Ratio in Relation to the Exclusion Probability

Summary The relation between the exclusion probability (E) and the paternity probability is derived by assuming the distributions of logarithm of paternity likelihood ratio, log (Y/X) for true fathers and unexcluded non-fathers as the normal distributions.Under this assumption the value log(l -E) is equal to the mean of the mean value for true fathers (a) and that for unexcluded non-fathers (b), i.e., log(l-E) = (a +b)/2. This relation holds quite well for the various actual distributions of log(Y/X) of father-child combinations and those of father-mother-child combinations using 14 blood group systems. Therefore, the derived relation is found to be a convenient way to deduce one of the three quantities (E, a, b) from the remaining two quantities in the actual distributions.     

Population genetic polymorphisms of 17 Y-chromosomal STR loci in South Koreans

Haplotypes and allele frequencies of 17 Y-chromosomal STR loci included in the AmpFlSTR^® Yfiler^® system were obtained from a sample of 1021 unrelated individuals living in 6 provinces of South Korea. A total of 938 haplotypes were observed in the 1021 individuals studied, of which 885 were unique. The overall haplotype diversity for the 17 Y-STR loci was 0.9998, and the discrimination capacity was 0.9187. We found 11 atypical alleles (null, duplicated, triplicated, and microvariant alleles), that have not previously been reported in South Korean populations. It seems that these 17 loci are useful genetic markers for forensic personal identification and paternity testing in the South Korean population.     

15 STR loci frequencies in the population from Paraná, Southern Brazil

Allele frequencies for 15 short tandem repeats (STR) loci were obtained from a sample of 4076 unrelated individuals undergoing paternity testing. The population is from Paraná, Southern Brazil. The loci are the most commonly used in forensic and paternity testing, being analyzed by the AmpFlSTR^® Identifiler™ (Applied Biosystems) commercial kit. The most polymorphic loci were D2S1338 and D18S51. Excepting the D13S317, all loci were in Hardy–Weinberg equilibrium. Comparative analyses between our population data and other populations are presented.     

Genetic structure and forensic parameters of 38 Indels for human identification purposes in eight Mexican populations

Insertion–deletions for human identification purposes (HID-Indels) offer advantages to solve particular forensic situations and complex paternity cases. In Mexico, admixed population known as Mestizos is the largest (∼90%), plus a number of Amerindian groups (∼10%), which have not been studied with HID-Indels. For this reason, allele frequencies and forensic parameters for 38 HID-Indels were estimated in 531 unrelated individuals from one Amerindian (Purépecha) and seven Mestizo populations from different regions of the country. Genotype distribution was in agreement with Hardy–Weinberg expectations in almost all loci/populations. The linkage disequilibrium (LD) test did not reveal possible associations between loci pairs in all eight Mexican populations. The combined power of discrimination was high in all populations (PD >99.99999999998%). However, the power of exclusion of the 38 HID-Indel system (PE >99.6863%) was reduced regarding most of autosomal STR kits. The assessment of genetic structure (AMOVA) and relationships between populations (F_ST) demonstrated significant differences among Mexican populations, mainly of the Purépecha Amerindian group. Among Mexican-Mestizos, three population clusters consistent with geography were defined: (i) North-West region: Chihuahua, Sinaloa, and Jalisco; (ii) Central-Southern region: Mexico City, Veracruz and Yucatan; (iii) South region: Chiapas. In brief, this report validates the inclusion of the 38 HID-Indel system in forensic casework and paternity cases in seven Mexican-Mestizo populations from different regions, and in one Mexican Amerindian group.     

Population data of 19 autosomal STR loci in the Li population from Hainan Province in southernmost China

In the present study, population data of 19 autosomal STR loci included in the Goldeneye™ DNA ID System 20A in 653 Li individuals was obtained and population genetic relationships among 13 populations were investigated. MDS and phylogenetic analysis suggested that the Hainan Li population kept a close genetic relationship with the Chinese Han populations, especially for Southern Han populations (Guangdong Han, Sichuan Han, and Hunan Han). Our results indicated that the 19 autosomal STRs are highly discriminative and polymorphic in the Hainan Li population suitable for personal forensic identification and paternity testing.

     

Application of the new insertion–deletion polymorphism kit for forensic identification and parentage testing on the Czech population

Insertion-deletion polymorphisms (INDELs) are diallelic markers derived from a single mutation event. Their low mutation frequency makes them suitable for forensic and parentage testing. The examination of INDELs thus combines advantages of both short tandem repeats (STR) and single nucleotide polymorphisms (SNP). This type of polymorphisms may be examined using as small amplicon size as SNP (about 100 bp) but could be analyzed by techniques used for routine STR analysis. For our population study, we genotyped 55 unrelated Czech individuals. We also genotyped 11 trios to analyze DIPplex Kit (QIAGEN, Germany) suitability for parentage testing. DIPplex Kit contains 30 diallelic autosomal markers. INDELs in DIPplex Kit were tested with linkage disequilibrium test, which showed that they could be treated as independent markers. All 30 loci fulfill Hardy–Weinberg equilibrium. There were several significant differences between Czech and African populations, but no significant ones within European population. Probability of a match in the Czech population was 1 in 6.8?×?10¹²; combined power of discrimination was 99.9999999999%. Average paternity index was 1.13–1.77 for each locus; combined paternity index reached about 27,000 for a set of 30 loci. We can conclude that DIPplex kit is useful as an additional panel of markers in paternity cases when mutations in STR polymorphisms are present. For application on degraded or inhibited samples, further optimization of buffer and primer concentrations is needed.     

Genetic diversity and haplotype analysis of Guizhou Miao identified with 19 X-chromosomal short tandem repeats

We analyzed Chinese Miao population samples (n = 268) from Guizhou province, Southwest China, with 19 X-chromosomal short tandem repeats (STRs) included in the AGCU X19 amplification kit. The combined PE is 0.999999922 and the combined PDs in males and females are 0.9999999999999999999994 and 0.9999999999998, respectively. The mean paternity exclusion change values are larger than 0.99999996. The HDs in seven linkage groups vary from 0.9324 to 0.9968. Subsequently, comparison among different Chinese populations shows that the substructures of Chinese were significantly influenced by ethno-linguistic rather than geographical boundaries, including most prominently Turkic-speaking and Tibeto-Burman-speaking populations.

     

Mathematical aspects of the paternity index I=X/Y,especially in relation to the chance of non-exclusion of non-fathers

Summary In a previous paper the author mentioned some aspects of the paternity index I (=X/Y): Among false triplets the frequency of those with I equal to or higher than an (observed) I value of I ^x is considerably lower than 1/I ^x; among false triplets the mean value of I is equal to 1, and among non-excluded non-fathers it is equal to the inverse of the chance of non-exclusion; among true triplets the mean value of 1/I (=i) is equal to the chance of non-exclusion of non-fathers. In a statistical material rather strong deviations from some of these expectations were observed.In the present paper further characteristics of the distribution of I values were taken into consideration, and especially those that should hold if lnI would fit in with a normal distribution. It was supposed that with the aid of such a distribution the deviations mentioned above could be recognized as chance variability. It appears, however, that neither the logarithms of the paternity index, nor those of the zygosity index of twins (chosen as an analogous model that is more easily analysable than the paternity index) are really normally distributed. This, in turn, makes that estimates of probability of paternity, based on such a supposition, are of doubtful reliability. Besides it is concluded that also for other reasons other estimates than Essen-Möller's W (or I or i), as probability of first type errors, lead in practice to conclusions that are equally subdue to a priori suppositions as are W values and may be, in fact, much more erroneous than those.Special attention is paid to the statistical analysis of paternity studies with more than one alleged father, and it is concluded that in such cases the general formula that may be considered to be equivalent with Essen-Möller's formula for one-man paternity cases, i.e., W=X/(X+Y) or I/(I+1), must be W ₁=I ₁/(I+n); W ₂=I ₂/(I+n) etc. and certainly not W ₁=I ₁/(I+1); W ₂=I ₂/(I+1) etc.Dedicated to Prof. Dr. Erik Essen-Möller on the occasion of his 80th birthday     

Genetic analysis of 15 STR loci in the population of Zhejiang Province (Southeast China)

Fifteen autosomal STR loci were analyzed from a population sample of 598 unrelated individuals residing in Zhejiang Province. We report allele frequencies distribution and statistical parameters for all 15 STR loci, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818 and FGA. Allele frequencies, the observed heterozygosity (Ho), the polymorphic information content (PIC), and the probability of paternity exclusion (PE) were calculated. All loci were in accordance with Hardy–Weinberg equilibrium (P > 0.05). Our studied population data were compared with the previously published population data of other ethnic groups or areas in China. Our results of present study were valuable for human identification and paternity tests in Zhejiang Province.     

Corrigendum to “Linkage disequilibrium analysis of D12S391 and vWA in U.S. population and paternity samples” [Forensic Sci. Int.: Genet. (in press), doi:10.1016/j.fsigen.2010.09.003]

Recently, the European Network of Forensic Science Institutes voted to adopt five additional STR loci (D12S391, D1S1656, D2S441, D10S1248, and D22S1045) to their existing European Standard Set of seven STRs (TH01, vWA, FGA, D8S1179, D18S51, D21S11, and D3S1358). The D12S391 and vWA loci are located 6.3 megabases (Mb) apart on chromosome 12. Ideally for use in forensic analyses, genetic markers on the same chromosome should be more than 50 Mb in physical distance in order to ensure full recombination and thus independent inheritance. The purpose of this study was to evaluate if the closely located D12S391 and vWA loci are independent and, consequently, if these loci can be included in the product rule calculation for forensic and kinship analyses. Departures from Hardy–Weinberg equilibrium and linkage disequilibrium between the D12S391 and vWA loci were tested using n = 654 unrelated U.S. African American, Caucasian, and Hispanic samples, and n = 764 father/son paternity samples. In the unrelated U.S. population samples, no significant departures from HWE were detected for D12S391 or vWA. No significant evidence of linkage disequilibrium was observed between the loci in the population samples. However, significant linkage disequilibrium was detected in U.S. African American, Caucasian, and Asian father/son samples with phased genotypes. No significant linkage disequilibrium was detected for U.S. Hispanic paternity samples. The use of phased father/son pairs allowed for robust detection of linkage disequilibrium between D12S391 and vWA. In unrelated population samples, linkage disequilibrium is present but more difficult to detect due to the large number of possible haplotype combinations and unknown allelic phase. For casework analyses that involve unrelated or related individuals, the single-locus genotype probabilities for D12S391 and vWA should not be multiplied to determine the match probability of an autosomal STR profile. Since the D12S391 and vWA loci are not independent, it is recommended that the observed combination of alleles at D12S391 and vWA should be treated as a non-independent diplotype for profile probability calculations. The observed haplotype frequencies for U.S. African American, Caucasian, Hispanic, and Asian populations are provided for match probability calculations.     

Forensic evaluation of STR data for the PowerPlex™ 16 System loci in a Bangladeshi population

Allele frequencies of 15 autosomal STR loci included in PowerPlex™ 16 System were determined from a sample of 148 unrelated Bangladeshi individuals. Forensic efficiency parameters such as, the power of discrimination (PD), observed and expected heterozygosity (H), polymorphism information content (PIC), probability of match (PM), power of exclusion (PE), and typical paternity index were calculated for the loci. These parameters indicated the usefulness of the loci in paternity testing and personal identification in the Bangladeshi population.     

Allele frequency distributions of 13 PCR-based systems in a population from North-East Spain

Population data studies were carried out on a Caucasian population from North-East Spain (n = 129– 292 individuals) for 13 PCR-based polymorphic DNA loci: six short tandem repeat loci (HumTH01, HumTPOX, HumCSF1PO, HumF13A01, HumFES/FPS, HumvWFA31), the six PM loci (HLA-DQα, LDLR, GYPA, HBGG, D7S8, GC) and one variable number tandem repeat locus (D1S80).The genotypes distributions were in accordance with Hardy-Weinberg expectations. The combined use of the 13 polymorphic systems provides a high power of discrimination and power of exclusion for use in forensic casework and paternity testing. Received: 18 November 1996 / Received in revised form: 19 February 1997     

The forensic application of the blood group antigens Lua and Lub

Summary Blood samples from 507 unrelated persons in Northrhine-Westphalia and from 254 paternity cases were tested for the Lutheran blood group antigens Lu^a and Lu^b. The gene frequencies were found to be 0.03 (=Lu ^a) and 0.969 (=Lu ^b).     

VWA STR genotyping: further inconsistencies between Perkin-Elmer and Promega kits

We report a simultaneous study of the VWA STR locus by the Perkin-Elmer Profiler Plus kit and the Promega GenePrint CTTv kit in a population sample from North Portugal and in 418 meiosis from family material and paternity cases. PCR amplification and genotyping were performed according to the manufacturer’s instructions using ABI 377 or ABI 310 automatic sequencers. Biological kinship in family material and paternity cases was validated by the use of the STR loci D3S1358, D5S818, D7S820, D8S1179, D13S317, D18S51, D21S11, FGA, CSF1PO, TH01 and TPOX. Out of 434 unrelated individuals we found 4 inconsistencies between the genotypes obtained using each kit. No exclusions were found in the meiotic analyses. In all cases, these inconsistencies were due to an annealing failure of the Perkin-Elmer forward primer resulting in false homozygotes. Sequencing analysis revealed an A-to-T substitution at position 1631 (GenBank sequence M25858), 52 bases upstream of the first TCTA motif of the repeat region. An estimate of the null allele frequency (s) in this study is thus obtainable from the expression s = 4/¶(2 × 434) = 0.46%. The relatively high frequency of these discrepancies in our population demonstrates the need for caution when comparing genotype or gene frequency estimates made from amplicons produced by different primers, when evaluating apparent exclusions in paternity testing and when searching for a match between individual genetic profiles in forensic databases. Our findings are also compared with those previously reported.