Paternity Investigation Cases Research Articles

Uniparental disomy of chromosome 21: A statistical approach and application in paternity tests

Considering the overall frequency of paternity investigation cases including mutational events, there is a real possibility that at least a fraction of all inconsistencies reported in paternity cases are caused not by polymerase slippage mutations, but to chromosomic abnormalities, as Uniparental Disomy (UPD). We report here the investigation of a trio paternity case (mother, child and alleged father), with observed inconsistencies that can alternatively be explained by occurrence of maternal uniparental isodisomy of chromosome 21 (miUPD21). A total of 350 short tandem repeat (STR) and single nucleotide polymorphism (SNP) markers were tested, statistically suggesting true biological linkage within the trio. Additionally, we propose miUPD21 explains, with significantly greater probability, the occurrence of detected inconsistencies, when compared to alternative hypothesis of multiple and simultaneous slippage mutations. Similar cases could have their statistical conclusions improved or even altered by including unusual chromosomal segregation patterns in the hypothesis formulation, as well as in mathematical calculations. Such reports of allelic inconsistencies being explained by chromosomal alterations are common in clinical genetics, and such situations might have impact on forensic investigation.

Mutation rate estimates for 13 STR loci in a large population from Rio Grande do Sul, Southern Brazil

Short tandem repeat (STR) polymorphisms have been extensively used in forensic genetics analysis. Knowledge about the locus-specific mutation rates of STRs improves forensic probability calculations and interpretations of diversity data. To incorporate single-locus diversity information into autosomal STR mutation rate estimations, 13 STR loci were studied during 2007-2009 in 10,959 paternity investigation cases from Rio Grande do Sul, the southernmost state of Brazil, covering an overall number of 284,934 allelic transfers. A total of 355 mutations were identified; 348 repeats were gains or losses of one step, three were gains or losses of two steps, and four were gains or losses of not stepwise mutation. The mutation rates ranged from 4.6 × 10(-5) to 2.3 × 10(-3), and the overall mutation rate estimate was 1.2 × 10(-3). The average of the paternal mutation rate (1.8 × 10(-3)) was five times higher than the maternal rate (0.36 × 10(-3)). The observed mutational features for STRs have important consequences for forensic applications, including the definition of criteria for exclusion in paternity testing and the interpretation of DNA profiles in identification analysis.

SNPs in paternity investigation: The simple future

Based on the 52 SNP-plex developed by the SNP forID 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.

Examples of combining genetic evidence—Bayesian network approach

Forensic experts are required to quantify their findings and to assess the range of uncertainties associated with the inferences that may be drawn from different genetic evidence. The practical application of probabilistic reasoning in forensic science can be assisted through the use of the formalism known as Bayesian networks. The aim of the study was to implement existing ways of probabilistic evaluation of DNA evidence in building appropriate network structures. We present a network models for identification of human remains and paternity investigation cases using different kinds of genetic markers, which have a different inheritance mode.

Use of eight X-chromosomal STRs in paternity investigation

A new commercial kit, Mentype ® Argus X-8, which analyzes eight X-chromosomal STR markers – DXS7132, DXS7423, DXS8378, DXS10074, DXS10101, DXS10134, DXS10135 and HPRTB, was used. A hundred and one South Portuguese Caucasian individuals and 60 paternity investigation cases, previously performed with routine STRs markers, were studied. Allele frequencies were estimated for the eight X-STRs. More than five exclusions between the alleged father and the female child were observed in almost all exclusion cases, especially in DXS10101, DXS10134 and DXS10135 loci. This set of eight X-chromosomal STRs appears to be quite useful for father–daughter studies and in some kinship investigations.

Autosomal SNPs in paternity investigation

Ten of the most polymorphic autosomal single nucleotide polymorphisms (SNPs) (∼50% heterozygosity) in European populations, especially NW Spain, selected from a 52 SNP panel for human identification reported by Sanchez et al. [J.J. Sanchez et al., A multiplex assay with 52 single nucleotide polymorphisms for human identification, Electrophoresis, 27 (2006), 1713–1724] were amplified in one PCR reaction followed by detection by single base extension reaction with SNaPshot ® multiplex kit. A total of 80 individuals from a South Portuguese population were typed and allele SNP frequencies were estimated which are in agreement with published population genetic studies. More than 20 paternity investigation cases, already performed routinely with STRs, were also studied. In exclusion cases, one, two or three exclusions, mainly in A08 and A12, have been detected. Even performing few SNP loci, but selecting SNPs with allele frequencies near 0.5, the SNP methodology can also be a useful tool in paternity investigation.

Power of exclusion of 18 autossomic STR loci in a Brazilian Middle–West region population sample

The aim of this work was to analyze the Power of Exclusion (PE) in paternity investigation cases from Federal District of Brazil (Center–West region of Brazil) using a local population sample (n=917) in comparison with Promega Corporation published databank, both for 18 autossomic STR loci. For this purpose, we analyzed 311 cases where the alleged father was excluded. The expected and observed values in the exclusion cases were compared by locus and by multiplex system. The values of χ2 show a P higher than 0.05 for each locus, except TPOX and D16S539 (0.05>P>0.01), where the observed number of exclusions was higher than the expected ones. The a priori Exclusion Probability to each locus did not differ significantly between the two databases, suggesting that, in the absence of a database population-specific, another databank can be used as reference for estimates of PE and Probability of Paternity, considering similar ancestry in both populations composition, which is the case of Brazil and the United States.

VWA STR locus structure and variability

More than 100 vWA alleles were sequenced to detect any possible sequence difference at this locus in Portuguese Caucasian and African populations. Internal variability was detected—the most common structure is TCTA (TCTG)4 (TCTA)n with a TCTA(TCTG)3(TCTA)n structure more frequent in small alleles and a TCTA (TCTG)5–6 (TCTA)n structure predominantly in large ones. Allele 17 has a unique structure in all 20 studied samples and the nonconsensus allele 14 structure has a prevalence of 60% in both populations. Performing more than 3000 paternity investigation cases with multiplex systems, eight vWA mutations were detected with a 0.0024 average mutation rate. Six mutations at the primer-binding site have also been detected when performing ProfilerPlus/SGMPlus versus Powerplex1.2.

Portuguese population study with 16 Y-STR loci

The aim of this study was to present a Portuguese Population Database of 214 Southern Portugal samples studied with 16 Y-STR loci including the eight minimal Y-STR haplotype—DYS19, DYS390, DYS391, DYS392, DYS393, DYS389I/II, DYS385 and other Y-STR loci—GATA A7.1 (DYS460), GATA C4, GATA A7.2 (DYS461), GATA A10, GATA H4, DYS437, DYS438 and DYS439. In this study, 209 different haplotypes could be defined and 205 haplotypes were found just once. This database has a discrimination power of 97.7%, a haplotype diversity of 99.6% and 2.3% of shared haplotypes. Some samples do not match any sample in the Y-STR Haplotype Reference Database which assigned specific region characteristics to these population samples. Forty-three alleged father–child non-exclusion cases were also studied and two possible mutations have been detected in DYS439 and DYS393. Complex paternity investigation cases without alleged father have also been studied. In an autosomal STR exclusion case, the same 16 Y-STR haplotype was obtained between the excluded alleged father and the child.

STR mutations in paternity investigations: a study of 1-year consecutive cases

A study of 1-year consecutive cases for STR mutations has been performed during 2000 with SGM Plus and PowerPlex 1.2 or PowerPlex 16. In paternity investigation cases, 18 STR mutations have been detected in several loci. Paternal and maternal mutation cases and a case with two paternal inconsistencies in D7S820 and CSF1PO are also presented. Maternal and paternal meioses were studied and the average mutation rates concerning several types of mutations were determined. During this 1-year study, multi-banded alleles and vWA genotype differences using different multiplex systems were also detected. The final probability paternity value (after inclusion of mutations) was always >99.99%, allowing to conclude confidently the presence of a mutation.

Portuguese population data on two pentanucleotide STR loci Penta E and Penta D

Two pentanucleotides—Penta E and Penta D—have been studied in 160 Portuguese Caucasian individuals and in 19 African origin individuals when the GenePrint® PowerPlex™ 16 System were introduced for paternity studies in our laboratory. Allele frequencies and forensic parameters were determined in these two populations. One-hundred fifty meioses were also studied and a paternal genetic inconsistency in Penta E was detected. Furthermore, 81 selected paternity investigation cases, including 60 nonexclusion cases, 14 exclusion cases and 7 mutation cases were studied with SGM Plus and PowerPlex 16. In nonexclusion cases, paternity probability (W) values were always >99.99%, even in mutation cases including the respective mutation rate. These data point to the conclusion that Penta E and Penta D are valuable STR loci for paternity investigation in the Portuguese population.

Portuguese population and paternity investigation studies with a multiplex PCR — the AmpFlSTR ® Profiler Plus™

A Portuguese Caucasian population of 146 unrelated individuals was studied. DNA samples were amplified by multiplex PCR for D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 using the AmpFlSTR ® Profiler Plus™ PCR Amplification Kit (Perkin-Elmer). All loci met Hardy–Weinberg expectations. Forensic statistical parameters were according to those obtained by other authors. Statistical differences were observed concerning three loci when comparing the Portuguese Caucasian population and an Italian Caucasian population, although these differences mainly concern the less frequent alleles. Eighty-three paternity investigation cases were analysed. Exclusions in between three and nine loci were observed in all the 23 exclusion cases obtained. Most of the non-exclusion cases had probability of paternity >99.9%. Two cases with an isolated genetic incompatibility between the alleged father and the child were detected, which may indicate probable mutation cases. These results demonstrate that the AmpFlSTR Profiler Plus is a suitable multiplex for paternity investigation in the Portuguese population.