Paternity Cases Research Articles

Assessment of Male Reproductive Skew via Highly Polymorphic STR Markers in Wild Vervet Monkeys, Chlorocebus pygerythrus

Male reproductive strategies have been well studied in primate species where the ability of males to monopolize reproductive access is high. Less is known about species where males cannot monopolize mating access. Vervet monkeys (Chlorocebus pygerythrus) are interesting in this regard as female codominance reduces the potential for male monopolization. Under this condition, we assessed whether male dominance rank still influences male mating and reproductive success, by assigning paternities to infants in a population of wild vervets in the Eastern Cape, South Africa. To determine paternity, we established microsatellite markers from noninvasive fecal samples via cross-species amplification. In addition, we evaluated male mating and reproductive success for 3 groups over 4 mating seasons. We identified 21 highly polymorphic microsatellites (number of alleles = 7.5 ± 3.1 [mean ± SD], observed heterozygosity = 0.691 ± 0.138 [mean ± SD]) and assigned paternity to 94 of 97 sampled infants (96.9%) with high confidence. Matings pooled over 4 seasons were significantly skewed across 3 groups, although skew indices were low (B index = 0.023-0.030) and mating success did not correlate with male dominance. Paternities pooled over 4 seasons were not consistently significantly skewed (B index = 0.005-0.062), with high-ranking males siring more offspring than subordinates only in some seasons. We detected 6 cases of extra-group paternity (6.4%) and 4 cases of natal breeding (4.3%). Our results suggest that alternative reproductive strategies besides priority of access for dominant males are likely to affect paternity success, warranting further investigation into the determinants of paternity among species with limited male monopolization potential.

Two loci concurrent mutations in non-exclusion parentage cases using 19 STR profiles.

Two loci concurrent mutations in non-exclusion paternity case were reported based on 19 STR loci available from Goldeneye™ DNA ID System 20A (Peoplespot, Beijing, China). When 9508 family trios with Paternity index (PI) threshold of >10,000 was analyzed, 14 families show mutations at two loci. The paternity was confirmed by using an additional 19 STR markers. When the probability of occurrence of two mutations was compared with the expected probability deduced from binomial model, the observed mutational probability was significantly larger than the expectation. However, the characteristics of mutations agree with those reported previously. Our result indicates that larger samples is still need to estimate mutation rates accurately and reveal the relationship between mutations with multiple loci and the characterization of human mutations based on microsatellites.

CHIIMP: An automated high-throughput microsatellite genotyping platform reveals greater allelic diversity in wild chimpanzees.

Short tandem repeats (STRs), also known as microsatellites, are commonly used to noninvasively genotype wild‐living endangered species, including African apes. Until recently, capillary electrophoresis has been the method of choice to determine the length of polymorphic STR loci. However, this technique is labor intensive, difficult to compare across platforms, and notoriously imprecise. Here we developed a MiSeq‐based approach and tested its performance using previously genotyped fecal samples from long‐term studied chimpanzees in Gombe National Park, Tanzania. Using data from eight microsatellite loci as a reference, we designed a bioinformatics platform that converts raw MiSeq reads into locus‐specific files and automatically calls alleles after filtering stutter sequences and other PCR artifacts. Applying this method to the entire Gombe population, we confirmed previously reported genotypes, but also identified 31 new alleles that had been missed due to sequence differences and size homoplasy. The new genotypes, which increased the allelic diversity and heterozygosity in Gombe by 61% and 8%, respectively, were validated by replicate amplification and pedigree analyses. This demonstrated inheritance and resolved one case of an ambiguous paternity. Using both singleplex and multiplex locus amplification, we also genotyped fecal samples from chimpanzees in the Greater Mahale Ecosystem in Tanzania, demonstrating the utility of the MiSeq‐based approach for genotyping nonhabituated populations and performing comparative analyses across field sites. The new automated high‐throughput analysis platform (available at https://github.com/ShawHahnLab/chiimp) will allow biologists to more accurately and effectively determine wildlife population size and structure, and thus obtain information critical for conservation efforts.

Mutation Analysis of Autosomal STR Loci Commonly Used in Paternity Testing in Bosnia and Herzegovina

Mutation analysis in forensic genetics and occurrence of mutations at short-tandem repeat (STR) loci, are very important in paternity testing and precise elucidation of obtained genetic profiles. To determine these locus-specific mutations in Bosnian-Herzegovinian population and their rate, 15 or 22 autosomal loci were typed using PowerPlex 16 and PowerPlex Fusion systems. In total, 1253 individuals within 583 parenthood testing cases were profiled at the Institute for Genetic Engineering and Biotechnology, University of Sarajevo during the period from 2009-2018. Out of total cases, in 13 cases 14 mutations were discovered at 11 loci. Among all tested DNA profiles two mutations occurred at D8S1179, D18S51 and FGA loci each, and one mutation at PENTA D, D3S1358, CSF1P0, D21S11, D5S818, vWA, D16S539, PENTA E. Mutation rates were calculated for 11 loci and were in consistency with mutation rates reported for correspondent locus. In our study, one mutation at locus PENTA D derives from maternal source. Also in one trio paternity case two single-step mutations at loci D16S539 and D18S51 were observed. Our results confirmed mutation analysis is important in paternity testing and therefore much attention should be directed at their analysis.

GWAS on family history of Alzheimer\u2019s disease

Alzheimer’s disease (AD) is a public health priority for the 21st century. Risk reduction currently revolves around lifestyle changes with much research trying to elucidate the biological underpinnings. We show that self-report of parental history of Alzheimer’s dementia for case ascertainment in a genome-wide association study of 314,278 participants from UK Biobank (27,696 maternal cases, 14,338 paternal cases) is a valid proxy for an AD genetic study. After meta-analysing with published consortium data (n = 74,046 with 25,580 cases across the discovery and replication analyses), three new AD-associated loci (P < 5 × 10−8) are identified. These contain genes relevant for AD and neurodegeneration: ADAM10, BCKDK/KAT8 and ACE. Novel gene-based loci include drug targets such as VKORC1 (warfarin dose). We report evidence that the association of SNPs in the TOMM40 gene with AD is potentially mediated by both gene expression and DNA methylation in the prefrontal cortex. However, it is likely that multiple variants are affecting the trait and gene methylation/expression. Our discovered loci may help to elucidate the biological mechanisms underlying AD and, as they contain genes that are drug targets for other diseases and disorders, warrant further exploration for potential precision medicine applications.

Should the Homeless Be Forcibly Helped?

When are we morally obligated as a society to help the homeless, and is coercive interference justified when help is not asked for, even refused? To answer this question, we propose a comprehensive taxonomy of different types of homelessness and argue that different levels of autonomy allow for interventions with varying degrees of pressure to accept help. There are only two categories, however, where paternalism proper is allowed, be it heavily qualified. The first case is the homeless person with severely diminished autonomy as a result of mental illness, and the second case is the homeless person who runs a risk of serious and imminent harm to self. In the first case, namely, that of soft paternalism, we argue that coercive intervention in the case of a refusal to accept help should be focused on the provision of housing that meets basic needs—needs that we outline in the article. In the case of imminent and severe harm to self, the case of hard paternalism, we argue that forced intervention can only be allowed if it is temporary and local, namely focused on getting someone out of harm’s way.

Inference of maternal uniparental disomy of the entire chromosome 2 from a paternity test.

Atypical situations arise during the constant resolution of paternity cases, which constitute challenges requiring additional genetic systems and non-standard methods. We report a paternity case presenting three alleged father (AF)-child incompatibilities for the markers TPOX, D2S441, and the indel locus B02 (11/11 vs 8/8; 14/14 vs 10/10; 2/2 vs1/1, respectively). Considering the presence of mutations/null alleles, the residual paternity indexes (PI) obtained with 23 autosomal short tandem repeats (STRs) and 38 indels suggest that the AF is the father (PI = 1.94e+011). Although the presence of few incompatibilities also could imply paternity of the AF brother, this hypothesis was less probable (PI = 3.20e+9) (W = 98.4 vs 1.6%, respectively). The inclusion of 23 Y-STR loci confirmed the paternity relationship in this case (global PI = 6.08e+15). However, the two multistep STRs and one indel incompatibilities allow discarding the mutation possibility. On the other hand, the confirmation of the homozygous STR genotypes with two different human identification kits and the low probability to find three null alleles (3.10e-8) allow rejecting the null allele presence hypothesis. Conversely, the child's homozygous genotype for maternal alleles in four markers located in the p and q arms of the chromosome 2 (TPOX, D2S441, D2S1338, and B02) suggests that maternal uniparental isodisomy better explains the relationship despite the presence of three paternal incompatibilities. In brief, when multiple incompatibilities are observed in paternity testing, the chromosomal location of the excluding loci and the use of additional genetic systems can be crucial to get confident kinship conclusions.

Paternity tests in Mexico: Results obtained in 3005 cases

National and international reports regarding the paternity testing activity scarcely include information from Mexico and other Latin American countries. Therefore, we report different results from the analysis of 3005 paternity cases analyzed during a period of five years in a Mexican paternity testing laboratory. Motherless tests were the most frequent (77.27%), followed by trio cases (20.70%); the remaining 2.04% included different cases of kinship reconstruction. The paternity exclusion rate was 29.58%, higher but into the range reported by the American Association of Blood Banks (average 24.12%). We detected 65 mutations, most of them involving one-step (93.8% and the remaining were two-step mutations (6.2%) thus, we were able to estimate the paternal mutation rate for 17 different STR loci: 0.0018 (95% CI 0.0005–0.0047). Five triallelic patterns and 12 suspected null alleles were detected during this period; however, re-amplification of these samples with a different Human Identification (HID) kit confirmed the homozygous genotypes, which suggests that most of these exclusions actually are one-step mutations. HID kits with ≥20 STRs detected more exclusions, diminishing the rate of inconclusive results with isolated exclusions (<3 loci), and leading to higher paternity indexes (PI). However, the Powerplex 21 kit (20 STRs) and Powerplex Fusion kit (22 STRs) offered similar PI (p = 0.379) and average number of exclusions (PE) (p = 0.339) when a daughter was involved in motherless tests. In brief, besides to report forensic parameters from paternity tests in Mexico, results describe improvements to solve motherless paternity tests using HID kits with ≥20 STRs instead of one including 15 STRs.

The application of next-generation sequencing to validate D12S391 microvariation

Objective: In a paternity case, the D12S391 locus was reported as a mismatch. To confirm the existence of mutations and mutations come from father or mother. Methods: STR and next-generation sequencing technology were used to validate the sequence. Results: NGS showed the loss of one adenine between the 19.3 allele of the child and allele 20 of the mother. Conclusion: The NGS can be applied in the paternity to validate the mutation.

A Single Step Mutation at D3S1358 Locus in a DNA Paternity Testing with 2 Alleged Fathers.

Genetic information is used very frequently in human identification in civil or judicial cases. Establishing the kinship relationship between a child and his biological father involves many ethical facts. We describe a DNA paternity case with two alleged fathers and an inconsistency between alleged father-2 and the child at D3S1358 locus. As biological samples we used saliva collected from inside the cheek of each person using buccal swabs (Copan, Italy). We collected the biological samples from each of person after each person gave the consent. In order to find the concentration of salivary DNA, the DNA samples were quantified by 7500 ABI Real-time PCR using the Quantifiler Human DNA kit (Applied Biosystems, USA). The next step was the amplification of the Salivary DNA samples by polymerase chain reaction (PCR). It was performed on a ProFlex PCR System (Applied Biosystems, USA) using the multiplex STR markers from the AmpFlSTR® Identifiler Plus Amplification Kit (Applied Biosystems, USA). After amplification, the PCR products were run on capillary electrophoresis on an ABI 3500 Genetic Analyzer (Applied Biosystems, USA). AF-1 was excluded as biological father. The DNA profiles of AF-2 and the child had one mismatch at D3S1358 locus. Further, we amplified the Y-STR markers to confirm the mutation, obtaining a perfect match between the 2 persons. In paternity testing, where one or two inconsistencies are present between the child and the alleged father on autosomal STR markers, the use of haploid markers X-STR or Y-STRs is needed for the confirmation or exclusion of paternity.

Application of SNP-STR Composed by D18S51 and Three SNPs of Its Flanking Region in Paternity Testing

To develop a SNP-STR haplotype by consisting of the SNP and STR genetic markers, both of which locate in a haplotype block. To investigate its distribution in Han population from Chengdu, and explore its application in some special cases of paternity testing. D18S51, one of the high mutation rate STR markers in combined DNA index system （CODIS）, and three SNP loci rs8089331, rs8094489 and rs7236090 in its flanking region, were chosen to establish SNP-STR. Its haplotype was obtained by nested allele-specific polymerase chain reaction, and the relevant distribution of 75 unrelated individuals were investigated in Han population from Chengdu. The SNP-STR haplotype was tentatively applied in duo paternity testing cases with D18S51 incompatibility. The SNP-STR typing method was established and a total of 43 haplotypes were obtained successfully in Han population from Chengdu. Its polymorphism was 0.948 6, and duo paternity testing cases were resolved by this method. SNP-STR shows high diversity and can be applied in the identifications of some special paternity testing cases.

Paternity Cases Within a Medicolegal Context: a Case Study of Heteropaternal Superfecundation in Iraq

A case of paternity was referred to the Medical-Legal Directorate( MLD)/ Baghdad in August 2011 .The family who were concerned was the Father (41 years old ) ,mother (23 years old) and 2 sons non identical twin (1.5year old) . Paternity test includes Conventional Blood Group Markers, DNA and Y chromosome STR Typing were investigated . The DNA and Y chromosome STR Typing were tested for the referred trios father and twins first , the results revealed an absolute exclusion of fatherhood relationship to both . , surprisingly the Y Chromosomeprofiles revealed obviously that the two non identical twins were from different fathers or paternal descent. Maternity test was ought to be examined for the assumed mother to rule out the possibility of switch of both babies in the hospital during their delivery and to prove their brotherhood relationship from mother side. The mother was referred and maternity was confirmed later using DNA Typing . Combined Maternity Index (CPI) was calculated for twins ,The probability of Maternity were 99.98% and 99.95% for the1st and 2 nd twin respectively. Key words : hetero paternal Superfecundation ,Non Identical twin,DNA Typing ,Y Chromosome STR Polymorphysim

Analysis of fortuitous matches in a STR genotype database from Mexico and its forensic efficiency parameters

BackgroundCommercial kits for Human Identification (HID) purposes, based on 15 short tandem repeat (STR) regions, allow the resolution of most forensic and paternity cases. However, some pitfalls arise in situations such as identification of missing persons, disaster victims, and in motherless paternities. We describe nine fortuitous matches found during the inclusion of new DNA profiles and/or searching for missing persons within a Mexican STR database (N = 2000). For these cases, we estimated both the likelihood ratio (LR) and the modified LR according to National Research Council (NRC) recommendations (i.e., LRNRC).ResultsIn most cases, low LRNRC values (~1 or <1) and elevated presence of modal STR alleles (>50% loci) were indicative of fortuitous matches. We estimated a significant increase in the observed frequency of fortuitous matches in this database when using the PowerPlex 16 DNA-typing system. In addition, forensic efficiency parameters for this HID kit are reported for the State of Mexico based on a population sample selected from the STR database (n = 493). We describe the population structure and relationships, which detail comparative homogeneity among Mexican-Mestizos from the Central region, excluding the Western region.ConclusionsThe results suggest that additional / more powerful HID systems should be used when searching for relatives within STR databases in order to enable definitive conclusions, which are also required in cases of motherless paternity and massive disasters. The genetic structure described herein allows forensic geneticists to use alternative STR population data during statistical interpretation, given that most Mexican populations do not have their own STR databases.

Inconsistent genotyping call at DYS389 locus and implications for interpretation.

The male-specific Y chromosome short tandem repeat (STR) locus is used widely in forensic case, which are useful molecular tool to providing the biological evidence for male/female mixture and paternal lineage cases. The Y-STR analysis has been greatly facilitated by advent of commercial multiplex kit. However, even with well-designed robust multiplex kit, abnormal genotyping profile may be observed when encountering with mutations, such as deletion/duplication within the target region or mutation at the primer binding site. In this study, a single-allele shift by five nucleotides for the DYS389I marker between the AmpFlSTR® Yfiler® and Yfiler® Plus PCR amplification kits while the same allele count for DYS389II was observed in eight unrelated Chinese male individuals. After further investigations by re-amplified with three additional multiplex kits, sanger, and next-generation sequencing, the discordance was finally proven caused by existing rare mutation in those sample, which contained two adjacent SNPs only one base apart in the sequence. This paper describes the molecular basis of the discordance at DYS389I genotyping between different commercial multiplex kits and could provide available information for enhancing of interpretation of abnormal Y-STR genotyping in forensic practice.

Multistep microsatellite mutation at D18S51 locus in a parentage testing case

Mutations of short tandem repeats (STRs) loci might cause allelic mismatchs between the child and the parents, which entangled the forensic inference in paternity testing. Most of the reported microsatellite mutations are confined to single-step mutations, and multistep mutations were rarely reported and only account for a very limited number of STR mutation events in previously studied cases. Here we reported a paternity case with a mismatch in locus D18S51. The genotypes of the alleged father, the mother and the child in D18S51 locus were 14/23, 15/16, and 15/20, respectively. Examination of 38 autosomal STR loci revealed no mismatches, and the paternity index is above 1.58E+15. These results suggested that the alleged father is the biological father of the child that a rare three-steps mutation had occurred in the paternal allele of D18S51.

AB103. A sequence variation of short tandem repeat observed in paternity cases using massively parallel sequencing technology

AB103. A sequence variation of short tandem repeat observed in paternity cases using massively parallel sequencing technology

AB103. A sequence variation of short tandem repeat observed in paternity cases using massively parallel sequencing technology

Background: STR has been regularly used as genetic marker in paternity testing. The current standard procedure of STR allele detection based on DNA fragment analysis using CE. However, the MPS offers the high-throughput sequencing with lower cost per nucleotide. This technology has increase an opportunity for STR allele detection in national database and paternity testing as well. The high degree polymorphism of STR makes them informative that is an influence of their high mutation rate. Moreover, the usefulness even in homozygous alleles is determined by sequence variation in particular STR marker. In this study, we compare a STR allele designation from CE and a STR sequencing from MPS. The sequence variation has observed in particular STR.

Mutation rates in 21 autosomal short tandem repeat loci in a population from Goiás, Brazil.

The appearance of new mutations in polymorphic markers plays a central role in a range of genetic applications, including dating phylogenetic events, informing disease studies, and evaluating forensic evidence. The present study estimated the mutation rates of 21 autosomal STR loci in a population from Central Brazil. We studied 15046 paternity cases from Goiás, Brazil from August 2012 to February 2015. We identified 262 mutations in the 21 loci. The loci that presented more mutations were FGA and D18S51, with a total of 46 and 28 mutations, respectively. The results showed mutational rates ranging from 1.7×10-5 to 7.6×10-4 mutations per site/region and the overall mutational rate was 2.1×10-4 ; these values were within the expected values for the STR markers. The most common type of mutation was one-step mutation, which totaled 96.2%. We found a higher rate of mutations of paternal origin (67.6%) than of mutations of maternal origin. The occurrence of mutations in STRs has important consequences for human identification, including the definition of criteria for exclusion in paternity testing and interpretation of genetic profiles in criminal cases.

Reconsidering paternalism in clinical research

The ethical standards that regulate clinical research have multiple rationales. Among them is the need to protect potential subjects from making imprudent decisions, which extends beyond the soft paternalistic concern to protect people from making uninformed decisions to participate in trials. This article argues that a plausible risk/benefit restriction on clinical trials is presumptively justified by hard paternalism, which in turn is supported by a deeper fairness-based rationale. This presumptive case for hard paternalism in research is not defeated by the alleged right to participate in clinical trials, by concerns about insult or status, by the need to conduct early phase trials that promise little to no benefit to participants, or by the recognition that some potential subjects are altruistically motivated.

Autosomal InDel polymorphisms for population genetic structure and differentiation analysis of Chinese Kazak ethnic group.

In the present study, we assessed the genetic diversities of the Chinese Kazak ethnic group on the basis of 30 well-chosen autosomal insertion and deletion loci and explored the genetic relationships between Kazak and 23 reference groups. We detected the level of the expected heterozygosity ranging from 0.3605 at HLD39 locus to 0.5000 at HLD136 locus and the observed heterozygosity ranging from 0.3548 at HLD39 locus to 0.5283 at HLD136 locus. The combined power of discrimination and the combined power of exclusion for all 30 loci in the studied Kazak group were 0.999999999999128 and 0.9945, respectively. The dataset generated in this study indicated the panel of 30 InDels was highly efficient in forensic individual identifcation but may not have enough power in paternity cases. The results of the interpopulation differentiations, PCA plots, phylogenetic trees and STRUCTURE analyses showed a close genetic affiliation between the Kazak and Uigur group.