Paternity Testing Research Articles

Development of a 17-plex STR typing system for the identification of individuals and parentage testing in cattle

Accurate identification of animals and the verification of their parentage can be used to pedigree populations and support selective breeding. The International Society for Animal Genetics recommended 16 cattle STRs for individual identification and parentage testing in cattle, but no multiplex STR typing system contains these 16 STRs. Here, we develop an efficient 17-plex multiplex typing system for cattle that contains the 16 ISAG recommend STRs and a sex-determining marker. Compared to the Bovine Parenting Typing Kit (containing 11 of the 16 ISAG recommend STRs), our new typing system not only increases the number of molecular markers, but also simplifies the PCR operation and shortens the time for the typing procedure (from 4.5 h to 1 h 37 min). Profile can be generated from a single PCR reaction using as little as 1 ng of DNA. The combined probabilities of paternity exclusion CPEduo and CPEtrio were 0.999804697 and 0.999999260, respectively. These results indicate that our 17-plex typing system is a fast, sensitive and species-specific method for the identification of individuals and their parentage for cattle. The application of this system will improve the efficiency of the identification of cattle individuals and their paternity, supporting population genetic research and the selective breeding of cattle.

Paternity Test: Is Mendel the Father of Genetics, and Why Should Science Educators Care?

Paternity Test: Is Mendel the Father of Genetics, and Why Should Science Educators Care?

An innovative approach: introducing novel sheep paternity testing panels

An innovative approach: introducing novel sheep paternity testing panels

Unveiling STRs instability in a colorectal cancer FFPE sample: a case report.

In forensic genetics, sometimes formalin-fixed paraffin-embedded (FFPE) biopsy material taken during life is the only biological sample available for individual identification or paternity testing. In most cases, this biological tissue is characterized by the presence of tumor cells characterized by instability and loss of heterozygosity of microsatellites (MSI/LOH) compared to the DNA present in cells of normal tissue.In this case report, two FFPE samples from the same male subject were available for genetic investigation: one sample with colorectal cancer tissue and the other with normal tissue (no cancerous histopathological features). The comparison of the genetic profiles obtained from DNA extracted from the two tissues showed in the tumor tissue the presence of three genomic instability phenomena affecting FGA, CSF1P0, D21S2055 loci, located on three distinct autosomal chromosomes, and one duplication phenomenon affecting the DYS438. Therefore, due to the MSI/LOH phenomena, the genetic profile acquired from the tumor tissue was distorted and thus generated a fictitious genetic profile, not corresponding to the subject's real one (normal tissue free of tumor cells).

B-219 Pseudo-exclusion From Paternity due to Maternal Uniparental Disomy of Chromosome 2

Abstract Background Uniparental disomy (UPD) is the abnormal situation in which both members of a chromosome pair exclusively comprise material of one of the parents. The incidence of uniparental disomy (UPD) of any chromosome is estimated in 1:3500 live births; this rare condition may be relevant not only for medical genetics, but also for parental testing. Methods We describe a case of trio paternity test using 55 informative STR loci, 30 of these were performed whith GlobalFiler Express KIT - Thermo Fisher (GFE) and Investigator HDPlex - Qiagen (IHDP); capillary electrophoresis using 3500XL - Applied BioSystems; analyses using Genemapper IDX 4.0 - Applied BioSystems. The Y haplotype and 8 additional autosomal STRs were performed by a reference laboratory, which assists us in complex cases. Genotyping with a 1,6 million marker SNP-array (GDA-cyto, Illumina) was analyzed using NxClinical software(Bionano). Results Inconsistencies were observed in four loci, namely TPOX, D2S441, D2S1338 and D2S1360. All four markers mapped on chromosome 2 and were compatible with the mother´s genotype, raising the suspicion of a maternal UPD2. SNP-array analyse showed 4 large blocks with absence of heterozygosity on chromosome 2 (AOH - arr[GRCh38] 2p25.3p24.1(10587_22202427)x2 hmz, 2p21p11.2(43674352_90357502)x2 hmz, 2q22.1q31.1(141240699_170583494)x2 hmz, 2q36.3q37.3(227133255_242119896)x2 hmz), comprising a total of 112,9 Mb. No large AOH blocks were observed in any other chromosome. Conclusions The results indicate the presence of a UPD2. As the result of an unusually high-number of crossing-overs (n=6), several heterozygous and homozygous blocks were present on chromosome 2 (see figure 1). Rare cases of pseudo-exclusions of either maternity or paternity due to UPD have been reported. Together with the case reported here, they highlight the necessity to consider inconsistencies of markers that map into a single chromosome as likely resulting from UPD.

Screening a new set of microhaplotypes in exonic regions for sample identity testing and paternity testing during whole exome sequencing analysis.

Whole exome sequencing (WES) is widely used in clinical diagnosis. Before obtaining an accurate diagnosis, it is essential to conduct sample identity testing and paternity testing on trio samples. Currently, there is a lack of optimal genetic markers for these purposes, with limited literature available in this area. Microhaplotypes (MHs) are promising genetic markers due to their high polymorphism, low mutation rate, short amplified fragments, absence of stutter and amplification bias. These characteristics make them suitable for sample tracking and paternity testing during WES analysis. In this study, we screened out a set of polymorphic MHs in exonic regions for the above purposes. The results showed that the power of discrimination (PD) and probability of exclusion (PE) of this set of markers ranged from 0.2682 to 0.8878 and 0.0178 to 0.4583, respectively. Both the cumulative power of discrimination (CPD) and cumulative probability of exclusion (CPE) exceeded 0.999999, indicating the great value of these markers in paternity testing and individual identification in the study population. However, these markers had the effective number of alleles (Ae) values ranging from 1.1784 to 3.8727 (average 2.1805) and informativeness (In) values ranging from 0.0151 to 0.2209 (average 0.0766), showing limited value in DNA mixture analysis and biogeographical ancestry inference.

NASTRA: accurate analysis of short tandem repeat markers by nanopore sequencing with repeat-structure-aware algorithm.

Short-tandem repeats (STRs) are the type of genetic markers extensively utilized in biomedical and forensic applications. Due to sequencing noise in nanopore sequencing, accurate analysis methods are lacking. We developed NASTRA, an innovative tool for Nanopore Autosomal Short Tandem Repeat Analysis, which overcomes traditional database-based methods' limitations and provides a precise germline analysis of STR genetic markers without the need for allele sequence reference. Demonstrating high accuracy in cell line authentication testing and paternity testing, NASTRA significantly surpasses existing methods in both speed and accuracy. This advancement makes it a promising solution for rapid cell line authentication and kinship testing, highlighting the potential of nanopore sequencing for in-field applications.

Accuracy in Pedigree Records in Hair Goats: New Microsatellite Based Paternity Test Panels

Objective: The aim of the study was to establish microsatellite-based paternity test panels that can be used in paternity tests for Hair goat populations bred in Aydın and Denizli provinces, and to evaluate them in terms of paternity test parameters. Material and Methods: The animal material of the study consisted of a total of 247 hair goats (42 bucks and 205 kids) in Hair goat farms in Aydın and Denizli provinces. The 18 microsatellites used in the study were evaluated in terms of molecular genetic parameters obtained from genotyping. After the evaluation, microsatellites were ranked from highest to lowest based on their individual exclusion probability values. Eighteen paternity test panels were created by sequentially adding a new microsatellite with a lower individual exclusion probability than the previous one to the microsatellite with the highest exclusion probability. Molecular genetic test statistics were obtained for the paternity test panels. Results: In the study, 306 alleles were observed. The observed heterozygosity ratio (Ho) ranged from 0.39 to 0.95, while the expected heterozygosity ratio (He) ranged from 0.72 to 0.92. In the study, individual P-probability of exclusion (PE) values ranged from 0.316 to 0.719, while the combined probability of exclusion (CPE) values for the paternity test panels ranged from 0.7188 to 0.9999. Among the paternity test panels, Panel -7 and the following panels showed values above the threshold value reported in the literature in terms of the combined probability of exclusion. Conclusion: According to the study findings, Panels 7 and 8, designed for paternity testing with fewer microsatellite markers, can be more cost-effective and practical for Hair goat populations compared to other panels. The findings obtained from the study make a significant contribution and provide a perspective for improving hand-mating practices. This is crucial within the framework of the "National Genetic Improvement Project for Small Ruminants at Breeders' Conditions" coordinated by the General Directorate of Agricultural Research and Policies.

PSIII-6 Multi-sire artificial insemination of beef heifers in the Nebraska Sandhills effect on pregnancy rate compared with single-sire insemination

Abstract The objective of this study was to compare pregnancy outcomes resulting from artificial insemination (AI) with multi-sire semen (MS) compared with single-sire semen (SS) in beef heifers. Another study observed pregnancy and paternity outcomes to sexed MS without a control treatment. In the first study, unrelated ABS Global Angus bulls (n = 3) were selected for AI to 441 (Yr 1) and 391 (Yr 2) Angus crossbred heifers. Heifers were synchronized with the melengestrol acetate – prostaglandin F2α timed-AI protocol. Conventional semen, from each bull, were labeled A, B, or C. Remaining semen was pooled in equal amounts to form conventional MS straws. Heifers were AI using alternating treatment of MS or SS: A, B, or C with one-half of inseminated heifers receiving either MS or SS. The GLIMMIX procedure in SAS 9.4 analyzed responses to treatments using the BIN distribution option and reported as LSMEANS. Contrasts and estimates analyzed responses between treatments. Ultrasound determined SS pregnancy rate averaged 60% (SS-A = 64%, SS-B = 58%, SS-C = 58%) and MS average 62% (P = 0.63). Paternity was determined in 57 MS calves and confirmed in 49 SS calves. In Yr 1, Bull A sired 7%, bull B sired 56%, and bull C sired 37%. Although bull A was much less successful than bull B or C, the values are not significantly different due to the small sample size (P = 0.11 and P = 0.24, respectively). Few conclusions can be made from the ongoing study, but it is hypothesized MS may improve consistency of pregnancy rate by equilibrating semen quality in herds subjected to timed AI. In the observational study, multiple 5-way cross bulls born from the ranch herd were selected for AI of 951 ± 41 heifers for 3 yr. Heifers were synchronized using the previously mentioned protocol with split-time AI. Unequal amounts of semen were collected, pooled, and sexed to favor heifer progeny at an expected ratio of 9:1. Semen from 2 to 4 random bulls were pooled making 3 to 4 MS groups each year. Heifers exhibiting estrus were administered sexed MS, but there was no control treatment. The observed ultrasound determined average pregnancy rate of heifers administered sexed MS was 65% (Yr 1), 75% (Yr 2), and 72% (Yr 3). Previous literature suggests average pregnancy rate to AI with sexed SS is 53%. Paternity testing in Yr 2 found semen contribution mirrored paternity ratios within some groups but the sire group with 2 bulls found one sired 15% and the other sired 85%. This study exemplified a viable method for AI that requires further research. Further research into semen quality of a single sire, and pooled semen could lead to optimization of fertilization among individuals within a herd.

Characterization of blood bank and transfusion medicine practices for pregnant individuals with fetuses at risk of hemolytic disease in the United States.

Hemolytic disease of the fetus and newborn (HDFN) is caused by maternal alloantibody-mediated destruction of fetal/neonatal red blood cells (RBCs). While the pathophysiology has been well-characterized, the clinical and laboratory monitoring practices are inconsistent. We surveyed 103 US institutions to characterize laboratory testing practices for individuals with fetuses at risk of HDFN. Questions included antibody testing and titration methodologies, the use of critical titers, paternal and cell-free fetal DNA testing, and result reporting and documentation practices. The response rate was 44% (45/103). Most respondents (96%, 43/45) assess maternal antibody titers, primarily using conventional tube-based methods only (79%, 34/43). Among respondents, 51% (23/45) rescreen all individuals for antibodies in the third trimester, and 60% (27/45) perform paternal RBC antigen testing. A minority (27%, 12/45) utilize cell-free fetal DNA (cffDNA) testing to predict fetal antigen status. Maternal antibody titers are performed even when the fetus is not considered to be at risk of HDFN based on cffDNA or paternal RBC antigen testing at 23% (10/43) of sites that assess titers. There is heterogeneity across US institutions regarding the testing, monitoring, and reporting practices for pregnant individuals with fetuses at risk of HDFN, including the use of antibody titers in screening and monitoring programs, the use of paternal RBC antigen testing and cffDNA, and documentation of fetal antigen results. Standardization of laboratory testing protocols and closer collaboration between the blood bank and transfusion medicine service and the obstetric/maternal-fetal medicine service are needed.

The Use of Genomic Screening for the Detection of Chromosomal Abnormalities in the Domestic Horse: Five New Cases of 65,XXY Syndrome in the Pura Raza Español Breed.

Sex chromosomal abnormalities are a well-established cause of reproductive failure in domestic horses. Because of its difficult diagnosis, the Pura Raza Español breeding program established a routine screening for chromosomal abnormalities in all the horses prior to enrolling in the studbook. This genomic procedure combines an initial assessment based on the results from Short Tandem Repeat (STR) parentage testing followed by a Single-Nucleotide Polymorphism (SNP) based copy number aberration (CNA) confirmative analysis in positive cases. Using this methodology, we identified five new individuals carrying a 65,XXY chromosomal number aberration (CNA) among 27,330 foals enrolled over the past two reproductive seasons. The animals were initially flagged as CNA candidates due to abnormal results in STR testing. Subsequent analysis genotyping using an STR sex-linked dedicated panel and a medium-density SNP array in ECAX and ECAY confirmed the diagnosis as 65,XXY carriers. Four cases (upon sample availability) underwent further analysis using in situ fluorescent hybridization with ECAX and ECAY probes, showing identical results. Phenotypic analysis revealed abnormal gonad development in one of the cases, showing that the remaining four had a normal reproductive morphology. To our knowledge, this represents the largest number of horses exhibiting the equine form of Klinefelter syndrome (65,XXY) reported to date. Our study highlights the importance of genomic screening in the accurate detection of chromosomal abnormalities in horses.

Genetic profile and ancestral polymorphism research of the Guizhou Shui and Dong ethnic groups using a novel self-developed AIM-InDel panel

Insertion or deletion (InDel), a genetic marker with short insertion/deletion fragment length polymorphism, is widely used in the field of forensic biological research. The Guizhou Shui (Shui) ethnic group and Guizhou Dong (Dong) ethnic group are located in the southwestern region of China, with rich historical and cultural background. In this study, a self-developed panel included 56 ancestry informative marker (AIM)-InDel loci on the autosomes, three InDel loci on the Y chromosome, and one sex-determined Amelogenin locus. Firstly, we used the 56 autosomal loci to assess the forensic individual identification and paternity testing abilities in both the Shui and Dong groups. The cumulative probability of match and probability of exclusion for the Shui and Dong groups were 2.228×10−15 and 0.991518139; 7.604×10−16 and 0.992253273, respectively. In addition, we also conducted in-depth analyses for the genetic backgrounds and structures of the Shui and Dong groups based on 56 AIM-InDel loci. This research has found that the Shui and Dong groups have close genetic relationships with the East Asian populations. Meanwhile, we also found that the Shui group has a close genetic distance with Chinese Dai in Xishuangbanna (CDX). These insights provide vital information for the genetic structures of the Shui and Dong groups, as well as basic population data and molecular biological evidence support for individual identification and biogeographic ancestry inference in forensic genetic field.

Polymorphism analysis of tri- and tetranucleotide repeat microsatellite markers in Hanwoo cattle.

The Hanwoo traceability system currently utilizes 11 dinucleotide repeat microsatellite (MS) markers. However, dinucleotide repeat markers are known to have a high incidence of polymerase chain reaction (PCR) artifacts, such as stutter bands, which can complicate the accurate reading of alleles. In this study, we examined the polymorphisms of the 11 dinucleotide repeat MS markers currently employed in traceability systems. Additionally, we explored four trinucleotide repeat MS markers and one tetranucleotide repeat MS marker in a sample of 1,106 Hanwoo cattle. We also assessed the potential utility of the tri- and tetranucleotide repeat MS markers. The polymorphic information content (PIC) of the five tri- and tetranucleotide repeat markers ranged from 0.663 to 0.767 (mean: 0.722), sufficiently polymorphic and slightly higher than the mean (0.716) of the current 11 dinucleotide repeat markers. Using all 16 markers, the mean PIC was 0.718. The estimated probability of identity (PI) was 3.13 × 10-12 using the 11 dinucleotide repeat markers, 7.03 × 10-6 using the five tri- and tetranucleotide repeat markers, and 2.39 × 10-17 using all 16 markers; the respective PIhalf-sibs values were 2.69 × 10-9, 1.29 × 10-4, and 3.42 × 10-13; and the respective PIsibs values were 3.89 × 10-5, 9.6 × 10-3, and 3.69 × 10-7. The probability of exclusion1 (PE1) was 0.999864 for the 11 dinucleotide repeat markers, 0.981141 for five of the tri- and tetranucleotide repeat markers, and > 0.99 for all 16 markers; the respective PE2 values were 0.994632, 0.901369, and > 0.99; and the respective PE3 values were 0.998702, > 0.99, and > 0.99. The five investigated tri- and tetranucleotide repeat MS markers can be used in combination with the 11 existing MS markers to improve the accuracy of individual identification and paternity testing in Hanwoo.

Application of a newly constructed NGS panel with 45 X-linked microhaplotypes demonstrates the unique value of X-MH for kinship testing and mixture analysis

X-linked microhaplotypes (X-MHs) have the potential to be a valuable supplementary tool in complex kinship identification or the resolution of DNA mixtures, because they bring together the distinctive genetic pattern of X chromosomal markers and the benefits of microhaplotypes (MHs). In this study, we used the 1000 Genome database to screen and select 63 X-MHs; 18 MHs were filtered out though a batch sequencing assessment of the DNA samples collected from 112 unrelated Chinese Han individuals. The resulting 45-plex panel performed well in comprehensive assessments including repeatability, sensitivity, species specificity, resistance to PCR inhibitors or degradation, mutation rate, and accuracy in detecting DNA mixture samples. The minimum amount of DNA template that can be tested with this panel is 0.5 ng. Additionally, the alleles of the minor contributor can be accurately detected when the mixture rate is larger than 1:9 in female-male mixture or 1:19 in male-male mixture. Then, we calculated population parameters on each MH based on the allele frequency data obtained from the sequence results of the aforementioned 112 unrelated samples. Combining these parameters on each MH, it can be calculated that TDPm, TDPf, CPET, CPEDFM, CPEDFF and CNCEP3 of the 45-plex system were 1–8.99×10−13, 1–1.62×10−19, 0.9999999995, 0.9999981, 0.9955, 0.9999971 and 0.99940, respectively, indicating that the panel is capable in personal identification and parentage testing. To reveal the unique advantage of X-MHs in the analyses of complex kinship and male DNA mixture, further assessments were made. For complex kinship identification, 22 types of individual pairs with different second-degree kinship were simulated and different types of likelihood ratios (LR) were calculated for each. The results revealed that the panel can achieve accuracy of approximately 70 %∼80 % when dividing each of the three types of second-degree kinships into three or four groups. Theoretically, such sub-division cannot be done by using independent autosomal markers. For male DNA mixture analysis without suspects, the maximum likelihood ratio strategy was derived and employed in the estimation of the number of male contributors (NOMC). Simulations were conducted to verify the efficacy of the 45-plex panel in the field and to compare it with autosomal markers by assuming the 45 MHs as autosomal ones. The results showed that X-MHs can achieve higher accuracy in the estimation of NOMC than autosomal ones when the mixed males were unrelated. The results highlighted the unique value of X-linked MHs in complex kinship and male mixture analyses.

Development of the first equine blastocyst produced by conventional IVF and in vitro culture in Europe resulting in the birth of a foal

In this case report, the production of the first equine blastocyst using conventional in vitro fertilization (IVF) and in vitro embryo culture methods in Europe is described. A healthy foal was born after transfer of a blastocyst using a complete in vitro production process, including in vitro oocyte maturation, in vitro sperm capacitation, fertilization in vitro and culture to the blastocyst stage in vitro. Oocytes were recovered from ovaries of slaughtered mares. After in vitro maturation, the oocytes were fertilized by conventional IVF and cultured for nine days. One embryo reached the blastocyst stage and was vitrified. After the selection of a suitable recipient mare that had ovulated four days earlier, the blastocyst was thawed and transferred. Five days after embryo transfer, a single embryonic vesicle was detected by transrectal ultrasonography. After a normal pregnancy of 323 days, a healthy colt was born. Parentage testing via microsatellite genotyping confirmed that the recipient was excluded as the foal’s dam and that the stallion whose semen was used, qualified as the sire.

Selective Retention of Cross-Fertilised Fruitlets during Premature Fruit Drop of Hass Avocado

The productivity of many tree crops is limited by low yield, partly due to high rates of fruitlet abscission during early fruit development. Early studies suggested that cross-pollinated fruitlets may be selectively retained during fruit development, although paternity testing of fruitlets to test this hypothesis was technically challenging. We used MassARRAY genotyping to determine the effects of pollen parentage on fruitlet retention and fruit quality of Hass avocado. We identified the paternity of abscised and retained fruitlets at 6 and 10 weeks, and mature fruit at 36 weeks, after peak anthesis. We measured the embryo mass, pericarp mass, total mass and nutrient concentrations of fruitlets, and the seed mass, flesh mass, total mass, diameter, length, nutrient concentrations and fatty-acid composition of mature fruit. The percentages of progeny on the tree that were cross-fertilised increased from 4.6% at 6 weeks after peak anthesis to 10.7% at fruit maturity. Only 1.0% of freshly abscised fruitlets on the ground at 10 weeks after peak anthesis were cross-pollinated even though 6.5% of retained fruitlets on the tree were cross-pollinated. At this stage, cross-pollinated fruitlets had similar nutrient concentrations to self-pollinated fruitlets, but they had higher total contents of P, K, Al, Ca, Fe, Mn and Zn due to having greater fruitlet mass. At maturity, cross-pollinated fruit were 6% heavier and had 2% greater diameter than self-pollinated fruit, without significant differences in flesh nutrient concentrations or fatty acid composition. The results demonstrate that Hass avocado trees selectively retain cross-pollinated fruitlets, which are larger than self-pollinated fruitlets and ultimately produce larger mature fruit. Avocado growers can increase fruit size and yield by improving the opportunities for cross-pollination, possibly by closely interplanting type A and type B cultivars and introducing more beehives into orchards.

Genetic assessment of eight zoo populations of golden snub-nosed monkey (Rhinopithecus roxellana) implication to the conservation management of captive populations.

Captive breeding programs play an important role in preserving the genetic diversity of endangered species. It is of utmost importance to conduct genetic assessment for captive populations in order to develop scientific breeding plans and conservation management strategies. Here, we genotyped 10 microsatellite loci and sequenced 368 bp of mitochondrial DNA control region for the golden snub-nosed monkey (Rhinopithecus roxellana) from eight captive populations in China, and compared the genetic indices of captive populations with a wild population. Meanwhile, we performed paternity tests to verify the genealogical records and established genetic lineages. A total of 157 individuals were identified from 161 fecal samples, including 135 captive individuals (approximately 25% of captive individuals in China). Microsatellite analysis showed that the nine populations had moderate levels of genetic diversity, with polymorphism information content (PIC) ranging from 0.43 to 0.542; the genetic diversity of captive populations (average PIC: 0.503) was slightly higher than that of the wild population (PIC: 0.438). The Structure analysis indicated that individuals of the eight captive populations contained two different genetic components. We conducted either single-blind or double-blind paternity testing on 40 offspring of captive individuals and found that five offspring from two zoos (Nanjing Hongshan Forest Zoo and Shanghai Wild Animal Park) showed discrepant kinships from their pedigree records, probably due to the inaccuracies in pedigree records. By constructing genetic pedigrees, inbred offspring were found in Beijing Zoo, Shanghai Zoo, Hangzhou Zoo, and Chengdu Zoo. Analysis based on mitochondrial DNA showed a high level of genetic diversity in the eight captive populations (mean nucleotide diversity: 0.047). However, no nucleotide diversity was found in the wild population. This study conducted a genetic survey for captive golden snub-nosed monkeys and will significantly benefit the genetic conservation management for captive populations in the future.

Genetic variation and phylogenetic analysis of 23 STR in Chinese Han population from Hainan, Southern China.

The forensic characteristics and genetic relationships of Hainan Han population are still not fully understood. The aim of this study was to investigate the forensic features and genetic variations of 23 short tandem repeat (STR) included in the HuaxiaTM Platinum system in Hainan Han and analyze the population genetic relationships between Hainan Han and other adjacent Chinese populations. The genetic polymorphisms of 23 STR loci included in the HuaxiaTM Platinum kit were evaluated from 2971 Hainan Han individuals. Comprehensive comparisons were conducted based on genetic distance, phylogenetic tree, multidimensional scaling and principal component analysis (PCA) to explore inter-population genetic relationship. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the 23 STR loci was 0.999 999 999 999 999 999 999 999 999 819 and 0.999 999 999 625 408, respectively. The investigated Hainan Han population has high genetic similarity with geographically close Han populations, while great genetic difference with other ethnic minorities, prominently in Yunnan Miao, Xinjiang Uygurs, Xinjiang Kazakh, and Tibetans. Our study found the 23 STR loci were highly polymorphic and suitable for forensic personal identification and paternity testing in Hainan Han population. Genetic similarity widely existed among Han populations from different regions, and significant genetic divergence existed between Han populations and some ethnic minorities. The populations genetic diversity and similarity were closely associated with ethnic origin and geographical distribution.

Development and validation of a novel 30-plex STR assay for canine individual identification and parentage testing

Domestic dogs are helpers in outdoor human work and companions for families; thus, individual canine identification and parentage testing are crucial in certain fields, including forensics and breeding programs. In this study, a six-dye fluorescent labeling multiplex amplification system containing 29 canine short tandem repeats (STRs) and the sex-determining marker DAmel was developed. The system was called the Tronfo Canine 30-plex STR Kit and was further validated according to the Scientific Working Group on DNA Analysis Methods and the Organization of Scientific Area Committees for Wildlife Forensics guidelines, including tests for PCR conditions, precision, species specificity, sensitivity, stability, repeatability and reproducibility, a population study, and a study of 16 paternity test cases. The results indicated that the novel canine STR assay was accurate, specific, reproducible, stable, and robust. Complete profiles were obtained with 31.25 pg of canine DNA. Additionally, 500 unrelated canine individuals were investigated using this novel system, and the combined power of discrimination and exclusion values were 0.999999999999999999 and 0.999996451039850, respectively. These results suggest that the Tronfo Canine 30-plex STR Kit is highly polymorphic, informative, and suitable for individual canine identification and parentage testing.

Mutational analysis of 23 autosomal short tandem repeats based on trio paternity testing in the Korean population

This study aimed to estimate A-STR mutation rates in 2,317 Korean parent–child trios by examining 20 Combined DNA Index System (CODIS) core loci (D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, CSF1PO, FGA, TH01, TPOX, vWA, D1S1656, D2S441, D2S1338, D10S1248, D12S391, D19S433, and D22S1045) and three non-CODIS loci (Penta E, Penta D, and SE33). Locus-specific mutation rate estimates varied from 0.00 to 8.63 × 10-3 per generation, with an average mutation rate of 1.62 × 10-3 (95 % CI, 1.39–1.88 × 10-3). We also combined data from previous studies to obtain comprehensive genetic values for the Korean population, and the average mutation rate was 1.59 × 10-3 (95 % CI, 1.38–1.82 × 10-3). Single-step mutations (95.69 %) and double-step mutations (3.35 %) were observed in the mutation pattern analysis, and cases expected to have multi-step mutations (0.96 %) were also observed. Large-sized alleles exhibited more loss mutations than gain mutations, and paternal mutations (62.68 %) were more frequently observed than maternal mutations (19.62 %). The calculated values and features of the 23 A-STRs explored in this study are expected to play a crucial role in establishing criteria for forensic genetic interpretation.