Utility of ForenSeq™ DNA Signature Prep Kit in the research of pairwise 2nd-degree kinship identification

Sequence-based genotyping of 58 STRs and 94 iiSNPs with Verogen's ForenSeq DNA signature prep kit in Mexican-Mestizos from Jalisco state (West, México)

Massively parallel sequencing (MPS) allows simultaneous detection of sequence variation of both Single nucleotide polymorphisms (SNPs) and Short tandem repeats (STRs) with different inheritance patterns, such as autosomal (aSTRs), patrilineal Y-linked (Y-STRs), and X-chromosomal (X-STRs). However, to apply these methodologies for Human Identification (HID), population databases with sequence-based (SB) allele frequencies are needed. For this reason, we sequenced 58 STRs (aSTRs, X-STRs, and Y-STRs) and 94 identity informative SNPs (iiSNPs) on 95 Mexican-Mestizo (admixed) individuals from the Jalisco state (West, Mexico), with the Primer Set-A of the ForenSeq™ DNA Signature Prep Kit. For SB allele calling, we used the recent ISFG recommendations for STR sequence nomenclature. The information provided by the SB variation (including flanking regions) in the STRs increased their allelic diversity regarding the length-based (LB) alleles, as follows: 46.2%, 47%, and 18.4% for aSTRs, X-STRs, and Y-STRs, respectively. The combined power of discrimination for aSTRs was virtually 100% based on LB and SB alleles, whereas the combined power of exclusion was 99.9999999977% and 99.9999999999%, respectively. The haplotypes based on X-STRs and Y-STRs show 100% of discriminatory capacity. Our results showed an increase in allele diversity and discriminatory capacity of this genomic system regarding forensic kits based on capillary electrophoresis. This study represents an effort to incorporate more genomic databases from Mexico and Latin America for the forensic application of MPS.

Improved second-degree kinship analysis using the FGID forensic four-in-one DNA typing kit

In general, using additional genetic markers can greatly improve the system power and accuracy of complex kinship identification. In this study, we employed the FGID Forensic Four-in-one DNA typing kit on the DNBSEQ-G99RS platform to gather sequence information for 66 autosomal STRs (A-STRs) and 132 autosomal SNPs (A-SNPs) of 24 pairs of second-degree relatives (13 grandparent-grandchild pairs and 11 uncle/aunt-nephew/niece pairs) from 9 families, along with 100 unrelated Han Chinese individuals. The likelihood ratio (LR) and identical-by-state (IBS) methods were applied to the kinship analysis, respectively. As anticipated, compared to the results using the ForenSeq™ DNA Signature Prep Kit, the LR values for second-degree relatives improved with the addition of more STR and SNP markers in this study, while LR values for unrelated individuals decreased. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) all exceeded 0.9600 at the cut-off values of t1 = -3 and t2 = 3, with 96.80% of simulated relationship pairs accurately classified as either second-degree relationships or unrelated individuals. Furthermore, IBS values based on sequence-based STRs were significantly lower than those based on length-based STRs. Overall, these results indicated that the FGID kit, which incorporates an increasing number of genetic markers, could effectively enhance the system performance in second-degree kinship analysis.

Systematically improving the efficiency of complex kinship identification through the addition of genetic markers and reference individuals

There is a growing demand for complex kinship identification due to the increasing complexity of social structures. However, the system efficiency of complex kinship identification systems, particularly for identifying second-degree and higher kinship relationships, needs improvement. This study aimed to further explore the selection of introduced relatives and genetic markers for second- and third-degree kinship identification by comparing the statistical parameters, such as likelihood ratio (LR), effectiveness, and error rate, of four different detection systems (19 STRs, 39 STRs, 55 STRs, and 55 STRs + 94 SNPs) in 109 common kinship identification scenarios. The study found that increasing the number of genetic markers or introducing more reference individuals generally enhanced the system efficiency for identifying complex genetic relationships by introducing various reference individuals into three-generation family lines to identify second- and third-degree kinships. The results were validated using true pedigree samples. Ranking the system efficiencies of kinship identification systems with different combinations of reference individuals and genetic markers provided insight into reference selection priorities and the optimal number of loci required. For second-degree relatives, adding one relative to the 39 STR marker set resulted in an effectiveness of over 90% with an error rate of less than 0.0005, while adding two known relatives achieved an effectiveness of over 95% with an error rate of less than 0.0001. Certain models could completely discriminate between related and unrelated individuals when using 55 STRs. For third-degree relatives, incorporating two known relatives in the 55 STR marker set resulted in an effectiveness of over 90% with an error rate of less than 0.0001 in most scenarios. In addition, when using both 55 STRs and 94 SNPs, a total of five models used for first-cousin relationships, that incorporated two reference individuals within second-degree relatives of both subjects, could completely distinguish between related and unrelated individuals. This study not only offers theoretical insights for complex kinship identification but also provides a valuable reference that can significantly improve the practice of identifying second- and third-degree kinships.

Pairwise kinship inference and pedigree reconstruction using 91 microhaplotypes

Kinship inference has been a major issue in forensic genetics, and it remains to be solved when there is no prior hypothesis and the relationships between multiple individuals are unknown. In this study, we genotyped 91 microhaplotypes from 46 pedigree samples using massive parallel sequencing and inferred their relatedness by calculating the likelihood ratio (LR). Based on simulated and real data, different treatments were applied in the presence and absence of relatedness assumptions. The pedigree of multiple individuals was reconstructed by calculating pedigree likelihoods based on real pedigree samples. The results showed that the 91 MHs could discriminate pairs of second-degree relatives from unrelated individuals. And more highly polymorphic loci were needed to discriminate the pairs of second-degree or more distant relative from other degrees of relationship, but correct classification could be obtained by expanding the suspected relationship searched to other relationships with lower LR values. Multiple individuals with unknown relationships can be successfully reconstructed if they are closely related. Our study provides a solution for kinship inference when there are no prior assumptions, and explores the possibility of pedigree reconstruction when the relationships of multiple individuals are unknown.

Applications and Performance of Precision ID GlobalFiler NGS STR, Identity, and Ancestry Panels in Forensic Genetics

Short Tandem Repeat (STR) testing via capillary electrophoresis is undoubtedly the most popular forensic genetic testing method. However, its low multiplexing capabilities and limited performance with challenging samples are among the factors pushing scientists towards new technologies. Next-generation sequencing (NGS) methods overcome some of these limitations while also enabling the testing of Single-Nucleotide Polymorphisms (SNPs). Nonetheless, these methods are still under optimization, and their adoption into practice is limited. Among the available kits, Thermo Fisher Scientific (Waltham, MA, USA) produces three Precision ID Panels: GlobalFiler NGS STR, Identity, and Ancestry. A clear review of these kits, providing information useful for the promotion of their use, is, however, lacking. To close the gap, a literature review was performed to investigate the popularity, applications, and performance of these kits. Following the PRISMA guidelines, 89 publications produced since 2015 were identified. China was the most active country in the field, and the Identity Panel was the most researched. All kits appeared robust and useful for low-quality and low-quantity samples, while performance with mixtures varied. The need for more population data was highlighted, as well as further research surrounding variables affecting the quality of the sequencing results.

Development and validation of YARN: A novel SE-400 MPS kit for East Asian paternal lineage analysis

Y-chromosomal short tandem repeat polymorphisms (Y-STRs) and Y-chromosomal single nucleotide polymorphisms (Y-SNPs) are valuable genetic markers used in paternal lineage identification and population genetics. Currently, there is a lack of an effective panel that integrates Y-STRs and Y-SNPs for studying paternal lineages, particularly in East Asian populations. Hence, we developed a novel Y-chromosomal targeted panel called YARN (Y-chromosome Ancestry and Region Network) based on multiplex PCR and a single-end 400 massive parallel sequencing (MPS) strategy, consisting of 44 patrilineage Y-STRs and 260 evolutionary Y-SNPs. A total of 386 reactions were validated for the effectiveness and applicability of YARN according to SWGDAM validation guidelines, including sensitivity (with a minimum input gDNA of 0.125 ng), mixture identification (ranging from 1:1-1:10), PCR inhibitor testing (using substances such as 50 μM hematin, 100 μM hemoglobin, 100 μM humic acid, and 2.5 mM indigo dye), species specificity (successfully distinguishing humans from other animals), repeatability study (achieved 100% accuracy), and concordance study (with 99.91% accuracy for 1121 Y-STR alleles). Furthermore, we conducted a pilot study using YARN in a cohort of 484 Han Chinese males from Huaiji County, Zhaoqing City, Guangdong, China (GDZQHJ cohort). In this cohort, we identified 52 different Y-haplogroups and 73 different surnames. We found weak to moderate correlations between the Y-haplogroups, Chinese surnames, and geographical locations of the GDZQHJ cohort (with λ values ranging from 0.050 to 0.340). However, when we combined two different categories into a new independent variable, we observed stronger correlations (with λ values ranging from 0.617 to 0.754). Overall, the YARN panel, which combines Y-STR and Y-SNP genetic markers, meets forensic DNA quality assurance guidelines and holds potential for East Asian geographical origin inference and paternal lineage analysis.

An overview of log likelihood ratio cost in forensic science - Where is it used and what values can we expect?

There is increasing support for reporting evidential strength as a likelihood ratio (LR) and increasing interest in (semi-)automated LR systems. The log-likelihood ratio cost (Cllr) is a popular metric for such systems, penalizing misleading LRs further from 1 more. Cllr = 0 indicates perfection while Cllr = 1 indicates an uninformative system. However, beyond this, what constitutes a "good" Cllr is unclear. Aiming to provide handles on when a Cllr is "good", we studied 136 publications on (semi-)automated LR systems. Results show Cllr use heavily depends on the field, e.g., being absent in DNA analysis. Despite more publications on automated LR systems over time, the proportion reporting Cllr remains stable. Noticeably, Cllr values lack clear patterns and depend on the area, analysis and dataset. As LR systems become more prevalent, comparing them becomes crucial. This is hampered by different studies using different datasets. We advocate using public benchmark datasets to advance the field.

Population genetic analyses of Eastern Chinese Han nationality using ForenSeq™ DNA Signature Prep Kit

Currently, the most commonly used method for human identification and kinship analysis in forensic genetics is the detection of length polymorphism in short tandem repeats (STRs) using polymerase chain reaction (PCR) and capillary electrophoresis (CE). However, numerous studies have shown that considerable sequence variations exist in the repeat and flanking regions of the STR loci, which cannot be identified by CE detection. Comparatively, massively parallel sequencing (MPS) technology can capture these sequence differences, thereby enhancing the identification capability of certain STRs. In this study, we used the ForenSeq™ DNA Signature Prep Kit to sequence 58 STRs and 94 individual identification SNPs (iiSNPs) in a sample of 220 unrelated individuals from the Eastern Chinese Han population. Our aim is to obtain MPS-based STR and SNP data, providing further evidence for the study of population genetics and forensic applications. The results showed that the MPS method, utilizing sequence information, identified a total of 486 alleles on autosomal STRs (A-STRs), 97 alleles on X-chromosome STRs (X-STRs), and 218 alleles on Y-chromosome STRs (Y-STRs). Compared with length polymorphism, we observed an increase of 260 alleles (157, 31, and 72 alleles on A-STRs, X-STRs, and Y-STRs, respectively) across 36 STRs. The most substantial increments were observed in DYF387S1 and DYS389II, with increases of 287.5% and 250%, respectively. The most increment in the number of alleles was found at DYF387S1 and DYS389II (287.5% and 250%, respectively). The length-based (LB) and sequence-based (SB) combined random match probability (RMP) of 27 A-STRs were 6.05E-31 and 1.53E-34, respectively. Furthermore, other forensic parameters such as total discrimination power (TDP), cumulative probability of exclusion of trios (CPEtrio), and duos (CPEduo) were significantly improved when using the SB data, and informative data were obtained for the 94 iiSNPs. Collectively, these findings highlight the advantages of MPS technology in forensic genetics, and the Eastern Chinese Han genetic data generated in this study could be used as a valuable reference for future research in this field.

Applications of 1993 single nucleotide polymorphism loci in forensic pairwise kinship identifications and inferences

Kinship testing plays critical roles in criminal investigations, missing person searches, civil disputes, as well as identifying disaster victims. The existing commonly used short tandem repeat (STR) loci have limited effectiveness in the identification of second-degree and more distant kinships. In this study, a total of 1993 SNP loci of 119 Chinese Han individuals from eight families were sequenced on the MGISEQ-2000RS platform. The system powers of this panel for kinship identifications were evaluated based on both the likelihood ratio (LR) and identical by state (IBS) methods. The results indicated that this panel could be used as an effective tool to kinship analyses including paternity testing, full sibling testing, second-degree kinships, and first cousin kinship analyses. Both the LR and IBS methods could be applied in distinguishing first-degree and second-degree pairs from unrelated individuals. Based on the 1993 SNP loci, LR>1000 and LR<0.001 are recommended as the thresholds of identifying first-cousin kinships from unrelated individuals, and the system power of such thresholds was 0.9470. Besides, kinship coefficients for different kinship pairs were estimated and then were used to predict the kinships for pairwise individuals. This panel performs an effective kinship inference power for the predictions of first-degree, second-degree kinships and unrelated individual pairs, while presenting low sensitivity in the prediction of first-cousin kinships.

High-resolution genotyping of 58 STRs in 635 Northern Han Chinese with MiSeq FGx ® Forensic Genomics System

Sequence polymorphisms were characterized at 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), and 24 Y chromosomal STRs (Y-STRs) in 635 Northern Han Chinese with the ForenSeq DNA Signature Prep Kit on the MiSeq FGx Forensic Genomics System. Since repeat region (RR) and flanking region (FR) variation can be detected by massively parallel sequencing (MPS), the increase in the number of unique alleles and the average of gene diversity was 78.18% and 3.51% between sequence and length, respectively. A total of 74 novel RR variants were identified at 33 STRs compared with STRSeq and previous studies, and 13 FR variants (rs1770275883, rs2053373277, rs2082557941, rs1925525766, rs1926380862, rs1569322793, rs2051848492, rs2051848696, rs2016239814, rs2053269960, rs2044518192, rs2044536444, and rs2089968964) were first submitted to dbSNP. Also, 99.94% of alleles were concordant between the ForenSeq DNA Signature Prep Kit and commercial CE kits. Discordance resulted from the low performance at D22S1045 and occasionally at DYS392, flanking region deletions at D7S820 and DXS10074, and the strict alignment algorithm at DXS7132. Null alleles at DYS505 and DYS448 and multialleles at DYS387S1a/b, DYS385a/b, DYS448, DYS505, DXS7132, and HPRTB were validated with other MPS and CE kits. Thus, a high-resolution sequence-based (SB) and length-based (LB) allele frequencies dataset from Northern Han Chinese has been established already. As expected, forensic parameters increased significantly on combined power of discrimination (PD) and combined power of exclusion (PE) at A-STRs, mildly on combined PD and combined mean exclusion chance (MEC) at X-STRs, and barely on discrimination capacity (DC) at Y-STRs. Additionally, MiSeq FGx quality metrics and MPS performance were evaluated in this study, which presented the high-quality of the dataset at 20 consecutive runs, such as ≥ 60% bases with a quality score of 20 or higher (%≥ Q20), > 60% of effective reads, > 2000 × of depth of coverage (DoC), ≥ 60% of allele coverage ratio (ACR) or heterozygote balance, ≥ 70% of inter-locus balance, and ≤ 0.4 of the absolute value of observed minus expected heterozygosity (|H_exp - H_obs|). In conclusion, MiSeq FGx can help us generate a high-resolution and high-quality dataset for human identification and population genetic studies.

Development and evaluation of a novel panel containing 188 microhaplotypes for 2nd-degree kinship testing in the Hebei Han population

Distant kinship identification is one of the critical problems in forensic genetics. As a new type of genetic marker defined and discussed in the last decade, the microhaplotype (MH) has drawn much attention in such identification owing to its specific advantages to traditional short tandem repeat (STR) or single nucleotide polymorphism (SNP) markers. In this study, MH markers were screened step by step from the 1000 Genomes Project database, and a novel multiplex panel containing 188 MHs (in which 181 are reported the first time, while 1 was reported in a previous study and the other 6 have partial overlaps with known markers) was constructed for application in 2nd- and 3rd-degree kinship identification. Along with the construction, a novel MH nomenclature was proposed, in which the SNP position information they contained was taken into account to eliminate the possibility that the same locus was named differently interlaboratory. After a series of evaluations, the panel was shown to have good sequencing accuracy, high sensitivity, species specificity, and resistance to anti-PCR inhibitors or degradation. Population data of the 188 MHs were calculated based on the genetic information of 221 unrelated Hebei Han individuals, and the effective number of alleles (Ae) ranged from 2.0925 to 8.2634 (with an average of 2.9267). For the whole system, the cumulative matching probability (CMP), the cumulative power of exclusion in paternity testing of duos (CPEduo) and that of trios (CPEtrio) reached 2.8422 × 10^-137, 1-1.3109 × 10^-21, and 1-2.8975 × 10^-39, respectively, indicating that this panel was satisfactory for individual identification and paternity testing. Then, the efficiency of the 188 MHs in 2nd- and 3rd-degree kinship testing was studied based on 30 extended families consisting of 179 2nd-degree and 121 3rd-degree relatives, as well as simulations of 0.5 million pairs of those two kinships. The results showed that clear opinions would be given in 83.36% of 2nd-degree identifications with a false rate less than 10^-5, when the confirming and excluding thresholds of cumulative likelihood ratio (CLR) were set as 10⁴ and 10^-4, respectively. This panel is still not sufficient to solve the problem of 3rd-degree kinship identification alone, and approximately 300 or 870 MH loci would be needed in 2nd- or 3rd-degree kinship identification, respectively, to achieve a system efficiency not less than 0.99 with such a threshold set; such necessary numbers would be used only as a reference in further research.

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019-2022

This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.

Classical and Non-Classical HLA Alleles as Supplementary Markers in Indirect Kinship Parentage Testing

A civil paternity investigation involving the parents of the deceased alleged father in order to establish a family relationship is presented. On the basis of the 23 autosomal short tandem repeat (aSTR) genotyping results, conclusive proof of paternity was not achieved, as the probability of paternity (W) was calculated to 0.99988. Additional genetic data of 17 classical and non-classical human leukocyte alleles (HLA) typing by next-generation sequencing (NGS) at a high-resolution level supported the hypothesis of grandpaternity over the hypothesis of coincidental paternal obligate allele (POA) sharing (total WaSTR&HLA = 0.9999998). The present study demonstrates the utility of 17 HLA genetic markers-typing in the solution of deficiency cases of disputed parentage.

Characterization of 58 STRs and 94 SNPs with the ForenSeq™ DNA signature prep kit in Mexican-Mestizos from the Monterrey city (Northeast, Mexico)

BACKGROUND

STR allele frequency databases from populations are necessary to take full advantage of the increased power of discrimination offered by massively parallel sequencing (MPS) platforms.

MATERIAL AND METHODS

For this reason, we sequenced 58 STRs (aSTRs, X-STRs, and Y-STRs) and 94 identity informative SNPs (iiSNPs) on 105 Mestizo (admixed) individuals from Monterrey City (Northeast, Mexico), with the Primer Set-A of the ForenSeq™ DNA Signature Prep Kit.

RESULTS

Most of the STR markers were in Hardy Weinberg equilibrium, with a few exceptions. We found 346 different length-based alleles for these 58 STRs; nevertheless, they became 528 alleles when the sequence was assessed. The combined power of discrimination from autosomal STRs (aSTRs) was -virtually- 100% in both length and sequence-based alleles, while the power of exclusion was 99.9999999976065 and 99.9999999999494%, respectively. Haplotypes based on X-STRs and Y-STRs showed 100% of discriminatory capacity.

CONCLUSIONS

These results provide -for the first time- forensic genomic population data from Mexico necessary for interpretation in kinship and criminal analyses.

Kinship assignment with the ForenSeq™ DNA Signature Prep Kit: Sources of error in simulated and real cases

Kinship recognition between anonymous DNA samples is becoming a relevant issue in forensics, more so with the increasing number of DNA profiles in databanks. Also, NGS-based genotyping is being increasingly used in routine personal identification, to simultaneously type large numbers of markers of different kind. In the present work, we explored computationally and experimentally the performance of the ForenSeq™ DNA Signature Prep Kit in identifying the true relationship between two anonymous samples, distinguishing it from other possible relationships. We analyzed with Familias R series of 10,000 pairs with 9 different simulated relationships, corresponding to different degrees of autosomal sharing. For each pair we obtained likelihood ratios for five kinship hypotheses vs. unrelatedness, and used their ranking to identify the preferred relationship. We also typed 21 subjects from two pedigrees, representing from parent-child to 4th cousins relationships. As expected, the power for identifying the true relationship decays in the order of autosomal sharing. Parent-child and full siblings can be robustly identified against other relationships. For half-siblings the chance of reaching a significant conclusion is already small. For more distant relationships the proportion of cases correctly and significantly identified is 10% or less. Bidirectional errors in kinship attribution include the suggestion of relatedness when this does not exist (10-50%), and the suggestion of independence in pairs of individuals more than 4 generations apart (25-60%). The real cases revealed a relevant effect of genotype miscalling at some loci, which could only be partly avoided by modulating the analysis parameters. In conclusion, with the exception of first degree relatives, the kit can be useful to inform additional investigations, but does not usually provide probatory results.

Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population

Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.

Pairwise kinship analysis of 17 pedigrees using massively parallel sequencing

With the tremendous development of massively parallel sequencing (MPS) in the last decade, it has been widely applied in basic science, clinical diagnostics, microbial genomics, as well as forensic genetics. MPS has lots of advantages that may facilitate the kinship analysis. In this study, 243 Chinese Han individuals from 17 families were involved and sequenced using the ForenSeq™ DNA Signature Prep Kit (Verogen, Inc., San Diego, USA), which provided the sequence information of 27 autosomal STRs (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative SNPs (iSNPs). A total of 275 pairs of parent-child, 123 pairs of full siblings, 1 pair of twins, 1 pair of half siblings, 158 pairs of grandparent-grandchild, 222 pairs of uncle/aunt-nephew/niece and 121 pairs of first cousins, as well as 701 pairs of unrelated individuals were identified. Using both likelihood ratio (LR) and identical by state (IBS) methods, the kinship analysis was conducted among these relative and non-relative pairs based on the A-STRs and SNPs. As a result, the ForenSeq Signature Kit could solve the analysis of parent-child (t1 = -4, t2 = 4), full siblings (t1 = -2, t2 = 2) and most second-degree kinships (t1 = -1, t2 = 1) using the LR method. When the IBS method was applied, 123 full sibling pairs had a higher average IBS value than other kinship groups in this study. And the IBS method could play a role in the testing of parent-child and full siblings.

Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing

Short tandem repeats (STRs) are the preferred genetic markers in forensic DNA analysis, routinely measured by capillary electrophoresis (CE) method based on the fragment length features. While, the massive parallel sequencing (MPS) technology could simultaneously target a large number of intriguing forensic STRs, bypassing the intrinsic limitations of amplicon size separation and accessible fluorophores in CE, which is efficient and promising for enabling the identification of forensic biological evidence. Here, we developed a novel MPS-based Forensic Analysis System Multiplecues SetB Kit of 133-plex forensic STR markers (52 STRs and 81 Y-STRs) and one Y-InDel (M175) based on multiplex PCR and single-end 400 bp sequencing strategy. This panel was subjected to developmental validation studies according to the SWGDAM Validation Guidelines. Approximately 2185 MPS-based reactions using 6 human DNA standards and 8 male donors were conducted for substrate studies (filter paper, gauze, cotton swab, four different types of FTA cards, peripheral venous blood, saliva, and exfoliated cells), sensitivity studies (from 2 ng down to 0.0625 ng), mixture studies (two-person DNA mixtures), PCR inhibitor studies (seven commonly encountered PCR inhibitors), species specificity studies (11 non-human species), and repeatability studies. Results of concordance studies (413 Han males and 6 human DNA standards) generated by STRait Razor and in-house Python scripts indicated 99.98% concordance rate in STR calling relative to CE for STRs between 41,900 genotypes at 100 STR markers. Moreover, the limitations of present studies, the nomenclature rules and forensic MPS applications were also described. In conclusion, the validation studies based on ~ 2200 MPS-based and ~ 2500 CE-based DNA profiles demonstrated that the novel MPS-based panel meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities, and the STR nomenclature rules should be further regulated to integrate the inconformity between MPS-based and CE-based methods.

BGISEQ-500RS sequencing of a 448-plex SNP panel for forensic individual identification and kinship analysis

Next generation sequencing (NGS)-based single nucleotide polymorphism (SNP) genotyping is widely used in the field of forensics. SNP genotyping data from several NGS platforms have been published, but forensic application trials of DNA nanoball sequencing platforms have been very limited. In this work, we developed a 448-plex SNP panel on the BGISEQ-500RS platform. The sequencing metrics of a total of 261 samples that were sequenced with this panel are reported in detail. The average sequencing depth was 8373 × and the average heterozygosity of the 448-plex assay was 0.85. Sensitivity analysis showed that 325 SNPs were successfully genotyped with as little as 50 pg of genomic DNA, with the mean quality score of the sequencing data above Q30. Forensic parameters were calculated based on the data of 142 unrelated Chinese Han individuals and the combined matching probability was as low as 5.21 × 10^-101. Kinship analyses based on experiments and computer simulations showed that the 448-panel was as effective as the ForenSeq™ DNA Signature Prep Kit for second-degree kinship identification, and when the two panels were merged, the related pairs were almost completely distinguished from unrelated pairs. The 448-plex SNP panel on the BGISEQ-500RS platform provides a powerful tool for forensic individual identification and kinship analysis.

The forensic landscape and the population genetic analyses of Hainan Li based on massively parallel sequencing DNA profiling

Due to the formation of the Qiongzhou Strait by climate change and marine transition, Hainan island was isolated from the mainland southern China during the Last Glacial Maximum. Hainan island, located at the southernmost part of China and separated from the Leizhou Peninsula by the Qiongzhou Strait, laid on one of the modern human northward migration routes from Southeast Asia to East Asia. The Hlai language-speaking Li minority, the second largest population after Han Chinese in Hainan island, is the direct descendants of the initial migrants in Hainan island and has unique ethnic properties and derived characteristics; however, the forensic-associated studies on Hainan Li population are still insufficient. Hence, 136 Hainan Li individuals were genotyped in this study using the MPS-based ForenSeq™ DNA Signature Prep Kit (DNA Primer Set A, DPMA) to characterize the forensic genetic polymorphism landscape, and DNA profiles were obtained from 152 different molecular genetic markers (27 autosomal STRs, 24 Y-STRs, 7 X-STRs, and 94 iiSNPs). A total of 419 distinct length variants and 586 repeat sequence sub-variants, with 31 novel alleles (at 17 loci), were identified across the 58 STR loci from the DNA profiles of Hainan Li population. We evaluated the forensic characteristics and efficiencies of DPMA, demonstrating that the STRs and iiSNPs in DPMA were highly polymorphic in Hainan Li population and could be employed in forensic applications. In addition, we set up three datasets, which included the genetic data of (i) iiSNPs (27 populations, 2640 individuals), (ii) Y-STRs (42 populations, 8281 individuals), and (iii) Y haplogroups (123 populations, 4837 individuals) along with the population ancestries and language families, to perform population genetic analyses separately from different perspectives. In conclusion, the phylogenetic analyses indicated that Hainan Li, with a southern East Asia origin and Tai-Kadai language-speaking language, is an isolated population relatively. But the genetic pool of Hainan Li influenced by the limited gene flows from other Tai-Kadai populations and Hainan populations. Furthermore, the establishment of isolated population models will be beneficial to clarify the exquisite population structures and develop specific genetic markers for subpopulations in forensic genetic fields.

Platinum-Quality Mitogenome Haplotypes from United States Populations

A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 × for low-frequency (5%) variant detection. Point heteroplasmies below 10% frequency were confirmed through replicate amplification, and length heteroplasmy was quantitatively assessed using a custom read count analysis tool. Data analysis involved a redundant, dual-analyst review to minimize errors in haplotype reporting with additional QC checks performed by EMPOP. Applying these methods, eight sample sets were processed from five U.S. metapopulations (African American, Caucasian, Hispanic, Asian American, and Native American) corresponding to self-reported identity at the time of sample collection. Population analyses (e.g., haplotype frequencies, random match probabilities, and genetic distance estimates) were performed to evaluate the eight datasets, with over 95% of haplotypes unique per dataset. The platinum-quality mitogenome haplotypes presented in this study will enable forensic statistical calculations and thereby support the usage of mitogenome sequencing in forensic laboratories.