Development a multiplex panel of AISNPs, multi-allelic InDels, microhaplotypes and Y-SNP/InDel loci for multiple forensic purposes via the NGS

Second- and third-degree kinship analysis by NGS-based SNP genotyping and evaluation of 2045-SNP performance on limited or degraded DNA

We developed a novel next-generation sequencing-based single-nucleotide polymorphism (SNP) genotyping method for second- and third-degree kinship analysis, and designed 1144- and 2045-SNP panels using one (Set A) and two sets (Sets A and B) of primers. These SNP loci were analyzed in 120 Japanese individuals, and likelihood ratios (LRs) for kinship discrimination were calculated to evaluate the effect of number of SNP loci in simulated analysis. Likelihood evaluation was performed using DNA profiles from two individuals, namely, the unknown and one reference relative. Genotyping of the 1144 and 2045 SNPs was informative to discriminate aunt-nephew/niece as second-degree relatives and unrelated pairs. In third-degree relationship analysis, distributions of log10LRs between the unknown and a first cousin (FC) were not separated from those of unrelated individuals even in 2045-SNP genotyping. To perform enhanced discrimination of third-degree relationships, we also evaluated the effectiveness of DNA profiles from three individuals, namely, the unknown and two first cousins (2FC). A likelihood evaluation from the 2045 SNPs using 2FC was more useful than the use of FC. Our method was applied to 12 kinship cases for second- and third-degree relationship analysis, and LRs from 1144- and 2045-SNP genotypes were markedly higher than those from conventional short tandem repeat profiles. Moreover, we evaluated the performance of the 2045 SNPs using limited or degraded DNA, compared with that with a larger amount of DNA. Using 0.1 ng of non-degraded DNA, the average concordance was higher than 97 %. In analysis with heavily degraded DNA (degradation index=32.2), we also detected high concordance (85.5 %) from 2045-SNP genotypes, compared with the lower rate (52.4 %) from 21 short tandem repeat profiles. Our method should be highly sensitive with discriminatory DNA profiles for analyzing second- and third-degree relationships.

Developmental and validation of a novel small and high-efficient panel of microhaplotypes for forensic genetics by the next generation sequencing

BACKGROUND

In the domain of forensic science, the application of kinship identification and mixture deconvolution techniques are of critical importance, providing robust scientific evidence for the resolution of complex cases. Microhaplotypes, as the emerging class of genetic markers, have been widely studied in forensics due to their high polymorphisms and excellent stability.

RESULTS AND DISCUSSION

In this research, a novel and high-efficient panel integrating 33 microhaplotype loci along with a sex-determining locus was developed by the next generation sequencing technology. In addition, we also assessed its forensic utility and delved into its capacity for kinship analysis and mixture deconvolution. The average effective number of alleles (Ae) of the 33 microhaplotype loci in the Guizhou Han population was 6.06, and the Ae values of 30 loci were greater than 5. The cumulative power of discrimination and cumulative power of exclusion values of the novel panel in the Guizhou Han population were 1-5.6 × 10- 43 and 1-1.6 × 10- 15, respectively. In the simulated kinship analysis, the panel could effectively distinguish between parent-child, full-sibling, half-sibling, grandfather-grandson, aunt-nephew and unrelated individuals, but uncertainty rates clearly increased when distinguishing between first cousins and unrelated individuals. For the mixtures, the novel panel had demonstrated excellent performance in estimating the number of contributors of mixtures with 1 to 5 contributors in combination with the machine learning methods.

CONCLUSIONS

In summary, we have developed a small and high-efficient panel for forensic genetics, which could provide novel insights into forensic complex kinships testing and mixture deconvolution.

Rapid genotyping of 32 insertion/deletion panel for human identification using fluorogenic probes-based multiplex real-time PCR

BACKGROUND

Insertion and deletion polymorphisms (InDels) have considerable potential in the field of forensic genetics because of their low mutation rate and small amplicons. At present, InDel polymorphisms detection based on the technique of capillary electrophoresis is the main technique used in forensic DNA laboratory. However, this method is complicated and time-consuming, and is not suitable for rapid on-site paternity and personal identification. Next-generation sequencing analysis of InDels polymorphisms requires expensive instruments, large upfront reagent and supply costs, computational requirements and complex bioinformatics, increased the time to obtain results. Thus, there is an urgent need to establish a method to provide reliable, rapid, sensitive and economical genotyping for InDels.

METHOD

A rapid InDels (32 InDels) panel was established using fluorogenic probes-based multiplex real-time PCR with microfluidic test cartridge and portable real-time PCR instrument. Then, we performed several validation studies including concordance, accuracy, sensitivity, stability, species specificity.

RESULTS

It showed that the complete genotypes could be obtained from ≥100 pg of input DNA and from a series of challenging samples with high accuracy and specificity within 90 min.

CONCLUSION

This method provides a rapid and cost-effective solution for InDels genotyping and personal identification in portable format.

State of the Art for Microhaplotypes

In recent years, the number of publications on microhaplotypes has averaged more than a dozen papers annually. Many have contributed to a significant increase in the number of highly polymorphic microhaplotype loci. This increase allows microhaplotypes to be very informative in four main areas of forensic uses of DNA: individualization, ancestry inference, kinship analysis, and mixture deconvolution. The random match Probability (RMP) can be as small as 10−100 for a large panel of microhaplotypes. It is possible to measure the heterozygosity of an MH as the effective number of alleles (Ae). Ae > 7.5 exists for African populations and >4.5 exists for Native American populations for a smaller panel of two dozen selected microhaplotypes. Using STRUCTURE, at least 10 different ancestral clusters can be defined by microhaplotypes. The Ae for a locus is also identical to the Paternity Index (PI), the measure of how informative a locus will be in parentage testing. High Ae loci can also be useful in missing persons cases. Finally, high Ae microhaplotypes allow the near certainty of seeing multiple additional alleles in a mixture of two or more individuals in a DNA sample. In summary, a panel of higher Ae microhaplotypes can outperform the standard CODIS markers.

Forensic Features and Genetic Structure Analyses of the Beijing Han Nationality Disclosed by a Self-Developed Panel Containing a Series of Ancestry Informative Deletion/Insertion Polymorphism Loci

The utilization of the ancestry informative markers to disclose the ancestral composition of a certain population and explore the genetic affinities between diverse populations is beneficial to inferring the biogeographic ancestry of unknown individuals and assisting in case detection, as well as avoiding the impacts of population stratification during genome-wide association analysis studies. In the present study, we applied an in-house ancestry informative deletion/insertion polymorphic multiplex amplification system to investigate the ancestral compositions of the Beijing Han population and analyze the genetic relationships between the Beijing Han population and 31 global reference populations. The results demonstrated that 32 loci of this self-developed panel containing 39 loci significantly contributed to the inference of genetic information for the Beijing Han population. The results of multiple population genetics statistical analyses indicated that the ancestral component and genetic architecture of the Beijing Han population were analogous to the reference East Asian populations, and that the Beijing Han population was genetically close to the reference East Asian populations.

Multivariate statistical approach and machine learning for the evaluation of biogeographical ancestry inference in the forensic field

The biogeographical ancestry (BGA) of a trace or a person/skeleton refers to the component of ethnicity, constituted of biological and cultural elements, that is biologically determined. Nowadays, many individuals are interested in exploring their genealogy, and the capability to distinguish biogeographic information about population groups and subgroups via DNA analysis plays an essential role in several fields such as in forensics. In fact, for investigative and intelligence purposes, it is beneficial to inference the biogeographical origins of perpetrators of crimes or victims of unsolved cold cases when no reference profile from perpetrators or database hits for comparative purposes are available. Current approaches for biogeographical ancestry estimation using SNPs data are usually based on PCA and Structure software. The present study provides an alternative method that involves multivariate data analysis and machine learning strategies to evaluate BGA discriminating power of unknown samples using different commercial panels. Starting from 1000 Genomes project, Simons Genome Diversity Project and Human Genome Diversity Project datasets involving African, American, Asian, European and Oceania individuals, and moving towards further and more geographically restricted populations, powerful multivariate techniques such as Partial Least Squares-Discriminant Analysis (PLS-DA) and machine learning techniques such as XGBoost were employed, and their discriminating power was compared. PLS-DA method provided more robust classifications than XGBoost method, showing that the adopted approach might be an interesting tool for forensic experts to infer BGA information from the DNA profile of unknown individuals, but also highlighting that the commercial forensic panels could be inadequate to discriminate populations at intra-continental level.