Analytical validation of the IBD segment-based tool KinSNP for human identification applications.

KinSNP v1.0, a software tool for human identification, has been widely used to measure IBD segment sharing between individuals using dense SNP data. Herein, the tool was validated using simulated pedigree data (up to 9 degree relationships) from five diverse populations from the 1000 Genomes Project.

A complete pipeline enables haplotyping and phasing macrohaplotype in long sequencing reads for polyploidy samples and a multi-source DNA mixture.

Macrohaplotype combines multiple types of phased DNA variants, increasing forensic discrimination power. High-quality long-sequencing reads, for example, PacBio HiFi reads, provide data to detect macrohaplotypes in multiploidy and DNA mixtures. However, the bioinformatics tools for detecting macrohaplotypes are lacking.

Determining lineages between individuals with high-density mitochondrial and Y-chromosomal single-nucleotide polymorphisms.

Genetic genealogy has been more frequently used in forensic investigations in identifying criminals. However, the current genetic genealogy applications usually do not consider lineage markers (including both Y and mitochondrial deoxyribonucleic acid (DNA)), which is probably because not all distant relatives share the same lineage markers. In addition, there is no study to show how to use lineage markers and what methods or thresholds should be applied in genetic genealogy.

TRcaller: a novel tool for precise and ultrafast tandem repeat variant genotyping in massively parallel sequencing reads.

Calling tandem repeat (TR) variants from DNA sequences is of both theoretical and practical significance. Some bioinformatics tools have been developed for detecting or genotyping TRs. However, little study has been done to genotyping TR alleles from long-read sequencing data, and the accuracy of genotyping TR alleles from next-generation sequencing data still needs to be improved.

MPKin-YSTR: Interpretation of Y chromosome STR haplotypes for missing persons cases.

Y chromosome Short Tandem Repeat (STR) haplotypes have been used in assisting forensic investigations primarily for identification and male lineage determination. The current SWGDAM interpretation guidelines for Y-STR typing provide helpful guidance on those purposes but do not address the issue of kinship analysis with Y-STR haplotypes. Because of the high mutation rate of Y-STRs, there are complex missing person cases in which inconsistent Y-STR haplotypes between true paternal lineage relatives will arise and cases with two or more male references in the same lineage and yet differ in their haplotypes.

USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences.

Background: Tandem repeats (TR), highly variable genomic variants, are widely used in individual identification, disease diagnostics, and evolutionary studies. The recent advances in sequencing technologies and bioinformatic tools facilitate calling TR haplotypes genome widely. Both length-based and sequence-based TR alleles are used in different applications.

A machine learning approach for missing persons cases with high genotyping errors.

Estimating the relationships between individuals is one of the fundamental challenges in many fields. In particular, relationship.ip estimation could provide valuable information for missing persons cases.

Optimized variant calling for estimating kinship.

One of the fundamental goals of forensic genetics is sample attribution, i.e., whether an item of evidence can be associated with some person or persons.

A prospective cost-benefit analysis for nylon 4N6FLOQSwabs®: example of the process and potential benefits.

Laboratories and their criminal justice systems are confronted with challenges for implementing new technologies, practices, and policies even when there appears to be demonstrative benefits to operational performance. Impacting decisions are the often higher costs associated with, for example, new technologies, limited current budgets, and making hard decisions on what to sacrifice to take on the seemingly better approach. A prospective cost-benefit analysis (CBA) could help an agency better formulate its strategies and plans and more importantly delineate how a relatively small increase to take on, for example, a new technology can have large impact on the system (e.

Evaluating the Impact of Dropout and Genotyping Error on SNP-Based Kinship Analysis With Forensic Samples.

Technological advances in sequencing and single nucleotide polymorphism (SNP) genotyping microarray technology have facilitated advances in forensic analysis beyond short tandem repeat (STR) profiling, enabling the identification of unknown DNA samples and distant relationships. Forensic genetic genealogy (FGG) has facilitated the identification of distant relatives of both unidentified remains and unknown donors of crime scene DNA, invigorating the use of biological samples to resolve open cases. Forensic samples are often degraded or contain only trace amounts of DNA.

vcferr: Development, validation, and application of a single nucleotide polymorphism genotyping error simulation framework.

Genotyping error can impact downstream single nucleotide polymorphism (SNP)-based analyses. Simulating various modes and levels of error can help investigators better understand potential biases caused by miscalled genotypes. We have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missingness in variant call format (VCF) files.

Genetic study with 21 autosomal STRs in five Peruvian macro regions for human identification purposes.

In this population study 1541 samples in total were collected and analyzed. The samples were collected from five jurisdictions: North macro region (n = 272), Central macro region (n = 404), South macro region (n = 272), East macro region (n = 197), and the Lima macro region (n = 396). The samples were analyzed using the Investigator 24 plex GO and Investigator 24 plex QS kits which enable typing of 21 autosomal STR loci and an amelogenin marker for sex determination.

skater: an R package for SNP-based kinship analysis, testing, and evaluation.

: SNP-based kinship analysis with genome-wide relationship estimation and IBD segment analysis methods produces results that often require further downstream process- ing and manipulation. A dedicated software package that consistently and intuitively imple- ments this analysis functionality is needed. : Here we present the skater R package for SNP-based kinship analysis, testing, and evaluation with R.

Precision DNA Mixture Interpretation with Single-Cell Profiling.

Wet-lab based studies have exploited emerging single-cell technologies to address the challenges of interpreting forensic mixture evidence. However, little effort has been dedicated to developing a systematic approach to interpreting the single-cell profiles derived from the mixtures. This study is the first attempt to develop a comprehensive interpretation workflow in which single-cell profiles from mixtures are interpreted individually and holistically.

Population data for 21 STRs for the Salvadoran population using GlobalFiler Express and GlobalFiler STR Amplification Kits.

With the advent of expanded STR (short tandem repeats) typing kits, it was necessary to determine allele frequencies and other appropriate population data parameters for El Salvador. Samples were collected from the central, east, and west regions of the country and typed for 21 forensically relevant STR loci. The data indicate that all loci are highly polymorphic, the three regions are genetically similar, and the population data are similar to those of US Hispanics.

Enhanced mixture interpretation with macrohaplotypes based on long-read DNA sequencing.

Deconvoluting mixture samples is one of the most challenging problems confronting DNA forensic laboratories. Efforts have been made to provide solutions regarding mixture interpretation. The probabilistic interpretation of Short Tandem Repeat (STR) profiles has increased the number of complex mixtures that can be analyzed.

Linkage and linkage disequilibrium among the markers in the forensic MPS panels.

For the past two to three decades, forensic DNA evidence has been analyzed with a limited number of short tandem repeats (STRs), and these STRs are usually assumed to be independent for statistical calculations. With the development and implementation of the MPS technologies, more autosomal markers, both single nucleotide polymorphisms (SNPs) and STRs, can be analyzed. A number of these markers are physically very close to each other, and it may not be appropriate to assume all these markers are genetically unlinked or in linkage equilibrium.

Developmental validation of VeriFiler™ Plus PCR Amplification Kit: A 6-dye multiplex assay designed for casework samples.

The VeriFiler™ Plus PCR Amplification Kit is a 6-dye multiplex assay that simultaneously amplifies a set of 23 autosomal markers (D3S1358, vWA, D16S539, CSF1PO, D6S1043, D8S1179, D21S11, D18S51, D5S818, D2S441, D19S433, FGA, D10S1248, D22S1045, D1S1656, D13S317, D7S820, Penta E, Penta D, TH01, D12S391, D2S1338, and TPOX), a quality indicator system, and two sex-identification markers. Combined, the markers satisfy the requirements of the Chinese National autosomal DNA database as well as expanded CODIS (Combined DNA Index System). The VeriFiler Plus kit was developed with an improved Master Mix which incorporates the brighter TED™ dye, and accommodates a higher sample loading volume thus allowing for increased sensitivity and enabling maximum information recovery from challenging casework samples including touch, degraded, and inhibited samples.

Forensic investigation approaches of searching relatives in DNA databases.

There are several indirect database searching approaches to identify the potential source of a forensic biological sample. These DNA-based approaches are familial searching, Y-STR database searching, and investigative genetic genealogy (IGG). The first two strategies use forensic DNA databases managed by the government, and the latter uses databases managed by private citizens or companies.

Ancestry inference and admixture component estimations of Chinese Kazak group based on 165 AIM-SNPs via NGS platform.

Predicting the biogeographical ancestries of populations and unknown individuals based on ancestry-informative markers (AIMs) has been widely applied in providing DNA clues to criminal investigations, correcting the factor of population stratification in genome-wide association studies (GWAS), and working as the basis of predicting the externally visible characteristics (EVCs) of individuals. The present study chose Chinese Xinjiang Kazak (XJK) group as research object using a 165 AIM-SNPs panel via next generation sequencing (NGS) technology to reveal its ancestral information and genetic background by referencing the populations' data from 1000 Genomes Phase 3. After the Bonferroni correction, there were no significant deviations at the 165 AIM-SNP loci except two loci with homozygote in the studied XJK group.

Developmental validation of the Huaxia™ Platinum PCR amplification kit: A 6-dye multiplex direct amplification assay designed for Chinese reference samples.

The Huaxia™ Platinum Kit for short tandem repeat (STR) amplification was designed to meet the needs of the rapidly growing Chinese forensic database. This PCR multiplex allows simultaneous amplification of the following autosomal loci: D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, Penta E, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, D6S1043, D10S1248, D1S1656, D12S391, D2S1338, Penta D and the gender-identification markers Yindel, and AMEL. The Huaxia™ Platinum Kit enables direct amplification from blood and buccal samples stored on treated and untreated paper, and features an optimized PCR protocol that yields time to results in less than 45 min.

SNP typing using the HID-Ion AmpliSeq™ Identity Panel in a southern Chinese population.

In the present study, 90 autosomal single nucleotide polymorphisms (SNPs) and 34 Y chromosomal SNPs were sequenced simultaneously using HID-Ion AmpliSeq™ Identity Panel on the Ion PGM™ platform for 125 samples in a southern Chinese population. Raw data were analyzed and forensic parameters were calculated. Haplogrouping concordance was also assessed using alternative methods based on Y-SNP haplotypes and Y-STR haplotypes.

Comparison of preprocessing methods and storage times for touch DNA samples.

Aim: To select appropriate preprocessing methods for different substrates by comparing the effects of four different preprocessing methods on touch DNA samples and to determine the effect of various storage times on the results of touch DNA sample analysis.

Method: Hand touch DNA samples were used to investigate the detection and inspection results of DNA on different substrates. Four preprocessing methods, including the direct cutting method, stubbing procedure, double swab technique, and vacuum cleaner method, were used in this study.

Paternity calculations in a di-spermy case.

In a criminal paternity case, which involved analysis of the product of conception, a rare circumstance was observed. The product of conception was triploidy, apparently due to an egg fertilized by two sperm. Since there is little guidance on how to calculate the probability of the DNA evidence given some basic hypotheses, the formulae were derived and are presented herein.