Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device.

The high variability characteristic of short tandem repeat (STR) markers is harnessed for human identification in forensic genetic analyses. Despite the power and reliability of current typing techniques, sequence-level information both within and around STRs are masked in the length-based profiles generated. Forensic STR typing using next generation sequencing (NGS) has therefore gained attention as an alternative to traditional capillary electrophoresis (CE) approaches.

mixIndependR: a R package for statistical independence testing of loci in database of multi-locus genotypes.

Background: Multi-locus genotype data are widely used in population genetics and disease studies. In evaluating the utility of multi-locus data, the independence of markers is commonly considered in many genomic assessments. Generally, pairwise non-random associations are tested by linkage disequilibrium; however, the dependence of one panel might be triplet, quartet, or other.

Differentiation of Hispanic biogeographic ancestry with 80 ancestry informative markers.

Ancestry informative single nucleotide polymorphisms (SNPs) can identify biogeographic ancestry (BGA); however, population substructure and relatively recent admixture can make differentiation difficult in heterogeneous Hispanic populations. Utilizing unrelated individuals from the Genomic Origins and Admixture in Latinos dataset (GOAL, n = 160), we designed an 80 SNP panel (Setser80) that accurately depicts BGA through STRUCTURE and PCA. We compared our Setser80 to the Seldin and Kidd panels via resampling simulations, which models data based on allele frequencies.

Potential applications of nanopore sequencing for forensic analysis.

Advancements in DNA sequencing technologies are occurring at a rapid rate. Various platforms have proven useful in all aspects of health and science research, from molecular diagnostics in cancer research to spore identification in bioterrorism. In the field of forensics, one particular single-molecule sequencing platform shows promise for becoming a viable solution for small to midsize forensic laboratories.

Approaches to Whole Mitochondrial Genome Sequencing on the Oxford Nanopore MinION.

Traditional approaches for interrogating the mitochondrial genome often involve laborious extraction and enrichment protocols followed by Sanger sequencing. Although preparation techniques are still demanding, the advent of next-generation or massively parallel sequencing has made it possible to routinely obtain nucleotide-level data with relative ease. These short-read sequencing platforms offer deep coverage with unparalleled read accuracy in high-complexity genomic regions but encounter numerous difficulties in the low-complexity homopolymeric sequences characteristic of the mitochondrial genome.

Admixture Effects on Coevolved Metabolic Systems.

Oxidative phosphorylation (OXPHOS) is the primary energy generating system in eukaryotic organisms. The complexes within the OXPHOS pathway are of mixed genomic origin. Although most subunit-coding genes are located within the nuclear genome, several genes are coded for in the mitochondrial genome.

Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing.

Mitochondrial DNA sequence data are often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require several rounds of PCR enrichment during Sanger or MPS protocols followed by fairly tedious assembly and analysis. Here we describe an efficient approach to sequencing directly from genomic DNA samples without prior enrichment or extensive library preparation steps.

PTPIP51 levels in glioblastoma cells depend on inhibition of the EGF-receptor.

Protein tyrosine phosphatase interacting protein 51 (PTPIP51) is upregulated in glioblastoma multiforme (GBM) and expression levels correlate with the grade of malignancy in gliomas. A similar correlation was reported for its interacting partner 14-3-3β, which has been shown to facilitate the interaction of PTPIP51 with cRAF (Raf1). Since the interaction of these signalling partners stimulates growth factor signalling downstream of the epidermal growth factor receptor (EGFR), a major drug target in GBM, we here investigated the impact of EGFR inhibition by small molecule inhibitors or monoclonal antibody on PTPIP51.

Cell Persistence of Allogeneic Keratinocytes and Fibroblasts Applied in a Fibrin Matrix to Acute, Full Thickness Wounds.

HP802-247 is a living cell suspension of cultured allogeneic growth-arrested human male keratinocytes and fibroblasts (1:9 ratio), intended for spray application to chronic wounds. In this study, a small wound was created on the arms of 28 healthy female volunteers (3-mm punch), followed by a single application of HP802-247. At each subsequent week for 8 weeks, a punch excision of the wounds was performed on a cohort of three subjects.

Deep-Sequencing Technologies and Potential Applications in Forensic DNA Testing.

Development of second- and third-generation DNA sequencing technologies have enabled an increasing number of applications in different areas such as molecular diagnostics, gene therapy, monitoring food and pharmaceutical products, biosecurity, and forensics. These technologies are based on different biochemical principles such as monitoring released pyrophosphate upon incorporation of a base (pyrosequencing), fluorescence detection subsequent to reversible incorporation of a fluorescently labeled terminator base, ligation based approach wherein fluorescence of cleaved nucleotide after ligation is measured, measuring the proton released after incorporation of a base (semiconductor-based sequencing), monitoring incorporation of a nucleotide by measuring the fluorescence of the fluorophore attached to the phosphate chain of the nucleotide, and by detecting the altered charge in a protein nanopore due to released nucleotide by exonuclease cleavage of a DNA strand. Analysis of multiple DNA fragments in parallel increases the depth of coverage while decreasing labor, cost, and time, highlighting some major advantages of deep-sequencing technologies.

Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry.

Short tandem repeats (STRs) are the primary genetic markers used for the analysis of biological samples in forensic and human identity testing. The discrimination power of a combination of STRs is sufficient in many human identity testing comparisons unless the evidence is substantially compromised and/or there are insufficient relatives or a potential mutation may have arisen in kinship analyses. An automated STR assay system that is based on electrospray ionization mass spectrometry (ESI-MS) has been developed that can increase the discrimination power of some of the CODIS core STR loci and thus provide more information in typical and challenged samples and cases.

Hidden Variation in Microsatellite Loci: Utility and Implications for Forensic DNA Analysis.

Short tandem repeat (STR) analysis has been the standard in forensic DNA examinations for almost 15 years. The purpose of this article is to provide some perspective on the biological nature of STR alleles themselves, examine underlying distributions of alleles in the STR loci that are routinely used, and to discuss features of these alleles that are not observable with the currently employed methods. Many of the internationally standardized STR loci contain variations of their interrupted repeat structures, either due to the compound or complex nature of the locus or due to nucleotide variations within the simple repeat motif, which inevitably leads them to become more stratified at the population level.

Genetic composition of six miniSTR in a Brazilian Mulatto sample population.

The present study characterizes the genetic variability of Mulatto population based on the polymorphism of six miniSTR autosomal loci, known as Non Codis 01 and 02 (NC01 and NC02) and evaluate their applicability in forensic genetics. A sample of 102 unrelated Brazilian mulattoes were genotyped for miniSTR loci D1S1677, D2S441, D4S2364 (miniplex NC02) and 45 individuals for D10S1248, D14S1434, D22S1045 (miniplex NC01). No significant deviations from Hardy-Weinberg equilibrium expectations were detected.

US forensic Y-chromosome short tandem repeats database.

A forensic Y-STR database generated in the US was compiled with profiles containing a portion or complete typing of 16 STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4. There were 17,447 samples in the version of database in which 77% and 20% were collected in North America and Asia, respectively. The database was separated into six general populations, African American, Asian, Caucasian, Hispanic, Indian, and Native American.

Haplotype block: a new type of forensic DNA markers.

Forensic DNA analysis is currently performed using highly discriminating short tandem repeat (STR) markers. SNPs are being investigated as adjunct tools for human identity testing because of their abundance in the human genome, utility for genotyping degraded DNA samples, and amenability to automation. While SNPs can provide an alternative approach, on a per locus basis they have a lower power of discrimination (PD) than STRs.

Texas population substructure and its impact on estimating the rarity of Y STR haplotypes from DNA evidence*.

Three sampled populations of unrelated males--African American, Caucasian, and Hispanic, all from Texas-were typed for 16 Y short tandem repeat (STR) markers using the AmpFlSTR Yfiler kit. These samples also were typed previously for the 13 core CODIS autosomal STR loci. Most of the 16 marker haplotypes (2478 out of 2551 distinct haplotypes) were observed only once in the data sets.

Mutation rates at Y chromosome short tandem repeats in Texas populations.

Father-son pairs from three populations (African American, Caucasian, and Hispanic) of Texas were typed for the 17 Y STR markers DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS456, DYS458, DYS635, DYS448, and Y GATA H4 using the AmpFlSTR YfilerTM kit. With 49,578 allele transfers, 102 mutations were detected. One three-step and four two-step mutations were found, and all others (95.

Null allele sequence structure at the DYS448 locus and implications for profile interpretation.

Null alleles can occur with any PCR-based STR typing system. They generally are due to deletions within the target region or primer binding sites or by primer binding site mutations that destabilize hybridization of at least one of the primers flanking the target region. Although not common, null types were detected at the DYS448 locus in seven out of 1,005 unrelated males in the Hispanic population.

Single Nucleotide Polymorphisms and Microarray Technology in Forensic Genetics - Development and Application to Mitochondrial DNA.

Variations in the genome, due to base substitutions, insertions, or deletions at single positions, are known as single nucleotide polymorphisms (SNPs). Approximately 85% of human variation is based on such polymorphisms. Therefore, there is an abundance of human SNPs that are available for forensic identity testing purposes.

New host and locality records of coccidia (Apicomplexa: Eimeriidae) from rodents in the southwestern and western United States.

One hundred forty-seven murid and heteromyid rodents were collected from various sites in the southwestern and western United States (Arizona, Colorado, New Mexico, Texas, and Utah) and Baja California Norte, Mexico, and their feces were examined for coccidial parasites. Of these, 53 (36%) were infected with at least 1 coccidian; 45 of 53 (85%) of the infected rodents harbored only 1 species of coccidian. Infected rodents included: 10 of 22 (45%) Neotoma albigula, 3 of 11 (27%) Neotoma floridana, 2 of 14 (14%) Neotoma lepida, 15 of 29 (52%) Neotoma micropus, 5 of 8 (63%) Peromyscus crinitis, 6 of 6 (100%) Peromyscus difficilis, 1 of 2 (50%) Peromyscus eremicus, 9 of 34 (26%) Sigmodon hispidis, and 2 of 3 (67%) Sigmodon ochrognathus; 4 Neotoma cinerea, 3 Neotoma devia, 3 Neotoma mexicana, 1 Peromyscus maniculatus, 1 Onychomys leucogaster, 1 Onychomys torridus, 3 Chaetodipus fallax, and 2 Chaetodipus penicillatus were negative.

A rapid procedure for isolating mitochondrial DNA.

A technique for the rapid isolation of mitochondrial DNA (mtDNA) from animal tissues is described that eliminates the time-consuming separation of nuclear and mtDNAs using cesium chloride gradient ultracentrifugation. The procedure utilizes digestion of the nuclear DNA with DNase, after which lysis of mitochondria and subsequent extraction of proteins results in relatively pure mtDNA. Up to 5 micrograms of mtDNA per gram of liver tissue resulted, a suitable yield for five digests with restriction enzymes and staining with ethidium bromide.