Assessment of impact of DNA extraction methods on analysis of human remain samples on massively parallel sequencing success

Skeletal remains recovered from missing persons' cases are often exposed to harsh environmental conditions resulting in the DNA being damaged, degraded, and/or the samples containing PCR inhibitors. In this study, the efficacy of common extraction methods was evaluated to remove high levels of PCR inhibitors commonly encountered with human remains, and their downstream compatibility with the two leading sequencing chemistries and platforms for human identification purposes. Blood, hair, and bone samples were spiked with high levels of inhibitors commonly identified in each particular substrate in order to test the efficiency of various DNA extraction methods prior to sequencing. Samples were extracted using three commercial extraction kits (DNA IQ™, DNA Investigator, and PrepFiler® BTA), organic (blood and hair only), and two total demineralization protocols (bone only)). Massively parallel sequencing (MPS) was performed using two different systems: Precision ID chemistry and a custom AmpliSeq™ STR and iiSNP panel on the Ion S5™ System and the ForenSeq DNA Signature Prep Kit on the MiSeq FGx™. The overall results showed that all DNA extraction methods were efficient and are fully compatible with both MPS systems. Key performance indicators such as STR and SNP reportable alleles, read depth, and heterozygote balance were comparable for each extraction method. In samples where CE-based STRs yielded partial profiles (bone), MPS-based STRs generated more complete or full profiles. Moreover, MPS panels contain more STR loci than current CE-based STR kits and also include SNPs, which can further increase the power of discrimination obtained from these samples, making MPS a desirable choice for the forensic analysis of such challenging samples.

Microbial enrichment and gene functional categories revealed on the walls of a spent fuel pool of a nuclear power plant

Microorganisms developing in the liner of the spent fuel pool (SFP) and the fuel transfer channel (FTC) of a Nuclear Power Plant (NPP) can form high radiation resistant biofilms and cause corrosion. Due to difficulties and limitations to obtain large samples from SFP and FTC, cotton swabs were used to collect the biofilm from the wall of these installations. Molecular characterization was performed using massively parallel sequencing to obtain a taxonomic and functional gene classification. Also, samples from the drainage system were evaluated because microorganisms may travel over the 12-meter column of the pool water of the Brazilian Nuclear Power Plant (Angra1), which has been functioning since 1985. Regardless of the treatment of the pool water, our data reveal the unexpected presence of Fungi (Basidiomycota and Ascomycota) as the main contaminators of the SFP and FTC. Ustilaginomycetes (Basidiomycota) was the major class contributor (70%) in the SFP and FTC reflecting the little diversity in these sites; nevertheless, Proteobacteria, Actinobacteria, Firmicutes (Bacilli) were present in small proportions. Mapping total reads against six fungal reference genomes indicate that there is, in fact, a high abundance of fungal sequences in samples collected from SFP and FTC. Analysis of the ribosomal internal transcribed spacer (ITS) 1 and 2 regions and the protein found in the mitochondria of eukaryotic cells, cytochrome b (cytb) grouped our sample fungi in the clade 7 as Ustilago and Pseudozyma. In contrast, in the drainage system, Alphaproteobacteria were present in high abundances (55%). The presence of Sphingopyxis, Mesorhizobium, Erythrobacter, Sphingomonas, Novosphingobium, Sphingobium, Chelativorans, Oceanicaulis, Acidovorax, and Cyanobacteria was observed. Based on genomic annotation data, the assessment of the biological function found a higher proportion of protein-coding sequences related to respiration and protein metabolism in SFP and FTC samples. The knowledge of this biological inventory present in the system may contribute to further studies of potential microorganisms that might be useful for bioremediation of nuclear waste.

The Probabilistic Genotyping Software STRmix: Utility and Evidence for its Validity

Forensic DNA interpretation is transitioning from manual interpretation based usually on binary decision-making toward computer-based systems that model the probability of the profile given different explanations for it, termed probabilistic genotyping (PG). Decision-making by laboratories to implement probability-based interpretation should be based on scientific principles for validity and information that supports its utility, such as criteria to support admissibility. The principles behind STRmix™ are outlined in this study and include standard mathematics and modeling of peak heights and variability in those heights. All PG methods generate a likelihood ratio (LR) and require the formulation of propositions. Principles underpinning formulations of propositions include the identification of reasonably assumed contributors. Substantial data have been produced that support precision, error rate, and reliability of PG, and in particular, STRmix™. A current issue is access to the code and quality processes used while coding. There are substantial data that describe the performance, strengths, and limitations of STRmix™, one of the available PG software.

Challenges in investigation of diabetes-related aviation fatalities-an analysis of 1491 subsequent aviation fatalities in USA during 2011-2016

Diabetes mellitus (DM) could cause pilot incapacitation and result in aviation fatalities. The mechanisms could be directly as a consequence of acute hypoglycemia/subacute diabetic ketoacidosis (DKA) or indirectly as an acute cardiovascular event by contributing to the development of atherosclerosis in coronary or carotid and cerebral arteries. In this study, DM-related fatal flight accidents in the US National Transport Bureau's database between years 2011-2016 were analyzed with special emphasis on postmortem (PM) glucose levels and correlation of toxicological reports with anamnestic information on DM. Additionally, autopsy results on coronary arteries were reviewed. In 43 out of 1491 (~ 3%) fatal accidents pilots had DM. Postmortem glucose or glycated hemoglobin percentage (Hb1Ac) was measured in 12 of the 43 cases; while antidiabetic medication was found in 14 of the cases (only two of the cases had both glucose measurements and medication). With the increasing prevalence of DM, a possibility of pilot incapacitation due to DM or complications of DM should be actively studied, even if no anamnestic information of DM was available. While PM hypoglycemia is difficult to assess, we propose a systematic investigation based on measurement of glucose, Hb1Ac%, and ketone bodies, and documentation of atherosclerotic lesions in major arteries to identify or rule out DM as a cause of pilot incapacitation.

Copycats in Pilot Aircraft-Assisted Suicides after the Germanwings Incident

Aircraft-assisted pilot suicide is a rare but serious phenomenon. The aim of this study was to evaluate changes in pilot aircraft-assisted suicide risks, i.e., a copycat effect, in the U.S. and Germany after the Germanwings 2015 incident in the French Alps. Aircraft-assisted pilot suicides were searched in the U.S. National Transportation Safety Board (NTSB) accident investigation database and in the German Bundestelle für Flugunfalluntersuchung (BFU) Reports of Investigation database five years before and two years after the deliberate crash of the Germanwings flight into the French Alps in 2015. The relative risk (RR) of the aircraft-assisted pilot suicides was calculated. Two years after the incident, three out of 454 (0.66%) fatal incidents were aircraft-assisted suicides compared with six out of 1292 (0.46%) in the prior five years in the NTSB database. There were no aircraft-assisted pilot suicides in the German database during the two years after or five years prior to the Germanwings crash. The relative aircraft-assisted pilot suicide risk for the U.S. was 1.4 (95% CI 0.3–4.2) which was not statistically significant. Six of the pilots who died by suicide had told someone of their suicidal intentions. We consider changes in the rate to be within a normal variation. Responsible media coverage of aircraft incidents is important due to the large amount of publicity that these events attract.

Planktonic microbial profiling in water samples from a Brazilian Amazonian reservoir

Our comprehension of the dynamics and diversity of freshwater planktonic bacterial communities is far from complete concerning the Brazilian Amazonian region. Therefore, reference studies are urgently needed. We mapped bacterial communities present in the planktonic communities of a freshwater artificial reservoir located in the western Amazonian basin. Two samples were obtained from rainy and dry seasons, the periods during which water quality and plankton diversity undergo the most significant changes. Hypervariable 16S rRNA and shotgun sequencing were performed to describe the first reference of a microbial community in an Amazonian lentic system. Microbial composition consisted mainly of Betaproteobacteria, Cyanobacteria, Alphaproteobacteria, and Actinobacteria in the dry period. The bacteria distribution in the rainy period was notably absent of Cyanobacteria. Microcystis was observed in the dry period in which the gene cluster for cyanotoxins was found. Iron acquisition gene group was higher in the sample from the rainy season. This work mapped the first inventory of the planktonic microbial community of a large water reservoir in the Amazon, providing a reference for future functional studies and determining other communities and how they interact.

Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification

The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals. Those studies utilize either targeted 16S rRNA or shotgun metagenomic sequencing to characterize skin microbiomes; however, these approaches have limited species and strain resolution and susceptibility to stochastic effects, respectively. Clade-specific markers from the skin microbiome, using supervised learning, can predict individual identity using skin microbiomes from their respective donors with high accuracy. In this study the hidSkinPlex is presented, a novel targeted sequencing method using skin microbiome markers developed for human identification. The hidSkinPlex (comprised of 286 bacterial (and phage) family-, genus-, species-, and subspecies-level markers), initially was evaluated on three bacterial control samples represented in the panel (i.e., Propionibacterium acnes, Propionibacterium granulosum, and Rothia dentocariosa) to assess the performance of the multiplex. The hidSkinPlex was further evaluated for prediction purposes. The hidSkinPlex markers were used to attribute skin microbiomes collected from eight individuals from three body sites (i.e., foot (Fb), hand (Hp) and manubrium (Mb)) to their host donor. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification were used to classify skin microbiomes to their hosts with up to 92% (Fb), 96% (Mb), and 100% (Hp) accuracy. All samples (n=72) regardless of body site origin were correctly classified with up to 94% accuracy, and body site origin could be predicted with up to 86% accuracy. Finally, human short tandem repeat and single-nucleotide polymorphism profiles were generated from skin swab extracts from a single subject to highlight the potential to use microbiome profiling in conjunction with low-biomass samples. The hidSkinPlex is a novel targeted enrichment approach to profile skin microbiomes for human forensic identification purposes and provides a method to further characterize the utility of skin microflora for human identification in future studies, such as the stability and diversity of the personal skin microbiome.

Investigation of the STR loci noise distributions of PowerSeq™ Auto System

Aim

To characterize the noise and stutter distribution of 23 short tandem repeats (STRs) included in the PowerSeq^TM Auto System.

Methods

Raw FASTQ files were analyzed using STRait Razor v2s to display alleles and coverage. The sequence noise was divided into several categories: noise at allele position, noise at -1 repeat position, and artifact. The average relative percentages of locus coverage for each noise, stutter, and allele were calculated from the samples used for this locus noise analysis.

Results

Stutter products could be routinely observed at the -2 repeat position, -1 repeat position, and +1 repeat position of alleles. Sequence noise at the allele position ranged from 10.22% to 28.81% of the total locus coverage. At the allele position, individual noise reads were relatively low.

Conclusion

The data indicate that noise generally will be low. In addition, the PowerSeq^TM Auto System could capture nine flanking region single nucleotide polymorphisms (SNPs) that would not be observed by other current kits for massively parallel sequencing (MPS) of STRs.

Attention-Deficit/Hyperactivity Disorder and Fatal Accidents in Aviation Medicine

BACKGROUND

Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder with symptoms of inattention and/or hyperactivity-impulsivity that interfere with functioning and/or development. ADHD occurs in about 2.5% of adults. ADHD can be an excluding medical condition among pilots due to the risk of attentional degradation and therefore impact on flight safety. Diagnosis of ADHD is complex, which complicates aeromedical assessment. This study highlights fatal accident cases among pilots with ADHD and discusses protocols to detect its presence to help to assess its importance to flight safety.

METHODS

To identify fatal accidents in aviation (including airplanes, helicopters, balloons, and gliders) in the United States between the years 2000 to 2015, the National Transportation Safety Board (NTSB) database was searched with the terms ADHD, attention deficit hyperactivity disorder, and attention deficit disorder (ADD).

RESULTS

The NTSB database search for fatal aviation accidents possibly associated with ADHD yielded four accident cases of interest in the United States [4/4894 (0.08%)]. Two of the pilots had ADHD diagnosed by a doctor, one was reported by a family member, and one by a flight instructor. An additional five cases were identified searching for ADD [5/4894 (0.1%)]. Altogether, combined ADHD and ADD cases yielded nine accident cases of interest (0.18%).

DISCUSSION

It is generally accepted by aviation regulatory authorities that ADHD is a disqualifying neurological condition. Yet FAA and CASA provide specific protocols for tailor-made pilot assessment. Accurate evaluation of ADHD is essential because of its potential negative impact on aviation safety.Laukkala T, Bor R, Budowle B, Sajantila A, Navathe P, Sainio M, Vuorio A. Attention-deficit/hyperactivity disorder and fatal accidents in aviation medicine. Aerosp Med Hum Perform. 2017; 88(9):871-875.

Evaluation of InnoTyper® 21 in a sample of Rio de Janeiro population as an alternative forensic panel

The use of bi-allelic markers such as retrotransposable element insertion polymorphisms or Innuls (for insertion/null) can overcome some limitations of short tandem repeat (STR) loci in typing forensic biological evidence. This study investigated the efficiency of the InnoTyper® 21 Innul markers in an urban admixed population sample in Rio de Janeiro (n = 40) and one highly compromised sample collected as evidence by the Rio de Janeiro police. No significant departures from Hardy-Weinberg equilibrium were detected after the Bonferroni correction (α' ≈ 0.05/20, p < 0.0025), and no significant linkage disequilibrium was observed between markers. Assuming loci independence, the cumulative random match probability (RMP) was 2.3 × 10^-8. A lower mean Fis value was obtained for this sample population compared with those of three North American populations (African-American, Southwest Hispanic, US Caucasian). Principal component analysis with the three North American populations and one from 21 East Asian population showed that African Americans segregated as an independent group while US Caucasian, Southwest Hispanic, East Asian, and Rio de Janeiro populations are in a single large heterogeneous group. Also, a full Innuls profile was produced from an evidence sample, despite the DNA being highly degraded. In conclusion, this system is a useful complement to standard STR kits.