Same-species Contamination Detection With Variant Calling Information From Next-generation Sequencing

Background: Same-species contamination detection is an important quality control step in genetic data analysis. Due to a scarcity of methods to detect and correct for this quality control issue, same-species contamination is more difficult to detect than cross-species contamination. We introduce a novel machine learning algorithm to detect same-species contamination in next-generation sequencing (NGS) data using a support vector machine (SVM) model. Our approach uniquely detects contamination using variant calling information stored in variant call format (VCF) files for DNA or RNA. Importantly, it can differentiate between same-species contamination and mixtures of tumor and normal cells.In the first stage, a change-point detection method is used to identify copy number variations (CNVs) and copy number aberrations (CNAs) for filtering. Next, single nucleotide polymorphism (SNP) data is used to test for same-species contamination using an SVM model. Based on the assumption that alternative allele frequencies in NGS follow the beta-binomial distribution, the deviation parameter ρ is estimated by the maximum likelihood method. All features of a radial basis function (RBF) kernel SVM are generated using publicly available or private training data. Results: We demonstrate our approach in simulation experiments. The datasets combine, in silico, exome sequencing data of DNA from two lymphoblastoid cell lines (NA12878 and NA10855). We generate VCF files using variants identified in these data and then evaluate the power and false-positive rate of our approach. Our approach can detect contamination levels as low as 5% with a reasonable false-positive rate. Results in real data have sensitivity above 99.99% and specificity of 90.24%, even in the presence of degraded samples with similar features as contaminated samples. We provide an R software implementation of our approach.Conclusions: Our approach addresses the gap in methods to test for same-species contamination in NGS. Due to its high sensitivity for degraded samples and tumor-normal samples, it represents an important tool that can be applied within the quality control process. Additionally, the user-friendly software has the unique ability to conduct quality control using the VCF format.

Degradation of Polyfurfuryl Alcohol-based Biopolymer by Soil-burial and Photo-degradation Methods

Recently, polyfurfuryl alcohol (PFA) based material has been gaining attention. Despite its use as an intermediate in various industries, the degradation process of PFA has rarely been reported. In this study, neat PFA (PF) and polylactic acid (PLA) incorporated PFA (PF-PL) based thermoset biopolymers were prepared by casting method. The degradation of the prepared biopolymer specimens was carried out under environmental conditions via soil-burial test and photo-degradation method for 21-months. The extent of degradation of PF and PF-PL was assessed by evaluating weight loss, structural and morphological change by Fourier transform infrared (FTIR) spectroscopy and scanning electron microscopy (SEM), respectively. Weight loss percentage in case of photo-degraded samples was found to be much higher compared to soil buried specimens. SEM micrographs showed a blistered surface with visible cracks on the surface of soil buried and photo-degraded samples. FTIR spectra of photo-degraded samples showed a new peak at 673 cm-1 indicating the furan ring opening during the degradation process. Significant variation in mechanical properties of PF and PF-PL specimens after soil-burial test also indicated biodegradable nature of the biopolymers. Approximately 45% and 63% of loss in tensile strength was obtained in PF and PF-PL soil buried specimens, respectively. All the obtained data revealed the fragmentation of biopolymers, hence supporting the biodegradable nature of PFA-based biopolymer.

Revisiting traditional SSR based methodologies available for elephant genetic studies

Asian elephant (Elephas maximus) plays a significant role in natural ecosystems and it is considered as an endangered animal. Molecular genetics studies on elephants’ dates back to 1990s. Microsatellite markers have been the preferred choice and have played a major role in ecological, evolutionary and conservation research on elephants over the past 20 years. However, technical constraints especially related to the specificity of traditionally developed microsatellite markers have brought to question their application, specifically when degraded samples are utilized for analysis. Therefore, we analyzed the specificity of 24 sets of microsatellite markers frequently used for elephant molecular work. Comparative wet lab analysis was done with blood and dung DNA in parallel with in silico work. Our data suggest cross-amplification of unspecific products when field-collected dung samples are utilized in assays. The necessity of Asian elephant specific set of microsatellites and or better molecular techniques are highlighted.

Water uptake dynamics in soybean seeds: influence in seeds performance and DNA integrity

ABSTRACT: Relationships among water uptake rate and temperatures were investigated in five soybean seeds lots cv. M 6410 IPRO. Germination, field emergence and electrical conductivity tests were applied to determine seed performance after fast (complete immersion in water), control (moist substrate) and slow (moist atmosphere) imbibitions both at 20 °C and 30 °C. The fresh weight increment over time in soybean seeds during imbibition was recorded. In parallel, analysis of the DNA integrity of seedlings obtained from such seeds was performed in gel electrophoresis. Absorption pattern of soybean seeds were similar among temperatures, but absorption characteristics vary with time progress according to the way of water entrance into the seeds. Upon fast imbibition seeds germinated lower than non-fast-imbibed seeds, besides loss of seed performance. In contrast, slow-imbibed seeds showed high germination, low abnormal seedlings and maintenance of seeds performance. DNA isolation from fast imbibed seeds was highly degraded; although, some considerably degraded samples were reported in controlled imbibed seeds and the best preserved DNA was found in slow-imbibed seeds. The pattern of DNA degradation is typically passive or non programmed cell death. Our results showed it is important to consider the water uptake rate during germination test, since DNA integrity plays a critical role during seed imbibition, preserving soybean seed performance.

Universal Fragment of mtDNA for Cervidae and Other Ungulate Species Identification

ObjectiveThe abundance of literature and many studies aimed at the identification of free-living animal species has helped to identify specific nucleotide marker sequences. In many cases, the best marker to distinguish species is the mitochondrial genome (mtDNA) or one of its fragments. In molecular analyses of Cervidae, biological material such as blood or muscle is easily obtained, as nearly all of these species are gaming animals.ResultsIn our research, we present the case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The proposed methodology is helpful as a routine identification procedure for a variety of tissue sources, even in cases where the samples are degraded. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base.

Using high-resolution melting to identify Calliphoridae (blowflies) species from Brazil

Forensic entomology is the study of insects and other arthropods used in the solution of crimes. Most of entomological evidences strongly depend on accurate species identification. Therefore, new methods are being developed due to difficulties in morphological identification, including molecular methods such as High-Resolution Melting. In this study, we reported a new HRM primer set to identify forensically important Calliphoridae (blowflies) from Brazil. For such purpose, Calliphoridae species of forensic importance in Brazil were listed and confirmed by specialists. Mitochondrial COI sequences of those species were downloaded from databases and aligned, and polymorphic variations were selected for distinction between species. Based on it, HRM primers were designed. Forty-three fly samples representing six species were tested in the HRM assay. All samples had the COI gene sequenced to validate the result. Identifying and differentiating the six species proposed using a combination of two amplicons was possible. The protocol was effective even for old insect specimens, collected and preserved dried for more than ten years, unlike the DNA sequencing technique that failed for those samples. The HRM technique proved to be an alternative tool to DNA sequencing, with advantage of amplifying degraded samples and being fast and cheaper than the sequencing technique.

Drag Reduction Performance of Mechanically Degraded Dilute Polyethylene Oxide Solutions

Mechanical degradation of dilute solutions of polyethylene oxide (PEO) via chain scission was investigated within a turbulent pipe flow. Comparisons of the drag reduction performance with and without degradation were made by matching the onset of drag reduction conditions, which has been shown for PEO to be related to the mean molecular weight. The bulk flow behavior of both the degraded and nondegraded samples were generally consistent with trends observed in the literature, but a subset of conditions showed significant deviation in the slope increment (drag reduction performance) between the degraded and nondegraded samples. When they deviated, the degraded samples were consistently more efficient than the nondegraded samples even though they had the same mean molecular weight. The deviations were shown to scale with the normalized difference between the initial and final molecular weights. The current data and analysis as well as the literature suggest that the deviations in the polymer performance (slope increment) are related to changes in the molecular weight distribution. More specifically, the improved performance of the degraded samples relative to the nondegraded ones at the mean molecular weight of the degraded sample indicates an excess of longer polymer chains since the higher chain fractions in a degraded solution more effectively control the flow properties when within a certain degree of degradation and Reynolds number.