A Comparison of Tools for Copy-Number Variation Detection in Germline Whole Exome and Whole Genome Sequencing Data

Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. Relevant CNVs are hard to detect because common structural variations define large parts of the human genome. CNV calling from short-read sequencing would allow single protocol full genomic profiling. We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a reference cohort encompassing 39 whole genome sequencing (WGS) samples paired current clinical standard—SNP-array based CNV calling. Additionally, for nine samples we also performed whole exome sequencing (WES), to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. Several tools had better performance for NA12878, which could be a result of overfitting. We suggest combining the best tools also based on different methodologies: GATK gCNV, Lumpy, DELLY, and cn.MOPS. Reducing the total number of called variants could potentially be assisted by the use of background panels for filtering of frequently called variants.

A comparison of tools for copy-number variation detection in germline whole exome and whole genome sequencing data

Background: Copy-number variations (CNVs) have important clinical implications for several diseases and cancers. The clinically relevant CNVs are hard to detect because CNVs are common structural variations that define large parts of the normal human genome. CNV calling from short-read sequencing data has the potential to leverage available cohort studies and allow full genomic profiling in the clinic without the need for additional data modalities. Questions regarding performance of CNV calling tools for clinical use and suitable sequencing protocols remain poorly addressed, mainly because of the lack of good reference data sets. Methods: We reviewed 50 popular CNV calling tools and included 11 tools for benchmarking in a unique reference cohort encompassing 39 whole genome sequencing (WGS) samples paired with analysis by the current clinical standard—SNP-array based CNV calling. Additionally, for nine of these samples we performed whole exome sequencing (WES) performed, in order to address the effect of sequencing protocol on CNV calling. Furthermore, we included Gold Standard reference sample NA12878, and tested 12 samples with CNVs confirmed by multiplex ligation-dependent probe amplification (MLPA). Results: Tool performance varied greatly in the number of called CNVs and bias for CNV lengths. Some tools had near-perfect recall of CNVs from arrays for some samples, but poor precision. Filtering output by CNV ranks from tools did not salvage precision. Several tools had better performance patterns for NA12878, and we hypothesize that this is the result of overfitting during the tool development. Conclusions: We suggest combining tools with the best recall: GATK gCNV, Lumpy, DELLY, and cn.MOPS. These tools also capture different CNVs. Further improvements in precision requires additional development of tools, reference data sets, and annotation of CNVs, potentially assisted by the use of background panels for filtering of frequently called variants.

Combined multi-isotopic and (S)TEM study of pre-solar silicates to probe the solar system’s prenatal history

<p><strong>Introduction </strong>Primitive extraterrestrial materials like carbonaceous chondrite matrices and interplanetary dust particles contain tiny dust grains that were formed in the winds of red giant branch, or asymptotic giant branch stars (AGB) and in the ejecta of novae and supernovae (SNe) explosions before the formation of our solar system. Presolar grains survived all the processes that created our solar system and carry the signatures of their parent stellar sources. Correlating isotopic data of individual presolar silicates with microstructural and chemical analyses obtained by STEM, provides a unique opportunity to provide better insights into physiochemical conditions of grain formation in stellar environments, grain alteration in the interstellar and parent body processes and also helps constraining various astrophysical grain condensation models. In this work, isotopic, structural and chemical analysis of nine presolar silicate grains from the CH3/CBb3 chondrite Isheyevo and CR2 chondrite NWA801 are reported.</p><p><strong>Experimental </strong>Presolar oxygen anomalous grain search using oxygen isotope imaging was done in-situ using NanoSIMS50 ion microprobe and five grains from AGB and four grains from SNe, were selected for (S)TEM investigations. The TEM lamellas were prepared using a TESCAN LYRA3 FIB-SEM at Curtin University. Structural and chemical analysis of presolar grains were performed by combining high-resolution scanning TEM imaging, spatially-resolved electron energy-loss spectroscopy (EELS) and spatially-resolved energy-dispersive X-ray spectroscopy (EDS) by using a FEI Titan Cubed Themis 60-300 microscope at Cádiz University which was operated at 200 kV. EDS quantification was corrected by using a standard reference sample of known composition and density and by taking into account the thickness of the probed area by using low-loss EELS. EELS spectrum images for fine structures (mostly, O-K, Si-L<sub>2,3 </sub>and Fe-L<sub>2,3</sub> edges) analyses were acquired with the monochromator excited allowing an energy resolution of about 0.4 eV. After denoising using principal components analysis and removal of the multiple scattering, we were able to map the heterogeneities related to the Fe oxidation state and to the oxygen local chemical environment. This allowed us to compare the degree of aqueous alteration of the grain with the surrounding rim and matrix grains.</p><p><strong>Results </strong>TEM and STEM data have revealed a strong heterogeneity and a broad range of structural and chemical compositions of the grains that enabled us to compare the stellar grain condensation environments (e.g. AGB stars and SNe), and suggest widely varying formation conditions for the presolar silicates identified in this study. Only one of the grains originally condensed as an amorphous grain has shown preferential sputtering of Mg, indicating that Mg-rich amorphous grains are not preferentially destroyed. Several grains are found with signatures that represent interstellar, nebular and parent body alteration. An oldhamite-like grain within a presolar enstatite grain is probably the first observation of an oldhamite grain as a seed grain for the condensation of an enstatite grain in stellar atmospheres. All these results, which will be discussed in detail, point out the importance of coordinated isotopic, microstructural and chemical studies of presolar silicates to investigate the processes that may have played a role in shaping our solar system.</p>

STUDYING THE PECULIARITIES OF SELF-CONSCIOUSNESS IN THE DISCOURSE OF THE PROBLEM OF FORENSIC-PSYCHOLOGICAL EXAMINATION OF A MINOR SUBJECT

The article deals with the problem of expert diagnosis of individual and personal characteristics of minors under subject. Systematic and generalized methodological approaches to the study of the parameters of self-consciousness in the context of forensic psychological examination of minors. It was determined that a mandatory component of expert research is a comparison of data on the state and characteristics of the mental development of a minor with the results of an analysis of the situation and behavior of the subject, taking into account the inter-individual variation of indicators of mental development and the peculiarity of the social situation of development. The conclusion is made about the expediency of selecting diagnostic methods in the context of the following personality characteristics: psychophysiological (implies the diagnosis of typological personality qualities of a general order, which are predominantly natural conditionality); psychological (includes determining the individual characteristics of self-consciousness, emotional sphere, anxiety, behavioral manifestations, motivation); social (orientation to the study of a real-life assessment system, which is set in the nearest microsocium of minors under the experts as a standard-reference sample and determines the tendency for the development of self-identity); sociocultural (includes the study of the system of value orientations of minors under expert and their immediate environment). It is noted that the basis of psychological diagnosis of individual psychological characteristics of the personality of minors under the expert are four basic principles that determine the construction of a psychodiagnostic study: the principle of methodical limitation, the principle of mutual verification and comparison of the results obtained among themselves, the principle of necessity-sufficiency, the principle of the relationship of diagnostic tool capabilities and depth sensing psychic reality. It was emphasized that the procedure of forensic psychological examination of minors subject (accused, witnesses, victims) is defined as a special kind of interpersonal interaction, in which the subject is assisted by psychological means in case of problems or difficulties of a communicative nature. This makes it possible not only to obtain information for expert opinions, but also relieves the psyche of minors from communication difficulties, relieves situational maladjustment, which naturally arises from the transition from spontaneous communication to targeted, planned, self-managed. The need to implement a system-integrative approach to the selection of diagnostic tools, which will increase the level of objectivity and validity of expert findings, has been determined. Key words: self-consciousness, forensic psychological examination, subject minors.

FTIR Spectroscopy Characterization of Si-C bonding in SiC Thin Film prepared at Room Temperature by Conventional 13.56MHz RF PECVD

SiC thin film has been synthesized by using conventional 13.56MHz radio frequency plasma enhanced chemical vapour deposition (PECVD). The mixture of silane (SiH4) and methane (CH4) were used as precursor gases while hydrogen as carrier gas. The SiH4/CH4 ratio and the substrate temperature have been varied in order to examine the reaction of the active species which can produce the Si-C bonding in the deposited film. FTIR spectroscopy was used to analyse the type of bonding and particularly to confirm the existence of Si-C bonding by comparing the spectrums obtained from deposited thin film samples and standard reference sample of bulk SiC single crystal wafer. The existence of Si-C bonding was confirmed and it was slightly shifted from the bulk SiC wafer at around 722cm-1 and 817cm-1.