Revision of the SNPforID 34-plex forensic ancestry test: Assay enhancements, standard reference sample genotypes and extended population studies

2013 ◽  
Vol 7 (1) ◽  
pp. 63-74 ◽  
Author(s):  
M. Fondevila ◽  
C. Phillips ◽  
C. Santos ◽  
A. Freire Aradas ◽  
P.M. Vallone ◽  
...  
Keyword(s):  
Population Studies ◽  
Reference Sample ◽  
Standard Reference Sample

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

Cancers ◽  
2021 ◽  
Vol 13 (24) ◽  
pp. 6283
Author(s):  
Migle Gabrielaite ◽  
Mathias Husted Torp ◽  
Malthe Sebro Rasmussen ◽  
Sergio Andreu-Sánchez ◽  
Filipe Garrett Vieira ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Reference Sample ◽  
Snp Array ◽  
Copy Number Variations ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Standard Reference Sample ◽  
Whole Exome

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.

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

2020 ◽  
Author(s):  
Luc Lajaunie ◽  
Manish N. Sanghani ◽  
William D.A. Rickard ◽  
José. J. Calvino ◽  
Kuljeet K. Marhas ◽  
...  
Keyword(s):  
Solar System ◽  
Chemical Analysis ◽  
Reference Sample ◽  
Parent Body ◽  
Stellar Atmospheres ◽  
Dust Particles ◽  
Chemical Compositions ◽  
Standard Reference Sample ◽  
Presolar Grains ◽  
Spatially Resolved

<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>

scholarly journals Alfnoor: assessing the information content of Ariel's low resolution spectra with planetary population studies.

2020 ◽  
Author(s):  
Lorenzo V. Mugnai ◽  
Enzo Pascale ◽  
Quentin Changeat ◽  
Ahmed Al-Refaie ◽  
Giovanna Tinetti
Keyword(s):  
Information Content ◽  
Population Studies ◽  
Reference Sample ◽  
Spectroscopic Observation ◽  
Performance Model ◽  
Atmospheric Composition ◽  
Transmission Spectra ◽  
Low Resolution ◽  
Reconnaissance Survey ◽  
Molecular Abundances

<p>In the next decade the Ariel Space Telescope will provide the first statistical dataset of exoplanet spectra, performing spectroscopic observation of about 1000 exoplanets in the wavelength range 0.5→7.8 μm thanks to its Reconnaissance Survey. About one half of these 1000 targets will be then selected for more accurate observations with higher spectral resolution.</p> <p>We present a novel metric to assess the information content of the Ariel Reconnaissance Survey low resolution transmission spectra. The proposed strategy will not only allow us to select candidate planets to be re-observed in Ariel higher resolution Tiers, but also to classify exoplanets by their atmospheric composition and to put the basis for the statistical analysis of such a large exoplanetary sample.</p> <p>To test our metric we use Alfnoor, a new package combining the TauRex spectral modelling with the ArielRad payload performance model, to produce populations of hundreds of exoplanets matching those presented in the Ariel Mission Reference Sample. For each of the planets in the Ariel candidate targets list we create an atmosphere with a randomised quantity of H<sub>2</sub>O, CH<sub>4</sub>, CO<sub>2</sub>, NH<sub>3</sub> and clouds. </p> <p>Our metric proves able to identify methane,  carbon  dioxide  and  water  rich  atmospheres in the cases of molecular abundances > 10<sup>−4</sup> in mixing ratio,  but it shows its limits in separating water from ammonia. </p> <p>We compare our metric with four different Deep Learning algorithms, they show only ∼10% better performance in identifying the molecular content.</p>

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

2012 ◽  
Vol 8 (4) ◽  
Author(s):  
Muhammad Firdaus Omar ◽  
Abd.Khamim Ismail ◽  
Imam Sumpono ◽  
Emilly Albert Alim ◽  
Mohd Nazri Nawi ◽  
...  
Keyword(s):  
Thin Film ◽  
Ftir Spectroscopy ◽  
Reference Sample ◽  
Chemical Vapour ◽  
Active Species ◽  
Standard Reference Sample ◽  
Frequency Plasma ◽  
Crystal Wafer ◽  
Sic Wafer

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.

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

2021 ◽  
Author(s):  
Migle Gabrielaite ◽  
Mathias Husted Torp ◽  
Sergio Andreu-Sánchez ◽  
Filipe Garrett Vieira ◽  
Christina Bligaard Pedersen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Reference Data ◽  
Reference Sample ◽  
Data Sets ◽  
Whole Genome ◽  
Sequencing Data ◽  
Standard Reference Sample ◽  
Whole Exome

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.

Increased dryness after pressing and wet web strength by utilizing foam application technology

TAPPI Journal ◽  
2016 ◽  
Vol 15 (11) ◽  
pp. 731-738 ◽  
Author(s):  
KARITA KINNUNEN-RAUDASKOSKI ◽  
KRISTIAN SALMINEN ◽  
JANI LEHMONEN ◽  
TUOMO HJELT
Keyword(s):  
Tensile Strength ◽  
Guar Gum ◽  
Paper Industry ◽  
Reference Sample ◽  
Strength Properties ◽  
Cellulose Microfibrils ◽  
Application Technology ◽  
Ethylene Vinyl Alcohol ◽  
Wet Pressing ◽  
Web Strength

Production cost savings by lowering basis weight has been a trend in papermaking. The strategy has been to decrease the amount of softwood kraft pulp and increase use of fillers and recycled fibers. These changes have a tendency to lower strength properties of both the wet and dry web. To compensate for the strength loss in the paper, a greater quantity of strength additives is often required, either dosed at the wet end or applied to the wet web by spray. In this pilot-scale study, it was shown how strength additives can be effectively applied with foam-based application technology. The technology can simultaneously increase dryness after wet pressing and enhance dry and wet web strength properties. Foam application of polyvinyl alcohol (PVA), ethylene vinyl alcohol (EVOH), carboxymethyl cellulose (CMC), guar gum, starch, and cellulose microfibrils (CMF) increased web dryness after wet pressing up to 5.2%-units compared to the reference sample. The enhanced dewatering with starch, guar gum, and CMF was detected with a bulk increase. Additionally, a significant increase in z-directional tensile strength of dry web and and in-plane tensile strength properties of wet web was obtained. Based on the results, foam application technology can be a very useful technology for several applications in the paper industry.

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