Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation

AbstractDevelopmental patterning in Caenorhabditis elegans is known to proceed in a highly stereotypical manner, which raises the question of how developmental robustness is achieved despite the inevitable stochastic noise. We focus here on a population of epidermal cells, the seam cells, which show stem cell-like behaviour and divide symmetrically and asymmetrically over post-embryonic development to generate epidermal and neuronal tissues. We have conducted a mutagenesis screen to identify mutants that introduce phenotypic variability in the normally invariant seam cell population. We report here that a null mutation in the fusogen eff-1 increases seam cell number variability. Using time-lapse microscopy and single molecule fluorescence hybridisation, we find that seam cell division and differentiation patterns are mostly unperturbed in eff-1 mutants, indicating that cell fusion is uncoupled from the cell differentiation programme. Nevertheless, seam cell losses due to the inappropriate differentiation of both daughter cells following division, as well as seam cell gains through symmetric divisions towards the seam cell fate were observed at low frequency. We show that these stochastic errors likely arise through accumulation of defects interrupting the continuity of the seam and changing seam cell shape, highlighting the role of tissue homeostasis in suppressing phenotypic variability during development.

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Complex Principal Component Analysis of Antarctic Ice Sheet Mass Balance

Remote Sensing ◽

10.3390/rs13030480 ◽

2021 ◽

Vol 13 (3) ◽

pp. 480

Author(s):

Jingang Zhan ◽

Hongling Shi ◽

Yong Wang ◽

Yixin Yao

Keyword(s):

Principal Component Analysis ◽

Ice Sheet ◽

Low Frequency ◽

Principal Component ◽

Equatorial Pacific ◽

Mass Change ◽

Frequency Variation ◽

Periodic Signal ◽

Time Frequency ◽

The Antarctic

Ice sheet changes of the Antarctic are the result of interactions among the ocean, atmosphere, and ice sheet. Studying the ice sheet mass variations helps us to understand the possible reasons for these changes. We used 164 months of Gravity Recovery and Climate Experiment (GRACE) satellite time-varying solutions to study the principal components (PCs) of the Antarctic ice sheet mass change and their time-frequency variation. This assessment was based on complex principal component analysis (CPCA) and the wavelet amplitude-period spectrum (WAPS) method to study the PCs and their time-frequency information. The CPCA results revealed the PCs that affect the ice sheet balance, and the wavelet analysis exposed the time-frequency variation of the quasi-periodic signal in each component. The results show that the first PC, which has a linear term and low-frequency signals with periods greater than five years, dominates the variation trend of ice sheet in the Antarctic. The ratio of its variance to the total variance shows that the first PC explains 83.73% of the mass change in the ice sheet. Similar low-frequency signals are also found in the meridional wind at 700 hPa in the South Pacific and the sea surface temperature anomaly (SSTA) in the equatorial Pacific, with the correlation between the low-frequency periodic signal of SSTA in the equatorial Pacific and the first PC of the ice sheet mass change in Antarctica found to be 0.73. The phase signals in the mass change of West Antarctica indicate the upstream propagation of mass loss information over time from the ocean–ice interface to the southward upslope, which mainly reflects ocean-driven factors such as enhanced ice–ocean interaction and the intrusion of warm saline water into the cavities under ice shelves associated with ice sheets which sit on retrograde slopes. Meanwhile, the phase signals in the mass change of East Antarctica indicate the downstream propagation of mass increase information from the South Pole toward Dronning Maud Land, which mainly reflects atmospheric factors such as precipitation accumulation.

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An Improved Time Integration Method Based on Galerkin Weak Form with Controllable Numerical Dissipation

Applied Sciences ◽

10.3390/app11041932 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1932

Author(s):

Weixuan Wang ◽

Qinyan Xing ◽

Qinghao Yang

Keyword(s):

High Frequency ◽

Integration Method ◽

Time Integration ◽

Low Frequency ◽

Weak Form ◽

High Accuracy ◽

Numerical Dissipation ◽

Frequency Range ◽

Time Integration Method ◽

Numerical Damping

Based on the newly proposed generalized Galerkin weak form (GGW) method, a two-step time integration method with controllable numerical dissipation is presented. In the first sub-step, the GGW method is used, and in the second sub-step, a new parameter is introduced by using the idea of a trapezoidal integral. According to the numerical analysis, it can be concluded that this method is unconditionally stable and its numerical damping is controllable with the change in introduced parameters. Compared with the GGW method, this two-step scheme avoids the fast numerical dissipation in a low-frequency range. To highlight the performance of the proposed method, some numerical problems are presented and illustrated which show that this method possesses superior accuracy, stability and efficiency compared with conventional trapezoidal rule, the Wilson method, and the Bathe method. High accuracy in a low-frequency range and controllable numerical dissipation in a high-frequency range are both the merits of the method.

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Identification of community-consensus clinically relevant variants and development of single molecule molecular inversion probes using the CIViC database

10.1101/479394 ◽

2018 ◽

Author(s):

Erica K. Barnell ◽

Adam Waalkes ◽

Kelsi Penewit ◽

Katie M. Campbell ◽

Zachary L. Skidmore ◽

...

Keyword(s):

Single Molecule ◽

Pearson Correlation ◽

Genomic Region ◽

Variant Annotation ◽

Design Paradigm ◽

Molecular Inversion Probes ◽

Sequencing Platforms ◽

Tumor Types ◽

Molecular Inversion Probe ◽

Actionable Variants

AbstractClinical targeted sequencing panels are important for identifying actionable variants for cancer patients, however, there are currently no strategies to create impartial and rationally-designed panels to accommodate rapidly growing knowledge within the field. Here we use the Clinical Interpretations of Variants in Cancer database (CIViC) in conjunction with single-molecule molecular inversion probe (smMIP) capture to identify and design probes targeting clinically relevant variants in cancer. In total, 2,027 smMIPs were designed to target 111 eligible CIViC variants. The total genomic region covered by the CIViC smMIPs reagent was 61.5 kb. When compared to existing genome or exome sequencing results (n = 27 cancer samples from 5 tumor types), CIViC smMIP sequencing demonstrated a 95% sensitivity for variant detection (n = 61/64 variants). Variant allele frequency for variants identified on both sequencing platforms were highly concordant (Pearson correlation = 0.885; n = 61 variants). Moreover, for individuals with paired tumor/normal samples (n = 12), 182 clinically relevant variants missed by original sequencing were discovered by CIViC smMIPs sequencing. This design paradigm demonstrates the utility of an open-sourced database built on attendant community contributions for each variant with peer-reviewed interpretations. Use of a public repository for variant identification, probe development, and variant annotation could provide a transparent approach to build a dynamic next-generation sequencing–based oncology panel.

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Publisher Correction: Deep learning enables fast and dense single-molecule localization with high accuracy

Nature Methods ◽

10.1038/s41592-021-01305-1 ◽

2021 ◽

Author(s):

Artur Speiser ◽

Lucas-Raphael Müller ◽

Philipp Hoess ◽

Ulf Matti ◽

Christopher J. Obara ◽

...

Keyword(s):

Deep Learning ◽

Single Molecule ◽

High Accuracy

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Deep learning enables fast and dense single-molecule localization with high accuracy

Nature Methods ◽

10.1038/s41592-021-01236-x ◽

2021 ◽

Author(s):

Artur Speiser ◽

Lucas-Raphael Müller ◽

Philipp Hoess ◽

Ulf Matti ◽

Christopher J. Obara ◽

...

Keyword(s):

Deep Learning ◽

Single Molecule ◽

High Accuracy

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BRCA Testing by Single-Molecule Molecular Inversion Probes

Clinical Chemistry ◽

10.1373/clinchem.2016.263897 ◽

2017 ◽

Vol 63 (2) ◽

pp. 503-512 ◽

Cited By ~ 28

Author(s):

Kornelia Neveling ◽

Arjen R Mensenkamp ◽

Ronny Derks ◽

Michael Kwint ◽

Hicham Ouchene ◽

...

Keyword(s):

Genetic Testing ◽

Copy Number Variation ◽

Single Molecule ◽

Copy Number ◽

Single Gene ◽

Work Flow ◽

Analytical Sensitivity ◽

Brca1 And Brca2 ◽

Number Variation ◽

Molecular Inversion Probes

Abstract BACKGROUND Despite advances in next generation DNA sequencing (NGS), NGS-based single gene tests for diagnostic purposes require improvements in terms of completeness, quality, speed, and cost. Single-molecule molecular inversion probes (smMIPs) are a technology with unrealized potential in the area of clinical genetic testing. In this proof-of-concept study, we selected 2 frequently requested gene tests, those for the breast cancer genes BRCA1 and BRCA2, and developed an automated work flow based on smMIPs. METHODS The BRCA1 and BRCA2 smMIPs were validated using 166 human genomic DNA samples with known variant status. A generic automated work flow was built to perform smMIP-based enrichment and sequencing for BRCA1, BRCA2, and the checkpoint kinase 2 (CHEK2) c.1100del variant. RESULTS Pathogenic and benign variants were analyzed in a subset of 152 previously BRCA-genotyped samples, yielding an analytical sensitivity and specificity of 100%. Following automation, blind analysis of 65 in-house samples and 267 Norwegian samples correctly identified all true-positive variants (>3000), with no false positives. Consequent to process optimization, turnaround times were reduced by 60% to currently 10–15 days. Copy number variants were detected with an analytical sensitivity of 100% and an analytical specificity of 88%. CONCLUSIONS smMIP-based genetic testing enables automated and reliable analysis of the coding sequences of BRCA1 and BRCA2. The use of single-molecule tags, double-tiled targeted enrichment, and capturing and sequencing in duplo, in combination with automated library preparation and data analysis, results in a robust process and reduces routine turnaround times. Furthermore, smMIP-based copy number variation analysis could make independent copy number variation tools like multiplex ligation-dependent probes amplification dispensable.

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Analysis of the Electron Traps at the 4H-SiC/SiO2 Interface of a Gate Oxide Obtained by Wet Oxidation of a Nitrogen Pre-Implanted Layer

Materials Science Forum ◽

10.4028/www.scientific.net/msf.615-617.533 ◽

2009 ◽

Vol 615-617 ◽

pp. 533-536

Author(s):

Ioana Pintilie ◽

Francesco Moscatelli ◽

Roberta Nipoti ◽

Antonella Poggi ◽

Sandro Solmi ◽

...

Keyword(s):

Low Frequency ◽

Gate Oxide ◽

High Accuracy ◽

Interface Trap Density ◽

Interface Trap ◽

High Concentration ◽

Mos Capacitors ◽

Order Of Magnitude ◽

Good Agreement

This work is focusing on the effect of a high concentration of nitrogen (N) introduced by ion implantation at the SiO2/4H-SiC interface in MOS capacitors. The N implanted sample (Ninterface ~1x1019cm-3) is compared with a non-implanted one (Ninterface ~1x1016cm-3) by means of the electron interface trap density (Dit). The Dit is determined via High-Low frequency C-V method and Thermal Dielectric Relaxation Current (TDRC) technique. It is shown that the TDRC method, mainly used so far for determination of near interface oxide charges, can be exploited to gain information about the Dit too. The determined value of Dit in the N-implanted sample is nearly one order of magnitude lower than that in the sample without N implantation. Good agreement between the TDRC results and those obtained from High-Low frequency C-V measurements is obtained. Furthermore, the TDRC method shows a high accuracy and resolution of Dit evaluation in the region close to the majority carrier band edge and gives information about the traps located into the oxide.

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Skeletal and Lattice Vibrations of Crystals of Dihalogenobis(pyridine)zinc(II)

Canadian Journal of Chemistry ◽

10.1139/v74-290 ◽

1974 ◽

Vol 52 (11) ◽

pp. 2005-2015 ◽

Cited By ~ 8

Author(s):

P. T. T. Wong

Keyword(s):

Single Molecule ◽

Room Temperature ◽

Normal Modes ◽

Low Frequency ◽

Far Infrared ◽

Liquid Nitrogen Temperature ◽

Lattice Vibrations ◽

Individual Molecule ◽

Stretching Vibrations ◽

The Individual

Detailed measurements of the low-frequency Raman spectra of the crystals of [ZnPy2Cl2] and [ZnPy2Br2] at room temperature, where Py is the pyridine molecule, and the far-infrared spectrum of the crystal of [ZnPy2Cl2] at liquid nitrogen temperature have been made. The vibrational frequencies for the single molecule and for the complete crystal of these two complexes have been calculated and compared with the observed spectra, and the distribution of the potential energy of the normal modes has also been calculated to assist the refinement of the calculation and the interpretation of the spectra. Apparently, the skeletal Zn–ligand vibrations of the individual molecule couple with the lattice vibrations in the crystal, except for the normal modes at 326 cm−1 for [ZnPy2Cl2] and at 250 cm−1 for [ZnPy2Br2] which are dominated by the Zn–halogen stretching vibrations. Reasonably good Zn–ligand stretching force constants were obtained. The nature of the coordination bonds of these complexes has been discussed.

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