Genome-wide analysis and visualization of copy number with CNVpytor in igv.js.

SUMMARY: Copy number variation (CNV) and alteration (CNA) analysis is a crucial component in many genomic studies and its applications span from basic research to clinic diagnostics and personalized medicine. CNVpytor is a tool featuring a read depth-based caller and combined read depth and B-allele frequency (BAF) based 2D caller to find CNVs and CNAs. The tool stores processed intermediate data and CNV/CNA calls in a compact HDF5 file-pytor file. Here, we describe a new track in igv.js that utilizes pytor and whole genome variant files as input for on-the-fly read depth and BAF visualization, CNV/CNA calling and analysis. Embedding into HTML pages and Jupiter Notebooks enables convenient remote data access and visualization simplifying interpretation and analysis of omics data. AVAILABILITY AND IMPLEMENTATION: The CNVpytor track is integrated with igv.js and available at https://github.com/igvteam/igv.js. The documentation is available at https://github.com/igvteam/igv.js/wiki/cnvpytor. Usage can be tested in the IGV-Web app at https://igv.org/app and also on https://github.com/abyzovlab/CNVpytor.

Toward Absolute Quantification of Soluble Proteins via Proton Nuclear Magnetic Resonance Spectroscopy: Total Protein Concentration in Blood Plasma.

For absolute protein quantification using nuclear magnetic resonance (NMR) spectroscopy, we considered proteins as homopolymers and effective amino acid (AA) residues (AAREff) as monomer units. For diverse classes of proteins, we determined the AAREff molecular weight as 111.5 ± 3.2 Da and the number of hydrogens per AA as 7.8 ± 0.2. Their ratio of 14.3 ± 0.3 (g/LP)/(mol/LH) remains constant across various protein classes and is equivalent to Kjeldahl's nitrogen-to-protein conversion constant of 5.78 ± 0.29 gN/gP. By analogy to the Kjeldahl method, we suggest that the total integral of a 1H NMR solution protein spectrum could be used for total protein quantification. We synthesized low-resolution protein spectra from the weighted sums of individual AA spectra and compared them with experimental spectra. In the methyl region, the ratio of the protein mass to the total number of protons in the synthetic spectra (corrected for the chemical shift mismatch) was ∼1 (mg/mL)/mM, which agrees with an earlier reported experimental ratio for urine (1.05 ± 0.06 (mg/mL)/mM). For human blood plasma, in the methyl region, we found empirical ratios of 1.115 ± 0.006 (mg/mL)/mM (using 96 patient samples) and 1.121 ± 0.011 (mg/mL)/mM for the NIST plasma standard. This numerical agreement points to universal conversion constants, i.e., protein mixtures with unknown compositions could be quantified without the need for calibration standards by measuring the millimolar proton concentration within the methyl region of the NMR spectrum using the same conversion constant.

Correction: All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons.

[This corrects the article DOI: 10.1371/journal.pcbi.1009487.].

All2: A tool for selecting mosaic mutations from comprehensive multi-cell comparisons.

Accurate discovery of somatic mutations in a cell is a challenge that partially lays in immaturity of dedicated analytical approaches. Approaches comparing a cell's genome to a control bulk sample miss common mutations, while approaches to find such mutations from bulk suffer from low sensitivity. We developed a tool, All2, which enables accurate filtering of mutations in a cell without the need for data from bulk(s). It is based on pair-wise comparisons of all cells to each other where every call for base pair substitution and indel is classified as either a germline variant, mosaic mutation, or false positive. As All2 allows for considering dropped-out regions, it is applicable to whole genome and exome analysis of cloned and amplified cells. By applying the approach to a variety of available data, we showed that its application reduces false positives, enables sensitive discovery of high frequency mutations, and is indispensable for conducting high resolution cell lineage tracing.

1H Nuclear Magnetic Resonance Spectroscopy-Based Methods for the Quantification of Proteins in Urine.

We described several postprocessing methods to measure protein concentrations in human urine from existing 1H nuclear magnetic resonance (NMR) metabolomic spectra: (1) direct spectral integration, (2) integration of NCD spectra (NCD = 1D NOESY-CPMG), (3) integration of SMolESY-filtered 1D NOESY spectra (SMolESY = Small Molecule Enhancement SpectroscopY), (4) matching protein patterns, and (5) TSP line integral and TSP linewidth. Postprocessing consists of (a) removal of the metabolite signals (demetabolization) and (b) extraction of the protein integral from the demetabolized spectra. For demetabolization, we tested subtraction of the spin-echo 1D spectrum (CPMG) from the regular 1D spectrum and low-pass filtering of 1D NOESY by its derivatives (c-SMolESY). Because of imperfections in the demetabolization, in addition to direct integration, we extracted protein integrals by the piecewise comparison of demetabolized spectra with the reference spectrum of albumin. We analyzed 42 urine samples with protein content known from the bicinchoninic acid (BCA) assay. We found excellent correlation between the BCA assay and the demetabolized NMR integrals. We have provided conversion factors for calculating protein concentrations in mg/mL from spectral integrals in mM. Additionally, we found the trimethylsilyl propionate (TSP, NMR standard) spectral linewidth and the TSP integral to be good indicators of protein concentration. The described methods increase the information content of urine NMR metabolomics spectra by informing clinical studies of protein concentration.

Magnetisation Processes in Geometrically Frustrated Spin Networks with Self-Assembled Cliques.

Functional designs of nanostructured materials seek to exploit the potential of complex morphologies and disorder. In this context, the spin dynamics in disordered antiferromagnetic materials present a significant challenge due to induced geometric frustration. Here we analyse the processes of magnetisation reversal driven by an external field in generalised spin networks with higher-order connectivity and antiferromagnetic defects. Using the model in (Tadic et al. Arxiv:1912.02433), we grow nanonetworks with geometrically constrained self-assemblies of simplexes (cliques) of a given size n, and with probability p each simplex possesses a defect edge affecting its binding, leading to a tree-like pattern of defects. The Ising spins are attached to vertices and have ferromagnetic interactions, while antiferromagnetic couplings apply between pairs of spins along each defect edge. Thus, a defect edge induces n - 2 frustrated triangles per n-clique participating in a larger-scale complex. We determine several topological, entropic, and graph-theoretic measures to characterise the structures of these assemblies. Further, we show how the sizes of simplexes building the aggregates with a given pattern of defects affects the magnetisation curves, the length of the domain walls and the shape of the hysteresis loop. The hysteresis shows a sequence of plateaus of fractional magnetisation and multiscale fluctuations in the passage between them. For fully antiferromagnetic interactions, the loop splits into two parts only in mono-disperse assemblies of cliques consisting of an odd number of vertices n. At the same time, remnant magnetisation occurs when n is even, and in poly-disperse assemblies of cliques in the range n ∈ [ 2 , 10 ] . These results shed light on spin dynamics in complex nanomagnetic assemblies in which geometric frustration arises in the interplay of higher-order connectivity and antiferromagnetic interactions.

Gravitational waves from periodic three-body systems.

Three bodies moving in a periodic orbit under the influence of Newtonian gravity ought to emit gravitational waves. We have calculated the gravitational radiation quadrupolar waveforms and the corresponding luminosities for the 13+11 recently discovered three-body periodic orbits in Newtonian gravity. These waves clearly allow one to distinguish between their sources: all 13+11 orbits have different waveforms and their luminosities (evaluated at the same orbit energy and body mass) vary by up to 13 orders of magnitude in the mean, and up to 20 orders of magnitude for the peak values.

Three classes of newtonian three-body planar periodic orbits.

We present the results of a numerical search for periodic orbits of three equal masses moving in a plane under the influence of Newtonian gravity, with zero angular momentum. A topological method is used to classify periodic three-body orbits into families, which fall into four classes, with all three previously known families belonging to one class. The classes are defined by the orbits' geometric and algebraic symmetries. In each class we present a few orbits' initial conditions, 15 in all; 13 of these correspond to distinct orbits.

Clonally Selected Lines After CRISPR-Cas Editing Are Not Isogenic.

The CRISPR-Cas9 system has enabled researchers to precisely modify/edit the sequence of a genome. A typical editing experiment consists of two steps: (1) editing cultured cells; (2) cell cloning and selection of clones with and without intended edit, presumed to be isogenic. The application of CRISPR-Cas9 system may result in off-target edits, whereas cloning will reveal culture-acquired mutations. We analyzed the extent of the former and the latter by whole genome sequencing in three experiments involving separate genomic loci and conducted by three independent laboratories. In all experiments we hardly found any off-target edits, whereas detecting hundreds to thousands of single nucleotide mutations unique to each clone after relatively short culture of 10-20 passages. Notably, clones also differed in copy number alterations (CNAs) that were several kb to several mb in size and represented the largest source of genomic divergence among clones. We suggest that screening of clones for mutations and CNAs acquired in culture is a necessary step to allow correct interpretation of DNA editing experiments. Furthermore, since culture associated mutations are inevitable, we propose that experiments involving derivation of clonal lines should compare a mix of multiple unedited lines and a mix of multiple edited lines.

Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis.

Idiopathic autism spectrum disorder (ASD) is highly heterogeneous, and it remains unclear how convergent biological processes in affected individuals may give rise to symptoms. Here, using cortical organoids and single-cell transcriptomics, we modeled alterations in the forebrain development between boys with idiopathic ASD and their unaffected fathers in 13 families. Transcriptomic changes suggest that ASD pathogenesis in macrocephalic and normocephalic probands involves an opposite disruption of the balance between excitatory neurons of the dorsal cortical plate and other lineages such as early-generated neurons from the putative preplate. The imbalance stemmed from divergent expression of transcription factors driving cell fate during early cortical development. While we did not find genomic variants in probands that explained the observed transcriptomic alterations, a significant overlap between altered transcripts and reported ASD risk genes affected by rare variants suggests a degree of gene convergence between rare forms of ASD and the developmental transcriptome in idiopathic ASD.

Analysis of somatic mutations in 131 human brains reveals aging-associated hypermutability.

We analyzed 131 human brains (44 neurotypical, 19 with Tourette syndrome, 9 with schizophrenia, and 59 with autism) for somatic mutations after whole genome sequencing to a depth of more than 200×. Typically, brains had 20 to 60 detectable single-nucleotide mutations, but ~6% of brains harbored hundreds of somatic mutations. Hypermutability was associated with age and damaging mutations in genes implicated in cancers and, in some brains, reflected in vivo clonal expansions. Somatic duplications, likely arising during development, were found in ~5% of normal and diseased brains, reflecting background mutagenesis. Brains with autism were associated with mutations creating putative transcription factor binding motifs in enhancer-like regions in the developing brain. The top-ranked affected motifs corresponded to MEIS (myeloid ectopic viral integration site) transcription factors, suggesting a potential link between their involvement in gene regulation and autism.

CNVpytor: a tool for copy number variation detection and analysis from read depth and allele imbalance in whole-genome sequencing.

BACKGROUND: Detecting copy number variations (CNVs) and copy number alterations (CNAs) based on whole-genome sequencing data is important for personalized genomics and treatment. CNVnator is one of the most popular tools for CNV/CNA discovery and analysis based on read depth. FINDINGS: Herein, we present an extension of CNVnator developed in Python-CNVpytor. CNVpytor inherits the reimplemented core engine of its predecessor and extends visualization, modularization, performance, and functionality. Additionally, CNVpytor uses B-allele frequency likelihood information from single-nucleotide polymorphisms and small indels data as additional evidence for CNVs/CNAs and as primary information for copy number-neutral losses of heterozygosity. CONCLUSIONS: CNVpytor is significantly faster than CNVnator-particularly for parsing alignment files (2-20 times faster)-and has (20-50 times) smaller intermediate files. CNV calls can be filtered using several criteria, annotated, and merged over multiple samples. Modular architecture allows it to be used in shared and cloud environments such as Google Colab and Jupyter notebook. Data can be exported into JBrowse, while a lightweight plugin version of CNVpytor for JBrowse enables nearly instant and GUI-assisted analysis of CNVs by any user. CNVpytor release and the source code are available on GitHub at https://github.com/abyzovlab/CNVpytor under the MIT license.

Large-scale influence of defect bonds in geometrically constrained self-assembly.

Recently, the importance of higher-order interactions in the physics of quantum systems and nanoparticle assemblies has prompted the exploration of new classes of networks that grow through geometrically constrained simplex aggregation. Based on the model of chemically tunable self-assembly of simplexes [Suvakov et al., Sci. Rep. 8, 1987 (2018)2045-232210.1038/s41598-018-20398-x], here we extend the model to allow the presence of a defect edge per simplex. Using a wide distribution of simplex sizes (from edges, triangles, tetrahedrons, etc., up to 10-cliques) and various chemical affinity parameters, we investigate the magnitude of the impact of defects on the self-assembly process and the emerging higher-order networks. Their essential characteristics are treelike patterns of defect bonds, hyperbolic geometry, and simplicial complexes, which are described using the algebraic topology method. Furthermore, we demonstrate how the presence of patterned defects can be used to alter the structure of the assembly after the growth process is complete. In the assemblies grown under different chemical affinities, we consider the removal of defect bonds and analyze the progressive changes in the hierarchical architecture of simplicial complexes and the hyperbolicity parameters of the underlying graphs. Within the framework of cooperative self-assembly of nanonetworks, these results shed light on the use of defects in the design of complex materials. They also provide a different perspective on the understanding of extended connectivity beyond pairwise interactions in many complex systems.

Hidden geometries in networks arising from cooperative self-assembly.

Multilevel self-assembly involving small structured groups of nano-particles provides new routes to development of functional materials with a sophisticated architecture. Apart from the inter-particle forces, the geometrical shapes and compatibility of the building blocks are decisive factors. Therefore, a comprehensive understanding of these processes is essential for the design of assemblies of desired properties. Here, we introduce a computational model for cooperative self-assembly with the simultaneous attachment of structured groups of particles, which can be described by simplexes (connected pairs, triangles, tetrahedrons and higher order cliques) to a growing network. The model incorporates geometric rules that provide suitable nesting spaces for the new group and the chemical affinity of the system to accept excess particles. For varying chemical affinity, we grow different classes of assemblies by binding the cliques of distributed sizes. Furthermore, we characterize the emergent structures by metrics of graph theory and algebraic topology of graphs, and 4-point test for the intrinsic hyperbolicity of the networks. Our results show that higher Q-connectedness of the appearing simplicial complexes can arise due to only geometric factors and that it can be efficiently modulated by changing the chemical potential and the polydispersity of the binding simplexes.

How the online social networks are used: dialogues-based structure of MySpace.

Quantitative study of collective dynamics in online social networks is a new challenge based on the abundance of empirical data. Conclusions, however, may depend on factors such as user's psychology profiles and their reasons to use the online contacts. In this study, we have compiled and analysed two datasets from MySpace. The data contain networked dialogues occurring within a specified time depth, high temporal resolution and texts of messages, in which the emotion valence is assessed by using the SentiStrength classifier. Performing a comprehensive analysis, we obtain three groups of results: dynamic topology of the dialogues-based networks have a characteristic structure with Zipf's distribution of communities, low link reciprocity and disassortative correlations. Overlaps supporting 'weak-ties' hypothesis are found to follow the laws recently conjectured for online games. Long-range temporal correlations and persistent fluctuations occur in the time series of messages carrying positive (negative) emotion; patterns of user communications have dominant positive emotion (attractiveness) and strong impact of circadian cycles and interactivity times longer than 1 day. Taken together, these results give a new insight into the functioning of online social networks and unveil the importance of the amount of information and emotion that is communicated along the social links. All data used in this study are fully anonymized.

Approximate action-angle variables for the figure-eight and periodic three-body orbits.

We use the maximally permutation-symmetric set of three-body coordinates that consist of the "hyper-radius" R=√[ρ(2)+λ(2)], the "rescaled area of the triangle" √[3]/2R(2) |ρ×λ|), and the (braiding) hyperangle Φ=arctan(2ρ·λ/λ(2)-ρ(2)) to analyze the "figure-eight" choreographic three-body motion discovered by Moore [Phys. Rev. Lett. 70, 3675 (1993)] in the Newtonian three-body problem. Here ρ,λ are the two Jacobi relative coordinate vectors. We show that the periodicity of this motion is closely related to the braiding hyperangle Φ. We construct an approximate integral of motion ̅G that together with the hyperangle Φ forms the action-angle pair of variables for this problem and show that it is the underlying cause of figure-eight motion's stability. We construct figure-eight orbits in two other attractive permutation-symmetric three-body potentials. We compare the figure-eight orbits in these three potentials and discuss their generic features, as well as their differences. We apply these variables to two new periodic, but nonchoreographic, orbits: One has a continuously rising Φ in time t, just like the figure-eight motion, but with a different, more complex, periodicity, whereas the other one has an oscillating Φ(t) temporal behavior.

Modeling collective charge transport in nanoparticle assemblies.

Mapping the assembled patterns of nanoparticles onto networks (mathematical graphs) provides a way for quantitative analysis of the structure effects on the physical properties of the assembly. Here we review the network modeling of the conduction with single-electron tunneling mechanisms in the assembled nanoparticle films. Simulations of the conduction predict the nonlinear current-voltage curves in different classes of the nanoparticle networks. Furthermore, the numerical analysis reveals how the I(V) nonlinearity is related to the collective charge fluctuations along the conducting paths through the sample, and stresses the role of the topology and quenched charge disorder.

Efficient hidden-variable simulation of measurements in quantum experiments.

We prove that the results of a finite set of general quantum measurements on an arbitrary dimensional quantum system can be simulated using a polynomial (in measurements) number of hidden-variable states. In the limit of infinitely many measurements, our method gives models with the minimal number of hidden-variable states, which scales linearly with the number of measurements. These results can find applications in foundations of quantum theory, complexity studies, and classical simulations of quantum systems.

Charge transport in cellular nanoparticle networks: meandering through nanoscale mazes.

The transport of electrons through topologically complex two-dimensional Au nanoparticle networks has been investigated using a combination of low temperature (4.5 K) direct current I(V) measurements and numerical simulations. Intricate, spatially correlated nanostructured networks were formed via spin-casting. The topological complexity of the nanoparticle assemblies produces I(V) curves associated with nonlinearity exponents, zeta approximately 4.0. Simulations based on tunneling transport in sparse and inhomogeneous planar networks are used to elucidate the influence of topology on the value of zeta.