GeTallele: A Method for Analysis of DNA and RNA Allele Frequency Distributions

This is the final version. Available on open access from Frontiers Media via the DOI in this recordData Availability Statement: The data analyzed in this study is subject to the following licenses/restrictions: The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. Requests to access these datasets should be directed to [email protected] allele frequencies (VAF) are an important measure of genetic variation that can be estimated at single-nucleotide variant (SNV) sites. RNA and DNA VAFs are used as indicators of a wide-range of biological traits, including tumor purity and ploidy changes, allele-specific expression and gene-dosage transcriptional response. Here we present a novel methodology to assess gene and chromosomal allele asymmetries and to aid in identifying genomic alterations in RNA and DNA datasets. Our approach is based on analysis of the VAF distributions in chromosomal segments (continuous multi-SNV genomic regions). In each segment we estimate variant probability, a parameter of a random process that can generate synthetic VAF samples that closely resemble the observed data. We show that variant probability is a biologically interpretable quantitative descriptor of the VAF distribution in chromosomal segments which is consistent with other approaches. To this end, we apply the proposed methodology on data from 72 samples obtained from patients with breast invasive carcinoma (BRCA) from The Cancer Genome Atlas (TCGA). We compare DNA and RNA VAF distributions from matched RNA and whole exome sequencing (WES) datasets and find that both genomic signals give very similar segmentation and estimated variant probability profiles. We also find a correlation between variant probability with copy number alterations (CNA). Finally, to demonstrate a practical application of variant probabilities, we use them to estimate tumor purity. Tumor purity estimates based on variant probabilities demonstrate good concordance with other approaches (Pearson's correlation between 0.44 and 0.76). Our evaluation suggests that variant probabilities can serve as a dependable descriptor of VAF distribution, further enabling the statistical comparison of matched DNA and RNA datasets. Finally, they provide conceptual and mechanistic insights into relations between structure of VAF distributions and genetic events. The methodology is implemented in a Matlab toolbox that provides a suite of functions for analysis, statistical assessment and visualization of Genome and Transcriptome allele frequencies distributions. GeTallele is available at: https://github.com/SlowinskiPiotr/GeTalleleMcCormick Genomic and Proteomic Center (MGPC)George Washington UniversityWellcome TrustEngineering and Physical Sciences Research Council (EPSRC

ReQTL: Identifying correlations between expressed SNVs and gene expression using RNA-sequencing data

This is the author accepted manuscript. The final version is available on open access from OUP via the DOI in this recordBy testing for associations between DNA genotypes and gene expression levels, expression quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands of single nucleotide variants (SNVs) may affect gene expression. As compared to DNA genotypes, RNA genetic variation represents a phenotypic trait that reflects the actual allele content of the studied system. RNA genetic variation at expressed SNV loci can be estimated using the proportion of alleles bearing the variant nucleotide (variant allele fraction, VAFRNA). VAFRNA is a continuous measure which allows for precise allele quantitation in loci where the RNA alleles do not scale with the genotype count. We describe a method to correlate VAFRNA to gene expression, and assess its ability to identify genetically regulated expression solely from RNA-sequencing (RNA-seq) datasets.We introduce ReQTL, an eQTL modification which substitutes the DNA allele count for the variant allele fraction at expressed SNV loci in the transcriptome (VAFRNA). We exemplify the method on sets of RNA-seq data from human tissues obtained though the Genotype-Tissue Expression Project (GTEx) and demonstrate that ReQTL analyses are computationally feasible and can identify a subset of expressed eQTL loci.A toolkit to perform ReQTL analyses is available at https://github.com/HorvathLab/ReQTL.Re_QTL_Supplementary_Data.zipMcCormick Genomic and Proteomic Center (MGPC), The George Washington UniversityNIH National Center for Advancing Translational Scienc

Early Mutants of Polyoma Virus (dl8 and dl23) with Altered Transformation Properties: Is Polyoma Virus Middle T Antigen a Transforming Gene Product?

The questions raised by Dulbecco (1975)—“Is transformation the result of provirus integration … or is it the consequence of the expression of genes present in the provirus?”—have not yet been satisfactorily answered. However, several lines of evidence from recent experiments on many different tumor viruses, as presented in this volume, strongly suggest that viral gene expression is required for transformation, the best evidence still arising from studies on the avian RNA tumor viruses (see Vogt 1977; Hanafusa 1977). With regard to polyoma virus, evidence also exists which indicates that viral gene expression is needed. Studies by Seif and Cuzin (1977) on transformation induced in rat cells by temperature-sensitive tsA mutants of polyoma virus suggest that the transformed phenotype is a complex interplay between various types of controls, including expression of a virus-coded protein, as well as cellular changes induced by the virus or selected for during growth in culture. Data..

Investigation of cirrus cloud properties in the tropical tropopause layer using high-altitude limb-scanning near-IR spectroscopy during NASA-ATTREX

Tropical-tropopause-layer cirrus clouds and their radiative effects represent a major uncertainty in the evaluation of Earth’s energy budget. High-altitude aircraft offer an opportunity to provide observations at cirrus cloud altitudes, most commonly using in situ measurements of ice particle optical properties and composition. In particular, remote sensing of scattering properties and near-IR ice water absorption in the limb can provide unique insights into thin and sub-visible cirrus clouds. Here we present novel spectroscopic observations of path-averaged ice water absorptions on board NASA’s Global Hawk aircraft during the Airborne Tropical TRopopause Experiment (ATTREX), which took place in 2011, 2013, and 2014. The University of California Los Angeles and University of Heidelberg mini-differential optical absorption spectroscopy (mini-DOAS) instrument provided multi-angle limb-scanning observations of scattered solar radiation in the near-IR (900–1726 nm), allowing the identification of ice and liquid water, O2, CO2, and H2O. The VLIDORT-QS radiative transfer (RT) code was specifically developed for this study and used to simulate high-altitude limb observations for varied cloud scenarios. We performed a comprehensive sensitivity study, developing a fundamental understanding of airborne near-IR limb observations of cirrus clouds. We identified two general distinct cases: a linear regime for optically thin clouds, where the ice absorption is proportional to ice water content (IWC), and a regime for optically thick cirrus clouds, where ice absorption is in saturation and independent of IWC. Results also demonstrate how molecular oxygen absorption can be used to infer information on optical properties of ice particles in the second regime only, with minimal information for thin cirrus clouds. We also explored the feasibility of retrieving IWC from mini-DOAS path-averaged ice water absorption (SIWP) measurements. This innovative interpolation-based approach requires a small number of RT calculations per observation to determine the sensitivity of SIWP to IWC. Spectral retrievals were applied for a particularly interesting case during Science Flight 2 over Guam in February 2014, during which the aircraft flew in circles in the same general area for an extended period of time. Retrieved IWC results are consistent with independent in situ measurements from other instruments on board. The measurements of ice particle scattering and absorption at different azimuths relative to the sun and at different altitudes represent a unique opportunity to test our approach and to infer properties of the ice particles, together with information on cirrus cloud radiative transfer.</p

scReQTL: an approach to correlate SNVs to gene expression from individual scRNA-seq datasets

This is the final version. Available from BMC via the DOI in this record. All data generated or analyzed during this study are included in this published article and its supplementary information files.Background: Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory single nucleotide variants (SNVs). Here, we present an alternative QTL-related approach applicable to transcribed SNV loci from scRNA-seq data: scReQTL. ScReQTL uses Variant Allele Fraction (VAFRNA) at expressed biallelic loci, and corelates it to gene expression from the corresponding cell. Results: Our approach employs the advantage that, when estimated from multiple cells, VAFRNA can be used to assess effects of SNVs in a single sample or individual. In this setting scReQTL operates in the context of identical genotypes, where it is likely to capture RNA-mediated genetic interactions with cell-specific and transient effects. Applying scReQTL on scRNA-seq data generated on the 10 × Genomics Chromium platform using 26,640 mesenchymal cells derived from adipose tissue obtained from three healthy female donors, we identified 1272 unique scReQTLs. ScReQTLs common between individuals or cell types were consistent in terms of the directionality of the relationship and the effect size. Comparative assessment with eQTLs from bulk sequencing data showed that scReQTL analysis identifies a distinct set of SNV-gene correlations, that are substantially enriched in known gene-gene interactions and significant genome-wide association studies (GWAS) loci. Conclusion: ScReQTL is relevant to the rapidly growing source of scRNA-seq data and can be applied to outline SNVs potentially contributing to cell type-specific and/or dynamic genetic interactions from an individual scRNA-seq dataset. Availability: https://github.com/HorvathLab/NGS/tree/master/scReQTLMcCormick Genomic and Proteomic Center (MGPC), The George Washington Universit

Polarization due to rotational distortion in the bright star Regulus

This is the full published article (retrieved from the 6 months post-publication posting on arXiv) including the Methods and Supplementary Information sections: 33 pages, 10 figures, 8 tablesPolarization in stars was first predicted by Chandrasekhar [1] who calculated a substantial linear polarization at the stellar limb for a pure electron-scattering atmosphere. This polarization will average to zero when integrated over a spherical star but could be detected if the symmetry is broken, for example by the eclipse of a binary companion. Nearly 50 years ago, Harrington and Collins [2] modeled another way of breaking the symmetry and producing net polarization - the distortion of a rapidly rotating hot star. Here we report the first detection of this effect. Observations of the linear polarization of Regulus, with two different high-precision polarimeters, range from +42 parts-per-million (ppm) at a wavelength of 741 nm to -22 ppm at 395 nm. The reversal from red to blue is a distinctive feature of rotation-induced polarization. Using a new set of models for the polarization of rapidly rotating stars we find that Regulus is rotating at 96.5(+0.6/-0.8)% of its critical angular velocity for breakup, and has an inclination greater than 76.5 degrees. The rotation axis of the star is at a position angle of 79.5+/-0.7 degrees. The conclusions are independent of, but in good agreement with, the results of previously published interferometric observations of Regulus [3]. The accurate measurement of rotation in early-type stars is important for understanding their stellar environments [4], and course of their evolution [5].Peer reviewedFinal Accepted Versio