A5064279895- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- RNA regulation and disease
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- Cancer Genomics and Diagnostics
- RNA modifications and cancer
- Plant Disease Resistance and Genetics
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- Gene expression and cancer classification
- Epigenetics and DNA Methylation
- Viral Infections and Immunology Research
- RNA Interference and Gene Delivery
- Graphene and Nanomaterials Applications
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- Extracellular vesicles in disease
- Genetic factors in colorectal cancer
- Genomics and Rare Diseases
- Nanoparticle-Based Drug Delivery
McCormick (United States)
2016-2021
George Washington University
2016-2021
Genomics (United Kingdom)
2019
King Saud bin Abdulaziz University for Health Sciences
2017
Institute of Developmental Physiology
2017
National Guard Health Affairs
2017
Georgetown University
2016
Abstract Background Recent studies have demonstrated the utility of scRNA-seq SNVs to distinguish tumor from normal cells, characterize intra-tumoral heterogeneity, and define mutation-associated expression signatures. In addition cancer studies, single cells been useful in transcriptional burst kinetics, allelic expression, chromosome X inactivation, ploidy estimations, haplotype inference. Results To aid these types we developed a tool, SCReadCounts, for cell-level tabulation sequencing...
With the recent advances in single-cell RNA-sequencing (scRNA-seq) technologies, estimation of allele expression from single cells is becoming increasingly reliable. Allele both quantitative and dynamic an essential component genomic interactome. Here, we systematically estimate heterozygous nucleotide variant (SNV) loci using scRNA-seq data generated on 10×Genomics Chromium platform. We analyzed 26,640 human adipose-derived mesenchymal stem (from three healthy donors), sequenced to average...
Purpose: Anastrozole (ANS) is an aromatase inhibitor that widely used as a treatment for breast cancer in postmenopausal women. Despite the wide use of ANS, it associated with serious side effects due to uncontrolled delivery. In addition, ANS exhibits low solubility and short plasma half-life. Nanotechnology-based drug delivery has potential enhance efficacy drugs overcome undesirable effects. this study, we aimed prepare novel ANS-loaded PLA-PEG-PLA nanoparticles (ANS-NPs) compare...
Abstract Imbalanced expression of somatic alleles in cancer can suggest functional and selective features, therefore indicate possible driving potential the underlying genetic variants. To explore correlation between allele frequency variants total gene their harboring gene, we used unique data set matched tumor normal RNA DNA sequencing 5523 distinct single nucleotide 381 individuals across 10 types obtained from The Cancer Genome Atlas (TCGA). We analyzed context variant features linked it...
Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory nucleotide variants (SNVs). Here, we present an alternative QTL-related approach applicable to transcribed SNV from scRNA-seq data: scReQTL. ScReQTL uses Variant Allele Fraction (VAFRNA) at expressed biallelic loci, corelates it gene the corresponding cell.Our employs advantage that, when estimated multiple cells, VAFRNA can be...
We introduce RNA2DNAlign, a computational framework for quantitative assessment of allele counts across paired RNA and DNA sequencing datasets. RNA2DNAlign is based on quantitation the relative abundance variant reference read counts, followed by binomial tests genotype allelic status at SNV positions between compatible sequences. detects with differential distribution, suggesting asymmetries due to regulatory/structural events. Based type asymmetry, outlines likely be implicated in editing,...
Abstract Motivation By testing for associations between DNA genotypes and gene expression levels, quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands of single nucleotide variants (SNVs) may affect expression. As compared to genotypes, RNA genetic variation represents a phenotypic that reflects the actual allele content studied system. at expressed SNV loci can be estimated using proportion alleles bearing variant (variant fraction, VAFRNA). VAFRNA...
Abstract With the recent advances in single-cell RNA-sequencing (scRNA-seq) technologies, estimation of allele expression from single cells is becoming increasingly reliable. Allele both quantitative and dynamic an essential component genomic interactome. Here, we systematically estimate heterozygous nucleotide variant (SNV) loci using scRNA-seq data generated on 10x Genomics platform. We include analysis 26,640 human adipose-derived mesenchymal stem (from three healthy donors), with average...
Asymmetric allele content in the transcriptome can be indicative of functional and selective features underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored cancer. Here we systematically quantify integrate variant fraction corresponding RNA DNA sequence data patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between prevalence functionality known cancer-implicated genes Gene Census...
Variant allele frequencies (VAF) are an important measure of genetic variation that can be estimated at single-nucleotide variant (SNV) sites. RNA and DNA VAFs used as indicators a wide-range biological traits, including tumor purity ploidy changes, allele-specific expression gene-dosage transcriptional response. Here we present novel methodology to assess gene chromosomal asymmetries aid in identifying genomic alterations datasets. Our approach is based on analysis the VAF distributions...
Summary: SCReadCounts is a method for cell-level estimation of the sequencing read counts bearing particular nucleotide at genomic positions interest from barcoded scRNA-seq alignments. generates an array outputs, including cell-SNV matrices with absolute variant-harboring counts, as well expressed Variant Allele Fraction (VAF RNA ); we demonstrate its application to estimate cell level expression somatic mutations and RNA-editing on cancer datasets. benchmarked against GATK Samtools freely...
Summary RsQTL is a tool for identification of splicing quantitative trait loci (sQTLs) from RNA-sequencing (RNA-seq) data by correlating the variant allele fraction at expressed SNV in transcriptome (VAF RNA ) with proportion molecules spanning local exon-exon junctions differential intron excision (percent spliced in, PSI). We exemplify method on sets RNA-seq human tissues obtained though Genotype-Tissue Expression Project (GTEx). does not require matched DNA and can identify subset sQTL...
Motivation By testing for association of DNA genotypes with gene expression levels, quantitative trait locus (eQTL) analyses have been instrumental in understanding how thousands single nucleotide variants (SNVs) may affect expression. As compared to genotypes, RNA genetic variation represents a phenotypic that reflects the actual allele content studied system. can be measured at expressed genome regions, and differs from genotype sites subjected regulatory forces. Therefore, assessment...
Abstract Recently, pioneering eQTLs studies on single cell RNA-seq (scRNA-seq) data have revealed new and cell-specific regulatory SNVs. Because correlate genotypes gene expression across multiple individuals, they are confined to SNVs with sufficient population frequency. Here, we present an alternative sc-eQTL approach – scReQTL - wherein substitute the expressed Variant Allele Fraction (VAF RNA ) at heterozygous SNV sites. Our employs advantage that, when estimated from cells, VAF can be...
Abstract Background Asymmetric allele expression typically indicates functional and/or structural features associated with the underlying genetic variants. When integrated, RNA and DNA frequencies can reveal patterns characteristic of a wide-range biological traits, including ploidy changes, genome admixture, allele-specific gene-dosage transcriptional response. Results To assess from matched sequencing datasets, we introduce method for generating model distributions variant (VAF) given read...