High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing [PDF]
Nature Communications, 2018 Functional characterization of disease-causing variants at risk loci in cancer is challenging. Here, in prostate cancer the authors report a pipeline for high-throughput single-nucleotide polymorphisms sequencing (SNPs-seq) for large scale screening of ...
Peng Zhang +16 more
doaj +5 more sources
Large scale single nucleotide polymorphism discovery in unsequenced genomes using second generation high throughput sequencing technology: applied to turkey [PDF]
BMC Genomics, 2009 Background - The development of second generation sequencing methods has enabled large scale DNA variation studies at moderate cost. For the high throughput discovery of single nucleotide polymorphisms (SNPs) in species lacking a sequenced reference ...
Hindrik H. D. Kerstens +6 more
core +10 more sources
Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies [PDF]
PeerJ, 2023 Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area.
Johan Rollin +21 more
openalex +11 more sources
Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms [PDF]
Foods, 2023 Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC.
Marie‐Alice Fraiture +9 more
openalex +7 more sources
Additional file 3 of Correcting nucleotide-specific biases in high-throughput sequencing data
, 2017 Figure S2. ChIP-seq and DNase-seq coverage in a super enhancer region (Hnisz D, Abraham BJ, Lee TI, et al. Transcriptional super-enhancers connected to cell identity and disease. Cell. 2013;155(4):10.1016/j.cell.2013.09.053). This region is also in a DNase hypersensitivity region.
Jeremy Wang +2 more
+4 more sources
A Systematic Evaluation of High-Throughput Sequencing Approaches to Identify Low-Frequency Single Nucleotide Variants in Viral Populations [PDF]
Viruses, 2020 High-throughput sequencing such as those provided by Illumina are an efficient way to understand sequence variation within viral populations. However, challenges exist in distinguishing process-introduced error from biological variance, which significantly impacts our ability to identify sub-consensus single-nucleotide variants (SNVs).
David J. King +7 more
openalex +5 more sources
Additional file 1 of Correcting nucleotide-specific biases in high-throughput sequencing data
, 2017 Figure S1. GM12878 DNase-seq 5-mer tile covariance matrix. The pairwise correlation is shown between bias values of 5-mer tiles in a 160bp window surrounding the 5â end of aligned reads. The block structure between tiles 0 and 3 indicates correlation between adjacent k-mer frequencies within DNase-seq reads. (PDF 203 kb)
Jeremy Wang +2 more
+4 more sources
Additional file 2 of Correcting nucleotide-specific biases in high-throughput sequencing data
, 2017 Table S1. Area under curve (AUC) values for the ROC curves representing sensitivity and specificity of footprint detection for several transcription factors. AUC values at increasing false positive rates (FPR) are computed independently for each motif before and after correction.
Jeremy Wang +2 more
+4 more sources
Ten simple rules for managing high-throughput nucleotide sequencing data [PDF]
, 2016 AbstractThe challenges posed by large data volumes produced by high-throughput nucleotide sequencing technologies are well known. This document establishes ten simple rules for coping with these challenges. At the level of master data management, (1) data triage reduces data volumes; (2) some lossless data representations are much more compact than ...
Rutger Vos
openalex +2 more sources
High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution [PDF]
Nucleic Acids Research, 2019 Abstract Targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S rRNA gene fragments is widely used to profile microbial communities. New long-read sequencing technologies can sequence the entire 16S rRNA gene, but higher error rates have limited their attractiveness when accuracy is important.
Benjamin J. Callahan +7 more
openalex +3 more sources