Monovar: single nucleotide variant detection in single cells [PDF]
Nature Methods, 2016 Current variant callers are not suitable for single-cell DNA sequencing, as they do not account for allelic dropout, false-positive errors and coverage nonuniformity.
Hamim Zafar +4 more
semanticscholar +5 more sources
Quantifying single nucleotide variant detection sensitivity in exome sequencing [PDF]
BMC Bioinformatics, 2013 The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to ...
A. Meynert +4 more
semanticscholar +5 more sources
SomatoSim: precision simulation of somatic single nucleotide variants [PDF]
BMC Bioinformatics, 2021 Background Somatic single nucleotide variants have gained increased attention because of their role in cancer development and the widespread use of high-throughput sequencing techniques.
Marwan A. Hawari +2 more
doaj +3 more sources
A framework for the estimation of the proportion of true discoveries in single nucleotide variant detection studies for human data. [PDF]
PLoS ONE, 2018 Any single nucleotide variant detection study could benefit from a fast and cheap method of measuring the quality of variant call list. It is advantageous to be able to see how the call list quality is affected by different variant filtering thresholds ...
Nik Tuzov
doaj +2 more sources
A resource of variant effect predictions of single nucleotide variants in model organisms
Molecular Systems Biology, 2018 The effect of single nucleotide variants (SNVs) in coding and noncoding regions is of great interest in genetics. Although many computational methods aim to elucidate the effects of SNVs on cellular mechanisms, it is not straightforward to ...
O. Wagih +5 more
semanticscholar +6 more sources
Programmable Argonaute-mediated single-nucleotide variant sequencing of cell-free DNA for multi-cancer early detection [PDF]
Nature CommunicationsMutation sequencing of cell-free DNA (cfDNA) in liquid biopsy is crucial for tumor precision medicine, resistance profiling, and clinical decision-making. However, cfDNA mutation profiling in blood samples remains challenging due to its low abundance and
Chong Guo +15 more
doaj +2 more sources
A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data
Computational and Structural Biotechnology Journal, 2018 Detection of somatic mutations holds great potential in cancer treatment and has been a very active research field in the past few years, especially since the breakthrough of the next-generation sequencing technology.
Chang Xu
doaj +2 more sources
Germline contamination and leakage in whole genome somatic single nucleotide variant detection
BMC Bioinformatics, 2018 Background The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be controlled.
Dorota H. Sendorek +10 more
doaj +2 more sources
Regulatory single nucleotide variant predictor (RSVP) increases predictive performance of functional regulatory variants [PDF]
Human Mutation, 2016 In silico methods for detecting functionally relevant genetic variants are important for identifying genetic markers of human inherited disease. Much research has focused on protein‐coding variants since coding regions have well‐defined physicochemical ...
Thomas A. Peterson +5 more
semanticscholar +4 more sources
Empirical Bayes single nucleotide variant-calling for next-generation sequencing data [PDF]
Scientific ReportsOne of the fundamental computational problems in cancer genomics is the identification of single nucleotide variants (SNVs) from DNA sequencing data.
Ali Karimnezhad, Theodore J. Perkins
doaj +2 more sources