An evaluation of copy number variation detection tools for cancer using whole exome sequencing data.

Abstract:

BACKGROUND:Recently copy number variation (CNV) has gained considerable interest as a type of genomic/genetic variation that plays an important role in disease susceptibility. Advances in sequencing technology have created an opportunity for detecting CNVs more accurately. Recently whole exome sequencing (WES) has become primary strategy for sequencing patient samples and study their genomics aberrations. However, compared to whole genome sequencing, WES introduces more biases and noise that make CNV detection very challenging. Additionally, tumors' complexity makes the detection of cancer specific CNVs even more difficult. Although many CNV detection tools have been developed since introducing NGS data, there are few tools for somatic CNV detection for WES data in cancer. RESULTS:In this study, we evaluated the performance of the most recent and commonly used CNV detection tools for WES data in cancer to address their limitations and provide guidelines for developing new ones. We focused on the tools that have been designed or have the ability to detect cancer somatic aberrations. We compared the performance of the tools in terms of sensitivity and false discovery rate (FDR) using real data and simulated data. Comparative analysis of the results of the tools showed that there is a low consensus among the tools in calling CNVs. Using real data, tools show moderate sensitivity (~50% - ~80%), fair specificity (~70% - ~94%) and poor FDRs (~27% - ~60%). Also, using simulated data we observed that increasing the coverage more than 10× in exonic regions does not improve the detection power of the tools significantly. CONCLUSIONS:The limited performance of the current CNV detection tools for WES data in cancer indicates the need for developing more efficient and precise CNV detection methods. Due to the complexity of tumors and high level of noise and biases in WES data, employing advanced novel segmentation, normalization and de-noising techniques that are designed specifically for cancer data is necessary. Also, CNV detection development suffers from the lack of a gold standard for performance evaluation. Finally, developing tools with user-friendly user interfaces and visualization features can enhance CNV studies for a broader range of users.

journal_name

BMC Bioinformatics

journal_title

BMC bioinformatics

authors

Zare F,Dow M,Monteleone N,Hosny A,Nabavi S

doi

10.1186/s12859-017-1705-x

subject

Has Abstract

pub_date

2017-05-31 00:00:00

pages

286

issue

1

issn

1471-2105

pii

10.1186/s12859-017-1705-x

journal_volume

18

pub_type

杂志文章
  • E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI).

    abstract:BACKGROUND:The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-9-65

    authors: Puigbò P,Bravo IG,Garcia-Vallvé S

    更新日期:2008-01-29 00:00:00

  • Automated NMR relaxation dispersion data analysis using NESSY.

    abstract:BACKGROUND:Proteins are dynamic molecules with motions ranging from picoseconds to longer than seconds. Many protein functions, however, appear to occur on the micro to millisecond timescale and therefore there has been intense research of the importance of these motions in catalysis and molecular interactions. Nuclear...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-421

    authors: Bieri M,Gooley PR

    更新日期:2011-10-27 00:00:00

  • Bayesian inference of biochemical kinetic parameters using the linear noise approximation.

    abstract:BACKGROUND:Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models requires the development of effective statistical methods to calibrat...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-10-343

    authors: Komorowski M,Finkenstädt B,Harper CV,Rand DA

    更新日期:2009-10-19 00:00:00

  • ModuleOrganizer: detecting modules in families of transposable elements.

    abstract:BACKGROUND:Most known eukaryotic genomes contain mobile copied elements called transposable elements. In some species, these elements account for the majority of the genome sequence. They have been subject to many mutations and other genomic events (copies, deletions, captures) during transposition. The identification ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-474

    authors: Tempel S,Rousseau C,Tahi F,Nicolas J

    更新日期:2010-09-22 00:00:00

  • DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference.

    abstract:BACKGROUND:Inferring molecular pathway activity is an important step towards reducing the complexity of genomic data, understanding the heterogeneity in clinical outcome, and obtaining molecular correlates of cancer imaging traits. Increasingly, approaches towards pathway activity inference combine molecular profiles (...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-403

    authors: Jiao Y,Lawler K,Patel GS,Purushotham A,Jones AF,Grigoriadis A,Tutt A,Ng T,Teschendorff AE

    更新日期:2011-10-19 00:00:00

  • Uncovering packaging features of co-regulated modules based on human protein interaction and transcriptional regulatory networks.

    abstract:BACKGROUND:Network co-regulated modules are believed to have the functionality of packaging multiple biological entities, and can thus be assumed to coordinate many biological functions in their network neighbouring regions. RESULTS:Here, we weighted edges of a human protein interaction network and a transcriptional r...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-392

    authors: Chen L,Wang H,Zhang L,Li W,Wang Q,Shang Y,He Y,He W,Li X,Tai J,Li X

    更新日期:2010-07-22 00:00:00

  • Evaluation of absolute quantitation by nonlinear regression in probe-based real-time PCR.

    abstract:BACKGROUND:In real-time PCR data analysis, the cycle threshold (CT) method is currently the gold standard. This method is based on an assumption of equal PCR efficiency in all reactions, and precision may suffer if this condition is not met. Nonlinear regression analysis (NLR) or curve fitting has therefore been sugges...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-107

    authors: Goll R,Olsen T,Cui G,Florholmen J

    更新日期:2006-03-03 00:00:00

  • BioIMAX: a Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data.

    abstract:BACKGROUND:Innovations in biological and biomedical imaging produce complex high-content and multivariate image data. For decision-making and generation of hypotheses, scientists need novel information technology tools that enable them to visually explore and analyze the data and to discuss and communicate results or f...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-297

    authors: Loyek C,Rajpoot NM,Khan M,Nattkemper TW

    更新日期:2011-07-21 00:00:00

  • Calibration and assessment of channel-specific biases in microarray data with extended dynamical range.

    abstract:BACKGROUND:Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channels being compared. Any step in a microarray process may introduce such offsets and in this article we study the biases introduced by the micro...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-5-177

    authors: Bengtsson H,Jönsson G,Vallon-Christersson J

    更新日期:2004-11-12 00:00:00

  • WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.

    abstract:BACKGROUND:Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientifi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-15-159

    authors: Durrant JD,Amaro RE

    更新日期:2014-05-23 00:00:00

  • BIOSMILE: a semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features.

    abstract:BACKGROUND:Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporate natural language processing (NLP) techniques have thus been developed for use in the biomedical fi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-325

    authors: Tsai RT,Chou WC,Su YS,Lin YC,Sung CL,Dai HJ,Yeh IT,Ku W,Sung TY,Hsu WL

    更新日期:2007-09-01 00:00:00

  • Rapid forward-in-time simulation at the chromosome and genome level.

    abstract:BACKGROUND:In population genetics, simulation is a fundamental tool for analyzing how basic evolutionary forces such as natural selection, recombination, and mutation shape the genetic landscape of a population. Forward simulation represents the most powerful, but, at the same time, most compute-intensive approach for ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-14-216

    authors: Aberer AJ,Stamatakis A

    更新日期:2013-07-09 00:00:00

  • Protein network prediction and topological analysis in Leishmania major as a tool for drug target selection.

    abstract:BACKGROUND:Leishmaniasis is a virulent parasitic infection that causes a worldwide disease burden. Most treatments have toxic side-effects and efficacy has decreased due to the emergence of resistant strains. The outlook is worsened by the absence of promising drug targets for this disease. We have taken a computationa...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-484

    authors: Flórez AF,Park D,Bhak J,Kim BC,Kuchinsky A,Morris JH,Espinosa J,Muskus C

    更新日期:2010-09-27 00:00:00

  • Integration of open access literature into the RCSB Protein Data Bank using BioLit.

    abstract:BACKGROUND:Biological data have traditionally been stored and made publicly available through a variety of on-line databases, whereas biological knowledge has traditionally been found in the printed literature. With journals now on-line and providing an increasing amount of open access content, often free of copyright ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-220

    authors: Prlić A,Martinez MA,Dimitropoulos D,Beran B,Yukich BT,Rose PW,Bourne PE,Fink JL

    更新日期:2010-04-29 00:00:00

  • PoGO: Prediction of Gene Ontology terms for fungal proteins.

    abstract:BACKGROUND:Automated protein function prediction methods are the only practical approach for assigning functions to genes obtained from model organisms. Many of the previously reported function annotation methods are of limited utility for fungal protein annotation. They are often trained only to one species, are not a...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-215

    authors: Jung J,Yi G,Sukno SA,Thon MR

    更新日期:2010-04-29 00:00:00

  • Simulating variance heterogeneity in quantitative genome wide association studies.

    abstract:BACKGROUND:Analyzing Variance heterogeneity in genome wide association studies (vGWAS) is an emerging approach for detecting genetic loci involved in gene-gene and gene-environment interactions. vGWAS analysis detects variability in phenotype values across genotypes, as opposed to typical GWAS analysis, which detects v...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-018-2061-1

    authors: Al Kawam A,Alshawaqfeh M,Cai JJ,Serpedin E,Datta A

    更新日期:2018-03-21 00:00:00

  • A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions.

    abstract:BACKGROUND:One very important functional domain of proteins is the protein-protein interacting region (PPIR), which forms the binding interface between interacting polypeptide chains. Post-translational modifications (PTMs) that occur in the PPIR can either interfere with or facilitate the interaction between proteins....

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-016-1165-8

    authors: Saethang T,Payne DM,Avihingsanon Y,Pisitkun T

    更新日期:2016-08-17 00:00:00

  • Constructing patch-based ligand-binding pocket database for predicting function of proteins.

    abstract:BACKGROUND:Many of solved tertiary structures of unknown functions do not have global sequence and structural similarities to proteins of known function. Often functional clues of unknown proteins can be obtained by predicting small ligand molecules that bind to the proteins. METHODS:In our previous work, we have deve...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-13-S2-S7

    authors: Sael L,Kihara D

    更新日期:2012-03-13 00:00:00

  • Stochastic models for the in silico simulation of synaptic processes.

    abstract:BACKGROUND:Research in life sciences is benefiting from a large availability of formal description techniques and analysis methodologies. These allow both the phenomena investigated to be precisely modeled and virtual experiments to be performed in silico. Such experiments may result in easier, faster, and satisfying a...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-9-S4-S7

    authors: Bracciali A,Brunelli M,Cataldo E,Degano P

    更新日期:2008-04-25 00:00:00

  • Parameterizing sequence alignment with an explicit evolutionary model.

    abstract:BACKGROUND:Inference of sequence homology is inherently an evolutionary question, dependent upon evolutionary divergence. However, the insertion and deletion penalties in the most widely used methods for inferring homology by sequence alignment, including BLAST and profile hidden Markov models (profile HMMs), are not b...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-015-0832-5

    authors: Rivas E,Eddy SR

    更新日期:2015-12-10 00:00:00

  • An improved method for identifying functionally linked proteins using phylogenetic profiles.

    abstract:BACKGROUND:Phylogenetic profiles record the occurrence of homologs of genes across fully sequenced organisms. Proteins with similar profiles are typically components of protein complexes or metabolic pathways. Various existing methods measure similarity between two profiles and, hence, the likelihood that the two prote...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-8-S4-S7

    authors: Cokus S,Mizutani S,Pellegrini M

    更新日期:2007-05-22 00:00:00

  • A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment.

    abstract:BACKGROUND:Many practical tasks in biomedicine require accessing specific types of information in scientific literature; e.g. information about the results or conclusions of the study in question. Several schemes have been developed to characterize such information in scientific journal articles. For example, a simple ...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-69

    authors: Guo Y,Korhonen A,Liakata M,Silins I,Hogberg J,Stenius U

    更新日期:2011-03-08 00:00:00

  • Mining locus tags in PubMed Central to improve microbial gene annotation.

    abstract:BACKGROUND:The scientific literature contains millions of microbial gene identifiers within the full text and tables, but these annotations rarely get incorporated into public sequence databases. We propose to utilize the Open Access (OA) subset of PubMed Central (PMC) as a gene annotation database and have developed a...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-15-43

    authors: Stubben CJ,Challacombe JF

    更新日期:2014-02-05 00:00:00

  • LDNFSGB: prediction of long non-coding rna and disease association using network feature similarity and gradient boosting.

    abstract:BACKGROUND:A large number of experimental studies show that the mutation and regulation of long non-coding RNAs (lncRNAs) are associated with various human diseases. Accurate prediction of lncRNA-disease associations can provide a new perspective for the diagnosis and treatment of diseases. The main function of many ln...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-020-03721-0

    authors: Zhang Y,Ye F,Xiong D,Gao X

    更新日期:2020-09-03 00:00:00

  • Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins.

    abstract:BACKGROUND:Protein-protein interactions play a key role in biological processes of proteins within a cell. Recent high-throughput techniques have generated protein-protein interaction data in a genome-scale. A wide range of computational approaches have been applied to interactome network analysis for uncovering functi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-11-S3-S3

    authors: Cho YR,Zhang A

    更新日期:2010-04-29 00:00:00

  • BIOZON: a system for unification, management and analysis of heterogeneous biological data.

    abstract:BACKGROUND:Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. DESCRIPTION:Here we present...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-70

    authors: Birkland A,Yona G

    更新日期:2006-02-15 00:00:00

  • Systematic exploration of guide-tree topology effects for small protein alignments.

    abstract:BACKGROUND:Guide-trees are used as part of an essential heuristic to enable the calculation of multiple sequence alignments. They have been the focus of much method development but there has been little effort at determining systematically, which guide-trees, if any, give the best alignments. Some guide-tree constructi...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-15-338

    authors: Sievers F,Hughes GM,Higgins DG

    更新日期:2014-10-04 00:00:00

  • Toward an interactive article: integrating journals and biological databases.

    abstract:BACKGROUND:Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-12-175

    authors: Rangarajan A,Schedl T,Yook K,Chan J,Haenel S,Otis L,Faelten S,DePellegrin-Connelly T,Isaacson R,Skrzypek MS,Marygold SJ,Stefancsik R,Cherry JM,Sternberg PW,Müller HM

    更新日期:2011-05-19 00:00:00

  • Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span.

    abstract:BACKGROUND:The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caeno...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/1471-2105-7-250

    authors: Blei DM,Franks K,Jordan MI,Mian IS

    更新日期:2006-05-08 00:00:00

  • A weighted string kernel for protein fold recognition.

    abstract:BACKGROUND:Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done before those methods provide reliable fold recognition for proteins whose sequences share little simila...

    journal_title:BMC bioinformatics

    pub_type: 杂志文章

    doi:10.1186/s12859-017-1795-5

    authors: Nojoomi S,Koehl P

    更新日期:2017-08-25 00:00:00