ReviewOncotarget2013
Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges.
Review in Oncotarget, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed.
- Benchmarking Ploidy Estimation Methods for Bulk and Single-Cell Whole Genome Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The dual role of whole-genome duplication: biological mechanisms, functional consequences, and detection advances.Acta biochimica et biophysica Sinica · 2025Review
- Review
- Domain generalization enables general cancer cell annotation in single-cell and spatial transcriptomics.Nature communications · 2024Article
- Article
- Whole Exome Analysis to Select Targeted Therapies for Patients with Metastatic Breast Cancer - A Feasibility Study.Geburtshilfe und Frauenheilkunde · 2023Article
- DOCEST-fast and accurate estimator of human NGS sequencing depth and error rate.Bioinformatics advances · 2023Article
- Detection of somatic structural variants from short-read next-generation sequencing data.Briefings in bioinformatics · 2021Review
- Identification of a prognostic signature based on copy number variations (CNVs) and CNV-modulated gene expression in acute myeloid leukemia.American journal of translational research · 2021Article
- Comprehensive Molecular Characterization of Chinese Patients with Glioma by Extensive Next-Generation Sequencing Panel Analysis.Cancer management and research · 2021Article
- Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology.Cancers · 2019Review
- Review
- Highly Multiplexed Fluorescence in Situ Hybridization for in Situ Genomics.The Journal of molecular diagnostics : JMD · 2019Article
- Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants.Bioinformatics (Oxford, England) · 2018Article
- A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing.Genome medicine · 2018Article
- Identification of copy number alterations in colon cancer from analysis of amplicon-based next generation sequencing data.Oncotarget · 2018Article
- Copy number variation in livestock: A mini review.Veterinary world · 2018Review
- Somatic evolutionary timings of driver mutations.BMC cancer · 2018Article
- Breaking point: the genesis and impact of structural variation in tumours.F1000Research · 2018Review
- Genomic copy number gains of ErbB family members predict poor clinical outcomes in glioma patients.Oncotarget · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Accurate detection of somatic copy number variations (CNVs) is an essential part of cancer genome analysis, and plays an important role in oncotarget identifications. Next generation sequencing (NGS) holds the promise to revolutionize somatic CNV detection. In this review, we provide an overview of current analytic tools used for CNV detection in NGS-based cancer studies. We summarize the NGS data types used for CNV detection, decipher the principles for data preprocessing, segmentation, and interpretation, and discuss the challenges in somatic CNV detection. This review aims to provide a guide to the analytic tools used in NGS-based cancer CNV studies, and to discuss the important factors that researchers need to consider when analyzing NGS data for somatic CNV detections.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.