ArticleGenome biology2007
Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 80 papers, 1 of them a synthesis that pooled it.
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Who cites it
80 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits.Nature genetics · 2014Pooled it
- Increased paternal age and the influence on burden of genomic copy number variation in the general population.Human genetics · 2013Trial
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- MicroRNAs Expression Profile in MN1-Altered Astroblastoma.Biomedicines · 2025Article
- Genome-wide association studies for economically important traits in mink using copy number variation.Scientific reports · 2024Article
- Improving CNV Detection Performance in Microarray Data Using a Machine Learning-Based Approach.Diagnostics (Basel, Switzerland) · 2023Article
- A pipeline for copy number profiling of single circulating tumour cells to assess intrapatient tumour heterogeneity.Molecular oncology · 2022Article
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- Genome-wide somatic copy number alteration analysis and database construction for cervical cancer.Molecular genetics and genomics : MGG · 2020Article
- Induction of Effective Immunity against Trypanosoma cruzi.Infection and immunity · 2020Article
- On the association analysis of CNV data: a fast and robust family-based association method.BMC bioinformatics · 2017Article
- Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis.BMC genomics · 2017Article
- CNVs into the wild: screening the genomes of conifer trees (Picea spp.) reveals fewer gene copy number variations in hybrids and links to adaptation.BMC genomics · 2017Article
- Whole exome association of rare deletions in multiplex oral cleft families.Genetic epidemiology · 2017Article
- Article
- Article
- Rawcopy: Improved copy number analysis with Affymetrix arrays.Scientific reports · 2016Article
- CNARA: reliability assessment for genomic copy number profiles.BMC genomics · 2016Article
- Copy number variants in the sheep genome detected using multiple approaches.BMC genomics · 2016Article
- Chromosomal copy number alterations and HPV integration in cervical precancer and invasive cancer.Carcinogenesis · 2016Article
20 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
backgroundLarge-scale high throughput studies using microarray technology have established that copy number variation (CNV) throughout the genome is more frequent than previously thought. Such variation is known to play an important role in the presence and development of phenotypes such as HIV-1 infection and Alzheimer's disease. However, methods for analyzing the complex data produced and identifying regions of CNV are still being refined.
resultsWe describe the presence of a genome-wide technical artifact, spatial autocorrelation or 'wave', which occurs in a large dataset used to determine the location of CNV across the genome. By removing this artifact we are able to obtain both a more biologically meaningful clustering of the data and an increase in the number of CNVs identified by current calling methods without a major increase in the number of false positives detected. Moreover, removing this artifact is critical for the development of a novel model-based CNV calling algorithm - CNVmix - that uses cross-sample information to identify regions of the genome where CNVs occur. For regions of CNV that are identified by both CNVmix and current methods, we demonstrate that CNVmix is better able to categorize samples into groups that represent copy number gains or losses.
conclusionRemoving artifactual 'waves' (which appear to be a general feature of array comparative genomic hybridization (aCGH) datasets) and using cross-sample information when identifying CNVs enables more biological information to be extracted from aCGH experiments designed to investigate copy number variation in normal individuals.
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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.