ReviewMicroarrays (Basel, Switzerland)2013
Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data.
Review in Microarrays (Basel, Switzerland), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- Mapping copy number variable regions correlated with reproduction and production traits in Karan Fries cattle mammalian genomics.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- Genetic analysis of two bladder exstrophy populations of South Asian and North American origin.Journal of pediatric urology · 2025Article
- Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population.BMC genomics · 2025Article
- Copy number variant scan in more than four thousand Holstein cows bred in Lombardy, Italy.PloS one · 2024Article
- Genome-wide identification of copy number variation and association with fat deposition in thin and fat-tailed sheep breeds.Scientific reports · 2022Article
- Increased Diagnostic Yield of Array Comparative Genomic Hybridization for Autism Spectrum Disorder in One Institution in Taiwan.Medicina (Kaunas, Lithuania) · 2021Article
- High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data.Scientific reports · 2020Article
- Article
- Array CGH-based detection of CNV regions and their potential association with reproduction and other economic traits in Holsteins.BMC genomics · 2019Article
- Characterization of copy number variants in a large multibreed population of beef and dairy cattle using high-density single nucleotide polymorphism genotype data.Journal of animal science · 2018Article
- Widespread modulation of gene expression by copy number variation in skeletal muscle.Scientific reports · 2018Article
- Genome-wide analysis reveals differential selection involved with copy number variation in diverse Chinese Cattle.Scientific reports · 2017Article
- Article
- In vivo and in vitro ageing results in accumulation of de novo copy number variations in bulls.Scientific reports · 2017Article
- Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array.Scientific reports · 2017Article
- Genome-wide copy number variation (CNV) detection in Nelore cattle reveals highly frequent variants in genome regions harboring QTLs affecting production traits.BMC genomics · 2016Article
- Population-genetic properties of differentiated copy number variations in cattle.Scientific reports · 2016Article
- Phenotypic Association Analyses With Copy Number Variation in Recurrent Depressive Disorder.Biological psychiatry · 2016Article
- Genome-wide identification of copy number variation using high-density single-nucleotide polymorphism array in Japanese Black cattle.BMC genetics · 2016Article
- A Method for Checking Genomic Integrity in Cultured Cell Lines from SNP Genotyping Data.PloS one · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detection. Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them. In this review, we first survey the literature on existing microarray platforms and CNV calling algorithms. We then examine a number of CNV calling tools to evaluate their impacts using bovine high-density SNP data. Large incongruities in the results from different CNV calling tools highlight the need for standardizing array data collection, quality assessment and experimental validation. Only after careful experimental design and rigorous data filtering can the impacts of CNVs on both normal phenotypic variability and disease susceptibility be fully revealed.
Indexed as
Identifiers
What OpenQuestion holds
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.