ArticleHuman mutation2011
Assessment of copy number variation using the Illumina Infinium 1M SNP-array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study.
Article in Human mutation, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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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.
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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.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure.Briefings in bioinformatics · 2022Pooled it
- Recurrent and Non-Recurrent Copy Number Variants in Native Americans and a Cosmopolitan Sample in Relation to Alcohol Use Disorder and Other Psychiatric Diseases.Molecular neurobiology · 2026Article
- Copy Number Variation Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Recurrent & non-recurrent copy number variants in Native Americans and a cosmopolitan sample in relation to Alcohol Use Disorder and other psychiatric diseases.Research square · 2025Article
- Rare copy number variant analysis in case-control studies using snp array data: a scalable and automated data analysis pipeline.BMC bioinformatics · 2024Article
- Descriptive Statistics and Genome-Wide Copy Number Analysis of Milk Production Traits of Jiangsu Chinese Holstein Cows.Animals : an open access journal from MDPI · 2023Article
- Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds.Scientific reports · 2022Article
- Genome-wide CNV investigation suggests a role for cadherin, Wnt, and p53 pathways in primary open-angle glaucoma.BMC genomics · 2021Article
- A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing.BMC genomics · 2021Article
- Increasing the resolution and precision of psychiatric genome-wide association studies by re-imputing summary statistics using a large, diverse reference panel.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2021Review
- Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail.Asian-Australasian journal of animal sciences · 2020Article
- Article
- Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays.BMC genomics · 2018Article
- Cytogenomic assessment of the diagnosis of 93 patients with developmental delay and multiple congenital abnormalities: The Brazilian experience.Clinics (Sao Paulo, Brazil) · 2017Article
- Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA.The Journal of molecular diagnostics : JMD · 2017Article
- Genome-wide detection of copy number variation in Chinese indigenous sheep using an ovine high-density 600 K SNP array.Scientific reports · 2017Article
- Article
- Genome-wide detection of CNVs in Chinese indigenous sheep with different types of tails using ovine high-density 600K SNP arrays.Scientific reports · 2016Article
- The Role of Constitutional Copy Number Variants in Breast Cancer.Microarrays (Basel, Switzerland) · 2015Review
- Causes of genome instability: the effect of low dose chemical exposures in modern society.Carcinogenesis · 2015Review
Corrections and comments
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Authors and funding
15 authors.
Funding
Abstract
High-throughput single nucleotide polymorphism (SNP)-array technologies allow to investigate copy number variants (CNVs) in genome-wide scans and specific calling algorithms have been developed to determine CNV location and copy number. We report the results of a reliability analysis comparing data from 96 pairs of samples processed with CNVpartition, PennCNV, and QuantiSNP for Infinium Illumina Human 1Million probe chip data. We also performed a validity assessment with multiplex ligation-dependent probe amplification (MLPA) as a reference standard. The number of CNVs per individual varied according to the calling algorithm. Higher numbers of CNVs were detected in saliva than in blood DNA samples regardless of the algorithm used. All algorithms presented low agreement with mean Kappa Index (KI) <66. PennCNV was the most reliable algorithm (KI(w=) 98.96) when assessing the number of copies. The agreement observed in detecting CNV was higher in blood than in saliva samples. When comparing to MLPA, all algorithms identified poorly known copy aberrations (sensitivity = 0.19-0.28). In contrast, specificity was very high (0.97-0.99). Once a CNV was detected, the number of copies was truly assessed (sensitivity >0.62). Our results indicate that the current calling algorithms should be improved for high performance CNV analysis in genome-wide scans. Further refinement is required to assess CNVs as risk factors in complex diseases.
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