ArticleBMC genomics2011
Accuracy and differential bias in copy number measurement of CCL3L1 in association studies with three auto-immune disorders.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 37 citations in OpenAlex.
- DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies.Bioinformatics (Oxford, England) · 2023Article
- CNVs Associated with Different Clinical Phenotypes of Psoriasis and Anti-TNF-Induced Palmoplantar Pustulosis.Journal of personalized medicine · 2022Article
- DNA Copy Number Variation Associated with Anti-tumour Necrosis Factor Drug Response and Paradoxical Psoriasiform Reactions in Patients with Moderate-to-severe Psoriasis.Acta dermato-venereologica · 2021Article
- An Update Evolving View of Copy Number Variations in Autoimmune Diseases.Frontiers in genetics · 2021Review
- Copy number variation of CCL3L1 among three major ethnic groups in Malaysia.BMC genetics · 2020Article
- Characterization of copy number variants for CCL3L1 gene in rheumatoid arthritis for French trio families and Tunisian cases and controls.Clinical rheumatology · 2016Article
- SRBreak: A Read-Depth and Split-Read Framework to Identify Breakpoints of Different Events Inside Simple Copy-Number Variable Regions.Frontiers in genetics · 2016Article
- Complex and multi-allelic copy number variation in human disease.Briefings in functional genomics · 2015Review
- Obesity, starch digestion and amylase: association between copy number variants at human salivary (AMY1) and pancreatic (AMY2) amylase genes.Human molecular genetics · 2015Article
- A comparison of assays for accurate copy number measurement of the low-affinity Fc gamma receptor genes FCGR3A and FCGR3B.PloS one · 2015Article
- Human gene copy number variation and infectious disease.Human genetics · 2014Review
- Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus.BMC genomics · 2014Article
- Digital genotyping of macrosatellites and multicopy genes reveals novel biological functions associated with copy number variation of large tandem repeats.PLoS genetics · 2014Article
- Technical considerations for genotyping multi-allelic copy number variation (CNV), in regions of segmental duplication.BMC genomics · 2014Article
- Low copy number of the salivary amylase gene predisposes to obesity.Nature genetics · 2014Article
- CCL3L1 copy number, CCR5 genotype and susceptibility to tuberculosis.BMC medical genetics · 2014Article
- The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data.Frontiers in genetics · 2014Article
- CCL3L1 copy number, HIV load, and immune reconstitution in sub-Saharan Africans.BMC infectious diseases · 2013Article
- Accurate measurement of gene copy number for human alpha-defensin DEFA1A3.BMC genomics · 2013Article
- Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions.Nature methods · 2013Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundCopy number variation (CNV) contributes to the variation observed between individuals and can influence human disease progression, but the accurate measurement of individual copy numbers is technically challenging. In the work presented here we describe a modification to a previously described paralogue ratio test (PRT) method for genotyping the CCL3L1/CCL4L1 copy variable region, which we use to ascertain CCL3L1/CCL4L1 copy number in 1581 European samples. As the products of CCL3L1 and CCL4L1 potentially play a role in autoimmunity we performed case control association studies with Crohn's disease, rheumatoid arthritis and psoriasis clinical cohorts.
resultsWe evaluate the PRT methodology used, paying particular attention to accuracy and precision, and highlight the problems of differential bias in copy number measurements. Our PRT methods for measuring copy number were of sufficient precision to detect very slight but systematic differential bias between results from case and control DNA samples in one study. We find no evidence for an association between CCL3L1 copy number and Crohn's disease, rheumatoid arthritis or psoriasis.
conclusionsDifferential bias of this small magnitude, but applied systematically across large numbers of samples, would create a serious risk of false positive associations in copy number, if measured using methods of lower precision, or methods relying on single uncorroborated measurements. In this study the small differential bias detected by PRT in one sample set was resolved by a simple pre-treatment by restriction enzyme digestion.
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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.