ArticleBMC genomics2013
Accurate measurement of gene copy number for human alpha-defensin DEFA1A3.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Digital droplet PCR is an accurate and precise method to measure DNA copy number.Scientific reports · 2025Article
- Complementary Experimental Methods in Genetics Open Up New Avenues of Research to Elucidate the Pathogenesis of Periodontitis.Advances in experimental medicine and biology · 2022Article
- Runaway multi-allelic copy number variation at the α-defensin locus in African and Asian populations.Scientific reports · 2020Article
- Improved the expression level of active transglutaminase by directional increasing copy of mtg gene in Pichia pastoris.BMC biotechnology · 2019Article
- Low-Copy Number Polymorphism in DEFA1/DEFA3 Is Associated with Susceptibility to Hospital-Acquired Infections in Critically Ill Patients.Mediators of inflammation · 2018Article
- The Role of Skin and Orogenital Microbiota in Protective Immunity and Chronic Immune-Mediated Inflammatory Disease.Frontiers in immunology · 2017Review
- Application of Droplet Digital PCR for Estimating Vector Copy Number States in Stem Cell Gene Therapy.Human gene therapy methods · 2016Article
- Polymorphisms in α-Defensin-Encoding DEFA1A3 Associate with Urinary Tract Infection Risk in Children with Vesicoureteral Reflux.Journal of the American Society of Nephrology : JASN · 2016Article
- Defensin gene variation and HIV/AIDS: a comprehensive perspective needed.Journal of leukocyte biology · 2016Review
- Identification of new susceptibility loci for IgA nephropathy in Han Chinese.Nature communications · 2015Article
- An evolutionary history of defensins: a role for copy number variation in maximizing host innate and adaptive immune responses.Frontiers in immunology · 2015Review
- 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
- The genetics and immunobiology of IgA nephropathy.The Journal of clinical investigation · 2014Review
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundMulti-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing.
resultsIn this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples.
conclusionsWe have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn's disease, type I diabetes, HIV progression and multiple sclerosis.
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