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      Detection of CAPN10 copy number variation in Thai patients with type 2 diabetes by denaturing high performance liquid chromatography and real-time quantitative polymerase chain reaction

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          Abstract

          Aims/Introduction

          A combination of multiple genetic and environmental factors contribute to the pathogenesis of type 2 diabetes. Copy number variations (CNVs) are associated with complex human diseases. However, CNVs can cause genotype deviation from the Hardy–Weinberg equilibrium (HWE). A genetic case–control association study in 216 Thai diabetic patients and 192 non-diabetic controls found that, after excluding genotyping errors, genotype distribution of calpain 10 ( CAPN10) SNP44 (rs2975760) deviated from HWE. Here, we aimed to detect CNV within the CAPN10 SNP44 region.

          Materials and Methods

          CNV within the CAPN10 SNP44 region was detected using denaturing high-performance liquid chromatography, and the results confirmed by real-time quantitative polymerase chain reaction with SYBR Green I.

          Results

          Both methods successfully identified CNV in the CAPN10 SNP44 region, obtaining concordant results. Correction of genotype calling based on the status of identified CNVs showed that the CAPN10 SNP44 genotype is in good agreement with HWE ( P > 0.05). However, no association between CNV genotypes and risk of type 2 diabetes was observed.

          Conclusions

          Identified CNVs for CAPN10 SNP44 genotypes lead to deviation from HWE. Furthermore, both denaturing high-performance liquid chromatography and real-time quantitative polymerase chain reaction are useful for detecting CNVs.

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          Most cited references27

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          Global variation in copy number in the human genome.

          Richard Redon, Shumpei Ishikawa, Karen R Fitch … (2006)
          Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.
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            Structural variation in the human genome.

            Lars Feuk, Andrew R. Carson, Stephen W Scherer (2006)
            The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term 'structural variation' in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants - collectively termed copy-number variants or copy-number polymorphisms - as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.
            Article 0 comments Cited 661 times – based on 0 reviews     Review now
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              Genotype, haplotype and copy-number variation in worldwide human populations.

              Mattias Jakobsson, Sonja W Scholz, Paul Scheet … (2008)
              Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups. Here we report the analysis of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations. Analysis of SNP genotypes yields strongly supported fine-scale inferences about population structure. Increasing linkage disequilibrium is observed with increasing geographic distance from Africa, as expected under a serial founder effect for the out-of-Africa spread of human populations. New approaches for haplotype analysis produce inferences about population structure that complement results based on unphased SNPs. Despite a difference from SNPs in the frequency spectrum of the copy-number variants (CNVs) detected--including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas--the global distribution of CNVs largely accords with population structure analyses for SNP data sets of similar size. Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations.
              Article 0 comments Cited 286 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): J Diabetes Investig
                Journal ID (iso-abbrev): J Diabetes Investig
                Journal ID (publisher-id): jdi
                Title: Journal of Diabetes Investigation
                Publisher: John Wiley & Sons, Ltd (Chichester, UK )
                ISSN (Print): 2040-1116
                ISSN (Electronic): 2040-1124
                Publication date (Print): November 2015
                Publication date (Electronic): 24 March 2015
                Volume: 6
                Issue: 6
                Pages: 632-639
                Affiliations
                [1 ]Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
                [2 ]Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
                [3 ]Division of Molecular Genetics, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
                [4 ]Division of Molecular Medicine, Departments of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University Bangkok, Thailand
                Author notes
                * Correspondence Pa-thai Yenchitsomanus, Tel.: +662-4192759, Fax: +662-4110169, E-mail address: ptyench@ 123456gmail.com
                Article
                DOI: 10.1111/jdi.12341
                PMC ID: 4627539
                SO-VID: 9a4b152c-9b85-4c85-b109-e1bcf8fdceab
                Copyright © © 2015 The Authors. Journal of Diabetes Investigation published by Asian Association of the Study of Diabetes (AASD) and Wiley Publishing Asia Pty Ltd
                License:

                This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.

                History
                Date received : 10 June 2014
                Date revision received : 11 February 2015
                Date accepted : 16 February 2015
                Categories
                Subject: Articles

                Keywords: capn10,copy number variations,denaturing high-performance liquid chromatography
                Data availability:
                Keywords: capn10, copy number variations, denaturing high-performance liquid chromatography

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