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Jin X, Guan Y, Shen H, Pang Y, Liu L, Jia Q, Meng F, Zhang X. Copy Number Variation of Immune-Related Genes and Their Association with Iodine in Adults with Autoimmune Thyroid Diseases. Int J Endocrinol 2018; 2018:1705478. [PMID: 29713342 PMCID: PMC5866896 DOI: 10.1155/2018/1705478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/31/2018] [Accepted: 02/06/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Autoimmune thyroid diseases (AITD) are complex conditions that are caused by an interaction between genetic susceptibility and environmental triggers. Iodine is already known to be an environmental trigger for AITD, but genes associated with susceptibility need to be further assessed. Therefore, the aims of this study were to assess the association between copy number variations (CNVs) and AITD, to identify genes related with susceptibility to AITD, and to investigate the interaction between iodine status and CNVs in the occurrence of AITD. METHODS Blood samples from 15 patients with AITD and 15 controls were assessed by chromosome microarray to identify candidate genes. The copy number of candidate genes and urinary iodine level was determined in adults from areas of different iodine statuses including 158 patients and 181 controls. RESULTS The immune-related genes, SIRPB1 and TMEM91, were selected as candidate genes. The distribution of SIRPB1 CNV in AITD patients and controls was significantly different and was considered a risk factor for AITD. There was no significant association between urinary iodine level and candidate gene CNVs. CONCLUSION SIRPB1 CNV and an excess of iodine were risk factors for AITD, but an association with the occurrence of AITD was not found.
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Affiliation(s)
- Xing Jin
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yunfeng Guan
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongmei Shen
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yi Pang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lixiang Liu
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Qingzhen Jia
- Institute for Endemic Disease Prevention and Treatment of Shanxi Province, Linfen, Shanxi, China
| | - Fangang Meng
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaoye Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
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Enigmatic in vivo GlcNAc-1-phosphotransferase (GNPTG) transcript correction to wild type in two mucolipidosis III gamma siblings homozygous for nonsense mutations. J Hum Genet 2016; 61:555-60. [PMID: 26935170 DOI: 10.1038/jhg.2016.13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/25/2022]
Abstract
Mucolipidosis (ML) III gamma is a rare autosomal-recessive disorder caused by pathogenic mutations in the GNPTG gene. GNPTG encodes the γ-subunit of GlcNAc-1-phosphotransferase that catalyzes mannose 6-phosphate targeting signal synthesis on soluble lysosomal enzymes. ML III gamma patients are characterized by missorting of lysosomal enzymes. In this report, we describe the probable occurrence of mRNA editing in two ML III gamma patients. Patients A and B (siblings) presented at the adult age with a typical clinical picture of ML III gamma, mainly compromising bone and joints, and high levels of lysosomal enzymes in plasma and low levels in fibroblasts. Both were found to be homozygous for c.-112C>G and c.328G>T (p.Glu110Ter) mutations in genomic DNA (gDNA) analysis of GNPTG. Analysis of complementary DNA (cDNA), however, showed normal genotypes for both patients. Low GNPTG mRNA expression was observed in both patients. The mRNA editing can explain the differences found in patients A and B regarding gDNA and cDNA analysis, and the mild clinical phenotype associated with homozygosity for a nonsense mutation. Our results suggest that mRNA editing can be more frequent than expected in monogenic disorders and that GNPTG analysis should be performed on gDNA.
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Jaczó Z, Pál E, Dénes R, Somogyi A, Sasvári-Székely M, Guttman A, Rónai Z. Rapid analysis of colipase gene variants by multicapillary electrophoresis. Electrophoresis 2015; 36:1237-43. [DOI: 10.1002/elps.201400551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 11/09/2022]
Affiliation(s)
- Zsuzsanna Jaczó
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
| | - Eszter Pál
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
| | - Réka Dénes
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
| | - Anikó Somogyi
- 2 Department of Internal Medicine; Semmelweis University; Budapest Hungary
| | - Mária Sasvári-Székely
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
| | - András Guttman
- Horváth Laboratory of Bioseparation Sciences; University of Debrecen; Debrecen Hungary
- MTA-PE Translational Glycomics Group; University of Pannonia; Veszprém Hungary
| | - Zsolt Rónai
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry; Semmelweis University; Budapest Hungary
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Ronai Z, Kovacs-Nagy R, Szantai E, Elek Z, Sasvari-Szekely M, Faludi G, Benkovits J, Rethelyi JM, Szekely A. Glycogen synthase kinase 3 beta gene structural variants as possible risk factors of bipolar depression. Am J Med Genet B Neuropsychiatr Genet 2014; 165B:217-22. [PMID: 24677591 PMCID: PMC3980030 DOI: 10.1002/ajmg.b.32223] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 01/10/2014] [Indexed: 11/07/2022]
Abstract
The glycogen synthase kinase 3B (GSK3B) is an important target protein of several antidepressants, such as lithium, a mood stabilizer. Recent studies associated structural variations of the GSK3B gene to bipolar disorder (BP), although replications were not conclusive. Here we present data on copy number variations (CNVs) of the GSK3B gene probing the 9th exon region in 846 individuals (414 controls, 172 patients with major depressive disorder (MDD) and 260 with BP). A significant accumulation (odds ratio: 5.5, P = 0.00051) of the amplified exon 9 region was found in patients (22 out of 432) compared to controls (4 of 414). Analyzing patient subgroups, GSK3B structural variants were found to be risk factors of BP particularly (P = 0.00001) with an odds ratio of 8.1 while no such effect was shown in the MDD group. The highest odds (19.7 ratio) for bipolar disorder was observed in females with the amplified exon 9 region. A more detailed analysis of the identified GSK3B CNV by a set of probes covering the GSK3B gene and the adjacent NR1I2 and C3orf15 genes showed that the amplified sequences contained 3' (downstream) segments of the GSK3B and NR1I2 genes but none of them involved the C3orf15 gene. Therefore, the copy number variation of the GSK3B gene could be described as a complex set of structural variants involving partial duplications and deletions, simultaneously. In summary, here we confirmed significant association of the GSK3B CNV and bipolar disorder pointing out that the copy number and extension of the CNV varies among individuals.
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Affiliation(s)
- Zsolt Ronai
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Reka Kovacs-Nagy
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Eszter Szantai
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Elek
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Maria Sasvari-Szekely
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Gabor Faludi
- Department of Clinical and Theoretical Mental Health, Kutvolgyi Clinical Center, Semmelweis University, Budapest, Hungary
| | - Judit Benkovits
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Janos M. Rethelyi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Anna Szekely
- Institute of Psychology, Eotvos Lorand University, Budapest, Hungary,Corresponding author Anna Szekely (associate professor) Institute of Psychology, Eotvos Lorand University, Budapest, Hungary Address: Izabella u. 46, Budapest, Hungary-1064 Tel: (+3620) 466-4554 Fax: (+361) 461-2691
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Shin GW, Jung SH, Yim SH, Chung B, Yeol Jung G, Chung YJ. Stuffer-free multiplex ligation-dependent probe amplification based on conformation-sensitive capillary electrophoresis: a novel technology for robust multiplex determination of copy number variation. Electrophoresis 2012; 33:3052-61. [PMID: 22965760 DOI: 10.1002/elps.201200334] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2012] [Revised: 07/18/2012] [Accepted: 07/23/2012] [Indexed: 01/12/2023]
Abstract
Developing diagnostic tools based on the application of known disease/phenotype-associated copy number variations (CNVs) requires the capacity to measure CNVs in a multiplex format with sufficient reliability and methodological simplicity. In this study, we developed a reliable and user-friendly multiplex CNV detection method, termed stuffer-free MLPA-CE-SSCP, that combines a variation of multiplex ligation-dependent probe amplification (MLPA) with CE-SSCP. In this variation, MLPA probes were designed without the conventionally required stuffer sequences. To separate the similar-sized stuffer-free MLPA products, we adopted CE-SSCP rather than length-dependent conventional CE analysis. An examination of the genomic DNA from five cell lines known to vary in X-chromosome copy number (1-5) revealed that copy number determinations using stuffer-free MLPA-CE-SSCP were more accurate than those of conventional MLPA, and the CV of the measured copy numbers was significantly lower. Applying our system to measure the CNVs on autosomes between two HapMap individuals, we found that all peaks for CNV targets showed the expected copy number changes. Taken together, our results indicate that this new strategy can overcome the limitations of conventional MLPA, which are mainly related to long probe length and difficulties of probe preparation.
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Affiliation(s)
- Gi Won Shin
- Institute of Environmental and Energy Technology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Korea
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Li SC, Hwu WL, Lin JL, Bali DS, Yang C, Chu SM, Chien YH, Chou HC, Chen CY, Hsieh WS, Tsao PN, Chen YT, Lee NC. Association of the congenital neuromuscular form of glycogen storage disease type IV with a large deletion and recurrent frameshift mutation. J Child Neurol 2012; 27:204-8. [PMID: 21917543 DOI: 10.1177/0883073811415107] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Anderson disease, also known as glycogen storage disease type IV (MIM 232500), is a rare autosomal recessive disorder caused by a deficiency of glycogen branching enzyme. Glycogen storage disease type IV has a broad clinical spectrum ranging from a perinatal lethal form to a nonprogressive later-onset disease in adults. Here, we report 2 unrelated infants who were born small for their gestational age and who had profound hypotonia at birth and thus needed mechanical ventilation. Both of these patients shared the same frameshift mutation (c.288delA, pGly97GlufsX46) in the GBE1 gene. In addition, both of these patients were found to have 2 different large deletions in the GBE1 gene; exon 7 and exons 2 to 7, respectively, on the other alleles. This case report also highlights the need for a more comprehensive search for large deletion mutations associated with glycogen storage disease type IV, especially if routine GBE1 gene sequencing results are equivocal.
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Affiliation(s)
- Sing-Chung Li
- School of Nutrition and Health Science, Taipei Medical University, Taipei, Taiwan
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Shin SH, Shin GW, Yim SH, Jung SH, Jung GY, Chung YJ. Strategy for high-fidelity multiplex DNA copy number assay system using capillary electrophoresis devices. Electrophoresis 2011; 32:1837-43. [DOI: 10.1002/elps.201100093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Revised: 03/13/2011] [Accepted: 03/15/2011] [Indexed: 01/31/2023]
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Rahman OA, Sasvari-Szekely M, Szekely A, Faludi G, Guttman A, Nemoda Z. Analysis of a polymorphic microRNA target site in the purinergic receptor P2RX7 gene. Electrophoresis 2010; 31:1790-5. [PMID: 20446288 DOI: 10.1002/elps.200900664] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The recent discovery of post-transcriptional regulation by microRNAs (miRNAs) drew our attention to SNPs of putative miRNA target sites in candidate genes of depression-related psychiatric disorders. The P2RX7 (purinergic receptor P2X, ligand-gated ion channel, 7) gene has been suggested as a candidate for major depressive and bipolar disorder, because of repeated associations with the rs2230912 (Gln460Arg) polymorphism. As this polymorphism is located at the end of the coding region, we considered a possible linkage with SNP(s) in putative miRNA target sites of the 3' untranslated region. Based on our in silico search, the rs1653625 fulfilled this criterion. This SNP, however, is surrounded with polycytosine and polyadenine tracts, which hindered its analysis until now. In this study, we describe a readily applicable genotyping method for rs1653625 by applying a primer that introduces mismatched nucleotides to create a restriction enzyme cleavage site. The resulting allele-specific products with 19 base pair difference were separated by both traditional horizontal agarose gel electrophoresis and multicapillary gel electrophoresis. The developed genotyping method was applied in our depression-related association study.
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Affiliation(s)
- Omar Abdul Rahman
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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