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Lack of Association of Polymorphism Located Upstream of ABCA1 (rs2472493), in FNDC3B (rs7636836), and Near ANKRD55–MAP3K1 Genes (rs61275591) in Primary Open-Angle Glaucoma Patients of Saudi Origin. Genes (Basel) 2023; 14:genes14030704. [PMID: 36980976 PMCID: PMC10048255 DOI: 10.3390/genes14030704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/06/2023] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Polymorphisms rs2472493 near ABCA1, rs7636836 in FNDC3B, and rs61275591 near the ANKRD55–MAP3K1 genes were previously reported to exhibit genome-wide significance in primary open-angle glaucoma (POAG). Since these polymorphisms have not been investigated in the Arab population of Saudi Arabia, we examined their association with POAG in a Saudi cohort. Genotyping was performed in 152 POAG cases and 246 controls using Taqman real-time assays and their associations with POAG and clinical markers, such as intraocular pressure, cup/disc ratio, and the number of antiglaucoma medications, were tested by statistical methods. There was no association observed between POAG and the minor allele frequencies of rs2472493[G], rs7636836[T], or rs61275591[A]. None of the genetic models such as co-dominant, dominant, recessive, over-dominant, and log-additive demonstrated any genotype link. The Rs2472493 genotype showed a modest association (p = 0.044) with the number of antiglaucoma medications in the POAG group, but no significant genotype effect on post hoc analysis. In addition, a G-T allelic haplotype of rs2472493 (ABCA1) and rs7636836 (FNDC3B) did show an over two-fold increased risk of POAG (odds ratio = 2.18), albeit non-significantly (p = 0.092). Similarly, no other allelic haplotype of the three variants showed any significant association with POAG. Our study did not replicate the genetic association of rs2472493 (ABCA1), rs763683 (FNDC3B), and rs61275591 (ANKRD55–MAP3K1) in POAG and related clinical phenotypes, suggesting that these polymorphisms are not associated with POAG in a Saudi cohort of Arab ethnicity. However, large population-based multicenter studies are needed to validate these results.
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Kondkar AA, Sultan T, Azad TA, Osman EA, Almobarak FA, Lobo GP, Al-Obeidan SA. Evaluation of ABCA1 and FNDC3B Gene Polymorphisms Associated With Pseudoexfoliation Glaucoma and Primary Angle-Closure Glaucoma in a Saudi Cohort. Front Genet 2022; 13:877174. [PMID: 35719397 PMCID: PMC9198278 DOI: 10.3389/fgene.2022.877174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: It is plausible that common disease mechanisms exist in glaucoma pathophysiology. Accordingly, we investigated the genetic association of two previously reported primary open-angle glaucoma (POAG)-related gene polymorphisms, rs2472493 (A > G) in ABCA1 and rs7636836 (C > T) in FNDC3B, in primary angle-closure glaucoma (PACG) and pseudoexfoliation glaucoma (PXG). Methods: TaqMan genotyping was performed in a total of 442 subjects consisting of 246 healthy controls, 102 PACG patients, and 94 PXG patients. Statistical evaluations were performed to detect allelic and genotype association of the variants with the disease and clinical variables such as intraocular pressure (IOP) and cup/disc ratio. Results: Overall, there was no allelic or genotype association of these variants in PACG and PXG. However, rs7636836[T] allele significantly increased the risk of PXG among men (p = 0.029, odds ratio [OR] = 2.69, 95% confidence interval = 1.11–6.51). Similarly, rs2472493 and rs7636836 genotypes also showed significant association with PXG among men in over-dominant model (p = 0.031, OR = 1.98, 95% CI = 1.06–3.71) and co-dominant model (p = 0.029, OR = 2.69, 95% CI = 1.11–6.51), respectively. However, none survived Bonferroni’s correction. Besides, the synergic presence of rs2472493[G] and rs7636836[T] alleles (G-T) was found to significantly increase the risk of PACG (p = 0.026, OR = 2.85, 95% CI = 1.09–7.46). No significant genotype influence was observed on IOP and cup/disc ratio. Conclusion: Our results suggest that the polymorphisms rs2472493 in ABCA1 and rs7636836 in FNDC3B genes may be associated with PXG among men, and a G-T allelic combination may confer an increased risk of PACG in the middle-eastern Saudi cohort. Further research in a larger population-based sample is needed to validate these findings.
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Affiliation(s)
- Altaf A Kondkar
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Tahira Sultan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Taif A Azad
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Essam A Osman
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Faisal A Almobarak
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Glenn P Lobo
- Department of Ophthalmology and Visual Neurosciences, University of Minnesota, Minneapolis, MN, United States
| | - Saleh A Al-Obeidan
- Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Glaucoma Research Chair in Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
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Darvish H, Omidvar ME, Ghaedi E, Ghaedi H. Association of rs3735025 and rs9656169 variants with autism, and schizophrenia: A GWAS-replication study in an Iranian population. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Al Bkhetan Z, Zobel J, Kowalczyk A, Verspoor K, Goudey B. Exploring effective approaches for haplotype block phasing. BMC Bioinformatics 2019; 20:540. [PMID: 31666002 PMCID: PMC6822470 DOI: 10.1186/s12859-019-3095-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for detecting certain classes of disease-associated mutations. One approach for detecting such mutations is through phased haplotype association analysis. While the accuracy of methods for phasing genotype data has been widely explored, there has been little attention given to phasing accuracy at haplotype block scale. Understanding the combined impact of the accuracy of phasing tool and the method used to determine haplotype blocks on the error rate within the determined blocks is essential to conduct accurate haplotype analyses. RESULTS We present a systematic study exploring the relationship between seven widely used phasing methods and two common methods for determining haplotype blocks. The evaluation focuses on the number of haplotype blocks that are incorrectly phased. Insights from these results are used to develop a haplotype estimator based on a consensus of three tools. The consensus estimator achieved the most accurate phasing in all applied tests. Individually, EAGLE2, BEAGLE and SHAPEIT2 alternate in being the best performing tool in different scenarios. Determining haplotype blocks based on linkage disequilibrium leads to more correctly phased blocks compared to a sliding window approach. We find that there is little difference between phasing sections of a genome (e.g. a gene) compared to phasing entire chromosomes. Finally, we show that the location of phasing error varies when the tools are applied to the same data several times, a finding that could be important for downstream analyses. CONCLUSIONS The choice of phasing and block determination algorithms and their interaction impacts the accuracy of phased haplotype blocks. This work provides guidance and evidence for the different design choices needed for analyses using haplotype blocks. The study highlights a number of issues that may have limited the replicability of previous haplotype analysis.
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Affiliation(s)
- Ziad Al Bkhetan
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia
| | - Justin Zobel
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia
| | - Adam Kowalczyk
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia.,Centre for Neural Engineering, University of Melbourne, Carlton, 3053, Australia.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, 00-662, Poland.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia
| | - Karin Verspoor
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia.
| | - Benjamin Goudey
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia.,IBM Australia - Research, Southgate, 3006, Australia
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Dou J, Guo H, Cheng F, Huang H, Fu L, Li L, Yang C, Ye L, Wen L, Cheng Y, Tang L, Zhu C, Zhu Z, Wang W, Sheng Y, Wang Z, Liu S, Fan X, Zuo X, Zhou F, Sun L, Zheng X, Zhang X. Genotype combination contributes to psoriasis: An exhaustive algorithm perspective. PLoS One 2017; 12:e0186067. [PMID: 29020033 PMCID: PMC5636117 DOI: 10.1371/journal.pone.0186067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 09/25/2017] [Indexed: 11/19/2022] Open
Abstract
Researchers have learned that nearly all conditions and diseases have a genetic component. With the benefit of technological advances, many single-nucleotide polymorphisms (SNPs) have been found to be associated with the risk of complex disorders by using genome wide association studies (GWASs). Disease-associated SNPs are sometimes shared by healthy controls and cannot clearly distinguish affected individuals from unaffected ones. The combined effects of multiple independent SNPs contribute to the disease process, but revealing the relationship between genotype and phenotype based on the combinations remains a great challenge. In this study, by considering the disease prevalence rate, we conducted an exhaustive process to identify whether a genotype combination pattern would have a decisive effect on complex disorders. Based on genotype data for 68 reported SNPs in 8,372 psoriasis patients and 8,510 healthy controls, we found that putative causal genotype combination patterns (CGCPs) were only present in psoriasis patients, not in healthy subjects. These results suggested that psoriasis might be contributed by combined genotypes, complementing the traditional modest susceptibility of a single variant in a single gene for a complex disease. This work is the first systematic study to analyze genotype combinations based on the reported susceptibility genes, considering each individual among the cases and controls from the Chinese population, and could potentially advance disease-gene mapping and precision medicine due to the causality relationship between the candidate CGCPs and complex diseases.
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Affiliation(s)
- Jinfa Dou
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Huimin Guo
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Fang Cheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Hequn Huang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Liying Fu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Longnian Li
- The Department of Dermatology, The First Affiliated Hospital, Gannan Medical University, Ganzhou, China
| | - Chao Yang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Lei Ye
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Leilei Wen
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Yuyan Cheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Lili Tang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Caihong Zhu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Zhengwei Zhu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Wenjun Wang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Yujun Sheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Zaixing Wang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Shengxiu Liu
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xing Fan
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xianbo Zuo
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Fusheng Zhou
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Liangdan Sun
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Xiaodong Zheng
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- * E-mail: (XDZ); (XJZ)
| | - Xuejun Zhang
- Institute of Dermatology and Department of Dermatology at No. 1 Hospital, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- * E-mail: (XDZ); (XJZ)
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Ali F, Zhang J. Mixture model-based association analysis with case-control data in genome wide association studies. Stat Appl Genet Mol Biol 2017; 16:173-187. [PMID: 28723613 DOI: 10.1515/sagmb-2016-0022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Multilocus haplotype analysis of candidate variants with genome wide association studies (GWAS) data may provide evidence of association with disease, even when the individual loci themselves do not. Unfortunately, when a large number of candidate variants are investigated, identifying risk haplotypes can be very difficult. To meet the challenge, a number of approaches have been put forward in recent years. However, most of them are not directly linked to the disease-penetrances of haplotypes and thus may not be efficient. To fill this gap, we propose a mixture model-based approach for detecting risk haplotypes. Under the mixture model, haplotypes are clustered directly according to their estimated disease penetrances. A theoretical justification of the above model is provided. Furthermore, we introduce a hypothesis test for haplotype inheritance patterns which underpin this model. The performance of the proposed approach is evaluated by simulations and real data analysis. The results show that the proposed approach outperforms an existing multiple testing method.
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7
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Ghaedi H, Tabasinezhad M, Alipoor B, Shokri F, Movafagh A, Mirfakhraie R, Omrani MD, Masotti A. The pre-mir-27a variant rs895819 may contribute to type 2 diabetes mellitus susceptibility in an Iranian cohort. J Endocrinol Invest 2016; 39:1187-93. [PMID: 27300034 DOI: 10.1007/s40618-016-0499-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 06/06/2016] [Indexed: 01/27/2023]
Abstract
PURPOSE The study was aimed at investigating the association between hsa-mir-27a polymorphism rs895819 (T/C) and type 2 diabetes mellitus (T2DM) susceptibility in a large Iranian cohort. METHODS In this case-control study, the investigated population consisted of T2DM patients (n = 204) and sex- and age-matched controls (n = 209). We used the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) for genotyping. RESULTS We observed significant differences between T2DM patients and controls for weight (p = 0.002), BMI (p < 0.001), systolic blood pressure (p < 0.001), diastolic blood pressure (p < 0.001), fasting plasma glucose (p < 0.001), triglyceride (p = 0.004) and LDL cholesterol (p = 0.051). Moreover, we found that genotype distributions were significantly different between groups (p < 0.05) and that the rs895819-C allele is more frequent in controls (p = 0.030, OR = 0.72, 95 % CI 0.53-0.97). CONCLUSION Our study shows that rs895819 in hsa-mir-27a is associated with T2DM susceptibility and that the C allele conveyed a protective role against T2DM. Larger multicentric and specific functional studies will be necessary to obtain a deeper comprehension of the role of rs895819 and hsa-mir-27a and how they are involved in the development of diabetes.
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Affiliation(s)
- H Ghaedi
- Medical Genetics Department, School of Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Tabasinezhad
- Medical Biotechnology Department, Pasteur Institute of Iran, Tehran, Iran
| | - B Alipoor
- Clinical Biochemistry Department, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - F Shokri
- Medical Genetics Department, School of Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Movafagh
- Medical Genetics Department, School of Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - R Mirfakhraie
- Medical Genetics Department, School of Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M D Omrani
- Medical Genetics Department, School of Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - A Masotti
- Gene Expression - Microarrays Laboratory, Bambino Gesù Children's Hospital-IRCCS, Viale di San Paolo 15, 00146, Rome, Italy.
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8
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Cocco P, Zucca M, Sanna S, Satta G, Nonne T, Angelucci E, Gabbas A, Rais M, Malpeli G, Campagna M, Scarpa A, G Ennas M. N-acetyltransferase polymorphisms are associated with risk of lymphoma subtypes. Hematol Oncol 2015; 34:79-83. [DOI: 10.1002/hon.2193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/14/2014] [Accepted: 12/29/2014] [Indexed: 01/23/2023]
Affiliation(s)
- Pierluigi Cocco
- Department of Public Health; Clinical and Molecular Medicine; Occupational Health Section; University of Cagliari; Monserrato Cagliari Italy
| | - Mariagrazia Zucca
- Department of Biomedical Sciences; Cytomorphology Section; University of Cagliari; Monserrato Cagliari Italy
| | - Sonia Sanna
- Department of Biomedical Sciences; Cytomorphology Section; University of Cagliari; Monserrato Cagliari Italy
| | - Giannina Satta
- Department of Public Health; Clinical and Molecular Medicine; Occupational Health Section; University of Cagliari; Monserrato Cagliari Italy
| | - Tinucia Nonne
- Department of Public Health; Clinical and Molecular Medicine; Occupational Health Section; University of Cagliari; Monserrato Cagliari Italy
| | | | - Attilio Gabbas
- Department of Public Health; Clinical and Molecular Medicine; Occupational Health Section; University of Cagliari; Monserrato Cagliari Italy
| | | | - Giorgio Malpeli
- ARC-NET Research Centre and Department of Pathology and Diagnostics; University of Verona; Verona Italy
| | - Marcello Campagna
- Department of Public Health; Clinical and Molecular Medicine; Occupational Health Section; University of Cagliari; Monserrato Cagliari Italy
| | - Aldo Scarpa
- ARC-NET Research Centre and Department of Pathology and Diagnostics; University of Verona; Verona Italy
| | - Maria G Ennas
- Department of Biomedical Sciences; Cytomorphology Section; University of Cagliari; Monserrato Cagliari Italy
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