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Chien CY, Tai SY, Li KH, Yang HL, Wang LF, Ho KY, Chang NC. Glucocorticoid receptor (NR3C1) genetic polymorphisms and the outcomes of sudden sensorineural hearing loss. J Otolaryngol Head Neck Surg 2023; 52:13. [PMID: 36782309 PMCID: PMC9926839 DOI: 10.1186/s40463-022-00601-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/17/2022] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND The glucocorticoid receptor gene (NR3C1) encodes the receptor to which cortisol and other glucocorticoids bind. Steroids in either oral, intratympanic, or intravascular forms are the treatment of choice for sudden sensorineural hearing loss (SSNHL), but the outcome varies. The outcomes of SSNHL have been investigated for related factors, including age, initial hearing loss severity and pattern, vertigo, genetic variations, and the time between onset and treatment. The objective of the present study was to analyze the association of genetic polymorphisms of NR3C1 with the outcomes of SSNHL. MATERIALS AND METHODS We conducted a comparison study of 93 cases with a poor outcome (control) and 100 cases with a good outcome (case) in SSNHL patients. Six single nucleotide polymorphisms (SNPs) were selected. The genotypes were determined using TaqMan technology. RESULTS The heterozygous AT genotype of rs17100289 was associated with a poor outcome in comparison with the major homozygous AA genotype after adjustments for age and sex (OR = 0.50; 95% CI 0.26-0.95; P = 0.035) in SSNHL patients. The CT genotype of rs4912912 was also associated with a poor outcome compared with the major homozygous TT genotype after the adjustments (OR = 0.47; 95% CI 0.24-0.92; P = 0.026). CONCLUSION These results suggest that NR3C1 genetic polymorphisms may influence the outcomes of SSNHL.
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Affiliation(s)
- Chen-Yu Chien
- grid.412019.f0000 0000 9476 5696Department of Otorhinolaryngology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, No. 100, Tzyou 1st Road, Kaohsiung, 807 Taiwan ,Department of Otorhinolaryngology, Kaohsiung Municipal Siaogang Hospital, Kaohsiung, Taiwan ,grid.412019.f0000 0000 9476 5696Department of Otorhinolaryngology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Yu Tai
- grid.412019.f0000 0000 9476 5696Department of Family Medicine, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan ,grid.415007.70000 0004 0477 6869Department of Family Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan ,grid.412019.f0000 0000 9476 5696Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuan-Hui Li
- grid.412019.f0000 0000 9476 5696Department of Otorhinolaryngology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, No. 100, Tzyou 1st Road, Kaohsiung, 807 Taiwan
| | - Hua-Ling Yang
- grid.412019.f0000 0000 9476 5696Division of Hepatobiliary and Pancreatic Medicine, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ling-Feng Wang
- grid.412019.f0000 0000 9476 5696Department of Otorhinolaryngology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, No. 100, Tzyou 1st Road, Kaohsiung, 807 Taiwan ,grid.412019.f0000 0000 9476 5696Department of Otorhinolaryngology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Kuen-Yao Ho
- grid.412019.f0000 0000 9476 5696Department of Otorhinolaryngology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, No. 100, Tzyou 1st Road, Kaohsiung, 807 Taiwan ,grid.412019.f0000 0000 9476 5696Department of Otorhinolaryngology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ning-Chia Chang
- Department of Otorhinolaryngology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, No. 100, Tzyou 1st Road, Kaohsiung, 807, Taiwan. .,Department of Otorhinolaryngology, Kaohsiung Municipal Siaogang Hospital, Kaohsiung, Taiwan. .,Department of Otorhinolaryngology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Amin USM, Parvez N, Rahman TA, Hasan MR, Das KC, Jahan S, Hasanat MA, Seraj ZI, Salimullah M. CDKAL1 gene rs7756992 A/G and rs7754840 G/C polymorphisms are associated with gestational diabetes mellitus in a sample of Bangladeshi population: implication for future T2DM prophylaxis. Diabetol Metab Syndr 2022; 14:18. [PMID: 35090536 PMCID: PMC8796445 DOI: 10.1186/s13098-021-00782-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/30/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Association of single nucleotide polymorphisms (SNP) rs7756992 A/G and rs7754840 G/C of cyclin-dependent kinase 5 regulatory subunit-associated protein 1-like 1 (CDKAL1) gene with the susceptibility of gestational diabetes mellitus (GDM) has been studied in a group of Bangladeshi women. METHODS In this case-control study, 212 GDM patients and 256 control subjects were genotyped for rs7756992 and rs7754840 by PCR-RFLP and TaqMan™ allelic discrimination assay method respectively. Genotyping results were confirmed by DNA sequencing and replicated TaqMan™ assay. The odds ratios and their 95% confidence interval were calculated by logistic regression to determine the associations between genotypes and GDM. RESULTS The genotype frequencies of rs7756992-AA/AG/GG in the GDM group and the control group were 37%/48%, 53%/45%, 10%/7% and those of rs7754840-CC/CG/GG were 51%/55%, 40.1%/39.8%, 9%/5% respectively. Under dominant and log additive models rs7756992 was revealed significantly associated with GDM after being adjusted for family history of diabetes (FHD) and gravidity. Conversely, rs7754840 was significantly associated (P = 0.047) with GDM only under the recessive model after the same adjustment. The risk allele frequency of both SNPs was higher in the GDM group but significantly (P = 0.029) increased prevalence was observed in the rs7756992 G allele. When positive FHD and risk alleles of these SNPs were synergistically present in any pregnant woman, the chance of developing GDM was augmented by many folds. The codominant model revealed 2.5 and 2.1 folds increase in odds by AG (rs7756992) and GC (rs7754840) genotypes and 3.7 and 4.5 folds by GG (rs7756992) and CC (rs7754840) genotypes respectively. A significant 2.7 folds (P = 0.038) increase in odds of GDM resulted from the interaction of rs7756992 and family history of diabetes under the dominant model. The cumulative effect of multigravidity and risk alleles of these SNPs increased the odds of GDM more than 1.5 folds in different genotypes. CONCLUSION This study not only revealed a significant association between rs7756992 and rs7754840 with GDM but also provided the possibility as potential markers for foretelling about GDM and type 2 diabetes mellitus in Bangladeshi women.
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Affiliation(s)
- U S Mahzabin Amin
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Nahid Parvez
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Tahia Anan Rahman
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Md Rakibul Hasan
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Keshob Chandra Das
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh
| | - Sharmin Jahan
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Muhammad Abul Hasanat
- Department of Endocrinology and Metabolism, Bangabandhu Sheikh Mujib Medical University (BSMMU), Dhaka, Bangladesh
| | - Zeba I Seraj
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Md Salimullah
- Molecular Biotechnology Division, National Institute of Biotechnology (NIB), Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.
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Escott-Price V, Schmidt KM. Probability of Alzheimer's disease based on common and rare genetic variants. ALZHEIMERS RESEARCH & THERAPY 2021; 13:140. [PMID: 34404470 PMCID: PMC8369699 DOI: 10.1186/s13195-021-00884-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/05/2021] [Indexed: 11/19/2022]
Abstract
Background Alzheimer’s disease, among other neurodegenerative disorders, spans decades in individuals’ life and exhibits complex progression, symptoms and pathophysiology. Early diagnosis is essential for disease prevention and therapeutic intervention. Genetics may help identify individuals at high risk. As thousands of genetic variants may contribute to the genetic risk of Alzheimer’s disease, the polygenic risk score (PRS) approach has been shown to be useful for disease risk prediction. The APOE-ε4 allele is a known common variant associated with high risk to AD, but also associated with earlier onset. Rare variants usually have higher effect sizes than common ones; their impact may not be well captured by the PRS. Instead of standardised PRS, we propose to calculate the disease probability as a measure of disease risk that allows comparison between individuals. Methods We estimate AD risk as a probability based on PRS and separately accounting for APOE, AD rare variants and the disease prevalence in age groups. The mathematical framework makes use of genetic variants effect sizes from summary statistics and AD disease prevalence in age groups. Results The AD probability varies with respect to age, APOE status and presence of rare variants. In age group 65+, the probability of AD grows from 0.03 to 0.18 (without APOE) and 0.07 to 0.7 (APOE e4e4 carriers) as PRS increases. In 85+, these values are 0.08–0.6 and 0.3–0.85. Presence of rare mutations, e.g. in TREM2, may increase the probability (in 65+) from 0.02 at the negative tail of the PRS to 0.3. Conclusions Our approach accounts for the varying disease prevalence in different genotype and age groups when modelling the APOE and rare genetic variants risk in addition to PRS. This approach has potential for use in a clinical setting and can easily be updated for novel rare variants and for other populations or confounding factors when appropriate genome-wide association data become available. Supplementary Information The online version contains supplementary material available at 10.1186/s13195-021-00884-7.
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Affiliation(s)
- Valentina Escott-Price
- Dementia Research Institute, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Hadyn Ellis Building, Maindy Rd, Cardiff, CF24 4HQ, UK.
| | - Karl Michael Schmidt
- School of Mathematics, Cardiff University, Senghennydd Road, Cardiff, CF24 4AG, UK
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Zhang L, Sun L. A generalized robust allele-based genetic association test. Biometrics 2021; 78:487-498. [PMID: 33729547 PMCID: PMC9544499 DOI: 10.1111/biom.13456] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 12/13/2020] [Accepted: 03/04/2021] [Indexed: 12/30/2022]
Abstract
The allele-based association test, comparing allele frequency difference between case and control groups, is locally most powerful. However, application of the classical allelic test is limited in practice, because the method is sensitive to the Hardy-Weinberg equilibrium (HWE) assumption, not applicable to continuous traits, and not easy to account for covariate effect or sample correlation. To develop a generalized robust allelic test, we propose a new allele-based regression model with individual allele as the response variable. We show that the score test statistic derived from this robust and unifying regression framework contains a correction factor that explicitly adjusts for potential departure from HWE and encompasses the classical allelic test as a special case. When the trait of interest is continuous, the corresponding allelic test evaluates a weighted difference between individual-level allele frequency estimate and sample estimate where the weight is proportional to an individual's trait value, and the test remains valid under Y-dependent sampling. Finally, the proposed allele-based method can analyze multiple (continuous or binary) phenotypes simultaneously and multiallelic genetic markers, while accounting for covariate effect, sample correlation, and population heterogeneity. To support our analytical findings, we provide empirical evidence from both simulation and application studies.
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Affiliation(s)
- Lin Zhang
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, Canada
| | - Lei Sun
- Department of Statistical Sciences, Faculty of Arts and Science, University of Toronto, Toronto, Canada.,Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
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Citterio F, Romano F, Ferrarotti F, Gualini G, Aimetti M. Quality of methods and reporting in association studies of chronic periodontitis and IL1A -889 and IL1B +3953/4 SNPs: A systematic review. J Periodontal Res 2019; 54:457-467. [PMID: 30982982 DOI: 10.1111/jre.12655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 11/30/2018] [Accepted: 12/10/2018] [Indexed: 11/29/2022]
Abstract
OBJECTIVE The aim of this systematic review was to evaluate the quality of reporting and methodology in genetic association studies between IL1A -889 and IL1B +3954 polymorphisms and chronic periodontitis. BACKGROUND Evidence provided by periodontal research on genetic risk factors is of uttermost importance in clinical practice as a possible diagnostic and prognostic tool for periodontitis. Inadequate reporting of results as well as high risk of bias due to methodological inconsistency hampers the integration of evidence in terms of clinical applicability. METHODS This review includes case-control studies in humans published between 1997 and July 2017. Searching was conducted through MEDLINE, EMBASE, and search handing. Specific scoring systems have been developed to evaluate the quality of methods and reporting. Each article was scored according to its adequacy, and then, the total number and the percentage of items positively qualified for both methods and reporting were calculated. The quality of methods in studies scoring 0-6, 7-12, and 13-16 was, respectively, considered poor, moderate, and good. For reporting, scores of 0-9, 10-18, and 19-26 were deemed of poor, moderate, and good quality, respectively. Pearson's correlation coefficient was calculated to explore the correlation between the year of publication and the quality in terms of methods and reporting. RESULTS From the 531 screened studies, 52 met the inclusion criteria and were thus included in the study. The quality of methods and reporting of published genetic association papers on IL1 and chronic periodontitis is moderate. On a scale from 0 to 16, the mean score for methods of the reviewed studies was 8.19 ± 1.93. The items more frequently considered inadequate concerned the handling of confounders in statistical analysis, especially oral hygiene habits, socioeconomic status, subgingival colonization of specific periodontal pathogens, and stress. A significant positive correlation was found between the year of publication and the quality scores in terms of method (r = 0.401, P = 0.003). In terms of reporting, the mean score was 14.83 ± 3.04 on a scale from 0 to 26 and it was considered overall moderate. No statistically significant correlation was found between the year of publication and the quality of reporting (P = 0.266). CONCLUSIONS The association between IL1A -889 and IL1B +3954 polymorphisms and chronic periodontitis is questionable due to methodological inconsistency. Evidence arising from meta-analysis is unreliable due to high risk of bias and moderate quality in terms of reporting.
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Affiliation(s)
- Filippo Citterio
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Federica Romano
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Francesco Ferrarotti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Gualini
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
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Sadr M, Moazzami B, Soleimanifar N, Elhamian N, Rezaei A, Ebrahimi Daryani N, Rezaei N. Single Nucleotide Polymorphisms of PTPN22 Gene in Iranian Patients with Ulcerative Colitis. Fetal Pediatr Pathol 2019; 38:8-13. [PMID: 30636557 DOI: 10.1080/15513815.2018.1543371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVES Protein tyrosine phosphatase non-receptor type 22 gene (PTPN22) single-nucleotide polymorphisms (SNP) have been associated with a number of different autoimmune diseases. This study aimed to investigate the association of five polymorphisms of PTPN22 gene with susceptibility to ulcerative colitis (UC) in Iran. MATERIALS AND METHODS A total of 67 patients diagnosed with UC (35 female and 32 male all under 18 years) and 93 healthy subjects were selected. The samples were genotyped for the, rs12760457, rs2476601, rs1310182, rs1217414, and rs33996649 in PTPN22 gene using real-time polymerase chain reaction (PCR) allelic discrimination TaqMan genotyping assays. RESULTS The frequencies of the rs1310182 A and G alleles, and also the AA and GG genotypes were significantly different between the patient and the control groups (p < 0.05). The carriage of G allele of rs1310182 was significantly associated with increased risk of UC (OR (95% CI) = 1.17 (0.70-1.98), p < 0.001). Moreover, the genotype GG of SNP rs1310182 was significantly associated with UC (OR (95% CI) = 2.32 (1.13-4.76), p < 0.01). No association was found between other PTPN22 gene SNPs among UC patients. CONCLUSION PTPN22 gene polymorphism in rs1310182 could play a crucial role in susceptibility to UC.
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Affiliation(s)
- Maryam Sadr
- a Molecular Immunology Research Center, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Bobak Moazzami
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Narjes Soleimanifar
- a Molecular Immunology Research Center, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Nazanin Elhamian
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Arezoo Rezaei
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Nasser Ebrahimi Daryani
- c Department of Gastroenterology and Hepatology , Tehran University of Medical Sciences , Tehran , Iran
| | - Nima Rezaei
- b Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran.,d Department of Immunology, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran.,e Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA) , Universal Scientific Education and Research Network (USERN) , Tehran , Iran
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Wang CH, Ning QF, Liu C, Lv TT, Cong EZ, Gu JY, Zhang YL, Nie HY, Zhang XL, Li Y, Zhang XY, Su LY. Associations of serotonin transporter gene promoter polymorphisms and monoamine oxidase A gene polymorphisms with oppositional defiant disorder in a Chinese Han population. Behav Brain Funct 2018; 14:15. [PMID: 30126429 PMCID: PMC6102835 DOI: 10.1186/s12993-018-0147-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 08/11/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oppositional defiant disorder (ODD) is a behavioral disorder that mainly refers to a recurrent pattern of disobedient, defiant, negativistic and hostile behaviors toward authority figures. Previous studies have showed associations of serotonin transporter (5-HTT) and monoamine oxidase A (MAOA) with behavioral and psychiatric disorders. The purposes of this study were to investigate the potential association of 5-HTT gene promoter polymorphism (5-HTTLPR) and MAOA gene polymorphism with susceptibility to ODD in a Han Chinese school population. METHODS The 5-HTTLPR gene polymorphism and the MAOA gene polymorphism were genotyped in a case-control study of 257 Han Chinese children (123 ODD and 134 healthy controls). RESULTS There was significant difference in the allele distribution of 5-HTTLPR (χ2 = 7.849, P = 0.005) between the ODD and control groups. Further, there were significant differences in genotype (χ2 = 5.168, P = 0.023) and allele distributions (χ2 = 10.336, P = 0.001) of the MAOA gene polymorphism that is variable-number tandem repeat (MAOA-uVNTR) between two groups. Moreover, there were significant differences in genotype (χ2 = 4.624, P = 0.032) and allele distributions (χ2 = 9.248, P = 0.002) of MAOA-uVNTR only in the male ODD and healthy groups. CONCLUSIONS Our results suggest that 5-HTTLPR and MAOA-uVNTR gene variants may contribute to susceptibility to ODD. Further, MAOA-uVNTR gene polymorphism may play a role in susceptibility to ODD only in male children.
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Affiliation(s)
- Chang-Hong Wang
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China.
| | - Qiu-Fen Ning
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China
| | - Cong Liu
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China
| | - Ting-Ting Lv
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China
| | - En-Zhao Cong
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China
| | - Jing-Yang Gu
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China
| | - Ying-Li Zhang
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China
| | - Hui-Yao Nie
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China
| | - Xiao-Li Zhang
- Department of Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University (Psychiatric Hospital of Henan Province China), Jianshe Road 388, Xinxiang, 453002, Henan, China
| | - Yan Li
- Department of Child and Adolescent, Public Health College, Zhengzhou University, Kexue Road 100, Zhengzhou, 450001, Henan, China
| | - Xiang-Yang Zhang
- Department of Psychiatry and Behavioral Sciences, UT Houston Medical School, The University of Texas Health Science Center at Houston, 1941 East Road, Houston, TX, 77054, USA
| | - Lin-Yan Su
- Department of Psychiatry, Mental Health Institute, Second Xiangya Hospital of Central South University, Changsha, 410011, China.
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Ebrahimi Daryani N, Saghazadeh A, Moossavi S, Sadr M, Shahkarami S, Soltani S, Farhadi E, Rezaei N. Interleukin-4 and Interleukin-10 Gene Polymorphisms in Patients with Inflammatory Bowel Disease. Immunol Invest 2018; 46:714-729. [PMID: 28872970 DOI: 10.1080/08820139.2017.1360343] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Changes in cytokine expression have been frequently found in patients with inflammatory bowel disease (IBD). Cytokine values outside the normal range may be somewhat related to common polymorphisms within cytokine genes. OBJECTIVE The present study was designed to investigate the possible association between polymorphisms within Interleukin IL-4 and IL-10 genes and susceptibility to and clinical features of IBD. METHODS The study population was composed of 140 healthy controls and 75 patients with IBD (40 patients with Crohn's disease (CD) and 35 patients with ulcerative colitis (UC)). Genotyping was performed using polymerase chain reaction with sequence-specific primers. RESULTS Higher frequencies for the C allele of IL-4-590 polymorphism (P < 0.0001; odds ratio [OR], 5.68; 95% confidence interval [95% CI], 3.28-9.83) and for the T allele of IL-4-1098 polymorphism (P = 0.016; OR, 1.83; 95% CI, 1.11-3.02) were observed in the whole group of IBD patients. The IL-4-590 C allele was also significantly overrepresented when IBD patients were subdivided into CD and UC (P < 0.0001; OR, 5.2-6.28). While the IL-4-1098 T allele was present at higher frequencies in patients with UC (P = 0.05; OR, 1.95), but not in CD (P = 0.09). Multiple pairwise comparisons indicated that genotypes of all polymorphisms investigated within IL-4 gene are correlated with IBD, CD, and UC. Haplotype analysis showed that the IL-4-1098/-590 TC haplotype might predispose individuals to IBD, CD, and UC whereas the IL-4-1098/-590 TT and GC haplotypes have a protective effect. On the contrary, neither allele nor genotype frequencies of IL-10 polymorphisms (IL-10-1082 A > G, IL-10-592 A > C, and IL-10-819 T > C) were associated with IBD, CD, or UC. CONCLUSIONS The present study suggests that IL-4 polymorphisms might play a role in susceptibility to IBD and its major subtypes in the Iranian population.
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Affiliation(s)
- Nasser Ebrahimi Daryani
- a Department of Gastroenterology and Hepatology , Tehran University of Medical Sciences , Tehran , Iran
| | - Amene Saghazadeh
- b Molecular Immunology Research Center , Tehran University of Medical Sciences , Tehran , Iran.,c Systematic Review and Mata-analysis Expert Group (SRMEG) , Universal Scientific Education and Research Network (USERN) , Tehran , Iran
| | - Shirin Moossavi
- d Digestive Oncology Research Center, Digestive Disease Research Institute , Tehran University of Medical Sciences , Tehran , Iran
| | - Maryam Sadr
- b Molecular Immunology Research Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Sepideh Shahkarami
- b Molecular Immunology Research Center , Tehran University of Medical Sciences , Tehran , Iran.,e Medical Genetics Network (MeGeNe) , Universal Scientific Education and Research Network (USERN) , Tehran , Iran
| | - Samaneh Soltani
- b Molecular Immunology Research Center , Tehran University of Medical Sciences , Tehran , Iran
| | - Elham Farhadi
- f Hematology Department , School of Allied Medical Science, Iran University of Medical Sciences , Tehran , Iran
| | - Nima Rezaei
- g Research Center for Immunodeficiencies, Children's Medical Center , Tehran University of Medical Sciences , Tehran , Iran.,h Department of Immunology , School of Medicine, Tehran University of Medical Sciences , Tehran , Iran.,i Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA) , Universal Scientific Education and Research Network (USERN) , Tehran , Iran
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Dimou NL, Pantavou KG, Bagos PG. Apolipoprotein E Polymorphism and Left Ventricular Failure in Beta-Thalassemia: A Multivariate Meta-Analysis. Ann Hum Genet 2017; 81:213-223. [DOI: 10.1111/ahg.12203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 06/05/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Niki L. Dimou
- Department of Computer Science and Biomedical Informatics; University of Thessaly; Papasiopoulou 2-4 Lamia 35100 Greece
| | - Katerina G. Pantavou
- Department of Computer Science and Biomedical Informatics; University of Thessaly; Papasiopoulou 2-4 Lamia 35100 Greece
| | - Pantelis G. Bagos
- Department of Computer Science and Biomedical Informatics; University of Thessaly; Papasiopoulou 2-4 Lamia 35100 Greece
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Abstract
The Hardy-Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, population stratification, and genotyping errors. For assessment of deviation from Hardy-Weinberg proportions in data, the most popular approaches include the asymptotic Pearson's chi-squared goodness-of-fit test and the exact test. Pearson's chi-squared goodness-of-fit test is simple and straightforward, but is very sensitive to a small sample size or rare allele frequency. The exact test of Hardy-Weinberg proportions is preferable in these situations. The exact test can be performed through complete enumeration of heterozygote genotypes or on the basis of the Markov chain Monte Carlo procedure. In this chapter, we describe the Hardy-Weinberg principle and the commonly used Hardy-Weinberg proportion tests and their applications, and we demonstrate how the chi-squared test and exact test of Hardy-Weinberg proportions can be performed step-by-step using the popular software programs SAS, R, and PLINK, which have been widely used in genetic association studies, along with numerical examples. We also discuss approaches for testing Hardy-Weinberg proportions in case-control study designs that are better than traditional approaches for testing Hardy-Weinberg proportions in controls only. Finally, we note that deviation from the Hardy-Weinberg proportions in affected individuals can provide evidence for an association between genetic variants and diseases.
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Affiliation(s)
- Jian Wang
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Sanjay Shete
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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11
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Saleem S, Azam A, Maqsood SI, Muslim I, Bashir S, Fazal N, Riaz M, Ali SHB, Niazi MK, Ishaq M, Waheed NK, Qamar R, Azam M. Role of ACE and PAI-1 Polymorphisms in the Development and Progression of Diabetic Retinopathy. PLoS One 2015; 10:e0144557. [PMID: 26658948 PMCID: PMC4679138 DOI: 10.1371/journal.pone.0144557] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/19/2015] [Indexed: 12/30/2022] Open
Abstract
In the present study we determined the association of angiotensin converting enzyme (ACE) and plasminogen activator inhibitor-1 (PAI-1) gene polymorphisms with diabetic retinopathy (DR) and its sub-clinical classes in Pakistani type 2 diabetic patients. A total of 353 diabetic subjects including 160 DR and 193 diabetic non retinopathy (DNR) as well as 198 healthy controls were genotyped by allele specific polymerase chain reaction (PCR) for ACE Insertion/Deletion (ID) polymorphism, rs4646994 in intron 16 and PAI-1 4G/5G (deletion/insertion) polymorphism, rs1799768 in promoter region of the gene. To statistically assess the genotype-phenotype association, multivariate logistic regression analysis was applied to the genotype data of DR, DNR and control individuals as well as the subtypes of DR. The ACE genotype ID was found to be significantly associated with DR (p = 0.009, odds ratio (OR) 1.870 [95% confidence interval (CI) = 1.04-3.36]) and its sub-clinical class non-proliferative DR (NPDR) (p = 0.006, OR 2.250 [95% CI = 1.098-4.620]), while PAI polymorphism did not show any association with DR in the current cohort. In conclusion in Pakistani population the ACE ID polymorphism was observed to be significantly associated with DR and NPDR, but not with the severe form of the disease i.e. proliferative DR (PDR).
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Affiliation(s)
- Saba Saleem
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Aisha Azam
- Institute of Ophthalmology, Mayo Hospital, Lahore, Pakistan
| | | | - Irfan Muslim
- Institute of Ophthalmology, Mayo Hospital, Lahore, Pakistan
| | - Shaheena Bashir
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Nosheen Fazal
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Moeen Riaz
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | | | - Muhammad Khizar Niazi
- Armed Forces Institute of Ophthalmology, Rawalpindi, Pakistan
- Army Medical College, Rawalpindi, Pakistan
| | - Mazhar Ishaq
- Armed Forces Institute of Ophthalmology, Rawalpindi, Pakistan
- Army Medical College, Rawalpindi, Pakistan
| | - Nadia Khalida Waheed
- Tufts University Medical School, Boston, Massachusetts, United States of America
| | - Raheel Qamar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
- Al-Nafees Medical College and Hospital, Isra University, Islamabad, Pakistan
- Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Maleeha Azam
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
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12
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Zang Y, Yuan Y. A shrinkage method for testing the Hardy-Weinberg equilibrium in case-control studies. Genet Epidemiol 2013; 37:743-50. [PMID: 23934751 DOI: 10.1002/gepi.21753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 06/14/2013] [Accepted: 07/15/2013] [Indexed: 12/23/2022]
Abstract
Testing for the Hardy-Weinberg equilibrium (HWE) is often used as an initial step for checking the quality of genotyping. When testing the HWE for case-control data, the impact of a potential genetic association between the marker and the disease must be controlled for otherwise the results may be biased. Li and Li [2008] proposed a likelihood ratio test (LRT) that accounts for this potential genetic association and it is more powerful than the commonly used control-only χ² test. However, the LRT is not efficient when the marker is independent of the disease, and also requires numerical optimization to calculate the test statistic. In this article, we propose a novel shrinkage test for assessing the HWE. The proposed shrinkage test yields higher statistical power than the LRT when the marker is independent of or weakly associated with the disease, and converges to the LRT when the marker is strongly associated with the disease. In addition, the proposed shrinkage test has a closed form and can be easily used to test the HWE for large datasets that result from genome-wide association studies. We compare the performance of the shrinkage test with existing methods using simulation studies, and apply the shrinkage test to a genome-wide association dataset for Alzheimer's disease.
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Affiliation(s)
- Yong Zang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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13
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Chowdhury S, Hobbs CA, MacLeod SL, Cleves MA, Melnyk S, James SJ, Hu P, Erickson SW. Associations between maternal genotypes and metabolites implicated in congenital heart defects. Mol Genet Metab 2012; 107:596-604. [PMID: 23059056 PMCID: PMC3523122 DOI: 10.1016/j.ymgme.2012.09.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 09/21/2012] [Accepted: 09/21/2012] [Indexed: 01/19/2023]
Abstract
BACKGROUND The development of non-syndromic congenital heart defects (CHDs) involves a complex interplay of genetics, metabolism, and lifestyle. Previous studies have implicated maternal single nucleotide polymorphisms (SNPs) and altered metabolism in folate-related pathways as CHD risk factors. OBJECTIVE We sought to discover associations between maternal SNPs and metabolites involved in the homocysteine, folate, and transsulfuration pathways, and determine if these associations differ between CHD cases and controls. DESIGN Genetic, metabolic, demographic, and lifestyle information was available for 335 mothers with CHD-affected pregnancies and 263 mothers with unaffected pregnancies. Analysis was conducted on 1160 SNPs, 13 plasma metabolites, and 2 metabolite ratios. A two-stage multiple linear regression was fitted to each combination of SNP and metabolite/ratio. RESULTS We identified 4 SNPs in the methionine adenosyltransferase II alpha (MAT2A) gene that were associated with methionine levels. Three SNPs in tRNA aspartic acid methyltransferase 1 (TRDMT1) gene were associated with total plasma folate levels. Glutamylcysteine (GluCys) levels were associated with multiple SNPs within the glutathione peroxidase 6 (GPX6) and O-6-methylguanine-DNA methyltransferase (MGMT) genes. The regression model revealed interactions between genotype and case-control status in the association of total plasma folate, total glutathione (GSH), and free GSH, to SNPs within the MGMT, 5,10-methenyltetrahydrofolate synthetase (MTHFS), and catalase (CAT) genes, respectively. CONCLUSIONS Our study provides further evidence that genetic variation within folate-related pathways accounts for inter-individual variability in key metabolites. We identified specific SNP-metabolite relationships that differed in mothers with CHD-affected pregnancies, compared to controls. Our results underscore the importance of multifactorial studies to define maternal CHD risk.
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Affiliation(s)
- Shimul Chowdhury
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
- Clinical Molecular Genetics Department, Providence Sacred Heart Medical Center, 101 W. Eighth Avenue, Spokane, WA 99204, USA
| | - Charlotte A. Hobbs
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Stewart L. MacLeod
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Mario A. Cleves
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Stepan Melnyk
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - S. Jill James
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Ping Hu
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
| | - Stephen W. Erickson
- Department of Pediatrics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 13 Children’s Way, Slot 512, Little Rock, AR 72202, USA
- Department of Biostatistics, College of Medicine, University of Arkansas for Medical Sciences, Arkansas Children’s Hospital Research Institute, 4301 W. Markham Street, Slot 781, Little Rock, AR 72205, USA
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14
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Abstract
The Hardy-Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, populations stratification, and genotyping errors. For assessment of deviation from the Hardy-Weinberg proportions in data, the most popular approaches include the asymptotic Pearson's chi-square goodness-of-fit test and the exact test. The Pearson's chi-square goodness-of-fit test is simple and straightforward, but it is very sensitive to small sample size or rare allele frequency. The exact test of Hardy-Weinberg proportions is preferable in these situations. The exact test can be performed through complete enumeration of heterozygote genotypes or on the basis of the Markov chain Monte Carlo procedure. In this chapter, we describe the Hardy-Weinberg principle and the commonly used Hardy-Weinberg proportions tests and their applications, and we demonstrate how the chi-square test and exact test of Hardy-Weinberg proportions can be performed step-by-step using the popular software programs SAS, R, and PLINK, which have been widely used in genetic association studies, along with numerical examples. We also discuss recent approaches for testing Hardy-Weinberg proportions in case-control study designs that are better than traditional approaches for testing Hardy-Weinberg proportions in controls only. Finally, we note that deviation from the Hardy-Weinberg proportions in affected individuals can provide evidence for an association between genetic variants and diseases.
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Affiliation(s)
- Jian Wang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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15
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Testing Hardy-Weinberg proportions in a frequency-matched case-control genetic association study. PLoS One 2011; 6:e27642. [PMID: 22110703 PMCID: PMC3215743 DOI: 10.1371/journal.pone.0027642] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 10/21/2011] [Indexed: 01/10/2023] Open
Abstract
In case-control genetic association studies, cases are subjects with the disease and controls are subjects without the disease. At the time of case-control data collection, information about secondary phenotypes is also collected. In addition to studies of primary diseases, there has been some interest in studying genetic variants associated with secondary phenotypes. In genetic association studies, the deviation from Hardy-Weinberg proportion (HWP) of each genetic marker is assessed as an initial quality check to identify questionable genotypes. Generally, HWP tests are performed based on the controls for the primary disease or secondary phenotype. However, when the disease or phenotype of interest is common, the controls do not represent the general population. Therefore, using only controls for testing HWP can result in a highly inflated type I error rate for the disease- and/or phenotype-associated variants. Recently, two approaches, the likelihood ratio test (LRT) approach and the mixture HWP (mHWP) exact test were proposed for testing HWP in samples from case-control studies. Here, we show that these two approaches result in inflated type I error rates and could lead to the removal from further analysis of potential causal genetic variants associated with the primary disease and/or secondary phenotype when the study of primary disease is frequency-matched on the secondary phenotype. Therefore, we proposed alternative approaches, which extend the LRT and mHWP approaches, for assessing HWP that account for frequency matching. The goal was to maintain more (possible causative) single-nucleotide polymorphisms in the sample for further analysis. Our simulation results showed that both extended approaches could control type I error probabilities. We also applied the proposed approaches to test HWP for SNPs from a genome-wide association study of lung cancer that was frequency-matched on smoking status and found that the proposed approaches can keep more genetic variants for association studies.
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16
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Sha Q, Zhang S. A test of Hardy-Weinberg equilibrium in structured populations. Genet Epidemiol 2011; 35:671-8. [PMID: 21818775 DOI: 10.1002/gepi.20617] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 06/15/2011] [Accepted: 06/15/2011] [Indexed: 01/05/2023]
Abstract
Testing for Hardy-Weinberg equilibrium (HWE) is used routinely as an important initial step for genotype data quality checking. Departure from HWE can be caused by many factors, such as genotyping errors, population stratification, and disease association, if we use affected individuals only. In a structured population, even if a marker is in HWE in each subpopulation, data may show departure from HWE if allele frequencies are different in different subpopulations and such a departure can be misinterpreted as a potential problem in genotyping quality, resulting in false exclusion from future analysis. In this article, we propose a new HWE test, a test for HWE in structured populations (HWES) that can assess departure from HWE and take into account of population stratification at the same time. Our proposed test can distinguish departure from HWE caused by population stratification and departure from HWE caused by other factors. We use simulation studies as well as applications to real data sets to evaluate the performance of the proposed test. Results show that, for a wide range of population structures, our proposed test has correct type I error rates while the traditional χ(2) test will lead to false-positive results. In homogenous populations, our proposed test has comparable power with the traditional χ(2) test.
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Affiliation(s)
- Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, USA
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