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Amin MM, Husada MS, Idaiani S, Effendy E, Nasution S, Purnama SD. The Effect of Interleukin-2 -330 T/G Polymorphism in People with Schizophrenia Among The Batak and Javanese Ethnic Groups. Med Arch 2023; 77:363-369. [PMID: 38299092 PMCID: PMC10825752 DOI: 10.5455/medarh.2023.77.363-369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 09/29/2023] [Indexed: 02/02/2024] Open
Abstract
Background Schizophrenia is a complex disorder involving multiple genes with mild to moderate effects and non-genetic risk factors such as environmental and psychological influences that alter brain chemistry. Significant reduction in interleukin-2 production by peripheral lymphocytes is an immunological finding replicated in schizophrenia across various countries. Investigations on the interleukin-2 -330 T/G polymorphism in people with schizophrenia (PWS) are still minimal, and the study location involves only a few countries with different results. Therefore, this study aims to examine the effect of interleukin-2 -330 T/G polymorphisms in people with schizophrenia among the Batak and Javanese ethnic groups in Indonesia, particularly in North Sumatra. Method This study used purposive non-probability sampling to recruit people with schizophrenia with 120 Batak and 120 Javanese subjects who were hospitalized at Prof. M. Ildrem Mental Hospital, Medan, Indonesia. The interleukin-2 -330 T/G polymorphism was examined by the PCR method. Result The results showed that the genotype frequency of the Batak people with schizophrenia is as follows: GG 11.7%, TG 53.3% and TT 35%. Furthermore, the group of Javanese people with schizophrenia is as follows: GG 23.3%, TG 44.2% and TT 32.5%. The OR for the genotypic comparison of GG was found to be 2.154 with 95% CI 0.992-4.678, p=0.053, while that of the TG genotype was 0.892 with 95% CI 0.505-1.574 and p=0.693. The T allele was higher than the G allele in Batak and Javanese ethnic groups, as demonstrated by p=0.713, OR=0.919 with 95% CI 0.641-1.318. Conclusion There is no statistically significant difference between the occurrence frequency of alleles. In addition, there is no significant relationship between the GG and the TG genotype of the interleukin-2 - 330T/G polymorphism in people with schizophrenia among the Batak and the Javanese ethnic groups.
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Affiliation(s)
- Mustafa M. Amin
- Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
| | | | - Sri Idaiani
- Centre of Preclinical and Clinical Medicine Research National Research and Innovation Agency
| | - Elmeida Effendy
- Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara
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van ‘t Hof LJ, Schotvanger N, Haasnoot GW, van der Keur C, Roelen DL, Lashley LEELO, Claas FHJ, Eikmans M, van der Hoorn MLP. Maternal-Fetal HLA Compatibility in Uncomplicated and Preeclamptic Naturally Conceived Pregnancies. Front Immunol 2021; 12:673131. [PMID: 34054856 PMCID: PMC8155594 DOI: 10.3389/fimmu.2021.673131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
Introduction In pregnancy, the mother and fetus differ in HLA antigens, and yet the maternal immune system generally tolerates the fetus. KIR receptors expressed by maternal uterine NK cells at the maternal-fetal interface directly interact with HLA-C on extravillous trophoblast cells for optimal placental development. In this study, we aimed to determine whether there is a preferential selection for HLA compatibility and specific KIR/HLA-C combinations in uncomplicated and preeclamptic naturally conceived pregnancies compared to what would be expected by chance. Methods Genotyping for maternal and fetal HLA-A, -B, -C, -DR, and -DQ, and maternal KIR was performed for 451 uncomplicated pregnancies and 77 pregnancies complicated with preeclampsia. The number of HLA antigen (mis)matches between mother and fetus was calculated and compared to expected values obtained by randomization of the HLA haplotype, inherited from the father, over the existing maternal haplotype of the fetuses. A similar methodology was executed for analysis of the KIR/HLA-C data (n=309). Results In uncomplicated pregnancies, the degree of maternal-fetal HLA matching was not different than expected-by-chance values. In preeclamptic pregnancies, the degree of maternal-fetal HLA matching was different in observed compared to expected-by-chance values (p=0.012). More specifically, the degree of maternal-fetal matching of HLA-C was higher in the actual preeclamptic pregnancies than was expected-by-chance (p=0.007). Preeclamptic pregnancies showed an overall tendency towards higher maternal-fetal HLA compatibility, for total HLA matches (p=0.021), HLA class I (p=0.038) and HLA-C (p=0.025) compared to uncomplicated pregnancies. Conclusion The data suggest that there is no preferential selection of maternal-fetal HLA compatibility in uncomplicated pregnancies. In contrast, increased total HLA, HLA class I and, especially, HLA-C compatibility is associated with preeclampsia, suggestive for a role of HLA mismatches in immune regulation leading to uncomplicated pregnancy.
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Affiliation(s)
- Liseanne J. van ‘t Hof
- Department of Obstetrics and Gynaecology, Leiden University Medical Center, Leiden, Netherlands
| | - Naomi Schotvanger
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Geert W. Haasnoot
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Carin van der Keur
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Dave L. Roelen
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Frans H. J. Claas
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
| | - Michael Eikmans
- Department of Immunology, Leiden University Medical Center, Leiden, Netherlands
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Gomez-Raya L, Rauw WM, Dekkers JCM. Vector space algebra for scaling and centering relationship matrices under non-Hardy-Weinberg equilibrium conditions. Genet Sel Evol 2021; 53:7. [PMID: 33461489 PMCID: PMC7812663 DOI: 10.1186/s12711-020-00589-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 11/03/2020] [Indexed: 11/13/2022] Open
Abstract
Background Scales are linear combinations of variables with coefficients that add up to zero and have a similar meaning to “contrast” in the analysis of variance. Scales are necessary in order to incorporate genomic information into relationship matrices for genomic selection. Statistical and biological parameterizations using scales under different assumptions have been proposed to construct alternative genomic relationship matrices. Except for the natural and orthogonal interactions approach (NOIA) method, current methods to construct relationship matrices assume Hardy–Weinberg equilibrium (HWE). The objective of this paper is to apply vector algebra to center and scale relationship matrices under non-HWE conditions, including orthogonalization by the Gram-Schmidt process. Theory and methods Vector space algebra provides an evaluation of current orthogonality between additive and dominance vectors of additive and dominance scales for each marker. Three alternative methods to center and scale additive and dominance relationship matrices based on the Gram-Schmidt process (GSP-A, GSP-D, and GSP-N) are proposed. GSP-A removes additive-dominance co-variation by first fitting the additive and then the dominance scales. GSP-D fits scales in the opposite order. We show that GSP-A is algebraically the same as the NOIA model. GSP-N orthonormalizes the additive and dominance scales that result from GSP-A. An example with genotype information on 32,645 single nucleotide polymorphisms from 903 Large-White × Landrace crossbred pigs is used to construct existing and newly proposed additive and dominance relationship matrices. Results An exact test for departures from HWE showed that a majority of loci were not in HWE in crossbred pigs. All methods, except the one that assumes HWE, performed well to attain an average of diagonal elements equal to one and an average of off diagonal elements equal to zero. Variance component estimation for a recorded quantitative phenotype showed that orthogonal methods (NOIA, GSP-A, GSP-N) can adjust for the additive-dominance co-variation when estimating the additive genetic variance, whereas GSP-D does it when estimating dominance components. However, different methods to orthogonalize relationship matrices resulted in different proportions of additive and dominance components of variance. Conclusions Vector space methodology can be applied to measure orthogonality between vectors of additive and dominance scales and to construct alternative orthogonal models such as GSP-A, GSP-D and an orthonormal model such as GSP-N. Under non-HWE conditions, GSP-A is algebraically the same as the previously developed NOIA model.
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Affiliation(s)
- Luis Gomez-Raya
- Department of Animal Science, Iowa State University, Ames, IA, USA. .,Dept Mejora Genética Animal, INIA, Madrid, Spain.
| | - Wendy M Rauw
- Department of Animal Science, Iowa State University, Ames, IA, USA.,Dept Mejora Genética Animal, INIA, Madrid, Spain
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, USA
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Ye Z, Wang Z, Hou Y. Does Bonferroni correction "rescue" the deviation from Hardy-Weinberg equilibrium? Forensic Sci Int Genet 2020; 46:102254. [PMID: 32006894 DOI: 10.1016/j.fsigen.2020.102254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/15/2020] [Accepted: 01/19/2020] [Indexed: 11/25/2022]
Abstract
The application of Bonferroni correction (BC) has been constantly controversial; nevertheless, in forensic population genetics research, it is common to apply it to Hardy-Weinberg equilibrium (HWE) tests referring to multiple loci. This letter aimed to discuss the problems of applying BC to HWE tests involving multiple loci by surveying population genetics research studies published over the last 10 years (2009-2019) from two major forensic genetic journals: Forensic Science International: Genetics (FSIG) and the International Journal of Legal Medicine (IJLM). The results showed that there was no uniform standard of whether to apply BC to HWE tests or not, and researchers commonly did not provide any explanation for the observation of deviations from HWE. Despite its widespread use in population genetics, BC may not guarantee a prudent result due to an irrelevant null hypothesis, reluctance to reject the null hypothesis, different interpretations of identical p-values, and inflated type Ⅱ error. We recommended a notable two-step approach suggested by Waples to evaluate the results of HWE tests: 1) identifying causes of departures from HWE and 2) evaluating the biological consequences of HW departures. In addition, for forensic researchers, we suggested that if a certain degree of deviation from HWE does occur, the first step to take should involve checking the technique and genotyping results carefully rather than recklessly using BC. In conclusion, according to the purpose of forensic population research, applying BC to HWE tests is unnecessary; rather, an unadjusted α should be used. BC does not "rescue" the deviation from HWE. To "rescue" it indeed, directly discussing the possible explanation for each departure from HWE and simply describing what has been done sequentially and why should be enough for readers to reach a reasonable conclusion even without the help of Bonferroni methods.
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Affiliation(s)
- Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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Rehman AU, Iqbal J, Shakeel A, Qamar ZU, Rana P. Hardy-Weinberg equilibrium study of six morphogenetic characters in a population of Punjab, Pakistan. ALL LIFE 2020. [DOI: 10.1080/26895293.2020.1750491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Aneeq-ur- Rehman
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Junaid Iqbal
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Amir Shakeel
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Zia ul Qamar
- Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Poonum Rana
- Department of Zoology, University of Agriculture Faisalabad, Faisalabad, Pakistan
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Johnson PCD, McAulay KA, Montgomery D, Lake A, Shield L, Gallagher A, Little AM, Shah A, Marsh SGE, Taylor GM, Jarrett RF. Modeling HLA associations with EBV-positive and -negative Hodgkin lymphoma suggests distinct mechanisms in disease pathogenesis. Int J Cancer 2015; 137:1066-75. [PMID: 25648508 PMCID: PMC4737225 DOI: 10.1002/ijc.29467] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 01/08/2015] [Indexed: 01/08/2023]
Abstract
HLA genotyping and genome wide association studies provide strong evidence for associations between Human Leukocyte Antigen (HLA) alleles and classical Hodgkin lymphoma (cHL). Analysis of these associations is complicated by the extensive linkage disequilibrium within the major histocompatibility region and recent data suggesting that associations with EBV‐positive and EBV‐negative cHL are largely distinct. To distinguish independent and therefore potentially causal associations from associations confounded by linkage disequilibrium, we applied a variable selection regression modeling procedure to directly typed HLA class I and II genes and selected SNPs from EBV‐stratified patient subgroups. In final models, HLA‐A*01:01 and B*37:01 were associated with an increased risk of EBV‐positive cHL whereas DRB1*15:01 and DPB1*01:01 were associated with decreased risk. Effects were independent of a prior history of infectious mononucleosis. For EBV‐negative cHL the class II SNP rs6903608 remained the strongest predictor of disease risk after adjusting for the effects of common HLA alleles. Associations with “all cHL” and differences by case EBV status reflected the subgroup analysis. In conclusion, this study extends previous findings by identifying novel HLA associations with EBV‐stratified subgroups of cHL, highlighting those alleles likely to be biologically relevant and strengthening evidence implicating genetic variation associated with the SNP rs6903608. What's new? Strong evidence exists for associations between HLA alleles and classical Hodgkin lymphoma (cHL). Analysis is however complicated by the linkage disequilibrium within the MHC region and data suggesting that associations with Epstein‐Barr virus (EBV)‐positive and negative cHL are distinct. In the largest study to date to investigate associations between EBV‐stratified cHL subgroups and directly typed HLA alleles, the authors extend associations with EBV‐positive cHL to novel HLA class II alleles, which are associated with decreased disease risk. For EBV‐negative disease, the class II SNP rs6903608 remains the strongest predictor of risk after adjusting for the effects of common HLA alleles.
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Affiliation(s)
- Paul C D Johnson
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Karen A McAulay
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Dorothy Montgomery
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Annette Lake
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Lesley Shield
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Alice Gallagher
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ann-Margaret Little
- Histocompatibility and Immunogenetics Laboratory, Gartnavel General Hospital, Glasgow, United Kingdom
| | - Anila Shah
- Anthony Nolan, Royal Free Hospital, Hampstead, London, United Kingdom
| | - Steven G E Marsh
- Anthony Nolan, Royal Free Hospital, Hampstead, London, United Kingdom.,Cancer Institute, University College London, Royal Free Campus, London, United Kingdom
| | - G Malcolm Taylor
- Immunogenetics Group, University of Manchester, St Mary's Hospital, Manchester, United Kingdom
| | - Ruth F Jarrett
- MRC - University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Roberts SJ, Nikitopoulos E, Cords M. Factors affecting low resident male siring success in one-male groups of blue monkeys. Behav Ecol 2014. [DOI: 10.1093/beheco/aru060] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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