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Thomford NE, Abraham SA, Nyarko SB, Biney RP. A consideration of CYP2D6 genetic variations in the Ghanaian population as a potential 'culprit' for the tramadol 'abuse crisis'. BMC Med Genomics 2024; 17:28. [PMID: 38254077 PMCID: PMC10804791 DOI: 10.1186/s12920-023-01773-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Cytochrome P450 2D6 is involved in the metabolism of several important medicines including opioids. Variations in CYP2D6 have been implicated in drug response and according to the Clinical Pharmacogenetics Implementation Consortium Guideline (CPIC) for CYP2D6, dosing for CYP2D6 substrates should be based on variants carried by individuals. Although CYP2D6 variations in Ghana had been previously recorded, not all variants have been reported in the Ghanaian population. In this exploratory study we set to investigate certain unreported variations in the Ghanaian population in addition to the previously reported ones and use that to understand the tramadol 'abuse' crisis that is currently being experienced in Ghana. METHODS This study employed a convenience sampling approach to include 106 unrelated participants who were recruited as part of the PHARMABIOME project. We successfully genotyped 106 samples using Iplex GOLD SNP genotyping protocol after extracting DNA from these individuals. Allele and diplotype frequencies were undertaken by counting from observed genotypes. Comparison of alleles reported from various studies were done. RESULTS Unreported alleles such as *3, *9 and *41 which are classified as no function and decreased function were observed in our study cohort. In addition, variants such as (*1, *2, *4, *5, *10, *17 and *29 were observed with different frequencies. Our study showed 26% representation of intermediate metabolizers (IM) and 2% poor metabolizers (PM) in the study population. CONCLUSION The implications for informal sector workers who use tramadol for recreational purposes, is that IMs and PMs will overdose as they may have reduced analgesic effects which will translate into increased risks of unforeseen adverse events. We therefore propose that CYP2D6 should be considered in opioid dosage while making use of these observed variations to implement new approaches to tackle the tramadol 'abuse crisis' in Ghana.
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Affiliation(s)
- Nicholas Ekow Thomford
- Department of Medical Biochemistry, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana.
- Pharmacogenomics and Genomic Medicine Group, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana.
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, Cape Town, 7925, South Africa.
| | - Susanna Aba Abraham
- Department of Adult Health, School of Nursing and Midwifery, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Samuel Badu Nyarko
- Department of Medical Biochemistry, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
- Pharmacogenomics and Genomic Medicine Group, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Robert Peter Biney
- Pharmacogenomics and Genomic Medicine Group, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
- Department of Pharmacotherapeutics and Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
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Boyanova L, Boyanova L, Hadzhiyski P, Kandilarov N, Yordanov D, Gergova R, Markovska R. Mixed (multiple-genotype) Helicobacter pylori infections in Bulgarian patients. Diagn Microbiol Infect Dis 2023; 107:116073. [PMID: 37717293 DOI: 10.1016/j.diagmicrobio.2023.116073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/19/2023]
Abstract
The aim of the study was to evaluate the frequency and characteristics of mixed (multiple-genotype) Helicobacter pylori infections (MGIs) in 155 Bulgarian symptomatic patients (21 children and 134 adults). MGIs were common (36.1%), including double-strain (34.8%) and triple-strain infections (1.3%). None of the 8 ulcer patients harbored multiple subtypes. We detected 18 multiple allelic combinations, of which the most frequent subtypes (17.4%) were vacA s1as2 and vacA s1cs2. The 2 patients with triple-strain infections had vacA s1bs1cs2i1i2/iceA1A2 and vacA s1as1cs2 subtypes. They were both adult men with chronic gastritis and both were examined in 2022. The prevalence of MGIs (51.7%) was 2-fold higher in 2020 to 2022 than in 2015 to 2019 (26.3%). Putative factors for the increase may be the patient's characteristics and COVID-19 pandemic-associated factors. MGI rates corresponded to the high infection seroprevalence (72.4% in 2011) in Bulgaria. The evolution and clinical importance of mixed H. pylori infections merit extensive evaluation.
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Affiliation(s)
- Lyudmila Boyanova
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria.
| | - Liliya Boyanova
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Petyo Hadzhiyski
- Specialized Hospital for Active Pediatric Treatment, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Nayden Kandilarov
- Department of General and Hepatobiliary Pancreatic Surgery, Department of Surgery, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Daniel Yordanov
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Raina Gergova
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Rumyana Markovska
- Department of Medical Microbiology, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
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Saremi L, Esmaeili S, Ghaffari ME, Shahbazi S, Lotfipanah S, Kadkhodazadeh M. Evaluation of matrix metalloproteinase-1, -2, -3, -7, and -13 gene polymorphisms in patients with chronic periodontitis and healthy controls. Clin Oral Investig 2023; 27:7417-7423. [PMID: 37848583 DOI: 10.1007/s00784-023-05331-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
OBJECTIVES The current study aimed to investigate the association of matrix metalloproteinase- (MMP-) 1, -2, -3, -7, and -13 gene polymorphisms with chronic periodontitis (CP) in an Iranian population. MATERIALS AND METHODS In this case-control study, 87 subjects with CP and 89 periodontally healthy subjects were allocated to case and control groups, respectively. Subjects' venous blood samples (5 cc) were collected, and DNA extraction was performed. A spectrophotometer was utilized to assess the concentration of extracted DNAs. The desired gene polymorphisms were examined using restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) followed by electrophoresis. Statistical analyses were done using the Pearson Chi-Square test, odds ratio, and t-Test using SPSS Version 28. RESULTS The MMP-1 (-1607 1G/2G) rs1799750, MMP-3 (-1171 5A/6A) rs3025058, and MMP-7 (-181 A/G) rs11568818 gene polymorphisms significantly differed between case and control groups (PV = 0.019, 0.007, and 0.028, respectively). In contrast, the gene polymorphisms of MMP-2 (-1306 C/T) rs243865 and MMP-13 (-77 A/G) rs2252070 did not make a significant difference. Regarding allele frequencies, the presence of the 2G allele in the MMP-1 (-1607) rs1799750 genotype increased the CP susceptibility significantly, while subjects with the 6A allele in their MMP-3 (-1171) rs3025058 genotype showed significantly lower susceptibility to CP (PV = 0.008 and < 0.001, respectively). CONCLUSION In the studied population, gene polymorphisms in the DNA sequences of MMP-1 (-1607 1G/2G) rs1799750, MMP-3 (-1171 5A/6A) rs3025058, and MMP-7 (-181 A/G) rs11568818 may have impacts on CP incidence. CLINICAL RELEVANCE Clinicians should be cautious about the association between MMP-1, MMP-3, and MMP-7 gene polymorphisms and the incidence of chronic periodontitis during periodontal treatment planning.
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Affiliation(s)
- Leila Saremi
- Dental Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Saharnaz Esmaeili
- Division of Oral and Maxillofacial Surgery, School of Dentistry, University of California, Los Angeles, Los Angeles, CA, USA
- Dentofacial Deformities Research Center, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Ebrahim Ghaffari
- Department of Epidemiology and Biostatistics, Faculty of Health, Qom University of Medical Sciences, Qom, Iran
| | - Soheil Shahbazi
- Dentofacial Deformities Research Center, Research Institute of Dental Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shirin Lotfipanah
- Department of Biology Education, Farhangian University, Tehran, Iran
| | - Mahdi Kadkhodazadeh
- Dental Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Ben Salem A, Ezzidi I, Ben Abdennebi H, Mahjoub T, Sarray S, Mtiraoui N. Interleukin 10 (IL-10) gene variants and haplotypes in Tunisian women with polycystic ovary syndrome (PCOS): a case-control study. Mol Biol Rep 2023; 50:8089-8096. [PMID: 37541999 DOI: 10.1007/s11033-023-08706-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/20/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder that affects women in their child-bearing age, and is associated with insulin resistance and type 2 diabetes. The etiology of PCOS involves multiple factors including genetic, metabolic and immunological factors. Interleukin - 10 (IL-10), as an anti-inflammatory cytokine, plays a critical role in this regard. We investigated the potential role of IL-10 gene variants in the development of PCOS in Tunisian population. METHODS AND RESULTS 115 cases and 120 controls were recruited in the current case control study. Rotterdam consensus criteria were used to diagnose PCOS patients. Genotyping for IL-10, rs1800896, rs1800871 and rs1800872 variants, was performed by real time PCR. The results obtained showed that the minor allele frequency of rs1800896, rs1800871and rs1800872 were comparable between PCOS cases and control subjects (P = 0.30, P = 0.71, and P = 0.57 respectively). The distribution analysis revealed an unsignificant association of the three tested variants, in all genetic models. Haplotype analysis identified one haplotype CCA with a protective role in PCOS development (P = 0.05; OR (95% CI) = 0.56 (0.32 - 0.99)). This association did not persist after adjustment for multiples covariates (Pc = 0.154). CONCLUSIONS Our study is the first to show how ethnicity influences the association of IL-10 gene variants with PCOS susceptibility. No allelic nor genetic association were observed between the tested variants and PCOS in Tunisian women, however, a particular IL-10 haplotype with a protective effect for PCOS was identified.
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Affiliation(s)
- Assila Ben Salem
- Laboratory of Human Genome and Multifactorial Diseases, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, LR12ES07, Tunisia.
| | - Intissar Ezzidi
- Laboratory of Human Genome and Multifactorial Diseases, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, LR12ES07, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
| | - Hassen Ben Abdennebi
- Laboratory of Human Genome and Multifactorial Diseases, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, LR12ES07, Tunisia
| | - Touhami Mahjoub
- Laboratory of Human Genome and Multifactorial Diseases, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, LR12ES07, Tunisia
| | - Sameh Sarray
- College of Medicine and Medical Sciences, Arabian Gulf University, Manama, Bahrain
- Faculty of Sciences of Tunis, University of Tunis EL Manar II, Tunis, Tunisia
| | - Nabil Mtiraoui
- Laboratory of Human Genome and Multifactorial Diseases, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, LR12ES07, Tunisia
- Higher Institute of Biotechnology of Monastir, University of Monastir, Monastir, Tunisia
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Diamantidis MD, Karanikola RA, Polyzoudi C, Delicou S, Manafas A, Savera H, Xydaki A, Kotsiafti A, Tsangalas E, Ikonomou G, Mani E, Ntoulas K, Alexiou E, Argyrakouli I, Koskinas J, Fotiou P. Clinical significance of mutational variants in beta and alpha genes in patients with hemoglobinopathies from two large Greek centers: a complex interplay between genotype and phenotype. J Mol Med (Berl) 2023; 101:1073-1082. [PMID: 37420139 DOI: 10.1007/s00109-023-02342-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 07/09/2023]
Abstract
Hemoglobinopathies affect patients in the wider Mediterranean area consisting of 4 distinct subgroups: beta thalassemia major (TM), beta thalassemia intermedia (TI), sickle cell disease (SCD) and hemoglobin H disease (alpha thalassemia). The clinical spectrum varies from mild to severe. Complex interactions between genes and environmental factors form the clinical manifestations. There is an unmet need to clarify these multifactorial mechanisms. This is the first Greek study describing mutational alleles (HBB and HBA1/HBA2 gene variants) in 217 patients with hemoglobinopathies of two large centers in Greece (Larissa and Athens) and associating particular genotypes or gene variants with clinical manifestations (transfusion frequency, complications). Thus, the complex interplay between corresponding genotypes and phenotypes was investigated. Our results are in accordance with previous national studies with limited variations, due to regional prevalence of specific gene variants, as expected. It is also a description of the prevalence of hemoglobinopathies in the Greek population. The type and prevalence of beta and alpha globin gene variants differ significantly among countries. We also confirm the well-known observation of many studies that in our beta thalassemic or SCD patients, co-inheritance of variants in the alpha globin genes, leading to absence or reduction of alpha globin synthesis were associated with milder clinical course, whereas the inheritance of additional alpha genes (triplication) led to a more severe clinical phenotype. In cases in whom the genotype and phenotype did not correlate, factors like the function or modification of possible regulatory genes or additional nutritional-environmental effects should be investigated. KEY MESSAGES: • This is the first Greek study, fully molecularly defining the beta and alpha mutational alleles in 217 patients with hemoglobinopathies of two large centers in Greece and correlating particular genotypes or gene variants with clinical manifestations (transfusion frequency, complications). • In the beta thalassemic or SCD patients of our cohort, co-inheritance of variants in the alpha globin genes, leading to absence or reduction of alpha globin synthesis were associated with milder clinical course (confirmation of a well-known previous observation). • The inheritance of additional alpha genes (triplication) led to a more severe clinical phenotype (confirmation of a well known previous observation). • The function or modification of possible regulatory genes should be investigated in cases in whom the genotype and phenotype did not correlate.
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Affiliation(s)
- Michael D Diamantidis
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece.
| | - Rebecca-Anastasia Karanikola
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
| | - Chrysoula Polyzoudi
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
| | - Sophia Delicou
- Thalassemia and Sickle Cell Disease Unit, Hippokration General Hospital of Athens, Athens, Greece
| | - Achilles Manafas
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
| | - Helen Savera
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
| | - Aikaterini Xydaki
- Thalassemia and Sickle Cell Disease Unit, Hippokration General Hospital of Athens, Athens, Greece
| | - Angeliki Kotsiafti
- Thalassemia and Sickle Cell Disease Unit, Hippokration General Hospital of Athens, Athens, Greece
| | - Evangelos Tsangalas
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
| | - Georgia Ikonomou
- Thalassemia Prevention Unit, General Hospital of Larissa, Larissa, Greece
| | - Eirini Mani
- Thalassemia Prevention Unit, General Hospital of Larissa, Larissa, Greece
| | - Konstantinos Ntoulas
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
| | - Evangelos Alexiou
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
| | - Ioanna Argyrakouli
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
| | - John Koskinas
- Thalassemia and Sickle Cell Disease Unit, Hippokration General Hospital of Athens, Athens, Greece
| | - Paraskevi Fotiou
- Thalassemia and Sickle Cell Disease Unit, Department of Hematology, First Department of Internal Medicine, General Hospital of Larissa, Tsakalov St. 1, 41 221, Larissa, Greece
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Yousef A, Yousef M, Chowdhury S, Abdilleh K, Knafl M, Edelkamp P, Alfaro-Munoz K, Chacko R, Peterson J, Smaglo BG, Wolff RA, Pant S, Lee MS, Willis J, Overman M, Doss S, Matrisian L, Hurd MW, Snyder R, Katz MH, Wang H, Maitra A, Shen JP, Zhao D. Impact of KRAS Mutations and Co-mutations on Clinical Outcomes in Pancreatic Ductal Adenocarcinoma. Res Sq 2023:rs.3.rs-3195257. [PMID: 37609177 PMCID: PMC10441514 DOI: 10.21203/rs.3.rs-3195257/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803 PDAC patients (42% with metastatic disease) at MD Anderson Cancer Center. Overall survival (OS) analysis demonstrated that KRAS mutation status and subtypes were prognostic (p<0.001). Relative to patients with KRAS wildtype tumors (median OS 38 months), patients with KRASG12R had a similar OS (median 34 months), while patients with KRASQ61 and KRASG12D mutated tumors had shorter OS (median 20 months [HR: 1.9, 95% CI 1.2-3.0, p=0.006] and 22 months [HR: 1.7, 95% CI 1.3-2.3, p<0.001], respectively). There was enrichment of KRASG12D mutation in metastatic tumors (34% vs 24%, OR: 1.7, 95% CI 1.2-2.4, p=0.001) and enrichment of KRASG12R in well and moderately differentiated tumors (14% vs 9%, OR: 1.7, 95% CI 1.05-2.99, p=0.04). Similar findings were observed in the external validation cohort (PanCAN's Know Your Tumor® dataset, n=408).
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Affiliation(s)
- Abdelrahman Yousef
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mahmoud Yousef
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kawther Abdilleh
- Pancreatic Cancer Action Network, Manhattan Beach, Los Angeles, CA, USA
| | - Mark Knafl
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Edelkamp
- Department of Data Engineering & Analytics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristin Alfaro-Munoz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ray Chacko
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Peterson
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brandon G. Smaglo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert A. Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shubham Pant
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael S. Lee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Willis
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sudheer Doss
- Pancreatic Cancer Action Network, Manhattan Beach, Los Angeles, CA, USA
| | - Lynn Matrisian
- Pancreatic Cancer Action Network, Manhattan Beach, Los Angeles, CA, USA
| | - Mark W. Hurd
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rebecca Snyder
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew H.G. Katz
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huamin Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Zhao
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Almawi WY, Nemr R, Atazhanova T, Malalla ZH, Sarray S, Mustafa FE, Mahmood NA. Differential Association of FTO Gene variants and Haplotypes with the Susceptibility to Polycystic Ovary Syndrome According To Obesity in Women with PCOS. Reprod Sci 2023; 30:2166-2176. [PMID: 36602653 DOI: 10.1007/s43032-022-01149-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/11/2022] [Indexed: 01/06/2023]
Abstract
We explored the relation between FTO single gene variants (rs1861868, rs9939973, rs1421085, rs1121980, rs17817449, rs8050136, rs9939609, rs9930506, and rs8044769) and polycystic ovary syndrome (PCOS), in particular, according to the obesity status. This retrospective population-based case-control study involved women with PCOS (583) and 713 eumenorrheic control women; genotyping was done by real-time PCR. Significantly higher minor allele frequency (MAF) of rs9939973, rs17817449, rs9939609, and rs9930506 and lower MAF of rs1121980 were seen in PCOS cases. Lower risk of PCOS was associated with rs1121980 and rs8050136 heterozygous and minor allele-homozygous genotypes, while an elevated risk of PCOS was seen with minor allele-homozygous rs9939973, rs17817449, and r9939609 heterozygous and genotypes and minor allele-homozygous rs9930506 and rs8044769 genotype. While none of the tested FTO SNPs variants was associated with PCOS in normal body weight/lean subjects, rs9939973, rs9939609, and rs9930506 were negatively associated with PCOS in overweight subjects. In comparison, rs1861868 was negatively, while rs8044769 was positively associated with PCOS in obese subjects. Haplotype analysis identified haplotypes GACCTCTAT, AACCTCTAT, AACCTATAT and AGTTGCAGC, and GACCTCTAC to be positively associated with PCOS, while haplotypes GGTTGAAGC, GACCTATAT, GGTTGCAGC, and GATCTATAT were negatively associated with PCOS. Apart from GGTTGAAGC, these haplotypes remained associated with altered risk of PCOS after adjusting for covariates. In addition to rs17817449, rs9939609, rs9930506, and rs1121980, this study is the first to demonstrate association of rs9939973 and rs8044769 with altered risk of PCOS and the first to confirm the BMI dependency on the association of FTO variants with PCOS. This underscores the role of FTO gene variants as predisposing factors of PCOS.
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Affiliation(s)
- Wassim Y Almawi
- School of Medicine, Nazarbayev University, Astana, Kazakhstan.
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.
| | - Rita Nemr
- School of Medicine, Lebanese American University, Beirut, Lebanon
| | | | - Zainab H Malalla
- Department of Medical Biochemistry, Arabian Gulf University, Manama, Bahrain
| | - Sameh Sarray
- Department of Medical Biochemistry, Arabian Gulf University, Manama, Bahrain
| | - Fekria E Mustafa
- Department of Obstetrics and Gynecology, Salmaniya Medical Complex, Manama, Bahrain
| | - Naeema A Mahmood
- Department of Obstetrics and Gynecology, Salmaniya Medical Complex, Manama, Bahrain
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Al Lawati M, Al Balushi B. RHD Positive Haplotype in D Negative Omani Blood Donor. Oman Med J 2023; 38:e488. [PMID: 37122416 PMCID: PMC10130977 DOI: 10.5001/omj.2023.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/09/2021] [Indexed: 11/03/2022] Open
Abstract
The frequency of Rhesus D negative blood group in Omanis is 8.35% but the molecular background of this phenotype is unknown in the Omani population. The Rhesus D negative phenotype has a high molecular diversity. We report a rare case of serological D negative with existence of complete RHD gene in a 43-year-old Omani male blood donor. Molecular analysis of RHD exons showed duplication across the boundary of intron 3 and exon 4. This is a 37 bp insert in RHD exon 4 along with c.609 G>A mutation. We are uncertain if the presence of RHDΨ is homozygous (RHDΨ/RHDΨ) or hemizygous (RHDΨ/del). Therefore, molecular basis of D zygosity determination would be a good approach to further explore the case.
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Affiliation(s)
- Mujtaba Al Lawati
- Department of Medical Lab Sciences, Oman College of Health Sciences, Muscat, Oman
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Firasat S, Raza A, Khan AR, Abid A. The prevalence of pharmacogenetic variants of vitamin K epoxide reductase complex subunit 1 gene (rs9923231), cytochrome P450 family 2 subfamily C member 9 gene (rs1799853) and cytochrome P450 family 3 subfamily-A member-5 gene (rs776746) among 13 ethnic groups of Pakistan. Mol Biol Rep 2023; 50:4017-4027. [PMID: 36849858 DOI: 10.1007/s11033-023-08304-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 01/26/2023] [Indexed: 03/01/2023]
Abstract
BACKGROUND Pharmacogenomics (PGx) plays a central role in the selection of targeted therapies that underpins precision-medicine. We investigated the prevalence of three important pharmacogenetic variants of VKORC1, CYP2C9, and CYP3A5 genes among Pakistani populations. METHODS A total of 1104 individuals were included representing thirteen major ethnicities. Samples were genotyped by using PCR-RFLP analysis. The allelic and genotypic frequencies of the three SNV's were calculated and were compared with the world's population data (ALFA, gnomAD, and 1000Genome, 1 K databases), using the chi-square test. RESULTS We found overall frequencies of functional-alleles of VKORC1 0.43, CYP2C9 0.94, and CYP3A5 0.14 in our population. Data showed a low prevalence of homozygous functional genotypes of VKORC1 (0.18; 0.0-0.45) and CYP3A5 (0.04; 0.0-0.22), and a high frequency of CYP2C9 (0.885; 0.80-1.0) across ethnicities. Genotyping distribution of VKCOR1 functional genotype was varied across ethnic groups such as 0.0-0.10 in Brahuis and Mohanas, Sindhis, Rajputs, and Gujjars populations, 0.11-0.20 in Makranis, Parsis, and Burusho populations, and 0.20-0.30 in Kalash, Kashmiris and Baloch populations. The highest VKORC1 (CC) was found in Pathans (0.45) and Hazaras (0.39) populations. Interestingly, we found a high prevalence of functional genotype CYP2C9 (rs1799853; C) and non-functional genotype of CYP3A5 (rs776746; T) across various ethnic groups of Pakistan. CONCLUSION Data regarding prevalence of clinically important pharmacogenomics SNVs could be useful in drug adjustment and avoiding adverse drug reactions in a specific ethnic population. This could help in moving current medical practices toward precision medicine in our part of the world.
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Affiliation(s)
- Sadaf Firasat
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Chand Bibi road, 74200, Karachi, Pakistan
| | - Ali Raza
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Chand Bibi road, 74200, Karachi, Pakistan
| | - Abdul Rafay Khan
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Chand Bibi road, 74200, Karachi, Pakistan
| | - Aiysha Abid
- Centre for Human Genetics and Molecular Medicine, Sindh Institute of Urology and Transplantation (SIUT), Chand Bibi road, 74200, Karachi, Pakistan.
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Aykur M, Calıskan Kurt C, Dirim Erdogan D, Biray Avcı C, Vardar R, Aydemir S, Girginkardesler N, Gunduz C, Dagci H. Distribution and Phylogenetic Analysis of Subtypes and Alleles of Blastocystis sp. in the Stool Samples Collected from Patients with Gastrointestinal Complaints in İzmir, Turkey. Acta Parasitol 2023. [PMID: 36806111 DOI: 10.1007/s11686-023-00665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/19/2023] [Indexed: 02/23/2023]
Abstract
PURPOSE Blastocystis sp. is one of the most prevalent intestinal protozoa found in humans and many other animals. The present study aimed to examine the distribution and genetic diversity of Blastocystis sp. in stool samples from patients with gastrointestinal complaints in İzmir, Turkey. METHODS All stool samples of 439 patients with gastrointestinal complaints were examined by native-Lugol and trichrome staining. To investigate the presence of Blastocystis sp. in stool samples, DNA was isolated, and PCR was performed with the barcode region in the SSU rRNA gene. PCR positive samples were sequenced to identify subtypes and alleles of Blastocystis sp. RESULTS The prevalence of Blastocystis sp. was found to be 16.6% (73/439) in patients with gastrointestinal complaints in İzmir, Turkey. Three different Blastocystis sp. subtypes were identified. ST3 (28/55; 51.0%) was the most common subtype followed by ST2 (19/55; 34.5%) and ST1 (8/55; 14.5%). Itching and diarrhea were the most prominent clinical symptoms in Blastocystis sp. positive patients. When clinical symptoms and subtypes were compared, diarrhea was found in 62.5%, 47.4%, and 46.4% of patients with ST1, ST2, and ST3 subtypes, respectively. In addition, itching was found in 37.5%, 32.1%, and 21.1% of patients with ST1, ST3, and ST2, respectively. Six distinct alleles were identified by allele analysis of Blastocystis 18S rRNA gene: allele 4 for ST1, alleles 9, 11, and 12 for ST2, and alleles 34 and 36 for ST3. In this study, Blastocystis sp. was detected in 16 of 21 districts, including the central and rural districts of İzmir. Although ST1 was detected in central districts, it was not found in rural districts. CONCLUSION This study provides comprehensive data on the prevalence and molecular epidemiology of the genetic diversity at the level of subtypes and alleles of Blastocystis sp. in different districts of İzmir province in Turkey. To the best of our knowledge, this is the first study which evaluates the distribution of subtypes and alleles of Blastocystis sp. according to PCR and SSU rRNA gene sequencing in patients with gastrointestinal complaints in different districts of İzmir province in Turkey.
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Al-Balushi M, Al-Badi S, Al-Yaarubi S, Al-Riyami H, Al-Shidhani A, Al-Hinai S, Alshirawi A, Hasson S, Said E, Al-Jabri A, Al Ansari A. The Association of Human Leukocyte Antigens Complex with Type 1 Diabetes in the Omani Population. Sultan Qaboos Univ Med J 2023; 23:68-75. [PMID: 36865417 PMCID: PMC9974035 DOI: 10.18295/squmj.2.2022.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/16/2021] [Accepted: 10/13/2021] [Indexed: 11/16/2022] Open
Abstract
Objectives Identification of the high risk alleles, genotypes and haplotypes of the human leukocyte antigens (HLA) in different populations is beneficial for understanding their roles in type 1 diabetes (T1D) pathogenesis and intervention practices. This study aimed to identify T1D-associated HLA gene alleles in the Omani population. Methods The present case-control study included 73 diabetic seropositive children (mean age 9.08 ± 3.27 years) attending the paediatric clinic at Sultan Qaboos University Hospital in Muscat, Oman, and 110 healthy controls. HLA-A, -B, -C, -DRB1 and -DQB1 genes were genotyped using a sequence-specific primer polymerase chain reaction (SSP-PCR). Results Two HLA class I alleles (B*08, B*58) and three class II alleles (DQB1*02, DRB1*03 and DRB1*04) were associated with T1D susceptibility, while one class I (B*51) and three class II (DQB1*05, DQB1*06 and DRB1*16) alleles were associated with T1D protection. HLA-DRB1*03 and DQB1*02 alleles showed the strongest risk association among all alleles. Six DRB1 residues (E9, S11, S13, Y30, V70 and K71) were significantly associated with T1D susceptibility. Heterozygous genotypes, HLA-DRB1*03/*04 and DQB1*02/*03 were significantly associated with T1D susceptibility (P <0.0001, odds ratio [OR] = 63.21 and P = 0.02, OR = 3.63, respectively). Furthermore, a significant combined action of DRB1*03-DQB1*02 haplotype in T1D risk (P = 0.000176, OR = 15) and DRB1*16-DQB1*05 haplotype in protection (P = 0.0312, OR = 0.48) was detected. Conclusion Known HLA class II gene alleles are associated with T1D in Omani children.
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Affiliation(s)
- Mohammed Al-Balushi
- Department of Microbiology & Immunology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Samiya Al-Badi
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Saif Al-Yaarubi
- Department of Child Health, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Hamad Al-Riyami
- Department of Genetics, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Azza Al-Shidhani
- Department of Child Health, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Shaima Al-Hinai
- Department of Child Health, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Ali Alshirawi
- Department of Medicine, College of Medicine, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Sidgi Hasson
- Department of Microbiology & Immunology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Elias Said
- Department of Microbiology & Immunology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Ali Al-Jabri
- Department of Microbiology & Immunology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Aliya Al Ansari
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman,Corresponding Author’s e-mail:
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Ahir-Bist S, Chavan V, Padmaja Samant M, Nanavati R, Mehta P, Mania-Pramanik J. Human leukocyte antigens class I and class II alleles associated with vertical human immunodeficiency virus transmission - an exploratory study from Mumbai, India. Indian J Dermatol Venereol Leprol 2023; 89:159. [PMID: 36331825 DOI: 10.25259/ijdvl_654_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/01/2022] [Indexed: 01/30/2023]
Abstract
Background Human leukocyte antigens (HLA) an important host genetic factor is responsible for influencing human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) transmission and disease progression. Contributions of HLA I and II alleles have not been reported in the Indian population with respect to vertical HIV transmission. Aim In the current study we determined the frequencies of HLA class I and class II alleles in a cohort of children exposed to HIV through their mothers. Method In this exploratory study children perinatally exposed to HIV-1 who fit the study criteria and had completed 18 month follow-up were typed for HLA class I and class II alleles using polymerase chain reaction combined with sequence-specific oligonucleotides probes (PCR-SSOP) and sequence-specific primer (SSP) method. HLA typing was done in 30 positive and 60 HIV negative children along with confounding factors such as treatment regimens, viral load and CD4 count of the mother, feeding option, etc. SPSS software was used for statistical analysis and online docking tools for in-silico analysis. Results HLA-B*40 (p = 0.018) was significantly higher in negative children and was associated with protection, whereas HLA-A*01 (p = 0.05), HLA-B*37 (p = 0.032) and HLA-DRB1*09 (p = 0.017) were associated with transmission. Known protective allele HLA-B*27 was only present in negative children. Many specific haplotypes were exclusively present in the negative children or the positive ones. In-silico analysis was performed to predict the ability of HLA-B*40 to bind to antigenic peptides obtained from HIV-1 sequences in our study group. Limitations Small sample size is a concerning limitation of the study. Nonetheless this is a comprehensive study on HLA alleles in HIV exposed Indian children Conclusion Our study highlights the contribution of HLA class I and II alleles in the Indian children and further adds to understanding the immunogenetic mechanisms. These can be developed as markers for prediction of infection transmission. The observations also contribute to the database of genetic makeup of our population and can help in designing vaccine strategies.
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Affiliation(s)
- Swati Ahir-Bist
- Department of Infectious Diseases Biology, ICMR-National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Vijay Chavan
- Department of Infectious Diseases Biology, ICMR-National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
| | - Mavani Padmaja Samant
- Department of Obstetrics and Gynaecology, Seth G. S. Medical College and K. E. M Hospital, Parel, Mumbai, Maharashtra, India
| | - Ruchi Nanavati
- Department of Neonatology, Seth G. S. Medical College and K. E. M Hospital, Parel, Mumbai, Maharashtra, India
| | - Preeti Mehta
- Department of Microbiology, Seth G. S. Medical College and K. E. M Hospital, Parel, Mumbai, Maharashtra, India
| | - Jayanti Mania-Pramanik
- Department of Infectious Diseases Biology, ICMR-National Institute for Research in Reproductive Health, Mumbai, Maharashtra, India
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Murthykumar K, Varghese S, Jayaseelan VP. Association of SRXN1 Receptor Gene Polymorphism with Susceptibility to Periodontitis. Contemp Clin Dent 2022; 13:363-368. [PMID: 36686993 PMCID: PMC9855261 DOI: 10.4103/ccd.ccd_309_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 10/31/2021] [Accepted: 12/26/2021] [Indexed: 11/06/2022] Open
Abstract
Background Emerging evidence suggests that oxidative stress forms a key component in the etiopathogenesis of periodontitis. Literature evidence have shown potential antioxidants responsible for combating the pro-oxidants which stress the periodontium, but the peroxiredoxin-sulfiredoxin system is explored very minimally in periodontal disease. Thus, the present study was aimed to evaluate the genetic association of SRXN1 receptor gene polymorphism (rs6053666). Materials and Methods A total of 100 subjects were recruited for this study, which included 50 Periodontitis patients (Stage II and above based on the criteria of American Association of Periodontology-2018) and 50 periodontally healthy or mild gingivitis. Genomic DNA was extracted from the whole blood collected from the subjects. DNA was amplified using specific primers flanking the BtgI region of the SRXN1 receptor gene. The amplicon was further subjected to genotyping using restriction fragment length using BtgI enzyme. The genotype obtained based on the restriction fragment length polymorphism pattern was recorded and used for statistical analysis. The distribution of genotypes and allele frequencies in the periodontitis and control groups were compared using the Chi-square test. The risk associated with individual alleles or genotypes was calculated as the odds ratio with 95% confidence intervals. Statistical significance in all tests was determined at P < 0.05. Results The genotype frequency and distributions of SRXN1 receptor BtgI polymorphism did not differ significantly at ꭕ2df (P = 0.557). Our study results showed that homozygous and heterozygous mutant genotypes had no significant difference (CC vs. CT + TT) between the periodontitis patients and control group with a P = 0.4266. The detected frequency of CT (38% vs. 34%) and TT (42% vs. 52%) genotype showed no significant difference between control and test group. There was no significant difference in C allele (39% vs. 31%) and T allele (61% vs. 69%) between the test and control group. Conclusion The present study denotes that SRXN1 receptor gene polymorphism is not associated with periodontitis in the study group analyzed.
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Affiliation(s)
| | - Sheeja Varghese
- Department of Periodontics, Saveetha Dental College, Chennai, Tamil Nadu, India
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Almawi WY, Nemr R, Finan RR, Saldhana FL, Hajjej A. HLA-A, -B, -C, -DRB1 and -DQB1 allele and haplotype frequencies in Lebanese and their relatedness to neighboring and distant populations. BMC Genomics 2022; 23:456. [PMID: 35725365 DOI: 10.1186/s12864-022-08682-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 06/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study examined the origin of present-day Lebanese using high-resolution HLA class I and class II allele and haplotype distributions. The study subjects comprised 152 unrelated individuals, and their HLA class I and class II alleles and two-locus and five-locus haplotypes were compared with those of neighboring and distant communities using genetic distances, neighbor-joining dendrograms, correspondence, and haplotype analyses. HLA class I (A, B, C) and class II (DRB1, DQB1) were genotyped at a high-resolution level by PCR-SSP. RESULTS In total, 76 alleles across the five HLA loci were detected: A*03:01 (17.1%), A*24:02 (16.5%), B*35:01 (25.7%), C*04:01 (25.3%), and C*07:01 (20.7%) were the most frequent class I alleles, while DRB1*11:01 (34.2%) and DQB1*03:01 (43.8%) were the most frequent class II alleles. All pairs of HLA loci were in significant linkage disequilibrium. The most frequent two-locus haplotypes recorded were DRB1*11:01 ~ DQB1*03:01 (30.9%), B*35:01-C*04:01 (20.7%), B*35:01 ~ DRB1*11:01 (13.8%), and A*24:02 ~ B*35:01 (10.3%). Lebanese appear to be closely related to East Mediterranean communities such as Levantines (Palestinians, Syrians, and Jordanians), Turks, Macedonians, and Albanians. However, Lebanese appear to be distinct from North African, Iberian, and Sub-Saharan communities. CONCLUSIONS Collectively, this indicates a limited genetic contribution of Arabic-speaking populations (from North Africa or the Arabian Peninsula) and Sub-Saharan communities to the present-day Lebanese gene pool. This confirms the notion that Lebanese population are of mixed East Mediterranean and Asian origin, with a marked European component.
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Almawi WY, Hajjej A, Abdrakhmanova S, Turganbekova A. Distribution of HLA-A, -C, -B, -DRB1, and -DQB1 polymorphisms in the Korean minority in Kazakhstan, and relatedness to neighboring and distant populations. Gene 2022; 823:146386. [PMID: 35248657 DOI: 10.1016/j.gene.2022.146386] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/28/2022] [Accepted: 02/28/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Among the 125 ethnicities and linguistic groups in Kazakhstan, Koreans represent the eighth minority numerically. HLA class I and class II allele frequencies and extended haplotypes were studied for the first time and were compared to related and distant populations worldwide. METHODS HLA class I (A, B, C) and class II (DRB1, DQB1) profile was investigated in Kazakhstani Koreans, and were compared to other populations using standard genetic distances (SGD), neighbor-joining dendrograms, correspondence, and haplotype analysis. RESULTS One hundred and thirty-one HLA alleles were identified in Koreans living in Kazakhstan, with A*02:01 (23.08%), B*35:01 (8.24%), C*01:02 (15.38%), DRB1*08:03 (9.89%), and DQB1*03:01 (21.98%) being the most frequent alleles. A*03:01 ∼ B*07:02 (3.85%), B*08:01 ∼ DRB1*03:01 (3.85%), B*07:02 ∼ C*07:02 (7.14%), and DRB1*08:03 ∼ DQB1*06:01 (9.34%) were the most frequent two-locus haplotypes, while A*02:01 ∼ B*18:01 ∼ C*07:01 ∼ DRB1*11:04 ∼ DQB1*03:01 and A*33:03 ∼ B*44:03 ∼ C*14:03 ∼ DRB1*13:02 ∼ DQB1*06:04 (2.2% each) were the most frequent five-locus haplotypes. CONCLUSION Korean minority in Kazakhstan was closely related to East Asians, including Mongolians (SGD, 0.044), Tuvans (East Siberia; SGD, 0.081), Burayts (Siberia; SGD, 0.094), but distant from East Mediterranean such as Lebanese (SGD, 0.367), Greek (SGD, 0.377), and Saudi (SGD, 0.414), and most Siberians (SGD, 0.473-0.699). This relatedness could be mainly attributed to massive migration of Koryo Saram to Kazakhstan in the 20th century.
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Affiliation(s)
- Wassim Y Almawi
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana, Kazakhstan; Faculty of Sciences, El-Manar University, Tunis, Tunisia.
| | - Abdelhafidh Hajjej
- Department of Immunogenetics, National Blood Transfusion Center, Tunis, Tunisia
| | - Saniya Abdrakhmanova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
| | - Aida Turganbekova
- Research and Production Center of Transfusion, Kazakhstan Ministry of Health, Astana, Kazakhstan
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Giantsis IA, Antonopoulou D, Dekolis N, Zaralis K, Avdi M. Origin, demographics, inbreeding, phylogenetics, and phenogenetics of Karamaniko breed, a major common ancestor of the autochthonous Greek sheep. Trop Anim Health Prod 2022; 54:73. [PMID: 35072809 DOI: 10.1007/s11250-022-03081-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/20/2022] [Indexed: 11/24/2022]
Abstract
Greece has a long history in autochthonous sheep, the genetic ancestry of which has been associated with four subtypes known to inhabit Greece at the end of the nineteenth century. Among them, the Karamaniko breed is still surviving, however endangered. This study was designed in order to (a) determine the phylogenetic status, (b) to evaluate the levels of inbreeding, and (c) to assess the genetic basis of coat color of Karamaniko breed. For these purposes, the mitochondrial cyt b gene was sequenced, the AFLP methodology was applied, and the MC1R was genotyped, respectively, in 72 female sheep from the Karamaniko breed. Four different novel cyt b haplotypes were defined and three MC1R genotypes were scored, whereas inbreeding levels estimated using AFLPs by the means of relatedness coefficient (r) were 0.287, with gene diversity at the levels of 0.105. Phylogenetic analysis indicated an eastern Asian tropical and subtropical origin of the Karamaniko breed, close with breeds originating from central Turkey, or a clustering within western European or Mediterranean sheep, mirroring a recent genetic divergence, with a non-random spread towards the formation of lowland breeds. The MC1R genotypes were all associated with the white coat color, in which selective breeding has probably been based on traditional morphological characters. Finally, levels of inbreeding do not constitute an indication for a particular mating plan to prevent unpleasant phenomena such as inbreeding depression, probably because of the special attention paid by the farmers towards the avoidance of relative recurrent mating.
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Affiliation(s)
- Ioannis A Giantsis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece.
| | - Danai Antonopoulou
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece.,Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikolaos Dekolis
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Zaralis
- Division of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, Florina, Greece
| | - Melpomeni Avdi
- Department of Animal Production, Faculty of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Güngörer V, Yorulmaz A, Arslan Ş. The clinical effect of gene mutations in familial Mediterranean fever disease. Pediatr Int 2022; 64:e15052. [PMID: 34743384 DOI: 10.1111/ped.15052] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/01/2021] [Accepted: 10/31/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND Familial Mediterranean fever (FMF) is a self-limiting, autoinflammatory disease characterized by inflammation of the serosal surfaces and recurrent episodes of fever. The aim of this study is to determine the effect of genetic mutations on clinical features in children with FMF. METHODS A total of 303 patients aged 0-18 years, who were diagnosed with FMF, according to Yalcinkaya-Özen diagnostic criteria and whose Mediterranean fever gene (MEFV) analysis was studied, were evaluated retrospectively. The clinical and demographic characteristics of the patients and the relationship between common alleles and genotypes were investigated. RESULTS The most common mutation in patients was M694V heterozygous. When the patients were divided into four groups, M694V homozygous, M694V heterozygous, M694V/other allele combined heterozygous, and other mutations, Arthritis was statistically significantly higher in the group that was M694V homozygous compared to the other groups. It was observed that the presence of the M694V allele significantly increased the frequency of periodic fever, aphthous stomatitis, pharyngitis, adenitis syndrome. The frequency of arthritis was significantly higher in patients who were E148Q homozygous than in patients who were heterozygous. Appendectomy history was significantly higher in the group carrying the V726A allele. CONCLUSIONS FMF disease and the effect of genetics on the disease can be better understood, thanks to studies evaluating the genotype-phenotype relationship. In this regard, we believe that studies evaluating the clinical and genotype relationship with a large series are needed.
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Affiliation(s)
- Vildan Güngörer
- Departments of Pediatric Rheumatology, Selcuk University Faculty of Medicine, Konya, Turkey
| | | | - Şükrü Arslan
- Departments of Pediatric Rheumatology, Selcuk University Faculty of Medicine, Konya, Turkey
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Ping J, Zhang J, Wan J, Banerjee A, Huang C, Yu J, Jiang T, Du B. Correlation of Four Single Nucleotide Polymorphisms of the RELN Gene With Schizophrenia. East Asian Arch Psychiatry 2021; 31:112-118. [PMID: 34987122 DOI: 10.12809/eaap2168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE This study aims to determine the association between single-nucleotide polymorphisms (SNPs) of the RELN gene and schizophrenia. METHODS 134 patients aged 16 to 58 (mean, 38.0) years who were diagnosed with acute or chronic schizophrenia at the Zhongshan Third People's Hospital between January 2018 and April 2020 were recruited, as were 64 healthy controls aged 22 to 59 (mean, 45.6) years who matched with the age and sex of the patients. MassARRAY mass spectrometry genotyping technology was used to determine the genotypes of four SNPs of RELN (rs2073559, rs2229864, rs362691, and rs736707). RESULTS There were no significant between-group or between-sex differences in terms of genotype, allele frequency, or haplotype frequency of the SNPs (all p > 0.05). In the association analysis between genotypes and quantitative traits in the Positive and Negative Syndrome Scale, rs2229864 and rs736707 were associated with the scores for items P3 (hallucinatory behaviour) and G11 (attention disorder), and rs362691 was associated with G10 (disorientation). However, the associations did not remain significant after Bonferroni correction. CONCLUSION Multiple pathogenic polymorphisms of RELN might be associated with hallucinatory behaviour and attention disorder in Chinese patients with schizophrenia.
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Affiliation(s)
- J Ping
- Joint Laboratory of Psychiatric Genetic Research and Department of Psychiatry, The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, PR China
| | - J Zhang
- Joint Laboratory of Psychiatric Genetic Research and Department of Psychiatry, The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, PR China
| | - J Wan
- Department of Early Intervention, The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, PR China
| | - A Banerjee
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - C Huang
- Department of Early Intervention, The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, PR China
| | - J Yu
- Department of Substance Dependence, The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, PR China
| | - T Jiang
- Department of Psychiatry, The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, PR China
| | - B Du
- Department of Clinical Psychology, The Third People's Hospital of Zhongshan, Zhongshan, Guangdong, PR China
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Pandi S, Chinniah R, Sevak V, Ravi PM, Raju M, Vellaiappan NA, Karuppiah B. Association of HLA-DRB1, DQA1 and DQB1 alleles and haplotype in Parkinson's disease from South India. Neurosci Lett 2021; 765:136296. [PMID: 34655711 DOI: 10.1016/j.neulet.2021.136296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
Parkinson's disease (PD) is a chronic, neurodegenerative motor disease exhibiting familial and sporadic forms. The present study was aimed to elucidate the association of HLA-DRB1*, DQA1* and DQB1* alleles with PD. A total of 105 PD patients and 100 healthy controls were typed by PCR-SSP method. We further carried out high-resolution genotyping for DQB1 and DQA1. Results revealed the increased frequencies of alleles DRB1*04 (OR = 2.36), DRB1* 13 (OR = 4.04), DQA1* 01:04:01 (OR = 4.51), DQB1*02:01 (OR = 2.66) and DQB1*06:03 (OR = 2.65) in PD patients suggesting susceptible associations. Further, decreased frequencies observed for alleles DRB1*10 (OR = 0.34), DRB1*15 (OR = 0.44), DQA1*04:01 (OR = 0.28), DQA1*06:01 (OR = 0.11) and HLA-DQB1*05:01 (OR = 0.37) among patients have suggested protective associations. Significant disease associations were observed for two-locus haplotype such as DRB1*13-DQB1*06:03 (OR = 11.52), DQA1*01:041-DQB1*06:03 (OR = 16.50), DQA1*01:041-DQB1*05:02 (OR = 5.38) and DQA1*04:01-DQB1*06:03 (OR = 3.027). Protective associations were observed for haplotypes DRB1*10-DQB1*05:01 (OR = 0.21), DRB1*15-DQB1*06 (OR = 0.006), DQA1*04:01-DQB1*05:01 (OR = 0.400) and DQA1*04:01-DQB1*05:03 (OR = 0.196). The critical amino acid residue analyses have revealed strong susceptible association for the residues of DQB1 alleles such as: L26, S28, K71, T71 and A74, Y9, S30, D37, I37, A38, A57 and S57; and for the residues of DQA1 alleles such as: C11, F61, I74, and M76. Similarly, amino acid residues such as A13, G26, Y26, A71, S74, L9 and V38 of HLA-DQB1 alleles and residues such as Y11, G61, S74 and L76 of DQA1 alleles showed protective associations. Thus, our study documented the susceptible and protective associations of DRB1*, DQB1 and DQA1 alleles and haplotypes in developing the disease and their influence on longevity of PD patients in south India.
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Affiliation(s)
- Sasiharan Pandi
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | - Rathika Chinniah
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | - Vandit Sevak
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | - Padma Malini Ravi
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | - Muthuppandi Raju
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | | | - Balakrishnan Karuppiah
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India.
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Xi N, Song X, Wang XY, Qin SF, He GN, Sun LL, Chen XM. 2+0 CYP21A2 deletion carrier — a limitation of the genetic testing and counseling: A case report. World J Clin Cases 2021; 9:6789-6797. [PMID: 34447826 PMCID: PMC8362542 DOI: 10.12998/wjcc.v9.i23.6789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/04/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND CYP21A2 gene mutations may all cause reduction or loss of 21-hydroxylase activity, leading to development of congenital adrenal hyperplasia (CAH) with different clinical phenotypes. For families with CAH children, genetic testing of the parents and genetic counseling are recommended to assess the risk of recurrence.
CASE SUMMARY We report a case of CAH with a high suspicion before delivery. The risk of the child suffering from CAH during the pregnancy had been underestimated due to the deviation of genetic counseling and genetic testing results. Our report confirmed a CYP21A2 homozygous deletion in this case, CYP21A2 heterozygous deletion in the mother, and a rare 2+0 CYP21A2 deletion in the father.
CONCLUSION It is important to analyze the distribution of CYP21A2 gene in the two alleles of parents of children with CAH.
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Affiliation(s)
- Na Xi
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Xiao Song
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Xue-Yan Wang
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Sheng-Fang Qin
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Guan-Nan He
- Department of Ultrasound, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Ling-Ling Sun
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
| | - Xi-Min Chen
- Department of Medical Genetics and Prenatal Diagnosis, Sichuan Provincial Hospital for Women and Children, Chengdu 610045, Sichuan Province, China
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Ebrahimi S, Ghasemi-Basir HR, Majzoobi MM, Rasouli-Saravani A, Hajilooi M, Solgi G. HLA-DRB1*04 may predict the severity of disease in a group of Iranian COVID-19 patients. Hum Immunol 2021; 82:719-725. [PMID: 34294460 PMCID: PMC8275473 DOI: 10.1016/j.humimm.2021.07.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 12/24/2022]
Abstract
Human leukocyte antigen (HLA) genes with extreme diversity can make a contribution for individual variations to the immune response against SARS-COV-2 infection. This study aimed to explore the distributions of HLA class II alleles frequencies and their relations with disease severity in a group of Iranian COVID-19 patients. This prospective and case-control study was conducted on 144 COVID-19 patients including 46 cases with moderate form, 54 cases with severe and 44 cases with critical disease. HLA-DRB1 and -DQB1 allele families were determined by PCR-SSP method and compared between three groups of the patients and in comparison to 153 ethnic-matched healthy controls. The patients group showed lower frequencies of HLA-DRB1*15 (OR = 0.57, P = 0.06), DRB1*15 ~ DQB1*05 haplotype (P = 0.04) and DRB1*15/DRB1*04 genotype (P = 0.04) in compare with healthy controls. Moderate COVID-19 patients had higher frequencies of HLA-DRB1*04 (P = 0.03), HLA-DRB1*10 (P = 0.05) and DRB1*04/DRB1*11 genotype (P = 0.01). Also, a higher significantly frequency of HLA-DRB1*03 allele group was observed in the critical patients versus controls (P = 0.01). Multiple logistic regression analysis revealed that the presence of DRB1*04 allele group was negatively associated with development of severe and critical disease (OR: 0.289, P = 0.005). Our results indicate a possible contribution of some HLA class II alleles in disease severity and clinical features of COVID-19 disease.
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Affiliation(s)
- Samaneh Ebrahimi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Hamid Reza Ghasemi-Basir
- Department of Pathology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | | | - Ashkan Rasouli-Saravani
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mehrdad Hajilooi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Ghasem Solgi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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Das M, Girirajan S. Genetic subtypes, allelic effects, and convergent neurodevelopmental mechanisms. Genome Med 2021; 13:99. [PMID: 34099044 PMCID: PMC8182898 DOI: 10.1186/s13073-021-00913-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/24/2021] [Indexed: 11/10/2022] Open
Abstract
High-throughput sequencing of large affected cohorts have helped uncover a plethora of risk genes for complex neurodevelopmental disorders. However, untangling complex disease etiology also involves understanding the functional consequences of these mutations in order to connect risk variants to resulting phenotypes. Here, we highlight the efforts of Mannucci and colleagues to define a novel molecular subtype of neurodevelopmental disorder associated with mutations in DHX30 and characterize location-specific mutational effects in cell culture and zebrafish models.
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Affiliation(s)
- Maitreya Das
- Department of Biochemistry and Molecular Biology and of Anthropology, Pennsylvania State University, 205A Life Sciences Building, University Park, PA, 16802, USA
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology and of Anthropology, Pennsylvania State University, 205A Life Sciences Building, University Park, PA, 16802, USA.
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23
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Oladosu OJ, Haruna IL, Hadebe SA, Zhou H, Hickford JGH. Nucleotide sequence variation of the major histocompatibility complex class II DQA1 gene in different cattle breeds from Nigeria and New Zealand. Vet Immunol Immunopathol 2021; 237:110273. [PMID: 34044268 DOI: 10.1016/j.vetimm.2021.110273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/17/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
The major histocompatibility complex (MHC) plays a role in immune response. Among other activities, the bovine MHC genes (BoLA) trigger immune responses, including the activation of antibody-producing B-cells. In this study, White Fulani (n = 24), Red Bororo (n = 5) and Holstein-White × Fulani-cross (n = 11) cattle from Nigeria, and New Zealand Holstein-Friesian × Jersey-cross (n = 40) cattle were used to investigate variability in exon 2 of BoLA-DQA1. Ten alleles were identified using a PCR-Single Strand Conformation Polymorphism (SSCP) approach and their nucleotide sequences confirmed by DNA sequencing. A total of 12.60 % of all nucleotide positions analysed were revealed to be variable and two novel BoLA-DQA1 alleles are reported here for the first time.
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Affiliation(s)
- Oyekunle J Oladosu
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Ishaku L Haruna
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Sibusiso A Hadebe
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Huitong Zhou
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand
| | - Jon G H Hickford
- Faculty of Agriculture and Life Sciences, Lincoln University, Lincoln, 7647, New Zealand.
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24
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Malik A, Saha S, Morya RK, Bhadada SK, Rana SV. Impact of serotonin transporter gene polymorphism on gut motility in patients with type 2 Diabetes mellitus. J Neurogastroenterol Motil 2021; 27:240-247. [PMID: 33526751 PMCID: PMC8026373 DOI: 10.5056/jnm20211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 11/20/2022] Open
Abstract
Background/Aims The pathogenesis of gastrointestinal (GI) symptoms in patients with type 2 diabetes mellitus (T2DM) is yet to be delineated clearly. Serotonin, a monoamine neurotransmitter, resides primarily in the gut and plays a vital role in GI system. However, no study has been documented the role of serotonin and serotonin transporter gene (SLC6A4) polymorphism in the development of GI symptoms in T2DM patients. Methods Three hundred diabetes patients attending diabetes clinic at Postgraduate Institute of Medical Education and Research, Chandigarh, and matched healthy controls were enrolled for this study. Plasma from collected blood sample was used for serotonin measurement by enzyme-linked immunosorbent assay method and buffy coat was used for isolation of DNA by phenol chloroform method. Serotonin transporter gene polymorphism was analyzed by polymerase chain reaction method. Results The frequency of short allele (S) and SS genotype was significantly higher in patients with T2DM than controls and was associated with increased risk of T2DM. The frequency of LS genotype showed an association with protection from the disease. Regarding GI symptoms, 78.2% of patients with constipation showed LL and LS genotypes, and 97.7% of patients with diarrhea had SS genotype. The patients without GI symptoms did not show any association of gut motility with genotype. Furthermore, serotonin was significantly higher in diabetic patients who belonged to SS genotype compared to LS or LL genotype and who presented with diarrhea. Conclusion SS genotypes are prone to develop diarrhea because of faster gut motility resulting from higher serotonin levels as compared to LS and LL genotype in T2DM patients.
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Affiliation(s)
- Aastha Malik
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sarama Saha
- Department of Biochemistry, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India
| | - Rajesh K Morya
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sanjay K Bhadada
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Satya V Rana
- Department of Gastroenterology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.,Department of Biochemistry, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India
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25
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Kabuye D, Ndibalema A. Lysosomal acid lipase gene single nucleotide polymorphism and pulmonary tuberculosis susceptibility. Indian J Tuberc 2021; 68:179-185. [PMID: 33845949 DOI: 10.1016/j.ijtb.2020.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/28/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND The factors that predispose to pulmonary tuberculosis (PTB) are not fully understood, However. Gene polymorphisms have been associated with PTB development. OBJECTIVES In this study, we investigated the relationship between LIPA gene polymorphisms and a predisposition to pulmonary tuberculosis caused by Mycobacterium tuberculosis. METHODS A total of 202 cases of PTB and 218 healthy controls (HCS) were included in this study. Analyses were done under allelic, homozygous, and heterozygous, dominant, recessive models, and were used to calculate values, odds ratios (ORs), and 95% confidence intervals (CIs) for assessing the association between single nucleotide polymorphisms (SNPs) and disease risk. Genotyping was conducted using the real time polymerase chain reaction with high resolution melting curve analysis. RESULTS When comparing PTB patients with healthy controls (HCS), significant associations with disease development were observed for both SNPs rs1051338 and rs7922269. Analysis was done based on models of genetic inheritance in man that is co-dominant, recessive and dominant models. Rs1051338, the heterozygous (AC vs. AA) P: 0.001, OR: 1.998, 95% CI: 1.312-3.042 and homozygous (CC vs. AA) P: < 0.001, OR: 4.078, 95% CI: 2.134-7.796 Co-dominant associated with increased risk for the disease. Under recessive (CC vs. AA + AC), P: 0.001, OR: 2.829: 95% CI: 1.543-5.185 and dominant model (AC + CC vs. AA) P: < 001, OR: 2.331, 95% CI: 1.564-3.474 the genotypes distribution increased the individual risk, plus its alleles distribution (P: < 0.001, OR: 2.004, 95% CI: 1.505-2.669). Considering SNP rs7922269 mutation significantly increased pulmonary tuberculosis risk as was observed in the homozygous GG vs. TT (P: 0.003, OR: 3.162, 95% CI: 1.431-6.989); heterozygous GT vs. TT (P: < 0.001, OR: 1.2.259, 95% CI: 1.503-3.394); dominant model (GT + GG vs. TT; P: < 0.001, OR: 2.061, 95% CI: 1.402-3.032) and the allele G (P: < 0.001, OR: 1.829, 95% CI:1.361-2.458), however no significant association was observed in the Recessive model (GG vs. TT + GT; P: 0.057, OR: 2.568, 95% CI: 0.965-4.432). CONCLUSION The findings of our study strengthen the hypothesis that LIPA rs1051338 and rs7922269 polymorphism associated with increased risk for pulmonary Tb in a sample of northern Chinese population.
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Affiliation(s)
- Deo Kabuye
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China; Kalisizo Hospital, Uganda.
| | - Angelamellisy Ndibalema
- Department of Laboratory Medicine, The First Affiliated Hospital of China Medical University, Shenyang, 110001, Liaoning Province, China; Kairuki Hospital, Tanzania.
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Mandefro A, Sisay T, Edea Z, Uzzaman MR, Kim KS, Dadi H. Genetic assessment of BoLA-DRB3 polymorphisms by comparing Bangladesh, Ethiopian, and Korean cattle. J Anim Sci Technol 2021; 63:248-261. [PMID: 33987601 PMCID: PMC8071750 DOI: 10.5187/jast.2021.e37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/03/2021] [Accepted: 01/10/2021] [Indexed: 12/20/2022]
Abstract
Attributable to their major function in pathogen recognition, the use of bovine
leukocyte antigens (BoLA) as disease markers in immunological traits in cattle
is well established. However, limited report exists on polymorphism of the BoLA
gene in zebu cattle breeds by high resolution typing methods. Thus, we used a
polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence
exon 2 of the BoLA class II DRB3 gene from 100 animals (Boran, n = 13; Sheko, n
= 20; Fogera, n = 16; Horro, n = 19), Hanwoo cattle (n = 18) and Bangladesh Red
Chittagong zebu (n = 14). Out of the 59 detected alleles, 43 were already
deposited under the Immuno Polymorphism Database for major histocompatibility
complex (IPD-MHC) while 16 were unique to this study. Assessment of the level of
genetic variability at the population and sequence levels with genetic distance
in the breeds considered in this study showed that Zebu breeds had a gene
diversity score greater than 0.752, nucleotide diversity score greater than
0.152, and mean number of pairwise differences higher than 14, being very
comparable to those investigated for other cattle breeds. Regarding neutrality
tests analyzed, we investigated that all the breeds except Hanwoo had an excess
number of alleles and could be expected from a recent population expansion or
genetic hitchhiking. Howbeit, the observed heterozygosity was not significantly
(p < 0.05) higher than the expected heterozygosity.
The Hardy Weinberg equilibrium (HWE) analysis revealed non-significant excess of
heterozygote animals, indicative of plausible over-dominant selection. The
pairwise FST values suggested a low genetic variation among all the breeds (FST
= 0.056; p < 0.05), besides the rooting from the
evolutionary or domestication history of the cattle. No detached clade was
observed in the evolutionary divergence study of the BoLA-DRB3 gene, inferred
from the phylogenetic tree based on the maximum likelihood model. The
investigation herein indicated the clear differences in BoLA-DRB3 gene
variability between African and Asian cattle breeds.
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Affiliation(s)
- Ayele Mandefro
- Department of Biotechnology, Addis Ababa Science and Technology University, Addis Ababa 16417, Ethiopia
| | - Tesfaye Sisay
- Institute of Biotechnology, Addis Ababa University, Addis Ababa 1176, Ethiopia
| | - Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Md Rasel Uzzaman
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Hailu Dadi
- Ethiopian Biotechnology Institute, Addis Ababa 5954, Ethiopia
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Aasdahl L, Nilsen TIL, Meisingset I, Nordstoga AL, Evensen KAI, Paulsen J, Mork PJ, Skarpsno ES. Genetic variants related to physical activity or sedentary behaviour: a systematic review. Int J Behav Nutr Phys Act 2021; 18:15. [PMID: 33482856 PMCID: PMC7821484 DOI: 10.1186/s12966-020-01077-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Research shows that part of the variation in physical activity and sedentary behaviour may be explained by genetic factors. Identifying genetic variants associated with physical activity and sedentary behaviour can improve causal inference in physical activity research. The aim of this systematic review was to provide an updated overview of the evidence of genetic variants associated with physical activity or sedentary behaviour. METHODS We performed systematic literature searches in PubMed and Embase for studies published from 1990 to April 2020 using keywords relating to "physical activity", "exercise", "sedentariness" and "genetics". Physical activity phenotypes were either based on self-report (e.g., questionnaires, diaries) or objective measures (e.g., accelerometry, pedometer). We considered original studies aiming to i) identify new genetic variants associated with physical activity or sedentary behaviour (i.e., genome wide association studies [GWAS]), or ii) assess the association between known genetic variants and physical activity or sedentary behaviour (i.e., candidate gene studies). Study selection, data extraction, and critical appraisal were carried out by independent researchers, and risk of bias and methodological quality was assessed for all included studies. RESULTS Fifty-four out of 5420 identified records met the inclusion criteria. Six of the included studies were GWAS, whereas 48 used a candidate gene approach. Only one GWAS and three candidate gene studies were considered high-quality. The six GWAS discovered up to 10 single nucleotide polymorphisms (SNPs) associated with physical activity or sedentariness that reached genome-wide significance. In total, the candidate gene studies reported 30 different genes that were associated (p < 0.05) with physical activity or sedentary behaviour. SNPs in or close to nine candidate genes were associated with physical activity or sedentary behaviour in more than one study. CONCLUSION GWAS have reported up to 10 loci associated with physical activity or sedentary behaviour. Candidate gene studies have pointed to some interesting genetic variants, but few have been replicated. Our review highlights the need for high-quality GWAS in large population-based samples, and with objectively assessed phenotypes, in order to establish robust genetic instruments for physical activity and sedentary behaviour. Furthermore, consistent replications in GWAS are needed to improve credibility of genetic variants. TRIAL REGISTRATION Prospero CRD42019119456 .
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Affiliation(s)
- Lene Aasdahl
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway. .,Unicare Helsefort Rehabilitation Centre, Rissa, Norway.
| | - Tom Ivar Lund Nilsen
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Clinic of Anaesthesia and Intensive Care, St. Olavs Hospital, Trondheim, Norway
| | - Ingebrigt Meisingset
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Anne Lovise Nordstoga
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Kari Anne I Evensen
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Department of Clinical and Molecular Medicine, NTNU, Trondheim, Norway.,Department of Physiotherapy, Oslo Metropolitan University, Oslo, Norway.,Unit for Physiotherapy Services, Trondheim, Norway
| | - Julie Paulsen
- Department of Medical Genetics, St. Olavs Hospital, Trondheim, Norway
| | - Paul Jarle Mork
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway
| | - Eivind Schjelderup Skarpsno
- Department of Public Health and Nursing, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Postboks 8905, MTFS, 7491, Trondheim, Norway.,Department of Neurology and Clinical Neurophysiology, St. Olavs Hospital, Trondheim, Norway
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Oboh MA, Ndiaye T, Diongue K, Ndiaye YD, Sy M, Deme AB, Diallo MA, Yade MS, Volkman SK, Badiane AS, Amambua-Ngwa A, Ndiaye D. Allelic diversity of MSP1 and MSP2 repeat loci correlate with levels of malaria endemicity in Senegal and Nigerian populations. Malar J 2021; 20:38. [PMID: 33436004 PMCID: PMC7805152 DOI: 10.1186/s12936-020-03563-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Characterizing the genetic diversity of malaria parasite populations in different endemic settings (from low to high) could be helpful in determining the effectiveness of malaria interventions. This study compared Plasmodium falciparum parasite population diversity from two sites with low (pre-elimination) and high transmission in Senegal and Nigeria, respectively. METHODS Parasite genomic DNA was extracted from 187 dried blood spot collected from confirmed uncomplicated P. falciparum malaria infected patients in Senegal (94) and Nigeria (93). Allelic polymorphism at merozoite surface protein 1 (msp1) and merozoite surface protein- 2 (msp2) genes were assessed by nested PCR. RESULTS The most frequent msp1 and msp2 allelic families are the K1 and IC3D7 allelotypes in both Senegal and Nigeria. Multiplicity of infection (MOI) of greater that 1 and thus complex infections was common in both study sites in Senegal (Thies:1.51/2.53; Kedougou:2.2/2.0 for msp1/2) than in Nigeria (Gbagada: 1.39/1.96; Oredo: 1.35/1.75]). The heterozygosity of msp1 gene was higher in P. falciparum isolates from Senegal (Thies: 0.62; Kedougou: 0.53) than isolates from Nigeria (Gbagada: 0.55; Oredo: 0.50). In Senegal, K1 alleles was associated with heavy than with moderate parasite density. Meanwhile, equal proportions of K1 were observed in both heavy and moderate infection types in Nigeria. The IC3D7 subtype allele of the msp2 family was the most frequent in heavily parasitaemic individuals from both countries than in the moderately infected participants. CONCLUSION The unexpectedly low genetic diversity of infections high endemic Nigerian setting compared to the low endemic settings in Senegal is suggestive of possible epidemic outbreak in Nigeria.
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Affiliation(s)
- Mary A Oboh
- Medical Research Council Unit, the Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
| | - Tolla Ndiaye
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal.
| | - Khadim Diongue
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Yaye D Ndiaye
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Mouhamad Sy
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Awa B Deme
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Mamadou A Diallo
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Mamadou S Yade
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| | - Aida S Badiane
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Alfred Amambua-Ngwa
- Medical Research Council Unit, the Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Aristide Le Dantec University Hospital, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
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Gergely L, Petrovič R, Feketová Z, Klimová D, Danihel Ľ, Mosná K, Mrázová H, Korbeľ M, Repiská V, Priščáková P. Partial hydatidiform moles with unclear histopathological profile - importance of genetic diagnostics. Ceska Gynekol 2021; 86:381-386. [PMID: 35038875 DOI: 10.48095/cccg2021381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
OBJECTIVE The aim of the study was the genetic characterization of a set of cases with an unclear morphological profile of the placental tissue suspected of a partial hydatidiform mole. PATIENTS AND METHODS This work presents the results of a genetic analysis of a group of 10 patients with various clinical manifestations of reproductive loss, where a partial hydatidiform mole was suspected on the basis of a histopathological examination. The composition of the genome of the products of conception was determined by short tandem repeats (STR) genotyping using a commercial kit;Devyser Compact v3 (Devyser). RESULTS AND CONCLUSIONS Out of 10 analyzed cases, five had diandric monogynic triploid genome, characteristic for a partial mole. Aneuploidies of chromosomes 13, 18, 21, X and Y were excluded in four cases and Pataus syndrome was dia-gnosed in one case. In the case of an unclear histopathological profile, consultative DNA analysis (ideally STR genotyping) can significantly help the pathologist in the differential dia-gnosis of a partial mole. The histopathological profile of a partial hydatidiform mole may be in some cases incomplete and unclear, especially in the early weeks of gestation, which can lead to false negativity of the examination. On the other hand, other pathologies, for example aneuploides or digynic triploidy, may produce a histopathological profile similar to a partial mole, which leads to false positivity. Accurate dia-gnosis of a partial hydatidiform mole using molecular genetic methods contributes to the determination of adequate dispensary care for patients.
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Li Q, Du Q. Associations between nine candidate genetic polymorphisms with coronary heart disease : A meta-analysis. Herz 2020; 45:15-28. [PMID: 31041492 DOI: 10.1007/s00059-019-4806-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 11/25/2018] [Accepted: 04/05/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND The aim of this study was to obtain a more accurate assessment of the potential association between nine genetic polymorphisms and the risk of coronary heart disease (CHD). METHODS A literature search was performed in PubMed, Embase, OVID, Web of Science, Wanfang, and Chinese National Knowledge Infrastructure (CNKI) databases to identify eligible studies. We analyzed the odds ratios (OR) and 95% confidence intervals (CI) to assess the strength of the associations. RESULTS A significant association was found between the PON1 -108C/T polymorphism and CHD risk (TT vs. CC: OR = 1.67, 95% CI = 1.14-2.47, p = 0.009; CT vs. CC: OR = 1.47, 95% CI = 1.17-1.85, p = 0.001; [TT + CT] vs. CC: OR = 1.56, 95% CI = 1.18-2.06, p = 0.002; T allele vs. C allele: OR = 1.28, 95%CI = 1.06-1.54, p = 0.011). There was a significant association between the hOGG1 +1245C/G polymorphism and CHD (GG vs. CC: OR = 2.33, 95% CI: 1.19-4.56, p = 0.014; CG vs. CC: OR = 1.36, 95% CI: 1.01-1.83, p = 0.046; [GG + CG] vs. CC: OR = 1.46, 95% CI: 1.10-1.94, p = 0.010; GG vs. [CC+CG]: OR = 2.11, 95% CI: 1.08-4.10, p = 0.028; G allele vs. C allele: OR = 1.45, 95% CI: 1.14-1.84, p = 0.002). The results also showed a statistically significant association of the SCARB1 +1050C/T polymorphism with CHD (TT vs. CC: OR = 1.30, 95% CI = 1.04-1.62, p = 0.022). Meta-analyses of the other six polymorphisms suggested a lack of any association with CHD risk. CONCLUSION Our results show that the susceptibility to CHD was associated with three polymorphisms: PON1 -108C/T, hOGG1 +1245C/G, and SCARB1 +1050C/T.
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da Silva FRP, Pessoa LDS, Shin JI, Alves EHP, Koga RS, Smith CV, Vasconcelos DFP, Pereira ACTDC. Polymorphisms in the interleukin genes and chronic periodontitis: A field synopsis and revaluation by Bayesian approaches. Cytokine 2020; 138:155361. [PMID: 33223448 DOI: 10.1016/j.cyto.2020.155361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/03/2020] [Accepted: 11/02/2020] [Indexed: 12/17/2022]
Abstract
Periodontitis is a high prevalent disease into the clinical dentistry. Genetic variations in interleukins (IL) genes were associated with chronic periodontitis (CP) and were focus of several meta-analyses. This study aimed to assess the noteworthiness in the meta-analyses by means of a Bayesian approach to determinate possible false report associations. A systematic search was performed for meta-analyses with associations between gene polymorphisms in interleukins and CP. The calculations for the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) were performed to assess the noteworthiness with a statistical power of 1.2 and 1.5 of Odds Ratio at a prior probability of 10-3 and 10-6. As results, eight meta-analyses approaching the IL1A/rs1800587, IL1B/rs1143634, IL1RN/rs2234663, IL4/rs2243250, IL6/rs1800795/rs1800796, IL17A/rs2275913 and IL18/rs1946518/rs187238 polymorphisms have been identified. Twenty-two from 270 calculations (8.15%) were noteworthy. Herein, we have identified the IL1A and IL1B polymorphisms as noteworthy biomarkers for CP susceptibility.
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Affiliation(s)
- Felipe Rodolfo Pereira da Silva
- Doctorate in Post-Graduation Program in Basic and Applied Immunology, Federal University of Amazonas, Manaus, Amazonas, Brazil
| | - Larissa Dos Santos Pessoa
- Laboratory of Histological Analysis and Preparation (LAPHis), Federal University of the Parnaiba Delta (UFDPar), Parnaiba, Piaui, Brazil
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, South Korea
| | - Even Herlany Pereira Alves
- Laboratory of Histological Analysis and Preparation (LAPHis), Federal University of the Parnaiba Delta (UFDPar), Parnaiba, Piaui, Brazil
| | - Reyce Santos Koga
- Doctorate in Post-Graduation Program in Basic and Applied Immunology, Federal University of Amazonas, Manaus, Amazonas, Brazil
| | - Camila Valente Smith
- Master Student in the Post-Graduation Program in Dentistry, Dentistry College, Federal University of Amazonas, Manaus, Amazonas, Brazil
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Gonzalez-Galarza FF, McCabe A, Melo Dos Santos EJ, Jones AR, Middleton D. A snapshot of human leukocyte antigen (HLA) diversity using data from the Allele Frequency Net Database. Hum Immunol 2020; 82:496-504. [PMID: 33755549 DOI: 10.1016/j.humimm.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/20/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022]
Abstract
The extensive allelic variability observed in several genes related to the immune response and its significance in different areas including transplantation, disease association studies, diversity in human populations, among many others, has led the scientific community to analyse these variants among individuals. Serving as an electronic data warehouse, the Allele Frequency Net Database (AFND, http://www.allelefrequencies.net) contains data on the frequency of immune related genes and their corresponding alleles from more than 1700 worldwide population samples covering more than ten million unrelated individuals. The collection of population data sets available in AFND encompasses different polymorphic regions including the highly-polymorphic human leukocyte antigen (HLA) system for which more than 1200 populations are available. In this article, we provide an insight of the high diversity found in the HLA region by examining population data sets stored in AFND, as well as a description of the available data sets for further analyses.
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Affiliation(s)
- Faviel F Gonzalez-Galarza
- Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico.
| | - Antony McCabe
- Computational Biology Facility, University of Liverpool, Biosciences Building, United Kingdom; Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, United Kingdom
| | - Eduardo J Melo Dos Santos
- Genetic of Complex Diseases Laboratory, Institute of Biological Sciences, Federal University of Pará, Brazil
| | - Andrew R Jones
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Biosciences Building, United Kingdom
| | - Derek Middleton
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom
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Bhembe NL, Green E. Characterization of mutations in the rpoB gene conferring rifampicin resistance in Mycobacterium tuberculosis complex isolated from lymph nodes of slaughtered cattle from South Africa. Braz J Microbiol 2020; 51:1919-27. [PMID: 32757138 DOI: 10.1007/s42770-020-00356-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022] Open
Abstract
Tuberculosis (TB) is an ongoing public health care, with the state of affairs exacerbated by the growth of anti-TB drug-resistant forms in South Africa. Not much attention is given to zoonotic TB. Thus, this study aimed to determine the presence of rpoB mutations among Mycobacterium tuberculosis complex (MTBC) isolates of lymph nodes from slaughtered cattle. A count of 14,950 carcasses from selected abattoirs were examined for nodular lesions and enlarged lymph nodes; 376 lymph nodes were cultured for MTBC. Positive isolates were tested for drug sensitivity against three anti-TB drugs, rifampicin, isoniazid, and ethambutol, using the Lowenstein-Jensen proportion method. Rifampicin-resistant isolates were sequenced, and spoligotyping was performed for lineage classification. A total of 162 isolates were confirmed as MTBC and 42 isolates were resistant to rifampicin. All rifampicin-resistant isolates carried the H526D rpoB mutation, and almost all of them carried an additional nonsynonymous nucleotide substitution in the hot spot region, in three other codons (510, 516 and 522). In total, 5 different mutations at four codons are reported, including one isolate showing 3 of them which has never been reported in South Africa. In addition, we report 4 different spoligo patterns, with 34 isolates known and 8 unknown spoligotype international types. From the known clades, 5 (11.9%) isolates were identified as Bov_4 caprae lineage, 29 (69%) Beijing, and 8 (19.1%) remaining unknown clades. The detection of MTBC-resistant patterns from cattle lymph nodes (Eastern Cape, South Africa) necessitates the investigation of other possible routes of MTBC transmission.
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Pahuja S, Jain S, Nain M, Goel R, Sehgal S, Jain M. Assessment of rhesus and kell blood group antigens, phenotypes, and their allelic frequencies in North Indian blood donors. Asian J Transfus Sci 2020; 14:137-141. [PMID: 33767540 PMCID: PMC7983148 DOI: 10.4103/ajts.ajts_9_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/19/2019] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Prevalence of rhesus (Rh) and Kell antigens in a population vary with race, ethnicity, and geographical location. With advances in immunohematology, non-D antigens, and their corresponding antibodies are increasingly being found to be culprits for alloimmunization. MATERIALS AND METHODS Assessment of the phenotype of Rh and Kell blood group antigen in the healthy donor population from North India was done, and estimation of the frequencies of these alleles in our population was performed. RESULTS The most common antigen in the North Indian donor population was "e" (95.6%) followed by "C" (89.6%), "c" (57.7%), and "E" (17.29%) in that order. The most prevalent phenotype in the Indian population was found to be "CDe" followed by "CcDe" and "CcDEe." "K" antigen was found to be positive in 1.81% of the population. DISCUSSION Knowledge of the Rh antigen profiles in a given population can be very helpful in formulating transfusion guidelines specific to a particular population with an aim to minimize the cost and maximize the benefits. With this aim in mind and considering the problems encountered in developing countries like ours, we conducted Rh and Kell antigen profiling of donors. Comparative analysis with other population studies and implications for transfusion protocols is evaluated. CONCLUSION Assessment of Rhesus antigen profile of a particular population is useful to develop cost effective ways of providing maximum benefits of blood transfusion with least resources.
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Affiliation(s)
- Sangeeta Pahuja
- Department of Immunohematology and Blood Transfusion, Lady Hardinge Medical College, Connaught Place, New Delhi, India
| | - Sonal Jain
- Department of Immunohematology and Blood Transfusion, Lady Hardinge Medical College, Connaught Place, New Delhi, India
| | - Manupriya Nain
- Department of Immunohematology and Blood Transfusion, Lady Hardinge Medical College, Connaught Place, New Delhi, India
| | - Ruchika Goel
- Department of Immunohematology and Blood Transfusion, Lady Hardinge Medical College, Connaught Place, New Delhi, India
| | - Shivali Sehgal
- Department of Immunohematology and Blood Transfusion, Lady Hardinge Medical College, Connaught Place, New Delhi, India
| | - Manjula Jain
- Department of Immunohematology and Blood Transfusion, Lady Hardinge Medical College, Connaught Place, New Delhi, India
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Abstract
Whipple’s disease is one of the rare maladies in terms of spread but very fatal one as it is linked with many disorders (like Gastroenteritis, Endocarditis etc.). Also, current regimens include less effective drugs which require long duration follows up. This exploratory study was conducted to commence the investigation for crafting multi target epitope vaccine against its bacterial pathogen Tropheryma whipplei. The modern bioinformatics tools like VaxiJen, NETMHCII PAN 3.2, ALLERGEN-FP, PATCH-DOCK, TOXIC-PRED, MHCPRED and IEDB were deployed, which makes the study more intensive in analyzing proteome of T. whipplei as these methods are based on robust result generating statistical algorithms ANN, HMM, and ML. This Immuno-Informatics approach leads us in the prediction of two epitopes: VLMVSAFPL and IRYLAALHL interacting with 4 and 6 HLA DRB1 alleles of MHC Class II respectively. VLMVSAFPL epitope is a part of DNA-directed RNA polymerase subunit beta, and IRYLAALHL epitope is a part of membranous protein insertase YidC of this bacterium. Molecular-Docking and Molecular-Simulation analysis yields the perfect interaction based on Atomic contact energy, binding scores along with RMSD values (0 to 1.5 Ǻ) in selection zone. The IEDB (Immune epitope database) population coverage analysis exhibits satisfactory relevance with respect to world population.
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Affiliation(s)
- Amit Joshi
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
| | - Vikas Kaushik
- Domain of Bioinformatics, School of Bio-Engineering and Bio-Sciences, Lovely Professional University, Punjab, India
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Nurul-Aain AF, Tan LK, Heselynn H, Nor-Shuhaila S, Eashwary M, Wahinuddin S, Lau IS, Gun SC, Mohd-Shahrir MS, Ainon MM, Azmillah R, Muhaini O, Shahnaz M, Too CL. HLA-A, -B, -C, -DRB1 and -DQB1 alleles and haplotypes in 271 Southeast Asia Indians from Peninsular Malaysia. Hum Immunol 2020; 81:263-4. [PMID: 32312605 DOI: 10.1016/j.humimm.2020.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 04/12/2020] [Indexed: 11/21/2022]
Abstract
A total of 271 Southeast Asia Indians from Peninsular Malaysia were genotyped for HLA-A, -B, -C, -DRB1, and -DQB1 loci using polymerase chain reaction sequence-specific oligonucleotide probe hybridization methods. In this report, HLA-B and HLA-DQB1 was in Hardy-Weinberg proportions (HWEP) (p > 0.05). We observed significant deviation from the HWEP for HLA-A (p < 0.05), HLA-C (p < 0.01) and HLA-DRB1 (p < 0.01) loci. This genotype data is available in Allele Frequencies Network Database (AFND) Dos Santos et al. (2016).
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Vanathi M, Shukla R, Balakrishnan P, Dwivedi R, Gupta N, Tandon R. Evaluation of thrombospondin-1 gene polymorphisms in corneal allograft rejection in Asian Indian patients. Indian J Ophthalmol 2020; 68:565-572. [PMID: 32174570 PMCID: PMC7210848 DOI: 10.4103/ijo.ijo_552_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Purpose: To evaluate the frequency and the association of Thrombospondin 1 (THBS1) gene single nucleotide polymorphisms (SNPs) in Asian Indian patients with optical full thickness corneal grafting surgery. Methods: Prospective case–control analysis of optical penetrating keratoplasty patients with and without immune rejection and controls for genotyping of 3 THBS1 gene SNPs (rs1478604 A>G; rs2228261 C>T; rs2228262 A>G) by Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS PCR). Results: Among 58 patients [45 with immune allograft rejection (DNA isolation was possible in 38 samples) and 13 without immune corneal allograft rejection] and 65 controls, allele frequencies observed for rs1478604 (A>G) are A: 69.7% and 72.6%, G: 30.2% and 27.3%; for rs2228261 (C>T) are T: 70.2% and 62.3%, C: 29.7% and 37.6%; and for rs2228262 (A>G) A: 97.4% and 98.4%; G 2.5% and 1.5% respectively. Genotype frequencies were rs1478604 (A>G) AA: 57.8% and 59.3%, AG 23.6% and 26.5%; GG 18.4% and 14%; for rs2228261 (C>T) TT: 40.5% and 33.8%, TC: 59% and 56.9%, CC: 0% and 9.2%; for rs2228262 (A>G) AA: 94.8% and 96.8%, AG: 5.1% and 3.1% in rejection and controls respectively. The allele and genotype frequency for the 3 described THSB1 SNPs did not show any difference between the corneal graft immune rejection patients and controls. Conclusion: Asian Indian population evaluated for THBS1 gene SNPs by ARMS PCR genotyping in Asian Indian population did not show any genetic association to immune rejection occurrence in our study.
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Affiliation(s)
- Murugesan Vanathi
- Cornea, Ocular Surface, Cataract and Refractive Services, Dr R P Centre for Ophthalmic Sciences, New Delhi, India
| | - Rashmi Shukla
- Department of Pediatric Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Prahlad Balakrishnan
- Department of Pediatric Genetics, All India Institute of Medical Sciences, New Delhi, India
| | - Roopa Dwivedi
- Cornea, Ocular Surface, Cataract and Refractive Services, Dr R P Centre for Ophthalmic Sciences, New Delhi, India
| | - Noopur Gupta
- Cornea, Ocular Surface, Cataract and Refractive Services, Dr R P Centre for Ophthalmic Sciences, New Delhi, India
| | - Radhika Tandon
- Cornea, Ocular Surface, Cataract and Refractive Services, Dr R P Centre for Ophthalmic Sciences, New Delhi, India
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Fichou Y, Berlivet I, Richard G, Tournamille C, Castilho L, Férec C. Defining Blood Group Gene Reference Alleles by Long-Read Sequencing: Proof of Concept in the ACKR1 Gene Encoding the Duffy Antigens. Transfus Med Hemother 2019; 47:23-32. [PMID: 32110191 DOI: 10.1159/000504584] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/01/2019] [Indexed: 01/31/2023] Open
Abstract
Background In the novel era of blood group genomics, (re-)defining reference gene/allele sequences of blood group genes has become an important goal to achieve, both for diagnostic and research purposes. As novel potent sequencing technologies are available, we thought to investigate the variability encountered in the three most common alleles of ACKR1, the gene encoding the clinically relevant Duffy antigens, at the haplotype level by a long-read sequencing approach. Materials and Methods After long-range PCR amplification spanning the whole ACKR1 gene locus (∼2.5 kilobases), amplicons generated from 81 samples with known genotypes were sequenced in a single read by using the Pacific Biosciences (PacBio) single molecule, real-time (SMRT) sequencing technology. Results High-quality sequencing reads were obtained for the 162 alleles (accuracy >0.999). Twenty-two nucleotide variations reported in databases were identified, defining 19 haplotypes: four, eight, and seven haplotypes in 46 ACKR1*01, 63 ACKR1*02, and 53 ACKR1*02N.01 alleles, respectively. Discussion Overall, we have defined a subset of reference alleles by third-generation (long-read) sequencing. This technology, which provides a "longitudinal" overview of the loci of interest (several thousand base pairs) and is complementary to the second-generation (short-read) next-generation sequencing technology, is of critical interest for resolving novel, rare, and null alleles.
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Affiliation(s)
- Yann Fichou
- EFS, Inserm, Univ Brest, UMR 1078, GGB, Brest, France.,Laboratoire d'Excellence GR-Ex, Paris, France
| | | | | | - Christophe Tournamille
- Laboratoire d'Excellence GR-Ex, Paris, France.,IMRB-Inserm U955 Equipe 2 Transfusion et Maladies du Globule Rouge, EFS Ile-de-France, Créteil, France
| | | | - Claude Férec
- EFS, Inserm, Univ Brest, UMR 1078, GGB, Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, CHU Morvan, Brest, France
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Sirisena ND, Samaranayake N, Dissanayake VHW. Electrophoretic mobility shift assays implicate XRCC2:rs3218550C>T as a potential low-penetrant susceptibility allele for sporadic breast cancer. BMC Res Notes 2019; 12:476. [PMID: 31370865 PMCID: PMC6676616 DOI: 10.1186/s13104-019-4512-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/23/2019] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE A previous study undertaken at our centre to identify common genetic variants associated with sporadic breast cancer in Sri Lankan women showed that the T allele of rs3218550, located in the 3'untranslated region of X-ray repair cross-complementing gene-2 (XRCC2), increased breast cancer risk by 1.5-fold. Dual luciferase reporter assays performed in MCF-7 breast cancer cells showed a putative transcriptional repressor effect exerted mainly by the T allele. Electrophoretic mobility shift assays were conducted to further investigate the interaction of this variant with DNA-binding protein, using nuclear protein extracts derived from MCF-7 cells. RESULTS An allele-specific differential binding was observed. The T allele resulted in differential DNA-protein complex binding as evidenced by the presence of multiple bands of increased intensity compared to the wild-type C allele. This implies possible alteration in binding of regulatory proteins by the variant allele. These results implicate XRCC2:rs3218550C>T as a potential low-penetrant susceptibility allele for sporadic breast cancer. XRCC2 is known to play an essential role in homologous recombination repair of DNA double-strand breaks. It is plausible that this variant may be exerting regulatory effects on XRCC2 gene expression leading to altered DNA repair capacity. Further functional studies are warranted to validate this finding.
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Affiliation(s)
- Nirmala D Sirisena
- Human Genetics Unit, Faculty of Medicine, University of Colombo, No. 25 Kynsey Road, Colombo 8, 00800, Sri Lanka.
| | - Nilakshi Samaranayake
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo 8, 00800, Sri Lanka
| | - Vajira H W Dissanayake
- Human Genetics Unit, Faculty of Medicine, University of Colombo, No. 25 Kynsey Road, Colombo 8, 00800, Sri Lanka
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Tiwari JK, Ali N, Devi S, Zinta R, Kumar V, Chakrabarti SK. Analysis of allelic variation in wild potato ( Solanum) species by simple sequence repeat (SSR) markers. 3 Biotech 2019; 9:262. [PMID: 31192087 DOI: 10.1007/s13205-019-1785-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/30/2019] [Indexed: 10/26/2022] Open
Abstract
Allelic variation in wild potato (Solanum) species was analysed using 14 simple sequence repeat (SSR) markers. SSR allelic profiles showed high polymorphism and distinctness among the wild species. A total of 109 alleles of 14 polymorphic SSR markers were scored in 82 accessions belonging to 22 wild potato species. Allele size ranged from a minimum of 104 bp (STI0030) to a maximum of 304 bp (STM5114). Number of SSR alleles per marker ranged from 4 (STM5127/STM1053) to 13 (STM0019), whereas PIC value varied between 0.66 (STM1053) and 0.91 (STM0019). Cluster analysis using SSR allelic profiles of 82 accessions grouped showed 5 major clusters (I-V) based on the Dice similarity coefficient using neighbour-joining clustering method. Distinct allelic variations were observed among the accessions irrespective of the origin country, series and species. Our study suggests that SSR-based molecular characterization of wild potato species is accession specific and development of an allelic dataset for all the accessions would strengthen their utilization in potato research in future.
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Hernández-Rivera JCH, Salazar-Mendoza M, Pérez-López MJ, González-Ramos J, Espinoza-Pérez R, Martínez-Álvarez JC, Trejo-Villeda M, Paniagua-Sierra R. Alelos HLA más comunes y asociados con riesgo o protección en enfermedad renal crónica de etiología no determinada. GAC MED MEX 2019; 155:243-248. [PMID: 31219464 DOI: 10.24875/gmm.19005033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Introduction Chronic kidney disease accounts for part of overall health expenditure; a potential etiology is related to variations, absence or presence of some human leukocyte antigen (HLA) alleles. Method An analysis of HLA reports of 1965 kidney recipients with no determined etiology, and 1361 kidney donors was performed. It was carried out with Luminex based in cell flow fluorometry for the A, B, DRB1 and DQA loci. An analysis was performed with contingency tables in order to determine the odds ratio (OR) and confidence intervals (CI). Quantitative analysis was also carried out. Results Of the 101 alleles found, 13 showed association, 7 with risk for chronic kidney disease, with the most significant being HLA-DR17 with an OR of 3.91 (95 % CI = 2.96-5.17) and the one with the highest significance for protection being HLA-DR9, with an OR of 0.043 (95 % CI = 0.005-0.3224). Conclusions It is necessary to understand that kidney diseases can be associated with yet unknown immune processes, where the association of the absence or presence of any allele should be known.
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Affiliation(s)
- Juan Carlos H Hernández-Rivera
- Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Unidad de Investigación Médica en Enfermedades Nefrológicas. Ciudad de México, México
| | - Mariana Salazar-Mendoza
- Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Hospital Regional "Lic. Adolfo López Mateos", Servicio de Urgencias. Ciudad de México, México
| | - María Juana Pérez-López
- Instituto Mexicano del Seguro Social, Centro Médico Nacional La Raza, Servicio de Nefrología. Ciudad de México, México
| | - Jaime González-Ramos
- Instituto Mexicano del Seguro Social, Centro Médico Nacional La Raza, Laboratorio de Histocompatibilidad. Ciudad de México, México
| | - Ramón Espinoza-Pérez
- Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Unidad de Trasplante Renal. Ciudad de México, México
| | - Julio César Martínez-Álvarez
- Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Laboratorio de Histocompatibilidad. Ciudad de México, México
| | - Miguel Trejo-Villeda
- Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Unidad de Investigación Médica en Enfermedades Nefrológicas. Ciudad de México, México
| | - Ramón Paniagua-Sierra
- Instituto Mexicano del Seguro Social, Centro Médico Nacional Siglo XXI, Unidad de Investigación Médica en Enfermedades Nefrológicas. Ciudad de México, México
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Zhang LN, Ma PF, Zhang YX, Zeng CX, Zhao L, Li DZ. Using nuclear loci and allelic variation to disentangle the phylogeny of Phyllostachys (Poaceae, Bambusoideae). Mol Phylogenet Evol 2019; 137:222-235. [PMID: 31112779 DOI: 10.1016/j.ympev.2019.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 11/18/2022]
Abstract
With the development of sequencing technologies, the use of multiple nuclear genes has become conventional for resolving difficult phylogenies. However, this technique also presents challenges due to gene-tree discordance, as a result of incomplete lineage sorting (ILS) and reticulate evolution. Although alleles can show sequence variation within individuals, which contain information regarding the evolution of organisms, they continue to be ignored in almost all phylogenetic analyses using randomly phased genome sequences. Here, we tried to incorporate alleles from multiple nuclear loci to study the phylogeny of the economically important bamboo genus Phyllostachys (Poaceae, Bambusoideae). Obtaining a total of 3926 sequences, we documented extensive allelic variation for 61 genes from 39 sampled species. Using datasets consisting of selected alleles, we demonstrated substantial discordance among phylogenetic relationships inferred from different alleles, as well as between concatenation and coalescent methods. Furthermore, ILS and hybridization were suggested to be underlying causes of the discordant phylogenetic signals. Taking these possible causes for conflicting phylogenetic results into consideration, we recovered the monophyly of Phyllostachys and its two morphology-defined sections. Our study also suggests that alleles deserve more attention in phylogenetic studies, since ignoring them can yield highly supported but spurious phylogenies. Meanwhile, alleles are helpful for unraveling complex evolutionary processes, particularly hybridization.
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Affiliation(s)
- Li-Na Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu-Xiao Zhang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, Yunnan 650224, China
| | - Chun-Xia Zeng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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Abstract
The IMGT/HLA Database has provided a repository for information regarding polymorphism in the genes of the immune system since 1998. In 2003, it was absorbed into the Immuno Polymorphism Database (IPD). The IPD project has enabled us to create and maintain a platform for curating and publishing locus-specific databases which are either involved directly with, or relate to, the function of the Major Histocompatibility Complex across a number of species. In collaboration with specialist groups and nomenclature committees individual sections have been curated prior to their submission to the IPD for online publication. The IPD consists of five core databases, with the primary database being the IMGT/HLA Database. With the work of various nomenclature committees, the HLA Informatics Group, and alongside the European Bioinformatics Institute, we provide access to this data through the website ( http://www.ebi.ac.uk/ipd/ ) to the public domain. The IPD project continually develops new tools in conjunction with on-going scientific developments-such as Next-Generation Sequencing-to maintain efficiency and usability in response to user feedback and requests. The website is updated on a regular basis to ensure that new and confirmatory sequences are distributed to the immunogenetics community, as well as the wider research and clinical communities.
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de Campos WN, Massaro JD, Cançado ELR, Wiezel CEV, Simões AL, Teixeira AC, Souza FFD, Mendes-Junior CT, Martinelli ADLC, Donadi EA. Comprehensive analysis of HFE gene in hereditary hemochromatosis and in diseases associated with acquired iron overload. World J Hepatol 2019; 11:186-198. [PMID: 30820268 PMCID: PMC6393716 DOI: 10.4254/wjh.v11.i2.186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/17/2019] [Accepted: 01/26/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Patients with hepatitis C virus (HCV) and hepatocellular carcinoma (HCC) may or not develop iron overload (IO), which is associated with worst prognosis, because can cause serious damage to organs. HFE gene controls the iron uptake from gut, particularly in patients with hereditary hemochromatosis (HH).
AIM To identify associations between HFE coding region in patients exhibiting hereditary hemochromatosis and in diseases associated with acquired IO.
METHODS We sequenced exons 2 to 5 and boundary introns of HFE gene, evaluating all polymorphic sites in patients presenting hereditary (hemochromatosis) or acquired iron overload HCV and HCC) and in healthy controls, using Sanger sequencing. We also determined the ensemble of extended haplotype in healthy control individuals, including several major histocompatibility complex loci, using sequence specific probes. Haplotype reconstruction was performed using the Arlequin and Phase softwares, and linkage disequilibrium (LD) between histocompatibility loci and HFE gene was performed using the Haploview software.
RESULTS The HFE*003 allele was overrepresented (f = 71%) and HFE*001 allele was underrepresented (f = 14%) in HH patients compared to all groups. A strong linkage disequilibrium was observed among the H63D-G, IVS2(+4)-C and C282Y-G gene variants, particularly in HH; however, the mutation IVS2(+4)T>C was not directly associated with HH susceptibility. The HFE*001/HFE*002 genotype conferred susceptibility to HCC in HCV patients exhibiting IO (P = 0.02, OR = 14.14). Although HFE is telomeric to other histocompatibility genes, the H63D-G/IVS2(+4)-C (P ≤ 0.00001/P ≤ 0.0057) combination was in LD with HLA-B*44 allele group in healthy controls. No LD was observed between HFE alleles and other major histocompatibility loci.
CONCLUSION A differential HFE association was observed for HH and for diseases associated with acquired IO (HCV, HCC). Since HFE is very distant from other histocompatibility loci, only weak associations were observed with these alleles.
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Affiliation(s)
- Wagner Narciso de Campos
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14048-900, Brazil
| | - Juliana Doblas Massaro
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14048-900, Brazil
| | - Eduardo Luiz Rachid Cançado
- Department of Gastroenterology, Clinical Gastroenterology and Clinical Hepatology of Clinical Hospital, University of São Paulo School of Medicine, São Paulo 01329-000, Brazil
| | - Cláudia Emília Vieira Wiezel
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14048-900, Brazil
| | - Aguinaldo Luiz Simões
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14048-900, Brazil
| | - Andreza Correa Teixeira
- Division of Gastroenterology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14048-900, Brazil
| | - Fernanda Fernandes de Souza
- Division of Gastroenterology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14048-900, Brazil
| | - Celso Teixeira Mendes-Junior
- Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, Brazil
| | - Ana de Lourdes Candolo Martinelli
- Division of Gastroenterology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14048-900, Brazil
| | - Eduardo Antônio Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14048-900, Brazil
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Klaassen MT, Bourke PM, Maliepaard C, Trindade LM. Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato. Euphytica 2019; 215:14. [PMID: 30872859 PMCID: PMC6390886 DOI: 10.1007/s10681-018-2331-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/22/2018] [Indexed: 05/26/2023]
Abstract
Protein content is a key quality trait for the potato starch industry. The objective of this study was to identify allele-specific quantitative trait loci (QTLs) for tuber protein content in cultivated potato (Solanum tuberosum L.) at the tetraploid level. We analysed 496 full-sib F1 clones in a 3-year field trial to dissect the complex genetic architecture of soluble tuber protein content. Genotypic data from a 60K single nucleotide polymorphism (SNP) array was used for SNP dosage scoring, constructing homologue specific linkage maps and assembly of a dense integrated chromosomal linkage map. From the integrated map, probabilistic multi-locus identity-by-descent (IBD) haplotypes (alleles) were estimated and used to detect associations between the IBD haplotypes and the phenotypic trait values. Moderate levels of trait heritability were estimated between 40 and 74% that correspond with previous studies. Our contemporary naive analysis identified potential additive QTLs on chromosomes 2, 3, 5 (top arm) and 9 across the years. Moreover, cofactor QTL analysis identified two masked QTLs on chromosomes 1 and 5 (lower arm). The QTLs on chromosomes 2, 5 (lower arm) and 9 are reported here for the first time. The QTLs that we identified on chromosomes 1, 3 and 5 (top arm) show overlap with previous studies for protein content in potato. Collectively the naive QTLs explained 12 to 17% of the phenotypic variance. The underlying alleles of the QTLs provided both positive and negative effects on the phenotype. Our work uncovers the complex genetic architecture of this trait and describes potential breeding strategies for improvement. As protein has emerged as a high-value component from industrial potato starch production, the dissection of the genetic architecture and subsequent improvement of this trait by breeding has great economic and environmental relevance.
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Affiliation(s)
- Michiel T. Klaassen
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
- Department of Applied Research, Aeres University of Applied Sciences, P.O. Box 374, 8250 AJ Dronten, The Netherlands
| | - Peter M. Bourke
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University and Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands
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Zhong LY, Wang F, Chen PS, Xie YJ, Tan JY, Liu M, Huang B, Lin WB. [Analysis of genotype and hematological phenotype of 14 patients with coinheritance HKαα and South-East deletion thalassemia]. Zhonghua Yi Xue Za Zhi 2018; 98:117-121. [PMID: 29343036 DOI: 10.3760/cma.j.issn.0376-2491.2018.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To analyze the genotype-phenotype correlations among those thalassemia samples with the presence of -α(3.7,) --(SEA) and normal α(2) alleles on their α-globin gene clusters. Methods: Fourteen patients(including 1fetus, 4 males and 9 females, aged 0- 56 years old)who were suspected diagnosed by hematologic analysis and genetic testing among 16 080 participants in our laboratory since from August 2011 to August 2016, were enrolled. Complete blood cell count was performed on XE4000i automatic hemocyte analyzer. HbA0, HbF and HbA2 were tested by high performance liquid chromatography (HPLC). Gap-PCR was adopted to detect three common deletional thalassemia deletions. Reverse dot-blot (RDB) assay was applied for detecting 17 common β-globin gene mutations and three common non-deletional α(2) gene mutations. Two-round nested PCR assay was established to detect the genotype of HKαα in α-thalassemia. Results: Fourteen cases were identified as HKαα/--(SEA) (14/16 080), including a pedigree and a rare case of HKαα/--(SEA) co-inheritance with IVS-Ⅱ-654(C→T) heterozygote. In HKαα/--(SEA) thalassemia group, mean cell volume(MCV) was (69.54±5.92)fl, and mean cell hemoglobin(MCH) was(22.11±2.22)pg and hemoglobin(Hb) was (117.64±18.14) g/L. Compared with normal group, MCV, MCH and Hb in HKαα/--(SEA) thalassemia group, was significantly decreased(P<0.05). There were no significant differences between α-thalassemia control group(--(SEA) /αα) in most hematological parameters (P>0.05). Conclusion: The two-round nested PCR could effectively detect the HKαα/--(SEA) genotype. The hematologic characteristics changed significantly in HKαα/--(SEA) group compared with HbH thalassemia and normal group. The genotype and phenotype non-correlation in patients with α-thalassemia should especially be causious to avoid a misdiagnosis of genetic tests, especially in prenatal diagnosis.
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Affiliation(s)
- L Y Zhong
- Department of Clinical Laboratoty, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
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Wu S, Wang Y, Chen G, Zhang M, Wang M, He JQ. 2'-5'-Oligoadenylate synthetase 1 polymorphisms are associated with tuberculosis: a case-control study. BMC Pulm Med 2018; 18:180. [PMID: 30497421 PMCID: PMC6267069 DOI: 10.1186/s12890-018-0746-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 11/19/2018] [Indexed: 02/08/2023] Open
Abstract
Background 2′-5′-Oligoadenylate synthetase 1 (OAS1) plays an important role in inflammatory immune reactions. OAS1 polymorphisms have been associated with increased susceptibility to various diseases. We investigated the association of polymorphisms in OAS1 with tuberculosis (TB). Methods A total of 1215 TB cases and 1114 healthy controls were enrolled from two independent studies. Genotyping was conducted using the improved multiplex ligase detection reaction (iMLDR) method. Associations between OAS1 polymorphisms (rs2240190, rs1131454, 10,774,671 and 11,066,453) and TB risk were established based on distributions of allelic frequencies using different genetic models. Results Significant association was observed between rs10774671, rs1131454 and TB. In the initial study, the G allele of rs10774671 was a significantly protective factor against TB (P = 0.006) and the genotype of GG differed significantly between TB patients and controls under the codominant model (P = 0.008) after Bonferroni correction. In the validation study, we also observed that the rs10774671 G allele (P = 0.001) and GG genotype (P = 0.001) were associated with TB. In addition, we found that the rs1131454 G allele (P = 0.004) and GG genotype (P = 0.001) were protective against TB in the Chinese Han population. Conclusions We report novel associations of polymorphisms in OAS1 with TB in the Chinese Tibetan and Han populations. Similar studies in different populations and functional studies are warranted to confirm our results.
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Affiliation(s)
- Shouquan Wu
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37, Guo Xue Alley, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yu Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37, Guo Xue Alley, Chengdu, 610041, Sichuan, People's Republic of China
| | - Guo Chen
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37, Guo Xue Alley, Chengdu, 610041, Sichuan, People's Republic of China.,Division of Geriatrics, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Miaomiao Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37, Guo Xue Alley, Chengdu, 610041, Sichuan, People's Republic of China
| | - Minggui Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37, Guo Xue Alley, Chengdu, 610041, Sichuan, People's Republic of China
| | - Jian-Qing He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, No. 37, Guo Xue Alley, Chengdu, 610041, Sichuan, People's Republic of China.
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Sirisena ND, Samaranayake N, Dissanayake VHW. Relative normalized luciferase activity for the recombinant vector constructs carrying the ancestral and variant alleles for XRCC2:rs3218550 and PHB:rs6917. BMC Res Notes 2018; 11:643. [PMID: 30180900 PMCID: PMC6122654 DOI: 10.1186/s13104-018-3760-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 08/31/2018] [Indexed: 12/05/2022] Open
Abstract
OBJECTIVE The data presented herein represents the preliminary results of the functional assays of a recently conducted larger study in which two single nucleotide polymorphisms (SNPs) [XRCC2:rs3218550 and PHB:rs6917] were significantly associated with risk of breast cancer among Sri Lankan postmenopausal women. The rs3218550 T allele and rs6917 A allele were found to increase breast cancer risk by 1.5-fold and 1.4-fold, respectively. Both SNPs are located in the 3'untranslated region (3'UTR) of the respective genes. It was hypothesized that these non-coding SNPs may be exerting some transcriptional regulatory effects on gene expression. Their putative functional effects were further investigated by generating bioluminescent recombinant experimental reporter gene constructs carrying the ancestral and variant alleles of these 2 SNPs, transiently transfecting them in MCF-7 breast cancer cell lines and performing dual-luciferase reporter gene assays to measure the luminescent signals. DATA DESCRIPTION The normalized relative luciferase activity for the recombinant vector constructs carrying the ancestral and variant alleles for XRCC2:rs3218550 and PHB:rs6917 are presented herein. This data might be of relevance to other researchers involved in delineating the functional mechanisms of SNPs located in the 3'UTR of the XRCC2 and PHB breast cancer related genes.
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Affiliation(s)
| | - Nilakshi Samaranayake
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo 8, Sri Lanka
| | - Vajira H. W. Dissanayake
- Human Genetics Unit, Faculty of Medicine, University of Colombo, No. 25 Kynsey Road, Colombo 8, Sri Lanka
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Abdi AA, Osman A. Prevalence of common hereditary risk factors for thrombophilia in Somalia and identification of a novel Gln544Arg mutation in coagulation factor V. J Thromb Thrombolysis 2018; 44:536-543. [PMID: 28889200 PMCID: PMC5658450 DOI: 10.1007/s11239-017-1543-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thrombophilia, commonly manifested as venous thromboembolism (VTE), is a worldwide concern but little is known on its genetic epidemiology in many parts of the globe particularly in the developing countries. Here we employed TaqMan genotyping and pyrosequencing to evaluate the prevalence of known common nucleotide polymorphisms associated with thrombophilia in a Somali population in the Puntland region of Somalia. We also employed next generation sequencing (NGS) to investigate other genetic variants in a Somali patient with deep venous thrombosis (DVT). As expected, we found no existence of factor V Leiden (rs6025) and prothrombin G20210A (rs1799963) in the Somali population. The G allele of ABO [261G/delG] polymorphism (rs8176719) was found at a frequency of 29%, similar to that observed in other African populations. We found the lowest so far reported frequency of MTHFR C677T (rs1801133) polymorphism in the Somali population (T allele frequency 1.5%). A novel and deleterious single nucleotide variation in exon 11 of coagulation factor V (c.1631A>G) causing Gln544Arg exchange in factor V was identified in a 29 years old Somali female with DVT. The same patient was heterozygous to VKORC1 Asp36Tyr polymorphism (rs61742245) that predisposes to warfarin resistance. In conclusion, this study shows that common hereditary factors for thromboembolism found in Caucasians are either less frequent or absent in the Somali population-similar to the situation in other Africans. NGS is possibly a better choice to detect genetic risk variants for thrombosis in this ethnic group.
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Affiliation(s)
- Abshir Ali Abdi
- Faculty of Medicine, East Africa University, Bosaso, Puntland, Somalia
| | - Abdimajid Osman
- Division of Clinical Chemistry, Region Östergötland, Ingång 64, 581 85, Linköping, Sweden. .,Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden.
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K RP, T S, B S, T MK, A J. LRP2 gene variants and their haplotypes strongly influence the risk of developing neural tube defects in the fetus: a family-triad study from South India. Metab Brain Dis 2018; 33:1343-1352. [PMID: 29728895 DOI: 10.1007/s11011-018-0242-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/16/2018] [Indexed: 10/17/2022]
Abstract
Neural tube defects (NTDs) are the leading cause of infant deaths worldwide. Lipoprotein related receptor 2 (LRP2) has been shown to play a crucial role in neural tube development in mouse models. However, the role of LRP2 gene in the development of human NTDs is not yet known. In view of this, family-based triad approach has been followed considering 924 subjects comprising 124 NTD case-parent trios and 184 control-parent trios diagnosed at Institute of Genetics and Hospital for Genetic Diseases, Hyderabad. Blood and tissue samples were genotyped for rs3755166 (-G759A) and rs2544390 (C835T) variants of LRP2 gene for their association with NTDs. Assessment of maternal-paternal genotype incompatibility risk for NTD revealed 3.77-folds risk with a combination of maternal GA and paternal GG genotypes (GAxGG = GA,p < 0.001), while CT genotypes of both the parents showed 4.19-folds risk for NTDs (CTxCT = CT,p = 0.009). Haplotype analysis revealed significant risk of maternal A-T (OR = 4.48,p < 0.001) and paternal G-T haplotypes (OR = 5.22,p < 0.001) for NTD development. Further, linkage analysis for parent-of-origin effects (POE) also revealed significant transmission of maternal 'A' allele (OR = 2.33,p = 0.028) and paternal 'T' allele (OR = 6.00,p = 0.016) to NTDs. Analysis of serum folate and active-B12 levels revealed significant association with LRP2 gene variants in the causation of NTDs. In conclusion, the present family-based triad study provides the first report on association of LRP2 gene variants with human NTDs.
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Affiliation(s)
- Rebekah Prasoona K
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, Telangana State, 500016, India
| | - Sunitha T
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, Telangana State, 500016, India
| | - Srinadh B
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, Telangana State, 500016, India
| | - Muni Kumari T
- Modern Government Maternity Hospital, Hyderabad, Telangana, 500012, India
| | - Jyothy A
- Institute of Genetics and Hospital for Genetic Diseases, Osmania University, Begumpet, Hyderabad, Telangana State, 500016, India.
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