Significant Allelic Association Research Articles

Genetic association of diabetic retinopathy with long noncoding RNA CDKN2B-AS1 gene polymorphism.

We attempted to test the influences of cyclin dependent kinase inhibitor 2B antisense RNA 1 (CDKN2B-AS1) gene polymorphisms on the susceptibility to Diabetic retinopathy (DR). Five single-nucleotide polymorphisms (SNPs) of the CDKN2B-AS1 gene, rs564398, rs1333048, rs1537373, rs2151280, and rs8181047 were examined in 280 DR cases and 455 DR-free diabetic controls. Among these loci tested, we demonstrated that diabetic carriers of at least one polymorphic allele (G) of rs2151280 (AG and GG; AOR, 1.613; 95% CI, 1.040-2.501; p = 0.033) are more susceptible to proliferative DR but not non-proliferative DR. This genetic association with the risk of developing proliferative DR was further strengthened in homozygotes for the polymorphic allele (G) of rs2151280 (GG; AOR, 2.194; 95% CI, 1.117-4.308; p = 0.023). We detected a significant association of the polymorphic allele (G) of rs2151280 with proliferative DR patients (OR, 1.503; 95% CI, 1.112-2.033; p = 0.008) but not with the entire DR or non-proliferative DR group. Moreover, as compared to those who do not possess the polymorphic allele of rs2151280 (AA), DR patients carrying at least one polymorphic allele of rs2151280 (AG + GG) exhibited a lower glomerular filtration rate and HDL cholesterol level, revealing a promotive role of rs2151280 in renal and cardiovascular complications of diabetes. Taken together, our findings implicate an impact of CDKN2B-AS1 gene polymorphisms on the progression of DR.

Association of liver function markers and apolipoprotein E ε4 with pathogenesis and cognitive decline in Alzheimer's disease.

Alzheimer's disease (AD) is a complex neurodegenerative disorder influenced by various factors, including liver function, which may impact the clearance of amyloid-β (Aβ) in the brain. This study aimed to explore how the apolipoprotein E (APOE) ε4 allele affects the relationship of liver function markers with AD pathology and cognition. We analyzed data from two independent cohorts, including 732 participants from the Hallym University Medical Center and 483 from the Alzheimer's Disease Neuroimaging Initiative, each group consisting of individuals with and without the APOE ε4 allele. Cross-sectional analyses evaluated the associations of liver enzymes (aspartate aminotransferase [AST], alanine aminotransferase [ALT], alkaline phosphatase, total bilirubin, and albumin) with AD diagnosis, amyloid positron emission tomography (PET) burden, and cerebrospinal fluid biomarkers for AD (Aβ42, total tau, and phosphorylated tau181) at baseline. Longitudinally, we investigated the associations between these liver enzymes and changes in cognitive performance over the course of a year. Logistic and linear regression models were used to analyze these associations and mediation analyses were conducted to assess whether age and amyloid PET burden mediated these associations. Only in the APOE ε4 carrier group, a high AST to ALT ratio and low ALT levels were significantly associated with AD diagnosis, increased amyloid PET burden, and faster longitudinal decline in cognitive function in both cohorts. In particular, the AST to ALT ratio was associated with cerebrospinal fluid Aβ42 levels exclusively in the APOE ε4 carrier group in the Alzheimer's Disease Neuroimaging Initiative cohort but not with phosphorylated tau181 or total tau levels. Moreover, mediation analyses from both cohorts revealed that in the APOE ε4 carriers group, age did not mediate the associations between liver enzymes and AD diagnosis or amyloid PET burden. However, amyloid PET burden partially mediated the association between liver enzymes and AD diagnosis exclusively in the APOE ε4 carriers group. This study provides valuable insights into the significant association of the APOE ε4 allele with liver enzymes and their potential role in Aβ-related pathogenesis and cognition in AD. Further research is required to elucidate the underlying mechanisms and potential therapeutic implications of these findings.

HLA Gene Polymorphism in Patients with Chronic HBV Infection. Fundeni Clinical Institute Experience

Introduction: Hepatitis B virus (HBV) infection is a serious health problem for the public health systems in many countries worldwide. According to the European Society for the Liver Study, more than 350 million people are diagnosed with hepatitis B virus infection. Chronic viral HBV infection could be caused by the inability of both the cellular and humoral immune systems to eliminate HBV. HLA genes control cellular and humoral immune responses and present the viral antigens to CD8+ (cytotoxic T cells) and CD4+ T (T helper cells). Aim: To look at the HLA allele polymorphisms in chronic hepatitis B-infected patients to search for significant HLA allele associations. Methods: We have included 240 patients with HBV infection from the Gastroenterology and Hepatology ward, at Fundeni Clinical Institute. As a control group, 300 unrelated healthy people with no hepatitis B infection were also included. We have genotyped the HLA class I and class II genes for both patients and the control group with Next Generation Sequencing Illumina (Immucor, Mia Fora NGS Flex, Norcross, GA, USA). Results: Our preliminary data showed that HLA-DQA1*01:02:02 and HLADRB5*02:02:01 alleles are associated with the risk of HBV infection persistence. Conclusions: Our study showed that a specific HLA genotype profile is associated with chronic HBV infection in our Romanian patients.

Genotyping the BCL11A Single Nucleotide Polymorphism and Associated Levels of Fetal Hemoglobin in Mauritanian Sickle Cell Patients.

Sickle cell disease (SCD) is a major heritable genetic disease in sub-Saharan Africa, including Mauritania. Fetal hemoglobin (HbF) can affect the pathophysiology, moderate the clinical course, and offer prospects for curative treatment of SCD. This study aimed to investigate the influence of single nucleotide polymorphisms (SNPs) in the BCL11A gene on the levels of HbF and hematological parameters in Mauritanian sickle cell (HbSS) patients. Complete blood count was assessed in 565 patients suspected to have SCD. Polymerase chain reaction (PCR)-restriction fragment length polymorphism was performed to identify the HbSS, and sequencing was used for genotyping three SNPs: rs4671393 (A>G) and rs11886868 (C>T) in the intron 2 and rs1052520 (G>A) in the 3'UTR regions of the BCL11A gene in 50 sickle cell patients. The prevalence of HbSS among the study population was 8.8% (50/565), and the mean (± standard deviation) of HbF level was 15.0% (± 6.0%). Sequencing showed the presence of three genotypes: AA (13.6%), AG (46.6%), GG (39.6%) in rs4671393; CC (17.6%), CT (48.7%), and TT (33.6%) in rs11886868. All samples from HbSS individuals displayed a wild-type genotype in the rs1052520 allele. The prevalence of minor alleles A (rs4671393) and C (rs11886868) were 37% and 39%, respectively. There was a statistically significant association (p = 0.034) between rs4671393 SNP and elevated HbF (mean 12.72 ± 6.26%). The study of three SNPs in the BCL11A locus in Mauritanian patients with SCD showed a significant association of rs4671393 allele with the HbF level. Further research is needed to explore additional SNPs in the BCL11A locus and investigate other genetic markers reported to modulate HbF levels, such as HBS1L-MYB and Xmn1-HBG2, to improve the management of this potentially life-threatening condition in Mauritania.

Clinical features, polysomnography, and genetics association study of restless legs syndrome in clinic based Chinese patients: A multicenter observational study

Study objectivesTo systemically describe the clinical features, polysomnography (PSG) finding, laboratory tests and single-nucleotide polymorphisms (SNPs) in a clinic based Chinese primary restless legs syndrome (RLS) population. MethodsThis observational study, conducted from January 2020 to October 2021 across 22 sleep labs in China, recruited 771 patients diagnosed with RLS following the 2014 RLSSG criteria. Clinical data, PSG testing, and laboratory examination and SNPs of patients with RLS were collected. A total of 32 SNPs in 24 loci were replicated using the Asian Screening Array chip, employing data from the Han Chinese Genomes Initiative as controls. ResultsIn this study with 771 RLS patients, 645 had primary RLS, and 617 has DNA available for SNP study. Among the 645 primary RLS, 59.7% were women. 33% had a family history of RLS, with stronger familial influence in early-onset cases. Clinical evaluations showed 10.4% had discomfort in body parts other than legs. PSG showed that 57.1% of RLS patients had periodic leg movement index (PLMI) of >5/h and 39.1% had PLMI >15/h, respectively; 73.8% of RLS patients had an Apnea-Hypopnea Index (AHI) > 5/h, and 45.3% had an AHI >15/h. The laboratory examinations revealed serum ferritin levels <75 ng/ml in 31.6%, and transferrin saturation (TSAT) of <45% in 88.7% of RLS patients. Seven new SNPs in 5 genes showed a significant allelic association with Chinese primary RLS, with one previously reported (BTBD9) and four new findings (TOX3, PRMT6, DCDC2C, NOS1). ConclusionsChinese RLS patients has specific characters in many aspects. A high family history with RLS not only indicates strong genetic influence, but also reminds us to consider the familial effect in the epidemiological study. Newly developed sequencing technique with large samples remains to be done.

Host genetic variants associated with COVID-19 reconsidered in a Slovak cohort

We present the results of an association study involving hospitalized coronavirus disease 2019 (COVID-19) patients with a clinical background during the 3rd pandemic wave of COVID-19 in Slovakia. Seventeen single nucleotide variants (SNVs) in the eleven most relevant genes, according to the COVID-19 Host Genetics Initiative, were investigated. Our study confirms the validity of the influence of LZTFL1 and 2′-5′-oligoadenylate synthetase (OAS)1/OAS3 genetic variants on the severity of COVID-19. For two LZTFL1 SNVs in complete linkage disequilibrium, rs17713054 and rs73064425, the odds ratios of baseline allelic associations and logistic regressions (LR) adjusted for age and sex ranged in the four tested designs from 2.04 to 2.41 and from 2.05 to 3.98, respectively. The OAS1/OAS3 haplotype ‘gttg’ carrying a functional allele G of splice-acceptor variant rs10774671 manifested its protective function in the Delta pandemic wave. Significant baseline allelic associations of two DPP9 variants in all tested designs and two IFNAR2 variants in the Omicron pandemic wave were not confirmed by adjusted LR. Nevertheless, adjusted LR showed significant associations of NOTCH4 rs3131294 and TYK2 rs2304256 variants with severity of COVID-19. Hospitalized patients' reported comorbidities were not correlated with genetic variants, except for obesity, smoking (IFNAR2), and hypertension (NOTCH4). The results of our study suggest that host genetic variations have an impact on the severity and duration of acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Considering the differences in allelic associations between pandemic waves, they support the hypothesis that every new SARS-CoV-2 variant may modify the host immune response by reconfiguring involved pathways.

Evaluation of Apolipoprotein e4 allele as Susceptible Factor for Neurodegenerative Diseases among Eastern Indians

Background &amp; Objectives: Apolipoprotein E (ApoE) and age have been identified as the major risk factors for several neurodegenerative disorders. Among the three major isoforms (ApoE2, ApoE3 &amp; ApoE4) of APOE, ApoE4 often shows ethnicity dependent association with neurodegenerative diseases. In the present study, we aim to determine the e4 allele/genotype frequency among the different neurodegenerative disorders and their correlation with several demographic and clinical parameters from eastern India. Methods: A total of 826 individuals were recruited for this study which includes 128 PD-MCI, 144 PDD, 90 DLB, 114 FTD, 94 AD and 256 unrelated neurologically controls from eastern India. Subjects were analysed for APOE genotype (E2, E3 and E4) by PCR-RFLP techniques and Sanger sequencing. Results: The APOE4 allele was significantly associated with each of the disease subtypes, selected for the study (P=0.016 to 0.000), while e3 allele was predominant among controls. Further stratification of subjects identified significant overrepresentation of (a) positive family history for FTD (P=0.0414) &amp; AD (P=0.029) and (b) early age at onset of for PDD (P=0.0316) and FTD (P=0.0034) among the e4 allele carriers. Furthermore, lowering of BMSE score was also observed among the e4 allele carriers of AD subjects (P=0.0324). Conclusion: There is a significant association of APOE4 allele with different neurodegenerative diseases influencing lowering of age at onset, BMSE score and positive family history among ethnic Bengali population of eastern India.

Association between Polymorphism rs61876744 in PNPLA2 Gene and Keratoconus in a Saudi Cohort.

The genetic etiology of Keratoconus (KC) in Middle Eastern Arabs of Saudi origin is still unclear. A recent genome-wide study identified two significant loci in the region of PNPLA2 (rs61876744) and CSNK1E (rs138380) for KC that may be associated with KC in the Saudi population. In addition, polymorphisms in the apolipoprotein E (APOE) gene, namely, rs429358 and rs7412, responsible for APOE allelic variants ε2, ε3, and ε4, may influence KC via oxidative stress mechanism(s). Thus, we investigated the possible association of polymorphisms rs61876744, rs138380, rs429358, rs7412, and APOE genotypes in KC patients of the Saudi population. This study included 98 KC cases and 167 controls. Polymorphisms rs6187644 and rs138380 were genotyped using TaqMan assays, and rs429358 and rs7412 were genotyped via Sanger sequencing. Although the allele frequency of rs61876744(T) in PNPLA2 was a protective effect against KC (odds ratio (OR) = 0.64, 95% confidence interval (CI) = 0.44-0.93), the p-value (p = 0.020) was not significant for multiple testing correction (p = 0.05/4 = 0.015). However, rs6187644 genotype showed a modestly significant protective effect in the dominant model (OR = 0.53, 95% CI = 0.32-0.88, p = 0.013). Polymorphisms rs138380, rs429358, and rs7412 showed no significant allelic or genotype association with KC. However, the ε2-carriers (ε2/ε2 and ε2/ε3 genotypes) exhibited a greater than 5-fold increased risk of KC, albeit non-significantly (p = 0.055). Regression analysis showed no significant effect of age, gender, and the four polymorphisms on KC. Our results suggest that polymorphism rs6187644 in PNPLA2 might be associated with KC in the Middle Eastern Arabs of Saudi origin but warrant a large-scale association analysis at this locus.

Genetic dissection of thousand-seed weight in linseed (Linum usitatissimum L.) using multi-locus genome-wide association study.

Flaxseed/linseed is an important oilseed crop having applications in the food, nutraceutical, and paint industry. Seed weight is one of the most crucial determinants of seed yield in linseed. Here, quantitative trait nucleotides (QTNs) associated with thousand-seed weight (TSW) have been identified using multi-locus genome-wide association study (ML-GWAS). Field evaluation was carried out in five environments in multi-year-location trials. SNP genotyping information of the AM panel of 131 accessions comprising 68,925 SNPs was employed for ML-GWAS. From the six ML-GWAS methods employed, five methods helped identify a total of 84 unique significant QTNs for TSW. QTNs identified in ≥ 2 methods/environments were designated as stable QTNs. Accordingly, 30 stable QTNs have been identified for TSW accounting up to 38.65% trait variation. Alleles with positive effect on trait were analyzed for 12 strong QTNs with r 2 ≥ 10.00%, which showed significant association of specific alleles with higher trait value in three or more environments. A total of 23 candidate genes have been identified for TSW, which included B3 domain-containing transcription factor, SUMO-activating enzyme, protein SCARECROW, shaggy-related protein kinase/BIN2, ANTIAUXIN-RESISTANT 3, RING-type E3 ubiquitin transferase E4, auxin response factors, WRKY transcription factor, and CBS domain-containing protein. In silico expression analysis of candidate genes was performed to validate their possible role in different stages of seed development process. The results from this study provide significant insight and elevate our understanding on genetic architecture of TSW trait in linseed.

VNTR Polymorphism in the Intron 5 of SIRT3 and Susceptibility to Breast Cancer.

Breast cancer recurrence and metastasis are associated with alterations in the cellular stress responses that influence tumour signalling. Sirtuin3 (SIRT3), a mitochondrial deacetylase is the regulator of mitochondrial metabolism and oxidative stress affecting tumour cell responses. Genetic variants or dysregulation of SIRT3 was known to associate with poor prognosis of recurrence and relapse in few cancers. The current case-control study was conducted in Hyderabad, India. A total of 200 primary female breast cancer cases were recruited, irrespective of age and clinical subtype. However, secondary or recurrent breast cancer cases were excluded from the study. A total of 202 age and gender-matched healthy controls without any familial inheritance of either breast or other cancer and having similar ethnicity as cases were recruited. The blood samples of both cases and controls were collected from Nizam's Institute of Medical Sciences (NIMS), Hyderabad. Our study is an attempt to evaluate the association of SIRT3 VNTR polymorphism in intron 5 with the development and progression of breast cancer by PCR-based genotyping. Result: The statistical analysis of the results with respect to epidemiological and clinical phenotypes revealed significant association of 0R allele and 0R/0R genotype with breast cancer risk (p<0.01). The odds ratios also were found to be significant i.e., 0R/0R [OR(CI): 2.67(1.54-4.65); p=0.000005] genotype. Also, the epidemiological and clinical variables have shown significant association with the risk of onset of the disease. Therefore, the influence of lack of repeats at intron 5 harbouring enhancer site on altered expression of SIRT3 might confer increased susceptibility to breast cancer. The VNTR polymorphism in the intron 5 region of SIRT3 gene could serve as a molecular marker for detection of breast cancer onset. Further studies are warranted to study the prognostic and therapeutic significance of this SIRT3 polymorphism.

Significant Association of Poly-A and Fok1 Polymorphic Alleles of the Vitamin D Receptor with Vitamin D Serum Levels and Incidence of Squamous Cutaneous Neoplasia

Vitamin D3, a prohormone, is converted to circulating calcidiol and then to calcitriol, the hormone that binds to the vitamin D receptor (VDR) (a nuclear transcription factor). Polymorphic genetic sequence variants of the VDR are associated with an increased risk of breast cancer and melanoma. However, the relationship between VDR allelic variants and the risk of squamous cell carcinoma and actinic keratosis remains unclear. We examined the associations between two VDR polymorphic sites, Fok1 and Poly-A, and serum calcidiol levels, actinic keratosis lesion incidence, and the history of cutaneous squamous cell carcinoma in 137 serially enrolled patients. By evaluating the Fok1 (F) and (f) alleles and the Poly-A long (L) and short (S) alleles together, a strong association between genotypes FFSS or FfSS and high calcidiol serum levels (50.0 ng/ml) was found; conversely, ffLL patients showed very low calcidiol levels (29.1 ng/ml). Interestingly, the FFSS and FfSS genotypes were also associated with reduced actinic keratosis incidence. For Poly-A, additive modeling showed that Poly-A (L) is a risk allele for squamous cell carcinoma, with an OR of 1.55 per copy of the L allele. We conclude that actinic keratosis and squamous cell carcinoma should be added to the list of squamous neoplasias that are differentially regulated by the VDR Poly-A allele.

Association of BDNF gene missense polymorphism rs6265 (Val66Met) with three quantitative traits, namely, intelligence quotient, body mass index, and blood pressure: A genetic association analysis from North India.

Brain-derived neurotrophic factor (BDNF), a neurotransmitter modulator, plays a significant role in neuronal survival and growth and participates in neuronal plasticity, thus being essential for learning, memory, and the development of cognition. Additionally, it is crucial for appetite, weight, and metabolic control and plays a pivotal role in the cardiovascular system. The Val66Met polymorphism (rs6265) of the BDNF gene causes a decrease in BDNF secretion and plays a role in impairments in cognition, energy homeostasis, and cardiovascular events. The present study aimed to evaluate the association of polymorphism (rs6265) of the BDNF gene with three quantitative traits simultaneously, namely, intelligence quotient (IQ), body mass index (BMI), and blood pressure (BP). Psychometric, morphometric, and physiometric data of the total participants (N = 246) were collected. WASI-IIINDIA was used to measure cognitive ability. Genotyping was carried out using allele-specific PCR for the rs6265 polymorphism (C196T), and genotypes were determined. Statistical analyses were performed at p < 0.05 significance level using MS-Excel and SigmaPlot. The odds ratio models with a 95% confidence interval were used to test the associations. The used models are co-dominant, recessive, dominant, over-dominant, and additive. The allelic frequencies of alleles C and T were 72 and 28%, respectively. Under the dominant genetic model, a significant susceptible association of minor allele T was observed with a lower average verbal comprehensive index (OR = 2.216, p = 0.003, CI (95%) =1.33-3.69), a lower average performance reasoning index (OR = 2.634, p < 0.001, CI (95%) = 1.573-4.41), and a lower average full-scale IQ-4 (OR = 3.159, p < 0.001, CI (95%) = 1.873-5.328). Carriers of Met-alleles were found to have an increased body mass index (OR = 2.538, p < 0.001, CI (95%) = 1.507-4.275), decreased systolic blood pressure (OR = 2.051, p = 0.012, CI (95%) = 1.202-3.502), and decreased diastolic blood pressure (OR = 2.162, p = 0.006, CI (95%) = 1.278-3.657). Under the recessive genetic model, several folds decrease in IQ and BP and an increase in BMI with the presence of the T allele was also detected. This novel study may improve our understanding of genetic alterations to the traits and hence be helpful for clinicians and researchers to investigate the diagnostic and prognostic value of this neurotrophic factor.

Replication of association at the LPP and UBASH3A loci in a UK autoimmune Addison's disease cohort.

Autoimmune Addison's disease (AAD) arises from a complex interplay between multiple genetic susceptibility polymorphisms and environmental factors. The first genome wide association study (GWAS) with patients from Scandinavian Addison's registries has identified association signals at four novel loci in the genes LPP, SH2B3, SIGLEC5, and UBASH3A. To verify these novel risk loci, we performed a case-control association study in our independent cohort of 420 patients with AAD from the across the UK. We report significant association of alleles of the LPP and UBASH3A genes [odds ratio (95% confidence intervals), 1.46 (1.21-1.75)and 1.40 (1.16-1.68), respectively] with AAD in our UK cohort. In addition, we report nominal association of AAD with SH2B3 [OR 1.18 (1.02-1.35)]. We confirm that variants at the LPP and UBASH3A loci confer susceptibility to AAD in a UK population. Further studies with larger patient cohorts are required to robustly confirm the association of SH2B3 and SIGLEC5/SPACA6 alleles.

TREM2 R47H variant and risk for Alzheimer’s disease: assessment in a Greek population and updated meta-analysis

Introduction Rare coding variants in TREM2 and their association with the susceptibility towards Alzheimer’s disease (AD) were recently studied in various ethnic groups with contradictory results. The T allele of the rs75932628 (p.R47H variant) has shown a positive risk association with AD in several studies; however, neither a study in Greece nor an updated meta-analysis have been conducted. Objective To assess the association between TREM2 rs75932628 and late-onset (sporadic) AD in a Greek population, and perform a meta-analysis of current data. Materials and Methods The rs75932628 was genotyped in a total of 327 patients with AD and 700 cognitively healthy controls. A systematic search and meta-analyses of studies presenting data regarding rs75932628 in AD cases and controls were also performed. Results Three patients vs. none of the controls were found to carry the heterozygous risk allele of the rs75932628, yielding a significant association (p = 0.032), in the Greek sample. In the meta-analysis, the overall odds ratio (OR) under a fixed-effects model was 2.98 (Confidence Interval (CI):2.52–3.53) showing a significant association of the rs75932628-T allele with AD in the overall dataset, based on data from 27 studies (26200 AD cases and 142084controls). Caucasian population-only studies (n = 16) revealed a similar OR of 2.93 (CI:2.45–3.51), whereas Asian population-only studies (n = 5) had a non-significant OR of 0.84 (CI:0.19–3.74). Conclusion The rs75932628 was associated with AD in the Greek sample. Our meta-analysis, covering a total population of over 168,000 people, also showed a significant association of the allele with AD in Caucasian populations.

Analysis of associations of genetic markers with the development of congenital scoliosis

Objective. To study the associations of single-nucleotide polymorphisms: rs6570507 in GPR126 gene, rs1800795 in IL-6 gene, rs1800469 in TGFB1 gene, rs731236 in VDR gene, rs625039 and rs11598564 polymorphisms in LBX1 gene, and rs12946942 in SOX9 gene with congenital scoliosis.Material and Methods. The study included 90 patients with verified congenital anomalies of the spine (single and multiple malformations of the spine, ICD-10 Code: Q76.3) and 157 clinically healthy volunteers without diagnosed spinal deformity and without family history of spinal malformations or osteoarticular system diseases. Molecular genetic testing was performed by PCR with real-time registration of a signal from the developed oligonucleotides used to determine rs6570507, rs1800795, rs1800469, rs625039, rs11598564, rs12946942, and rs731236 polymorphisms. Reference sequences were selected from the dbSNP database, and sequence design was performed on the BLAST platform. Data analysis was performed using the R free software computing environment. Data were compared using Pearson’s c2 test, and 95 % confidence interval limits were calculated to assess the significance of OR.Results. Statistically significant association of the G allele and GG genotype of the rs1800795 polymorphism in the interleukin-6 gene with congenital scoliosis was found in group of Russian patients (p &lt; 0.001). No significant association of alleles and genotypes of polymorphic variants of rs6570507, rs1800469, rs625039, rs11598564, rs12946942, and rs731236 with congenital scoliosis was found.Conclusion. The rs1800795 polymorphism can be considered as a promising marker for molecular genetic diagnostics of congenital scoliosis.

Lack of impact of OCTN1 gene polymorphisms on clinical outcomes of gabapentinoids in Pakistani patients with neuropathic pain.

Gabapentinoids are the first-line drugs for neuropathic pain. These drugs are the substrate of organic cation transporter (OCTN1) for renal excretion and absorption across the intestinal epithelium. Gabapentinoids exhibit wide interindividual variability in daily dosage and therapeutic efficacy which makes titration regimens prolonged for optimal efficacy. The present study aimed to investigate the possible influence of the single nucleotide polymorphism (SNP) of OCTN1 on therapeutic efficacy and safety of gabapentinoids in neuropathic pain patients of the Pakistani population. Four hundred and twenty-six patients were enrolled in the study. All participants were genotyped for OCTN1 rs1050152 and rs3792876 by PCR-RFLP method and followed up for eight weeks. The therapeutic outcomes of gabapentinoids, reduction in pain score, inadequate or complete lack of response, adverse events (AEs) in responders and discontinuation of treatment on account of AEs were recorded for all patients. There was no significant association of genotypes and alleles of both SNPs on the clinical response of gabapentinoids (P ˃ 0.05). Similarly, significant differences were not found in the reduction of pain scores and AEs among different genotypes in the responders. The present study has reported the association of OCTN1 rs1050152 and rs3792876 polymorphisms with clinical outcomes of gabapentinoids for the first time in the real-world clinical setting. Our results suggest a lack of influence of OCTN1 genetic variants in the determination of clinical response to gabapentinoids in patients with neuropathic pain in the Pakistani population. These findings signify the role of renal functions in predicting the interindividual variability to therapeutic responsiveness of gabapentinoids.

Gene polymorphism among hypertensive patients with coronary artery disease.

The obstruction of the coronary arteries causes Coronary Artery Disease (CAD). It has been reported that interleukin-6 gene is related to the development of cardiovascular diseases such as atherosclerosis and coronary artery disease. This was due to the large variability and short half-life of interleukin 6 (IL-6). There are few studies on the link between interleukin 6 and CAD on the patients with hypertension. Therefore, goal of this study was to see if there is a link between IL-6 gene polymorphisms and coronary artery disease with hypertension patients. The polymorphisms were carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The data was determined for statistical significance using chi-square analysis. A significant difference was found in the GG genotype of IL-6 -174, which was more frequent in cases of CAD (48.67 %) than in controls (8%) and 95% CI was 0.473455 - 0.500326; P<0.010620511. The GG genotype of IL-6-572C/G polymorphism was more frequent in cases of CAD (42.6%) compared with controls (8%) and 95% CI 0.386724 - 0.480945; P<0.017939631). likewise, significant association of variant allele G with CAD patients was reported. Hypertension was significantly higher among patients as compared to controls (P<0.022847535). Our findings indicated that both gene polymorphisms may be associated with development of CAD.

Polymorphism rs3742330 in microRNA Biogenesis Gene DICER1 Is Associated with Pseudoexfoliation Glaucoma in Saudi Cohort.

We investigated the association between DICER1 (rs3742330) and DROSHA (rs10719) polymorphisms and pseudoexfoliation glaucoma (PXG) and related clinical phenotypes in a Saudi cohort. In a retrospective case-control study, TaqMan real-time, PCR-based genotyping was performed in 340 participants with 246 controls and 94 PXG cases. The minor (G) allele frequency of rs3742330 in PXG (0.03) was significantly different from that in the controls (0.08) and protective against PXG (odds ratio (OR) = 0.38, 95% confidence interval (CI) = 0.16–0.92), p = 0.017). Similarly, the rs3742330 genotypes showed a significant protective association with PXG in dominant (p = 0.019, OR = 0.38, 95% CI = 0.15–0.92), over-dominant (p = 0.024, OR = 0.39, 95% CI = 0.16–0.95), and log-additive models (p = 0.017, OR = 0.38, 95% CI = 0.16–0.92). However, none remained significant after an adjustment for age, sex, and multiple testing. Rs10719 in DROSHA did not show any significant allelic or genotype association with PXG. However, a protective effect of the GA haplotype in DICER1 and DROSHA and PXG (p = 0.034) was observed. Both polymorphisms showed no significant effect on intraocular pressure and the cup–disk ratio. In conclusion, we report a significant genetic association between variant rs3742330 in DICER1, a gene involved in miRNA biogenesis, and PXG. Further investigation in a larger group of patients of different ethnicities and functional studies are warranted to replicate and validate its potential role in PXG.

Association between matrix metalloproteinases-2 and -9 gene polymorphism with basement membrane disruption in oral lichen planus: A case-control pilot study

ObjectivesThis study investigated genetic polymorphism of matrix metalloproteinases (MMP) −2 and −9 in oral lichen planus (OLP) and their association with the basement membrane status. Study designThis case-control study involved genotyping of peripheral blood sample of 32 OLP patients and 106 ethnically matched controls. Single nucleotide polymorphisms (SNP) that were assessed in the groups were- MMP9 rs3918242, MMP9 rs17576 and MMP2 rs865094. Basement membrane status of the OLP biopsy samples was microscopically assessed and recorded following Periodic acid Schiff staining. ResultsMMP9 rs3918242 showed significant genotypic and allelic associations between OLP subjects and controls. It was also significantly associated with intact basement membranes in OLP cases with increased frequency of ‘TT’ genotype and ‘T’ allele. No association was found with regard to MMP9 rs17576 and MMP2 rs865094. ConclusionBiallelic substitution at the promoter region of MMP9 (rs3918242) gene may be associated with increased risk of development of OLP. It may be involved in compromising the integrity of the basement membrane junction.

HLA-disease association and pleiotropy landscape in over 235,000 Finns

The human leukocyte antigen (HLA) system is the single most important genetic susceptibility factor for many autoimmune diseases and immunological traits. For systematic population-level analysis of HLA-phenotype association landscape we imputed the alleles of classical HLA genes in a discovery cohort of 146,630 and replication cohort of 89,340 Finns of whom SNP genotype data and 3,355 disease phenotypes were available as part of the FinnGen project. In total, 3,649 statistically significant single HLA allele associations in 368 phenotypes were found. Known susceptibility associations clearly dominated the landscape but we discovered also a few previously poorly established HLA associations such as DQA1*01:03 and DQB1*06:03 with mental and behavioural disorders due to cannabinoids (p-value = 10-5; beta = 0.6). As certain HLAs were found to be involved in both autoimmune and infectious diseases, we studied further the independence of their associations and statistical pleiotropy. We found that altogether 11 shared HLA alleles were associated independently with both autoimmune and infectious diseases. The most prominent of these were DQA1*03:01 and DQB1*03:02 both of which associated with three infectious and three autoimmune phenotypes. All the shared HLAs showed risk effects in both disease groups, suggesting that infections can increase the risk for autoimmune diseases. The population-level landscape analysis is an excellent resource for estimating the contribution and genetic models of HLA genes in many different phenotypes and for fine-mapping primary associations.