Association of FSHR gene polymorphisms with endometriosis in women visiting tertiary-care hospitals of Lahore, Pakistan

2021 ◽  
pp. 1-14
Author(s):  
Irfana Liaqat ◽  
Najiya al Arifa ◽  
Saba Asif ◽  
Khalid Parvaiz Lone ◽  
Admin
Keyword(s):  
Tertiary Care ◽  
Nucleotide Polymorphisms ◽  
Yale University ◽  
Blood Leukocytes ◽  
Single Nucleotide ◽  
Direct Dna Sequencing ◽  
Control Subjects ◽  
Fshr Gene ◽  
High Incidence ◽  
Tertiary Care Hospitals

Abstract Objectives: The study was aimed to explore the association of endometriosis risk factors with single nucleotide polymorphisms rs6166 and rs6165 (Asn680Ser and Ala307Thr) of follicle stimulating hormone receptor (FSHR) gene in Pakistani women. Methods: This study was conducted from 2013 to 2016. The sampling and extraction of DNA was done in Department of Zoology GC University Lahore while the sequencing was performed at Yale University USA. This case control study consists of 364 subjects including 156 women diagnosed with endometriosis and 208 randomly recruited controls. Subjects diagnosed at stage II-IV endometriosis with infertility were pooled for study. The women with adenomyosis, ovarian cancer and leiomyoma were excluded. The whole blood leukocytes were used for DNA extraction. Two important polymorphisms of exon 10 of FSHR gene were analyzed by direct DNA sequencing both in endometriosis and controls. Results: SNP rs6166 in the affected endometriosis subjects exhibited high incidence of allele “A” (Asn/Asn) 68.3% as compared to controls 33.7% (OR= 4.240; P =0.001). Similarly, the allele “A” of SNP rs6165 (Thr/Thr) was more frequent in endometriosis 67.3% than in control subjects 37.5% (OR =3.430, P =0.001). The occurrence of haplotype AA (Asn/Thr) was 45.5% in endometriosis and 11 % in control subjects (P= 0.001).  Remarkably, the incidence of haplotype GG (Ser/Ala) was contrary to previous observations, since only 9.9% occurred in endometriosis as opposed to 45.2% in controls (P= 0.001). Continuous...  

Association of systemic lupus erythematosus (SLE) genetic susceptibility loci with lupus nephritis in childhood-onset and adult-onset SLE

Rheumatology ◽  
2019 ◽  
Vol 59 (1) ◽  
pp. 90-98 ◽  
Author(s):  
Declan Webber ◽  
Jingjing Cao ◽  
Daniela Dominguez ◽  
Dafna D Gladman ◽  
Deborah M Levy ◽  
...  
Keyword(s):  
Lupus Erythematosus ◽  
Tertiary Care ◽  
Logistic Models ◽  
Risk Scores ◽  
Nucleotide Polymorphisms ◽  
Adult Onset ◽  
Susceptibility Loci ◽  
Childhood Onset ◽  
Single Nucleotide ◽  
Independent Cohort

Abstract Objective LN is one of the most common and severe manifestations of SLE. Our aim was to test the association of SLE risk loci with LN risk in childhood-onset SLE (cSLE) and adult-onset SLE (aSLE). Methods Two Toronto-based tertiary care SLE cohorts included cSLE (diagnosed <18 years) and aSLE patients (diagnosed ⩾18 years). Patients met ACR and/or SLICC SLE criteria and were genotyped on the Illumina Multi-Ethnic Global Array or Omni1-Quad arrays. We identified those with and without biopsy-confirmed LN. HLA and non-HLA additive SLE risk-weighted genetic risk scores (GRSs) were tested for association with LN risk in logistic models, stratified by cSLE/aSLE and ancestry. Stratified effect estimates were meta-analysed. Results Of 1237 participants, 572 had cSLE (41% with LN) and 665 had aSLE (30% with LN). Increasing non-HLA GRS was significantly associated with increased LN risk [odds ratio (OR) = 1.26; 95% CI 1.09, 1.46; P = 0.0006], as was increasing HLA GRS in Europeans (OR = 1.55; 95% CI 1.07, 2.25; P = 0.03). There was a trend for stronger associations between both GRSs and LN risk in Europeans with cSLE compared with aSLE. When restricting cases to proliferative LN, the magnitude of these associations increased for both the non-HLA (OR = 1.30; 95% CI 1.10, 1.52; P = 0.002) and HLA GRS (OR = 1.99; 95% CI 1.29, 3.08; P = 0.002). Conclusion We observed an association between known SLE risk loci and LN risk in children and adults with SLE, with the strongest effect observed among Europeans with cSLE. Future studies will include SLE-risk single nucleotide polymorphisms specific to non-European ancestral groups and validate findings in an independent cohort.

scholarly journals Analytical Validation of the Tag-It High-Throughput Microsphere-Based Universal Array Genotyping Platform: Application to the Multiplex Detection of a Panel of Thrombophilia-Associated Single-Nucleotide Polymorphisms

2004 ◽  
Vol 50 (11) ◽  
pp. 2028-2036 ◽  
Author(s):  
Susan Bortolin ◽  
Margot Black ◽  
Hemanshu Modi ◽  
Ihor Boszko ◽  
Daniel Kobler ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Throughput ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Single Nucleotide ◽  
Direct Dna Sequencing ◽  
Array Platform ◽  
Genotyping Platform ◽  
Universal Array ◽  
Primer Sets

Abstract Background: We have developed a novel, microsphere-based universal array platform referred to as the Tag-It™ platform. This platform is suitable for high-throughput clinical genotyping applications and was used for multiplex analysis of a panel of thrombophilia-associated single-nucleotide polymorphisms (SNPs). Methods: Genomic DNA from 132 patients was amplified by multiplex PCR using 6 primer sets, followed by multiplex allele-specific primer extension using 12 universally tagged genotyping primers. The products were then sorted on the Tag-It array and detected by use of the Luminex xMAP™ system. Genotypes were also determined by sequencing. Results: Empirical validation of the universal array showed that the highest nonspecific signal was 3.7% of the specific signal. Patient genotypes showed 100% concordance with direct DNA sequencing data for 736 SNP determinations. Conclusions: The Tag-It microsphere-based universal array platform is a highly accurate, multiplexed, high-throughput SNP-detection platform.

scholarly journals Variants in the 5α-Reductase Type 1 and Type 2 Genes Are Associated with Polycystic Ovary Syndrome and the Severity of Hirsutism in Affected Women

2006 ◽  
Vol 91 (10) ◽  
pp. 4085-4091 ◽  
Author(s):  
Mark O. Goodarzi ◽  
Nissar A. Shah ◽  
Heath J. Antoine ◽  
Marita Pall ◽  
Xiuqing Guo ◽  
...  
Keyword(s):  
Risk Factors ◽  
Los Angeles ◽  
Single Nucleotide Polymorphisms ◽  
Polycystic Ovary Syndrome ◽  
White Women ◽  
Polycystic Ovary ◽  
Nucleotide Polymorphisms ◽  
Ovary Syndrome ◽  
Single Nucleotide ◽  
Control Subjects

Abstract Context: Despite the importance of dihydrotestosterone in androgen action, polymorphisms in the genes for the two isoforms of 5α-reductase (SRD5A1 and SRD5A2) have not been evaluated as risk factors for polycystic ovary syndrome (PCOS). Objective: The objective of the study was to test the hypothesis that haplotypes in the SRD5A1 and SRD5A2 genes are risk factors for PCOS and the severity of hirsutism in affected women. Design: PCOS and control subjects were genotyped for seven single-nucleotide polymorphisms in SRD5A1 and eight single-nucleotide polymorphisms in SRD5A2. Haplotypes were determined and tested for association with PCOS diagnosis and component phenotypes. Setting: Subjects were recruited from the reproductive endocrinology clinic at the University of Alabama at Birmingham; control subjects were recruited from the general surrounding community. Genotyping took place at Cedars-Sinai Medical Center in Los Angeles. Participants: A total of 287 White women with PCOS and 187 controls participated. Main Measurements: SRD5A1 and SRD5A2 genotype, quantitative hirsutism score, and hormonal and metabolic phenotypes were assessed. Results: Haplotypes within both genes were associated with PCOS risk. The Leu allele of the Val89Leu variant in SRD5A2 was associated with protection against PCOS; this allele is known to modestly reduce 5α-reductase activity. Haplotypes in SRD5A1 but not SRD5A2 were also associated with the degree of hirsutism in affected women. Conclusions: This study presents genetic evidence suggesting an important role of both isoforms of 5α-reductase in the pathogenesis of PCOS. That only SRD5A1 haplotypes were associated with hirsutism suggests that only this isoform is important in the hair follicle.

scholarly journals Screening of single nucleotide polymorphisms among fuchs’ endothelial corneal dystrophy subjects in Malaysia

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Ker Hsin Ng ◽  
Visvaraja Subrayan ◽  
Vasudevan Ramachandran ◽  
Fazliana Ismail
Keyword(s):  
Tertiary Care ◽  
Corneal Dystrophy ◽  
Nucleotide Polymorphisms ◽  
Older Individuals ◽  
Single Nucleotide ◽  
Genetic Studies ◽  
Novel Variant ◽  
Different Populations ◽  
Larger Sample ◽  
Control Study

Abstract Background The pathophysiology underlying Fuchs' Endothelial Corneal Dystrophy (FECD), especially in older individuals, remains unclear, with a genetic predisposition being reported as the single best predictor of the disease. Genetic studies have shown that several genes in various loci such as COL8A2, SLC4A11, TCF8/ZEB1 and TCF4 are associated with FECD in different populations and ethnicities. A case–control study was conducted to determine the association between genetic variants and FECD in a tertiary care setting in Malaysia. A total number of 12 patients with clinically diagnosed FECD and 12 age, gender and race matched control subjects were recruited. Extracted genomic DNA were genotyped using Infinium Global Screening Array (GSA)-24 version 1.0 BeadChip with iScan high-throughput system. Illumina GenomeStudio 2.0 Data Analysis and PLINK version 1.9 software were used to perform association tests and determine the distribution of obtained variants among the cases and controls. Results A significant novel genetic variant, rs11626651, a variant of the LOC105370676 gene or known as the LINC02320 gene, located at chromosome 14, has been identified as a suggestive association with FECD (p < 5 × 10−6). Further analysis in this study suggested that candidate genes such as COL8A2, ZEB1/TCF8, TCF4 and SLC4A11 had no significant associations with FECD. Conclusions The discovery of a novel variant may influence the underlying pathogenic basis of FECD in Malaysia. The current study is the first genetic study on FECD to use Infinium GSA. It is the first comprehensive report in Malaysia to provide genetic information of potential relevance to FECD, which may pave the way for new therapeutic strategies in the future. A detailed analysis with a larger sample size is recommended for further evaluation.

scholarly journals The First Report of Genetic Polymorphisms of the Equine SPRN Gene in Outbred Horses, Jeju and Halla Horses

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2574
Author(s):  
Sae-Young Won ◽  
Yong-Chan Kim ◽  
Kyoungtag Do ◽  
Byung-Hoon Jeong
Keyword(s):  
Prion Protein ◽  
Prion Disease ◽  
Protein Gene ◽  
Prion Diseases ◽  
Minimum Free Energy ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Reading Frame ◽  
Direct Dna Sequencing ◽  
Thoroughbred Horses

Prion disease is a fatal infectious disease caused by the accumulation of pathogenic prion protein (PrPSc) in several mammals. However, to date, prion disease has not been reported in horses. The Sho protein encoded by the shadow of the prion protein gene (SPRN) plays an essential role in the pathomechanism of prion diseases. To date, the only genetic study of the equine SPRN gene has been reported in the inbred horse, Thoroughbred horse. We first discovered four SPRN single nucleotide polymorphisms (SNPs) in 141 Jeju and 88 Halla horses by direct DNA sequencing. In addition, we found that the genotype, allele and haplotype frequencies of these SNPs of Jeju horses were significantly different from those of Halla and Thoroughbred horses, this latter breed is also included in this study. Furthermore, we observed that the minimum free energy and mRNA secondary structure were significantly different according to haplotypes of equine SPRN polymorphisms by the RNAsnp program. Finally, we compared the SNPs in the coding sequence (CDS) of the SPRN gene between horses and prion disease-susceptible species. Notably, prion disease-susceptible animals had polymorphisms that cause amino acid changes in the open reading frame (ORF) of the SPRN gene, while these polymorphisms were not found in horses.

scholarly journals Genetic Variations of Cytokines and Cytokine Receptors in Psoriasis Patients from China

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Xiao-Lan Li ◽  
Chun-Feng Wu ◽  
Gui-Sheng Wu
Keyword(s):  
Protective Factor ◽  
Chinese Patients ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Control Subjects ◽  
Genetic Patterns ◽  
Il12b Gene ◽  
Genetic And Environmental Factors ◽  
And Control ◽  
Control Study

Psoriasis is a chronic inflammatory and hyperproliferative skin disease affected by both genetic and environmental factors. The aim of the present study was to investigate polymorphisms in a candidate gene family of interleukin (IL) in unrelated Chinese patients with psoriasis and control subjects without psoriasis. In this case-control study, 200 unrelated Chinese psoriasis patients and 298 age- and sex-matched control subjects were enrolled. Genomic DNA was prepared from peripheral blood obtained from all psoriasis patients and control subjects. We genotyped seven single-nucleotide polymorphisms (SNPs) in candidate genes of six ILs: IL4, IL10, IL12B, IL13, IL15, and IL23R, which have been shown in the literature to be associated with psoriasis in other ethnic groups. Among the seven SNPs in the six IL genes studied, only the rs3212227 in the IL12B gene was found to be associated with psoriasis at genotypic level in the studied population. The C/C genotype in the IL12B gene is a protective factor of psoriasis (P = 0.0218; OR = 0.51; 95% CI: 0.27–0.96) in Chinese. Furthermore, the studied Chinese population has extremely low minor allele frequency for IL23R. Together, the data reveal unique genetic patterns in Chinese that may be in part responsible for the lower risk for psoriasis in this population.

scholarly journals ecRESCUE: a novel ecDHFR-regulated RESCUE system with reduced RNA off-targeting activity

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Yihan Wang ◽  
Guo Li ◽  
Xiangyang Li ◽  
Yuzhe Wang ◽  
Xingxu Huang ◽  
...  
Keyword(s):  
Genetic Diseases ◽  
Transcriptional Level ◽  
In Vitro Experiments ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Considerable Potential ◽  
Base Editing ◽  
High Incidence ◽  
Rescue System

AbstractThe currently available RESCUE RNA base editing system demonstrates considerable potential for the treatment of genetic diseases at the transcriptional level. However, the relatively high incidence of off-target events hampers the precise RNA editing, thereby limiting its use in the clinical setting. This study describes a new RNA base editing method, named ecRESCUE, which utilizes inducible stabilization of the protein ecDHFR DD fused at the C-terminal of the original RESCUE system. In vitro experiments in 293T cells showed that the ecRESCUE editor markedly reduced the incidence of off-target single nucleotide polymorphisms without affecting the RNA A-to-I and C-to-U base editing efficiency. Altogether, these results demonstrate that the inducible ecRESCUE system represents an attractive approach to regulate and improve the outcome of the available RNA base editor with reduced off-targeting activity.

scholarly journals ecRESCUE: a novel ecDHFR-regulated RESCUE system with reduced RNA off-targeting activity

2021 ◽  
Author(s):  
Jianen Gao ◽  
Yihan Wang ◽  
Guo Li ◽  
Xiangyang Li ◽  
Yuzhe Wang ◽  
...  
Keyword(s):  
Genetic Diseases ◽  
Transcriptional Level ◽  
In Vitro Experiments ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Considerable Potential ◽  
Base Editing ◽  
High Incidence ◽  
Rescue System

Abstract The currently available RESCUE RNA base editing system demonstrates considerable potential for the treatment of genetic diseases at the transcriptional level. However, the relatively high incidence of off-target events hampers the precise RNA editing, thereby limiting its use in the clinical setting. This study describes a new RNA base editing method, named ecRESCUE, which utilizes inducible stabilization of the protein ecDHFR DD fused at the C-terminal of the original RESCUE system. In vitro experiments in 293T cells showed that the ecRESCUE editor markedly reduced the incidence of off-target single nucleotide polymorphisms without affecting the RNA A-to-I and C-to-U base editing efficiency. Altogether, these results demonstrate that the inducible ecRESCUE system represents an attractive approach to regulate and improve the outcome of the available RNA base editor with reduced off-targeting activity.

Association of CYP19A1 gene polymorphisms with anoestrus in water buffaloes

2018 ◽  
Vol 30 (3) ◽  
pp. 487 ◽  
Author(s):  
Khairy M. El-Bayomi ◽  
Ayman A. Saleh ◽  
Ashraf Awad ◽  
Mahmoud S. El-Tarabany ◽  
Hadeel S. El-Qaliouby ◽  
...  
Keyword(s):  
Blood Levels ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Association Analyses ◽  
Water Buffaloes ◽  
Risk Alleles ◽  
Lower Blood ◽  
High Incidence ◽  
Control Study ◽  
Selection Of

Cytochrome P450 aromatase (encoded by the CYP19A1 gene) regulates oestrogen biosynthesis and so plays an essential role in female fertility. We investigated the genetic association of CYP19A1 with the risk of anoestrus in Egyptian water buffaloes. A total of 651 animals (326 anoestrous and 325 cycling) were used in this case-control study. Using single-strand conformation polymorphisms and sequencing, four single nucleotide polymorphisms (SNPs) were detected; c.−135T > C SNP in the 5′UTR and three non-synonymous SNPs: c.559G > A (p. V187M) in Exon 5, c.1285C > T (p. P429S) and c.1394A > G (p. D465G) in Exon 10. Individual SNP-anoestrus association analyses revealed that genotypes (CC, AA and GG) and alleles (C, A and G) of the −135T > C, c.559G > A and c.1394A > G SNPs respectively were high risk for anoestrus. A further analysis confirmed that these three SNPs were in linkage disequilibrium. Additionally, haplotypes with two (TAG/122 and CAA/221) or three (CAG/222) risk alleles were significantly associated with susceptibility to anoestrus, lower blood levels of both oestradiol and antioxidant enzymes (superoxide dismutase, glutathione peroxidase (GPX) and catalase) and downregulated expression levels of CYP19A1, oestrogen receptor α and Gpx3 in the ovary, as well as increased serum level of malondialdehyde. This suggests the occurrence of a high incidence of oxidative ovarian damage and subsequently ovarian inactivity in buffaloes carrying risk alleles. Therefore, with this study we suggest the selection of buffaloes with protective alleles at these SNPs to improve the reproductive efficiency of the herd.

scholarly journals Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country

2016 ◽  
Vol 54 (7) ◽  
pp. 1862-1870 ◽  
Author(s):  
David Stucki ◽  
Marie Ballif ◽  
Matthias Egger ◽  
Hansjakob Furrer ◽  
Ekkehardt Altpeter ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Nucleotide Polymorphisms ◽  
Foreign Born ◽  
Single Nucleotide ◽  
Content Type ◽  
Weak Evidence ◽  
High Incidence ◽  
Low Incidence

Immigrants from regions with a high incidence of tuberculosis (TB) are a risk group for TB in low-incidence countries such as Switzerland. In a previous analysis of a nationwide collection of 520Mycobacterium tuberculosisisolates from 2000 to 2008, we identified 35 clusters comprising 90 patients based on standard genotyping (24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat [MIRU-VNTR] typing and spoligotyping). Here, we used whole-genome sequencing (WGS) to revisit these transmission clusters. Genome-based transmission clusters were defined as isolate pairs separated by ≤12 single nucleotide polymorphisms (SNPs). WGS confirmed 17/35 (49%) MIRU-VNTR typing clusters; the other 18 clusters contained pairs separated by >12 SNPs. Most transmission clusters (3/4) of Swiss-born patients were confirmed by WGS, as opposed to 25% (4/16) of the clusters involving only foreign-born patients. The overall clustering proportion was 17% (90 patients; 95% confidence interval [CI], 14 to 21%) by standard genotyping but only 8% (43 patients; 95% CI, 6 to 11%) by WGS. The clustering proportion was 17% (67/401; 95% CI, 13 to 21%) by standard genotyping and 7% (26/401; 95% CI, 4 to 9%) by WGS among foreign-born patients and 19% (23/119; 95% CI, 13 to 28%) and 14% (17/119; 95% CI, 9 to 22%), respectively, among Swiss-born patients. Using weighted logistic regression, we found weak evidence of an association between birth origin and transmission (adjusted odds ratio of 2.2 and 95% CI of 0.9 to 5.5 comparing Swiss-born patients to others). In conclusion, standard genotyping overestimated recent TB transmission in Switzerland compared to WGS, particularly among immigrants from regions with a high TB incidence, where genetically closely related strains often predominate. We recommend the use of WGS to identify transmission clusters in settings with a low incidence of TB.

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