Sadia Rehman

Investigation of the Greek ancestry of populations from northern Pakistan

Three populations from northern Pakistan, the Burusho, Kalash, and Pathan, claim descent from soldiers left behind by Alexander the Great after his invasion of the Indo-Pak subcontinent. In order to investigate their genetic relationships, we analyzed nine Alu insertion polymorphisms and 113 autosomal microsatellites in the extant Pakistani and Greek populations. Principal component, phylogenetic, and structure analyses show that the Kalash are genetically distinct, and that the Burusho and Pathan populations are genetically close to each other and the Greek population. Admixture estimates suggest a small Greek contribution to the genetic pool of the Burusho and Pathan and demonstrate that these two northern Pakistani populations share a common Indo-European gene pool that probably predates Alexander’s invasion. The genetically isolated Kalash population may represent the genetic pool of ancestral Eurasian populations of Central Asia or early Indo-European nomadic pastoral tribes that became sequestered in the valleys of the Hindu Kush Mountains.

A study on the association of TNF-α-308, IL-6-174, IL-10-1082 and IL-1RaVNTR gene polymorphisms with rheumatic heart disease in Pakistani patients

Inflammation is an important contributor to the pathogenesis of rheumatic heart disease (RHD), a disorder of heart valves caused by a combination of immune, genetic and environmental factors. Cytokines are important mediators of inflammatory and immune responses. The aim of this study was to investigate the role of cytokine gene polymorphisms and their potential usefulness as biomarkers in RHD patients from Pakistan. We screened 150 RHD patients and 204 ethnically matched controls for tumor necrosis factor (TNF)-α(-308)G/A, interleukin (IL)-10(-1082) G/A, interleukin (IL)-6(-174) G/C and a variable number of tandem repeats (VNTRs) polymorphism of the IL-1Ra gene using polymerase chain reaction. The results showed that TNF-α(-308) A and IL-6(-174) G alleles were associated with susceptibility to RHD (p=0.000; OR=2.81; CI=1.5-5.14 and p=0.025; OR=1.50; CI=1.04-2.16 respectively). The TNF-α(-308) AA and GA genotypes were associated with susceptibility to RHD (p=0.012; OR=9.94; CI; 1.21-217.3 and p=0.046; OR=1.97; CI=0.98-3.97 respectively) while the GG genotype seemed to confer resistance (p=0.003; OR=0.39; CI=0.20-0.76). The GG genotype for IL-6(-174) was significantly associated with predisposition to RHD (p=0.015; OR=2.6; CI=1.17-5.85). The A1 (four repeats) and A2 (two repeats) alleles at the IL-1Ra VNTR polymorphism were associated with resistance and susceptibility to RHD respectively. However, this polymorphism deviated from Hardy-Weinberg equilibrium in both patients and controls in our population. TNF-α(-308) and IL-6(-174) polymorphisms may be useful markers for the identification of individuals susceptible to RHD in Pakistan. These individuals could be provided aggressive prophylactic intervention to prevent the morbidity and mortality associated with RHD.

Association analysis of GWAS and candidate gene loci in a Pakistani population with psoriasis

Psoriasis is a common inflammatory and hyper proliferative condition of the skin and a serious chronic systemic autoimmune disease. We undertook an association study to investigate the genetic etiology of psoriasis in a Pakistani population by genotyping single-nucleotide polymorphisms (SNPs) previously reported to be associated in genome-wide association (GWAS) or in candidate gene studies of psoriasis. Fifty seven single-nucleotide polymorphisms (SNPs) from 42 loci were genotyped in 533 psoriasis patients and 373 controls. Our results showed genome wide significant association of the MHC region (rs1265181 being the most significant from five SNPs used with overall OR=3.38; p=2.97E-18), as well as nominally significant associations at ten other loci (p<0.05) in the Pakistani population (LCE3B, REL, IL13/IL4, TNIP1, IL12B, TRAF3IP2, ZC3H12C, NOS2 and RNF114 from GWAS and PRR9 from a previous candidate gene study). Overall, only nine SNPs out of the 42 GWAS loci, displayed an odds ratio in the opposite allelic direction and only three did not reach similar odds ratio within 95% confidence interval as previously reported (SLC45A1/TNFRSF9, ELMO1 and IL28RA). This indicates similar genetic risk factors and molecular mechanisms behind disease in Pakistani psoriasis patients as in other populations. In addition, we show that the MHC and TNIP1 regions are significantly different in patients with psoriasis onset before the age of 40 (type I) compared to after 40 years of age (type II). MHC being associated mainly with type I while TNIP1 with type II patients.

The frequency of HLA class I and II alleles in Pakistani patients with aplastic anemia.

Hematological disorders like Aplastic anemia are quite frequent in Pakistan. Human leukocyte antigen (HLA) system, have been implicated in the development of Aplastic anemia in various population-based studies, The aim of this study was to determine the role of the HLA Class I and Class II alleles in genetic susceptibility to Aplastic anemia in Pakistani patients. HLA A*, B* and DRB1* alleles were analyzed, in 61 Pakistani patients (Females n = 22, Males n = 39) and the control group consisted of 200 ethnically matched individuals (Females n = 89, Males n = 111). The allele frequency of DRB1*15 was found significantly higher in patients 0.36 (p = 0.001 with odds ratio = 1.97), as compared to the controls 0.212. Although DRB1*03 percent frequency was significantly higher in controls 0.175 (p = 0.023) with odds ratio = 0.514, as compared to patients 0.106.Therefore DRB1*15 emerged as a susceptible allele and DRB1*03 as a protective allele in Pakistani Aplastic anemia patients and control samples. No significant difference was found in allele frequencies of other HLA class I and HLA class II alleles for both patients and controls. Three haplotypes A*02 B*40 DRB1*15 (p = 0.021), A*31 B*51 DRB1*13 (p = 0.12) and A*33 B*58 DRB1*15 (p = 0.000) showed significant variations in the two groups.

The angiotensin-converting enzyme gene insertion polymorphism: a higher risk for psoriasis in male patients

DEAR EDITOR, I would like to clarify a point related to the article ‘Prevalence of fragrance contact allergy in the general population in five European countries: a cross-sectional study’ by Diepgen et al. The authors are to be commended for the considerable effort that they expended to ensure standardization of as many aspects of the study as possible. Some readers may not have taken the time to review the details of the patch testing procedures, which are included in an appendix in the Supporting Information posted on the journal’s website. However, there they can learn that the authors went to the trouble of procuring ingredients for the fragrance mixes tested in the study so that the TRUE Test patches and petrolatum mixes could be manufactured from the same batches. This extra step to ensure that patch testing was conducted with a consistent product represents an admirable commitment to controlling as many variables in their study as possible – an often elusive goal in the field of patch testing for many well-established reasons. However, patch testing is a moving a target. Consequently, I would like to point out that the formulation of Fragrance Mix (FM) I in TRUE Test has changed since Diepgen et al. conducted their study (August 2008 to October 2011). As used in their study, the TRUE Test FM I patches were formulated with hydroxypropyl cellulose as the vehicle to match the formulation used in the commercial product at the time. However, since then the FM I formulation in TRUE Test has changed. The vehicle was changed to polyvinylpyrrolidone and the thickness of the gel layer was increased. As a result, the dose was increased from 0 43 mg 1 cm 2 to 0 50 mg 1 cm 2 and the stability of the patch was improved. The newly formulated FM I was introduced to TRUE Test in the U.S.A. and Japan in 2015 and is currently awaiting regulatory approval in Europe. These changes were made in response to concerns about the sensitivity of the product as expressed by the patch testing community, and were in progress long before Diepgen and coworkers published their article. However, it is important for readers to be aware of the lag between the time that their study was conducted and its more recent publication relative to the changes in the TRUE Test FM I formulation. Through no fault of these accomplished investigators, their conclusions about the performance of the FM I in TRUE Test can no longer be generalized to the product as it exists today in the U.S.A. and Japan, and should soon be outdated in terms of the European market as well.

Single-Nucleotide Polymorphisms of FAS and FASL Genes and Risk of Idiopathic Aplastic Anemia

ABSTRACT FAS/FASL signaling system plays a vital role in the regulation of apoptosis, envisaged as a death process required for immune surveillance to prevent autoimmunity and tumorigenesis along with several other biological activities. Several single-nucleotide polymorphisms (SNPs) of FAS/FASL system can result in aberrant apoptosis, which can cause different cancers and autoimmune diseases. Aplastic anemia (AA) is an autoimmune dysfunction characterized by peripheral blood pancytopenia associated with hypoplasia of bone marrow. The aim of this study was to screen Pakistani AA patients and controls for two Fas SNPs rs2234767 and rs1800682 and two FASLG SNPs rs763110 and rs5030772. Genotyping of 392 DNA samples was done by Tetra-ARMS polymerase chain reaction. Genotypic frequencies of Fas rs1800682 and FASLG rs5030772 showed significance difference in their distribution in both controls and patients, while Fas rs2234767 and FASLG rs763110 SNPs had no such difference. Carriers of rs1800682 AG+GG had a very odd ratio of 4.63, with 95% confidence interval (CI) of 3.01–7.11, while individuals with FASLG rs5030772 AG+GG were more common in controls than patients with OR 0.53 and 95% CI of 0.34–0.83. Cumulative effects of these SNPs were analyzed, and they showed almost similar trends; however, Fas rs2234767 and FASLG rs763110 genotypes in combination with Fas rs1800682 and FASLG rs5030772 demonstrated significant association. This study provided information that endorsed the involvement of FAS/FASL system SNPs in the pathogenesis of AA; further studies should be designed to understand the exact role of SNPs that can help in early diagnosis and treatment.

Single nucleotide polymorphisms in asthma candidate genes TBXA2R , ADAM33 FCER1B and ORMDL3 in Pakistani asthmatics a case control study

BackgroundGenetic variations in different loci and genes are important in asthma pathogenesis. There is much importance of various immunological pathways in the IgE secretion regulation. Alterations in any main part of these pathways can increase the risk of asthma development. Polymorphisms in these genetic markers can effect certain pathways which predict the asthma susceptibility. In the present study, SNPs directly or indirectly affecting the immunological process pathways are selected.MethodsThis study was conducted to determine association of 16 SNPs in 10 candidate genes with asthma in Pakistani population in 333 asthmatic cases and 220 healthy controls. Genotyping was performed using the Sequenom Mass ARRAY iPLEX platform (14 SNPs) and TaqMan assay (2 SNPs).ResultsThe minor allele at two of the SNPs showed association with protection from asthma, rs1131882 in TBXA2R gene (OR 0.73, 95% CI 0.52–1.01, P = 0.05) and rs2280091 in the ADAM33 gene (OR 0.69, 95% CI 0.50–0.97, P = 0.03). For FCER1B gene, rs2583476 the asthmatic male gender had higher TT genotype counts as compared to controls (OR = 1.86, 95% CI = 1.09–3.17, p = 0.01). In rs11650680 of ORMDL3 gene the CT genotype is more prevalent in female asthma cases in comparison with female controls (OR = 1.99, 95% CI = 1.02–3.89, p = 0.03).ConclusionsThis data suggests that variations at TBXA2R and ADAM33 genes are found to be associated with asthma susceptibility in Pakistan. FCER1B gene is associated with male and ORMDL3 in female asthmatics. These genetic markers can be important source of asthma risk in Pakistani population.

An angiotensin I-converting enzyme insertion/deletion polymorphism is associated with Pakistani asthmatic cases and controls

Asthma is a chronic disease due to inflammation of the airways of lungs that is clinically characterized by variable symptoms including wheezing, coughing and shortness of breath. Angiotensin I-converting enzyme (ACE) plays a major role in fibrous tissue formation and is highly expressed in lungs. The main aim of this research work was to study the role of ACE insertion/deletion (I/D) polymorphism, rs4646994, in asthma in Pakistani patients. A total of 854 subjects, including 333 asthma patients and 521 ethnically matched controls, were studied. The ACE (I/D) polymorphism was genotyped using polymerase chain reaction (PCR). Chi-square, Fisher’s exact and Hardy–Weinberg equilibrium tests were used to compare groups. Homozygous insertion genotype II (p<0.0001, OR=3.38) and insertion allele (I) was significantly more frequent in Pakistani asthmatics than in healthy controls (p=0.0007, OR=1.40). The ID genotype (p<0.0001, OR=0.43) and the deletion allele (D) were associated with protection of disease in Pakistani patients (p=0.0007, OR=0.71). These data suggest the involvement of ACE I/D polymorphism in asthma risk in the Pakistani population. This marker may be an important indication in the molecular mechanism of asthma and can become a useful tool in risk assessment and help in designing strategy to combat disease.

Mutation Screening of MEFV and TNF Gene in Pakistani Patients with Rheumatic Heart Disease: A Case Control-Study

Background: Rheumatic heart disease (RHD) is an inflammatory autoimmune cardiovascular disorder. The disease is highly prevalent in both urban (22 per 1000 individuals) and rural (5.7 per 1000 individuals) areas of Pakistan. The main purpose of this research work was to examine the role of two most widely studied genes, MEFV and TNF in the susceptibility of RHD in Pakistani patients.Methods and Materials: In total 360 samples, including 156 clinically diagnosed RHD patients and 204 healthy controls were included in the study. Single strand conformational polymorphism (SSCP) and direct DNA sequencing approach were used to identify the genetic changes in TNF exons and hot spots of MEFV gene.Results: No genetic variation in the two genes was detected in this study except a novel mutation (g.G2,096A) in exon 2 of MEFV gene. Computational analysis revealed that this mutation (p.S179N) severely affect the threedimensional structure of the protein and thus probably has a pathogenic role. However, this mutation was identified in two patients only.Conclusion: Hence, contribution of this mutation is expected to be very small in Pakistani patients. Our results showed a novel mutation with pathogenic effect in a very small proportion of the RHD patients in Pakistan. However, majority of the patients may have mutation outside the hot spot region of MEFV gene or there are other susceptibility factors that are contributing toward high prevalence of RHD in Pakistan. Therefore, it is important to screen the complete MEFV gene and other genetic susceptibility factors to understand etiology of RHD and thus manage its increasing incidence.