High risk association of IL-4 VNTR polymorphism with asthma in a North Indian population.

BACKGROUND: A case-control study was conducted to evaluate the role of IL-4 VNTR polymorphism in asthma that has been associated with various inflammatory diseases worldwide. This is the first case-control study conducted in India, investigating the role of IL-4 VNTR polymorphism in asthma pathogenesis. METHODS: A case-control study was performed with a total of 824 adult subjects, inducting 410 asthma patients and 414 healthy controls from North India. The genotypes were identified by polymerase chain reaction. RESULTS: Statistical analysis for the IL-4 VNTR polymorphism revealed that the Rp1 allele was significantly associated with asthma with OR=1.47, 95% CI (1.11-1.94) and p=0.005. The Rp1/Rp1 homozygous mutant genotype posed a high risk towards asthma with OR=2.39, 95% CI (0.96-6.14) and p=0.040. The Rp2/Rp1 heterozygous genotype also posed a risk towards asthma with OR=1.39, 95% CI (1.00-1.94) and p=0.040. Most of the phenotypic traits were significantly associated with the disease. CONCLUSIONS: IL-4 VNTR polymorphism is a high risk factor for asthma in the studied North Indian population.

Association of 24 bp duplication of human CHIT1 gene with asthma in a heterozygous population of north India: a case-control study.

PURPOSE: CHIT1 is expressed by pulmonary macrophages, which is typically the site of entry for many environmental fungi that may increase the risk of pulmonary fungal infection and lead to hypersensitivity. The conserved expression of this gene in humans suggests its physiological importance in the mammalian lung. METHODS: The present study was conducted with a total of 964 subjects, including 483 healthy controls and 481 asthma patients. DNA samples were extracted from blood, and the genotyping was done using polymerase chain reaction method. RESULTS: Statistical analysis revealed that the 24 bp duplication in CHIT1 gene polymorphism shows highly significant association in heterozygous (wild/dup) genotype with OR 1.74, 95 % CI (1.29-2.36), and p = 0.000. However, the homozygous mutant genotype (dup/dup) was found to be non-significant with OR 1.06, 95% CI (0.69-1.63), and p = 0.786. The combination of both wild/dup and dup/dup was also found to be highly significant with OR 1.57, 95% CI (1.18-2.11), and p = 0.002. CONCLUSIONS: This is the first study conducted in India which reports a significant association between 24 bp duplication in CHIT1 gene polymorphism and asthma in the studied North Indian population.

Protective role of IL-18 -137G/C polymorphism in a North Indian population with asthma: a pilot study.

BACKGROUND: IL-18, a pleiotropic, pro-inflammatory cytokine that plays a major role in innate as well as acquired immunity, has been implicated in asthma etiology and this is the first study investigating the role of IL-18 -137G/C (rs 187238) promoter polymorphism in asthma pathogenesis in a North Indian population. METHODS: A pilot study was conducted with a total of 824 subjects, out of which 410 were asthma patients including 323 patients suffering from allergic rhinitis and 414 healthy controls from regions of North India. Tetra-Primer Amplification Refractory Mutation System Polymerase Chain Reaction (Tetra-Primer ARMS PCR) was used for genotyping the IL-18 -137G/C polymorphism. RESULTS: While the homozygous wild (GG) genotype was equally prevalent in asthma patients as well as control subjects (70.0%), the homozygous mutant (CC) genotype was more prevalent among the controls (8.0%) than in asthma patients (3.4%), which yielded a significant protection or decreased risk towards asthma. Statistical analysis revealed Odds Ratio (OR)=0.43 (95% CI=0.21-0.85), Chi2 (χ2)=6.93 and p-value=0.008 (p<0.005). Moreover, a few asthma phenotypic traits also revealed significant protective associations with the polymorphism. CONCLUSIONS: The IL-18 -137G/C polymorphism confers a significant protection from asthma in the studied North Indian population. This is the first study to report the protective association of the polymorphism with the disease.

High risk association of IL-1 receptor antagonist (IL-1RN) VNTR polymorphism with asthma in a North Indian population: a pilot study.

BACKGROUND: A pilot case-control study was conducted to evaluate the role of IL-1 receptor antagonist (IL-1RN) VNTR penta-allelic polymorphism in asthma that has been associated with various inflammatory diseases worldwide. This is the first case-control study conducted in India, investigating the role of IL-1RN VNTR polymorphism in asthma pathogenesis. METHODS: A case-control study was performed with a total of 824 adult subjects, inducting 410 asthma patients and 414 healthy controls from North India. The genotypes were identified by polymerase chain reaction. RESULTS: Statistical analysis for the IL-1RN VNTR polymorphism revealed that the IL-1RN(*)2 allele was significantly associated with asthma with OR=1.45, 95% CI (1.15-1.85) and p=0.001. The IL-1RN(*)2/2 genotype posed a risk towards asthma with OR=1.66, 95% CI (0.97-2.86) and p=0.048. Most of the phenotypic traits were significantly associated with the disease. CONCLUSIONS: IL-1RN(*)2 allele is a high risk factor for asthma in the studied North Indian population.

Association of mannose-binding lectin gene polymorphism with tuberculosis susceptibility and sputum conversion time.

Mannose-binding lectin (MBL) plays an important role in innate immunity. The effect of low MBL levels producing variants of MBL2 gene on tuberculosis (TB) has been controversial with some studies reporting it to confer protection against the disease, whereas others estimating a susceptibility relation. Other than conducting a case-control study to evaluate the role of MBL A/B polymorphism on TB, we conducted a longitudinal study to check whether this MBL variant can influence the host response to Mycobacterium tuberculosis infection. A total of 357 TB patients (286 pulmonary TB, 71 extrapulmonary (EP) TB) and 392 healthy controls belonging to same ethnicity were included in the study. We found the mutant allele 'B' allele confers a protective role against TB in our study population. This effect was absent in EP patients. On stratification on the basis of sex, the protective role of the 'B' allele was found to be limited to females only and males reported no significant difference. No effect of MBL A/B polymorphism on sputum conversion time was reported. We conclude that MBL 'B' allele is associated with protection against TB, but no influence was found on sputum conversion rate.

Association of ß(2)-adrenergic receptor polymorphisms with asthma in a North Indian population.

BACKGROUND: ß(2)-Adrenergic receptor (ß(2)AR), a G-protein coupled receptor, is present on the bronchial smooth muscle cells and results in bronchodilation upon activation. The genetic factors determining ß(2)AR expression and function may not only alter the response of an individual to the therapy but also may serve as predictive markers for response to the agonists used in the therapy. The present study aimed at evaluating the role of ß(2)AR-16 and ß(2)AR-27 gene polymorphisms in asthma. METHODS: A case-control study was performed with a total of 824 adult subjects, including 410 asthmatics and 414 healthy controls from regions of North India. The ß(2)AR-16 and ß(2)AR-27 polymorphisms were genotyped by PCR-RFLP. RESULTS: Statistical analysis for the ß(2)AR-16 polymorphism revealed that the mutant Gly16 allele was significantly associated with asthma, with OR = 0.80, 95 % CI = 0.65-0.99, and P = 0.032. The Gly16/Gly16 mutant genotype also confers decreased risk toward asthma, with OR = 0.65, 95 % CI = 0.41-1.02, and P = 0.049. However, the ß(2)AR-27 polymorphism was not associated with asthma as it did not reach statistical significance, with OR = 0.86, 95 % CI = 0.69-1.07, and P = 0.163. CONCLUSION: The ß(2)AR-16 polymorphism confers a decreased risk toward asthma while the ß(2)AR-27 polymorphism is not associated with asthma in the studied North Indian population.

GSTT1 and GSTM1 gene polymorphisms as major risk factors for asthma in a North Indian population.

BACKGROUND: According to the National Family Health Survey, asthma is one of the leading diseases in India. In order to understand the complexity of asthma, the susceptibility genes need to be targeted for their association. Glutathione S-transferases play a major role in the detoxification of metabolites of oxidative stress resulting in inflammation and asthma. In the present study, the hypothesis that GSTT1 and GSTM1 gene polymorphisms are associated with asthma was examined. METHODS: This is the first study to investigate the role of GSTT1 and GSTM1 gene polymorphisms in asthma pathogenesis in a North Indian population. A total of 824 subjects were recruited, of which 410 were asthma patients, including 323 patients suffering from allergic rhinitis. The other 414 recruits were healthy controls from regions of North India. Multiplex PCR was used for genotyping the GSTT1 and GSTM1 gene polymorphisms. RESULTS: The GSTT1 null allele was more prevalent in asthma patients (40 %) than in the control subjects (13.3 %), which yielded a nearly fourfold risk towards asthma with odds ratio (OR) (95 % CI) = 4.35 (3.04-6.24), χ(2) = 75.34, and p = 0.000. The GSTM1 polymorphism also revealed a greater prevalence of the GSTM1 null allele in asthma patients (46.6 %) than in controls (39.4 %). Statistical analysis yielded a marginal risk toward asthma with OR (95 % CI) = 1.34 (1.01-1.79), χ(2) = 4.37, and p = 0.036. CONCLUSIONS: Polymorphisms as a result of deletions in the GSTT1 and GSTM1 genes confer an increased risk towards asthma thereby suggesting the protective role of these functional genes in the development of the disease.

Association of IL13R alpha 1 +1398A/G polymorphism in a North Indian population with asthma: A case-control study.

BACKGROUND: Interleukin 13 (IL13) is directly involved in the secretion of total serum immunoglobulin E (IgE), which plays a major role in the asthma pathogenesis. OBJECTIVE: One of the polymorphic receptor of IL13 is IL13Rα1, which after binding to IL13, initiates signal transduction that results in mucin secretion, airway hyperreactivity, fibrosis, and chitinase up-regulation, which increases asthma risk. METHODS: In the present study, the role of IL13Rα1 +1398A/G gene polymorphisms in asthma was detected with a total of 964 individuals, including 483 healthy controls and 481 asthma patients from a North Indian population using polymerase chain reaction-restriction fragment length polymorphism method. RESULTS: Statistical analysis revealed that the mutant allele (G) is predominant in asthma patients (42.7%) than the controls (38.2%), which shows an increased risk toward asthma with odds ratio = 1.21, 95% confidence interval (1.00-1.45), χ(2) = 4.10 and p = 0.043. Furthermore, the phenotypic characteristics also reveal a significant association with the disease (p < 0.05). CONCLUSIONS: This is the first study conducted in India and +1398A/G polymorphism in noncoding region of IL13Rα1 confer risk toward asthma in the studied population.

Association of NAT2, GST and CYP2E1 polymorphisms and anti-tuberculosis drug-induced hepatotoxicity.

Adherence to the prescribed anti-tuberculosis drug (ATD) treatment is crucial for curing patients with active TB. Anti-tuberculosis drug (ATD) induced hepatotoxicity (ATDH) may contribute to ATD's poor compliance in patients with tuberculosis (TB) as interruption of treatment and the switch to second-line anti-tuberculosis drugs, which is required in patients who do not tolerate standard drugs, may result in a sub-optimal treatment response. Isoniazid (INH) is a part of ATD and involved with ATDH due to toxic metabolites produced on its metabolism in liver, attributed to the variation in enzymes involved in this pathway like N-acetyltransferase 2 (NAT2), cytochrome P4502E1 (CYP2E1) and glutathione S-transferases (GSTs). The present study aimed at analysis of polymorphism at three loci of NAT2, two loci of GST and one locus on CYP2E1 and development of ATDH in patients undergoing ATD therapy. A total of 408 newly diagnosed patients with tuberculosis were enrolled for this study and at the end of sampling, 17 ATDH cases and 391 non-ATDH cases were reported. The genetic polymorphisms of the NAT2 and CYP2E1 genes were studied by PCR-RFLP and GSTM1 and GSTT1 were evaluated by multiplex PCR. Slow phenotype of NAT2 was found to be a risk factor for developing ATDH when compared to fast acetylators. Slow haplotype C481A590G857 and an intermediate acetylator haplotype T481A590G857 were found to be significantly associated with development of ATDH. GSTM1 and GSTT1 double null genotype was also reported to be associated with ATDH development. The heterozygote genotype 'c1c2' of CYP2E1 was also seen to contribute towards elevated risk of ATDH. 'c2' allele absence in females ATDH group can be considered as a protective factor against development of ATDH. In males, presence of 'c1c2' allele was seen to contribute towards elevated risk of ATDH development.

Highly Protective Association of MMP-2-1306C/T Promoter Polymorphism With Asthma in a North Indian Population: A Pilot Study.

PURPOSE: Asthma is the most prevalent disease in India according to the national survey conducted by NFHS 2 in 1998-1999. Matrix metalloproteinase-2 (MMP-2), a collagenase encoded by the MMP-2 gene, degrades the type IV collagen and is responsible for inflammatory responses. This is a pilot study evaluating the role of MMP-2 -1306C/T promoter single nucleotide polymorphism (SNP) in asthma pathogenesis. METHODS: A case-control study was performed with a total of 824 adult subjects, including 410 adult asthmatics and 414 healthy controls from regions of North India. The MMP-2 -1306C/T polymorphism was genotyped by the Tetra-Primer Amplification Refractory Mutation System Polymerase Chain Reaction (Tetra-Primer ARMS PCR). RESULTS: Statistical analysis of the results for the MMP-2 -1306C/T polymorphism revealed an extremely protective role of the mutant T allele in asthma pathogenesis with OR=0.45, 95% CI (0.35-0.58) and P=0.000. The heterozygous CT genotype also conferred protection from asthma with OR=0.37, 95% CI (0.27-0.51) and P=0.000. The homozygous TT genotype was also significantly associated with asthma with OR=0.35, 95% CI (0.16-0.72) and P=0.002. Moreover, the polymorphism was significantly associated with all the phenotypic traits of the disease. CONCLUSION: The MMP-2 -1306C/T promoter polymorphism confers significant protection from asthma in the studied North Indian population.

Association of the wild-type A/A genotype of MBL2 codon 54 with asthma in a North Indian population.

BACKGROUND: High serum MBL level as well as polymorphisms in the mannose-binding lectin 2 (MBL2) gene resulting in MBL deficiency are involved in the mechanism of a number of non-infectious diseases such as asthma, conferring either risk or protection in different population studies. MBL being the first reactant of the MBL pathway is also a major determinant of the fate of the anaphylatoxins such as C3a and C5a, which are also pro-inflammatory mediators. The MBL2 gene polymorphisms thus control the serum levels of MBL as well as C3a and C5a. OBJECTIVE: This is the first case-control study conducted in India, investigating the role of MBL2 codon 54 A/B polymorphism in asthma pathogenesis. METHODS: A case-control study was performed with a total of 992 adult subjects, including 410 adult asthmatics and 582 healthy controls from regions of North India. The MBL2 codon 54 A/B polymorphism was genotyped by PCR-RFLP. RESULTS: Statistical analysis for the codon 54 polymorphism revealed that the wild (A) allele was significantly associated with asthma with OR=1.9, 95% CI (1.4-2.4), and p< 0.001. CONCLUSION: The MBL2 codon 54 A/B polymorphism is significantly associated with asthma and its phenotypic traits as the wild (A/A) genotype confers a significant risk towards the disease in the studied North Indian population.

No association of PTGDR -441C/T polymorphism with asthma in a North Indian population.

BACKGROUND: Asthma is the most prevalent disease in India according to the national survey conducted by NFHS 2 in 1998-399. Prostaglandin D2 (PGD2) is a bronchoconstriction inducing metabolite of arachidonic acid in the mast cells, which is produced on exposure to allergens and acts as a ligand for the Prostaglandin D2 Receptor (PTGDR). Polymorphisms in the PTGDR gene have been suggested to be involved in the mechanism of asthma. OBJECTIVE: This is the first study conducted in India, investigating the role of PTGDR -441C/T} promoter polymorphism in asthma pathogenesis. METHODS: A case-control study was performed with a total of 992 subjects, including 410 adult asthmatics and 582 healthy controls from regions of North India. The PTGDR -441C/T polymorphism was genotyped by Tetra-Primer Amplification Refractory Mutation System Polymerase Chain Reaction (Tetra-Primer ARMS PCR). RESULTS: Statistical analysis of the results between asthma cases and controls for the PTGDR −441C/T polymorphism showed Chi² (χ²) = 0.29, OR = 0.95, 95% CI (0.70-1.15) and p = 0.599. Neither the genotypic nor the allelic frequencies observed for the PTGDR −441C/T polymorphism, were significantly associated with asthma or asthma phenotypes. CONCLUSIONS: The PTGDR -441C/T polymorphism is not associated with asthma or its phenotypes in the studied North Indian population.

Metagenomics: Concept, methodology, ecological inference and recent advances.

Microorganisms constitute two third of the Earth's biological diversity. As many as 99% of the microorganisms present in certain environments cannot be cultured by standard techniques. Culture-independent methods are required to understand the genetic diversity, population structure and ecological roles of the majority of organisms. Metagenomics is the genomic analysis of microorganisms by direct extraction and cloning of DNA from their natural environment. Protocols have been developed to capture unexplored microbial diversity to overcome the existing barriers in estimation of diversity. New screening methods have been designed to select specific functional genes within metagenomic libraries to detect novel biocatalysts as well as bioactive molecules applicable to mankind. To study the complete gene or operon clusters, various vectors including cosmid, fosmid or bacterial artificial chromosomes are being developed. Bioinformatics tools and databases have added much to the study of microbial diversity. This review describes the various methodologies and tools developed to understand the biology of uncultured microbes including bacteria, archaea and viruses through metagenomic analysis.