Dataset Information

Association of single nucleotide polymorphism rs113420705 of CASP3 in children with Kawasaki disease from North India.

ABSTRACT:

Background

Kawasaki disease is a pediatric, systemic, vasculitic disorder. Its exact etiology is still unknown. Genetic polymorphisms are being investigated as susceptibility factor for this disorder. These are likely to vary among different populations.

Aim

To investigate the association of single nucleotide polymorphism (SNP) rs113420705 of CASP3 in Kawasaki disease (KD) from North India.

Settings and design

Observational, case-control study.

Methods

Polymerase chain reaction and bidirectional Sanger sequencing was used for determining genotypes of SNP rs113420705 in 45 cases of KD and 50 healthy age- and sex-matched controls. Allele and genotype frequencies were assessed and compared between the groups.

Results

Among 45 cases, 32 had TT (71.1%), 13 had CT (28.9%) and none had CC genotype of SNP rs113420705. No significant differences in allele, genotype, or carrier frequencies of rs113420705 were found between the two groups. A comparison was also made between subgroups of KD with coronary abnormality (7 children; 15.5%) and KD with normal coronaries (38 children; 84.4%). The C allele was significantly overexpressed in KD with coronary abnormality group (P = 0.005). However, no difference was noted in the genotype frequencies.

Conclusion

CT genotype of rs113420705 of CASP3 showed a trend to significance with the occurrence of KD in children in North India. However, we could not establish any association between minor allele C and susceptibility to KD. C allele appeared to be over expressed in children with KD with coronary abnormalities. Larger studies will help us to reach conclusive evidence applicable to all ethnicities.

SUBMITTER: Das KG

PROVIDER: S-EPMC9731064 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Association of single nucleotide polymorphism rs113420705 of <i>CASP3</i> in children with Kawasaki disease from North India.

Das K Gokul KG Bhattarai Dharmagat D Kaur Anupriya A Kaur Anit A Kumrah Rajni R Srivastava Priyanka P Rawat Amit A Singh Surjit S

Journal of family medicine and primary care 20220901 9

<h4>Background</h4>Kawasaki disease is a pediatric, systemic, vasculitic disorder. Its exact etiology is still unknown. Genetic polymorphisms are being investigated as susceptibility factor for this disorder. These are likely to vary among different populations.<h4>Aim</h4>To investigate the association of single nucleotide polymorphism (SNP) rs113420705 of <i>CASP3</i> in Kawasaki disease (KD) from North India.<h4>Settings and design</h4>Observational, case-control study.<h4>Methods</h4>Polymer ...[more]

PMID: 36505637

Similar Datasets

Project description:The C-C motif chemokine ligand-2 (CCL2) was evidenced to be associated with tuberculosis susceptibility in some ethnic groups. In the present study, effort was made to find out the association of CCL2-2518 A>G and -362 G>C variants with susceptibility to TB in a population from North India. The genotyping was carried out in 373 participants with pulmonary TB (PTB) and 248 healthy controls (HCs) for CCL2-2518 A>G and -362 G>C polymorphisms by PCR-RFLP and by melting curve analysis using fluorescence-labeled hybridization fluorescent resonance energy transfer (FRET) probes, respectively, followed by DNA sequencing in a few representative samples. Genotype and allele frequencies were compared by the chi-squared test and crude and Mantel-Haenszel (M-H) odds ratio (OR). OR was calculated using STATA/MP16.1 software. Further, CCL2, IL-12p70, IFN-γ, TNF-α, and TGF-β levels were measured in serum samples of these participants using commercially available kits. Our analysis indicated that the homozygous mutant in both -2518 GG (OR = 2.07, p = 0.02) and -362 CC (OR = 1.92, p = 0.03) genotypes was associated with susceptibility to pulmonary TB. Further, heterozygous genotypes -2518AG (OR = 0.60, p = 0.003) and -362GC (OR = 0.64, p = 0.013) provide resistance from PTB disease. Haplotype analysis revealed AC haplotype (p = 0.006) to be a risk factor associated with PTB susceptibility. The serum CCL2 level was significantly elevated among participants with -2518 AA genotype compared to -2518 GG genotype. CCL2 level was observed to be positively correlated with IL12p70, IFN-γ and TNF-α, thus suggesting the immunological regulatory role of CCL2 against pulmonary tuberculosis. CCL2-2518 GG and -362 CC genotypes were found to be associated with susceptibility to pulmonary tuberculosis and CCL2-2518AG and CCL2-362GC with resistance from PTB. AC haplotype was found to be a risk factor for PTB in the present study. It may be hypothesized from the findings that -2518G allele could be responsible for lower production of CCL2 which leads to defective Th1 response and makes a host susceptible for pulmonary tuberculosis.

Project description:BackgroundCurrent breeding approaches in potato rely almost entirely on phenotypic evaluations; molecular markers, with the exception of a few linked to disease resistance traits, are not widely used. Large-scale sequence datasets generated primarily through Sanger Expressed Sequence Tag projects are available from a limited number of potato cultivars and access to next generation sequencing technologies permits rapid generation of sequence data for additional cultivars. When coupled with the advent of high throughput genotyping methods, an opportunity now exists for potato breeders to incorporate considerably more genotypic data into their decision-making.ResultsTo identify a large number of Single Nucleotide Polymorphisms (SNPs) in elite potato germplasm, we sequenced normalized cDNA prepared from three commercial potato cultivars: 'Atlantic', 'Premier Russet' and 'Snowden'. For each cultivar, we generated 2 Gb of sequence which was assembled into a representative transcriptome of ~28-29 Mb for each cultivar. Using the Maq SNP filter that filters read depth, density, and quality, 575,340 SNPs were identified within these three cultivars. In parallel, 2,358 SNPs were identified within existing Sanger sequences for three additional cultivars, 'Bintje', 'Kennebec', and 'Shepody'. Using a stringent set of filters in conjunction with the potato reference genome, we identified 69,011 high confidence SNPs from these six cultivars for use in genotyping with the Infinium platform. Ninety-six of these SNPs were used with a BeadXpress assay to assess allelic diversity in a germplasm panel of 248 lines; 82 of the SNPs proved sufficiently informative for subsequent analyses. Within diverse North American germplasm, the chip processing market class was most distinct, clearly separated from all other market classes. The round white and russet market classes both include fresh market and processing cultivars. Nevertheless, the russet and round white market classes are more distant from each other than processing are from fresh market types within these two groups.ConclusionsThe genotype data generated in this study, albeit limited in number, has revealed distinct relationships among the market classes of potato. The SNPs identified in this study will enable high-throughput genotyping of germplasm and populations, which in turn will enable more efficient marker-assisted breeding efforts in potato.