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A Fast Method for DEFB1 - 44C/G SNP Genotyping in Brazilian Patients with Periodontitis.

ABSTRACT: Defensins are cationic antimicrobial peptides expressed in epithelial cells. Such peptides exhibit antibacterial, antifungal and antiviral properties, and are a component of the innate immune response. It has been suggested that they have a protective role in the oral cavity. This study evaluated the DEFB1 polymorphism in diabetic patients with or without periodontitis in comparison to healthy controls.We used Hairpin-Shaped Primer (HP) assay to study the distribution of the -44 C/G SNP (rs1800972) in 119 human DNAs obtained from diabetic patients and healthy control patients.The results indicate that there are no differences in distribution between groups and that in diabetic periodontitis patients the homozygous mutant could be found more frequently.Further studies are necessary in order to investigate the role of DEFB1 polymorphisms in diabetic periodontitis patients and the influence of the peptide in periodontal pathogens.

SUBMITTER: Cimoes R

PROVIDER: S-EPMC4872829 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

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A Fast Method for DEFB1 - 44C/G SNP Genotyping in Brazilian Patients with Periodontitis.

Cimőes Renata R Cavalcanti de Siqueira Rafael Rafael Amorim RR Crovella Sergio S Eleutério de Souza Paulo Roberto PR Donos Nikos N

Acta stomatologica Croatica 20140901 3

<h4>Aim</h4>Defensins are cationic antimicrobial peptides expressed in epithelial cells. Such peptides exhibit antibacterial, antifungal and antiviral properties, and are a component of the innate immune response. It has been suggested that they have a protective role in the oral cavity. This study evaluated the DEFB1 polymorphism in diabetic patients with or without periodontitis in comparison to healthy controls.<h4>Material and methods</h4>We used Hairpin-Shaped Primer (HP) assay to study the ...[more]

PMID: 27688368

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Project description:BackgroundSingle nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays.ResultsCollating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays.ConclusionsOur results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future studies of non-model organisms.

Project description:BackgroundCommon bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availability of the complete sequences of the two common bean genomes has dramatically accelerated and has enabled new experimental strategies to be applied for genetic research. DArTseq has been widely used as a method of SNP genotyping allowing comprehensive genome coverage with genetic applications in common bean breeding programs.ResultsUsing this technology, 6286 SNPs (1 SNP/86.5 Kbp) were genotyped in genic (43.3%) and non-genic regions (56.7%). Genetic subdivision associated to the common bean gene pools (K = 2) and related to grain types (K = 3 and K = 5) were reported. A total of 83% and 91% of all SNPs were polymorphic within the Andean and Mesoamerican gene pools, respectively, and 26% were able to differentiate the gene pools. Genetic diversity analysis revealed an average H E of 0.442 for the whole collection, 0.102 for Andean and 0.168 for Mesoamerican gene pools (F ST = 0.747 between gene pools), 0.440 for the group of cultivars and lines, and 0.448 for the group of landrace accessions (F ST = 0.002 between cultivar/line and landrace groups). The SNP effects were predicted with predominance of impact on non-coding regions (77.8%). SNPs under selection were identified within gene pools comparing landrace and cultivar/line germplasm groups (Andean: 18; Mesoamerican: 69) and between the gene pools (59 SNPs), predominantly on chromosomes 1 and 9. The LD extension estimate corrected for population structure and relatedness (r2SV) was ~ 88 kbp, while for the Andean gene pool was ~ 395 kbp, and for the Mesoamerican was ~ 130 kbp.ConclusionsFor common bean, DArTseq provides an efficient and cost-effective strategy of generating SNPs for large-scale genome-wide studies. The DArTseq resulted in an operational panel of 560 polymorphic SNPs in linkage equilibrium, providing high genome coverage. This SNP set could be used in genotyping platforms with many applications, such as population genetics, phylogeny relation between common bean varieties and support to molecular breeding approaches.

Dataset Information

A Fast Method for DEFB1 - 44C/G SNP Genotyping in Brazilian Patients with Periodontitis.

Publications

A Fast Method for DEFB1 - 44C/G SNP Genotyping in Brazilian Patients with Periodontitis.

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