Dataset Information

Nonrandom Distribution of miRNAs Genes and Single Nucleotide Variants in Keratoconus Loci.

ABSTRACT: Despite numerous studies, the causes of both development and progression of keratoconus remain elusive. Previous studies of this disorder focused mainly on one or two genetic factors only. However, in the analysis of such complex diseases all potential factors should be taken into consideration. The purpose of this study was a comprehensive analysis of known keratoconus loci to uncover genetic factors involved in this disease causation in the general population, which could be omitted in the original studies. In this investigation genomic data available in various databases and experimental own data were assessed. The lists of single nucleotide variants and miRNA genes localized in reported keratoconus loci were obtained from Ensembl and miRBase, respectively. The potential impact of nonsynonymous amino acid substitutions on protein structure and function was assessed with PolyPhen-2 and SIFT. For selected protein genes the ranking was made to choose those most promising for keratoconus development. Ranking results were based on topological features in the protein-protein interaction network. High specificity for the populations in which the causative sequence variants have been identified was found. In addition, the possibility of links between previously analyzed keratoconus loci was confirmed including miRNA-gene interactions. Identified number of genes associated with oxidative stress and inflammatory agents corroborated the hypothesis of their effect on the disease etiology. Distribution of the numerous sequences variants within both exons and mature miRNA which forces you to search for a broader look at the determinants of keratoconus. Our findings highlight the complexity of the keratoconus genetics.

SUBMITTER: Nowak DM

PROVIDER: S-EPMC4503774 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Nonrandom Distribution of miRNAs Genes and Single Nucleotide Variants in Keratoconus Loci.

Nowak Dorota M DM Gajecka Marzena M

PloS one 20150715 7

Despite numerous studies, the causes of both development and progression of keratoconus remain elusive. Previous studies of this disorder focused mainly on one or two genetic factors only. However, in the analysis of such complex diseases all potential factors should be taken into consideration. The purpose of this study was a comprehensive analysis of known keratoconus loci to uncover genetic factors involved in this disease causation in the general population, which could be omitted in the ori ...[more]

PMID: 26176855

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Project description:Although LGALS3 has been widely studied, the genotypes of the LGALS3 single nucleotide polymorphism (SNP) loci in skull base chordoma (SBC) have been not well defined. The aim of the current study was to analyze two LGALS3 SNP genotypes in patients with SBC. A total of 48 patients with SBC who underwent surgical treatment in Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University (Beijing, China) and 66 healthy participants were included in the present study. A total of two SNPs (LGALS3+191 C>A and LGALS3 +292 A>C) were selected for sequencing analysis of amplified target fragments from DNA that was extracted from blood samples. The clinical features of the patients were recorded, follow-up was conducted and statistical analysis was performed with SPSS 20.0. There were no differences in age and sex between the patients and control group. In addition, there were no significant differences in the distribution of genotypes (P=0.662) and allelic frequencies (P=0.638) at LGALS3+191 C>A between the two groups. However, significant difference was observed in the allelic distributions at LGALS3 +292 A>C between them (P=0.016), and allele A was associated with the occurrence of SBC. The distribution of the genotypes at LGALS3 +292 A>C was not significantly different in the additive model (CC vs. AC vs. AA, P=0.083) but was significantly different in the dominant model (CC+AC vs. AA, P=0.043). In the Kaplan-Meier analysis, there were no significant differences in the overall survival and progression analysis between different genotypes at LGALS3 +191 C>A (P=0.168 and P=0.120) in patients with SBC. There was no significant difference in overall survival was observed between the genotypes at +292 A>C (P=0.595). However, the progression-free survival (PFS) time of the CC+AC genotype group was longer compared with the AA genotype group (P<0.001). In the univariate and multivariate analysis of tumor progression, PFS was shorter in the AA genotype group compared with the CC+AC genotype group (P<0.001). The allele A and AA genotype at LGALS3 +292 A>C were observed to be associated with a higher risk of SBC, and the AA genotype at +292 A>C was associated with a shorter PFS time.

Project description:BACKGROUND:Although mosaic variation has been known to cause disease for decades, high-throughput sequencing technologies with the analytical sensitivity to consistently detect variants at reduced allelic fractions have only recently emerged as routine clinical diagnostic tests. To date, few systematic analyses of mosaic variants detected by diagnostic exome sequencing for diverse clinical indications have been performed. METHODS:To investigate the frequency, type, allelic fraction, and phenotypic consequences of clinically relevant somatic mosaic single nucleotide variants (SNVs) and characteristics of the corresponding genes, we retrospectively queried reported mosaic variants from a cohort of ~?12,000 samples submitted for clinical exome sequencing (ES) at Baylor Genetics. RESULTS:We found 120 mosaic variants involving 107 genes, including 80 mosaic SNVs in proband samples and 40 in parental/grandparental samples. Average mosaic alternate allele fraction (AAF) detected in autosomes and in X-linked disease genes in females was 18.2% compared with 34.8% in X-linked disease genes in males. Of these mosaic variants, 74 variants (61.7%) were classified as pathogenic or likely pathogenic and 46 (38.3%) as variants of uncertain significance. Mosaic variants occurred in disease genes associated with autosomal dominant (AD) or AD/autosomal recessive (AR) (67/120, 55.8%), X-linked (33/120, 27.5%), AD/somatic (10/120, 8.3%), and AR (8/120, 6.7%) inheritance. Of note, 1.7% (2/120) of variants were found in genes in which only somatic events have been described. Nine genes had recurrent mosaic events in unrelated individuals which accounted for 18.3% (22/120) of all detected mosaic variants in this study. The proband group was enriched for mosaicism affecting Ras signaling pathway genes. CONCLUSIONS:In sum, an estimated 1.5% of all molecular diagnoses made in this cohort could be attributed to a mosaic variant detected in the proband, while parental mosaicism was identified in 0.3% of families analyzed. As ES design favors breadth over depth of coverage, this estimate of the prevalence of mosaic variants likely represents an underestimate of the total number of clinically relevant mosaic variants in our cohort.

Dataset Information

Nonrandom Distribution of miRNAs Genes and Single Nucleotide Variants in Keratoconus Loci.

Publications

Nonrandom Distribution of miRNAs Genes and Single Nucleotide Variants in Keratoconus Loci.

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