New Dombrock variant
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ABSTRACT:
PROVIDER: PRJEB28375 | ENA |
REPOSITORIES: ENA
Similar Datasets
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Project description:Alpha 1-Antitrypsin Deficiency (AATD) is a rare genetic disorder caused by mutations in the SERPINA1 gene, which encodes the Alpha 1-Antitrypsin (AAT) protein. Individuals carrying pathogenic SERPINA1 variants are predisposed to lung and liver damage. The most common AATD-associated SERPINA1 alleles are the S and Z alleles, though additional variants have been identified. This case report describes the discovery of a new SERPINA1 variant detected in two cities in southeastern France. This variant, named PiZmarseille, results from in cis combination of the PiZ allele and a rare variant known as PiZbristol. PiZmarseille has been associated with early-onset liver disease in childhood. To further investigate this new variant, we performed its molecular characterization, revealing that PiZmarseille shares the pathogenic properties of both the PiZ and PiZbristol variants. These properties include its retention in the endoplasmic reticulum as aggregates and its degradation through the autophagy and proteasome pathways. Additionally, we conducted proteomic profiling to explore the association of this mutant with liver disease. Our analysis revealed that the neutrophil degranulation pathway is particularly deregulated in PiZmarseille liver samples. Furthermore, when compared to other AAT genotypes, the proteomic profile of PiZmarseille most closely resembles that of the PiZ variant, rather than other SERPINA1 variants.
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Project description:Most psoriasis-related genes or loci identified through genome-wide association studies (GWASs) represent common clusters and are located in non-coding regions of the human genome, providing only limited evidence for the role of coding variants in psoriasis. Two exome-wide case-control genotyping data sets were obtained from our previous study. Quality control was established for each data set, and the remaining markers in each were annotated using ANNOVAR. Gene-based analysis was performed on the annotation results. A total of 250 and 35 genes in the Exome_Fine and Exome_Asian Array cohorts, respectively, exceeded the threshold (P < 4.43 × 10-6). Merged gene-based analysis was then conducted on the same set of SNPs from seven genes common to both arrays, and the chi-square test was used to confirm all gene-based results. Ultimately, four new susceptibility genes were identified: BBS7 (Pcombine = 1.38 × 10−29), GSTCD (Pcombine = 8.35 × 10−47), LIPK (Pcombine = 1.02 × 10−19) and PPP4R3B (Pcombine = 1.79 × 10−33). This study identified four new susceptibility genes for psoriasis through a gene-based method using rare variants, contributing to our understanding of the pathogenesis of psoriasis.
2019-05-25 | GSE131670 | GEO
Project description:Most psoriasis-related genes or loci identified through genome-wide association studies (GWASs) represent common clusters and are located in non-coding regions of the human genome, providing only limited evidence for the role of coding variants in psoriasis. Two exome-wide case-control genotyping data sets were obtained from our previous study. Quality control was established for each data set, and the remaining markers in each were annotated using ANNOVAR. Gene-based analysis was performed on the annotation results. A total of 250 and 35 genes in the Exome_Fine and Exome_Asian Array cohorts, respectively, exceeded the threshold (P < 4.43 × 10-6). Merged gene-based analysis was then conducted on the same set of SNPs from seven genes common to both arrays, and the chi-square test was used to confirm all gene-based results. Ultimately, four new susceptibility genes were identified: BBS7 (Pcombine = 1.38 × 10−29), GSTCD (Pcombine = 8.35 × 10−47), LIPK (Pcombine = 1.02 × 10−19) and PPP4R3B (Pcombine = 1.79 × 10−33). This study identified four new susceptibility genes for psoriasis through a gene-based method using rare variants, contributing to our understanding of the pathogenesis of psoriasis.
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Project description:The discovery of copy number variation in healthy individuals is far from complete, and due to the resolution of detection systems used, the majority of loci reported so far are relatively large (~65% > 10kb). Applying a two-stage high-resolution array CGH approach to analyse 50 healthy Caucasian males from northern France, we discovered 2208 copy number variants (CNVs) detected by more than one consecutive probe. These clustered into 1469 copy number variant regions (CNVRs), of which 721 are thought to be novel. The majority of these are small (median size 4.4kb) and most have common boundaries, with a coefficient of variation less than 0.1 for 83% of end-points in those observed in multiple samples. Only 6% of the CNVRs analysed showed evidence of both copy number losses and gains at the same site. A further 6089 variants were detected by single probes: 48% of these were observed in more than one individual. In total, 2570 genes were seen to intersect variants: 1284 in novel loci. Genes involved in differentiation and development were significantly overrepresented, and approximately half the genes identified feature in the OMIM database. The biological importance of many of the genes affected, along with the well-conserved nature of the majority of the copy number variants, suggests they could have important implications for phenotype and, thus, be useful for association studies of complex diseases. Keywords: comparative genomic hybridization
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Project description:New variant of Salmonella Genomic Island 1 in S. Kentucky
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