Identification of a Locus on the X Chromosome Linked to Familial Membranous Nephropathy

Puntuació de risc genètic; Glomerulonefritis; Nefropatia membranosaPuntuación de riesgo genético; Glomerulonefritis; Nefropatía membranosaGenetic risk score; Glomerulonephritis; Membranous nephropathyIntroduction Membranous nephropathy (MN) is the most common cause of nephrotic syndrome (NS) in adults and is a leading cause of end-stage renal disease due to glomerulonephritis. Primary MN has a strong male predominance, accounting for approximately 65% of cases; yet, currently associated genetic loci are all located on autosomes. Previous reports of familial MN have suggested the existence of a potential X-linked susceptibility locus. Identification of such risk locus may provide clues to the etiology of MN. Methods We identified 3 families with 8 members affected by primary MN. Genotyping was performed using single-nucleotide polymorphism microarrays, and serum was sent for anti-phospholipase A2 receptor (PLA2R) antibody testing. All affected members were male and connected through the maternal line, consistent with X-linked inheritance. Genome-wide multipoint parametric linkage analysis using a model of X-linked recessive inheritance was conducted, and genetic risk scores (GRSs) based on known MN-associated variants were determined. Results Anti-PLA2R testing was negative in all affected family members. Linkage analysis revealed a significant logarithm of the odds score (3.260) on the short arm of the X chromosome at a locus of approximately 11 megabases (Mb). Haplotype reconstruction further uncovered a shared haplotype spanning 2 Mb present in all affected individuals from the 3 families. GRSs in familial MN were significantly lower than in anti-PLA2R–associated MN and were not different from controls. Conclusions Our study identifies linkage of familial membranous nephropathy to chromosome Xp11.3-11.22. Family members affected with MN have a significantly lower GRS than individuals with anti-PLA2R–associated MN, suggesting that X-linked familial MN represents a separate etiologic entity

Noncoding deletions reveal a gene that is critical for intestinal function.

Large-scale genome sequencing is poised to provide a substantial increase in the rate of discovery of disease-associated mutations, but the functional interpretation of such mutations remains challenging. Here we show that deletions of a sequence on human chromosome 16 that we term the intestine-critical region (ICR) cause intractable congenital diarrhoea in infants1,2. Reporter assays in transgenic mice show that the ICR contains a regulatory sequence that activates transcription during the development of the gastrointestinal system. Targeted deletion of the ICR in mice caused symptoms that recapitulated the human condition. Transcriptome analysis revealed that an unannotated open reading frame (Percc1) flanks the regulatory sequence, and the expression of this gene was lost in the developing gut of mice that lacked the ICR. Percc1-knockout mice displayed phenotypes similar to those observed upon ICR deletion in mice and patients, whereas an ICR-driven Percc1 transgene was sufficient to rescue the phenotypes found in mice that lacked the ICR. Together, our results identify a gene that is critical for intestinal function and underscore the need for targeted in vivo studies to interpret the growing number of clinical genetic findings that do not affect known protein-coding genes

STAG3 truncating variant as the cause of primary ovarian insufficiency

Primary ovarian insufficiency (POI) is a distressing cause of infertility in young women. POI is heterogeneous with only a few causative genes having been discovered so far. Our objective was to determine the genetic cause of POI in a consanguineous Lebanese family with two affected sisters presenting with primary amenorrhoea and an absence of any pubertal development. Multipoint parametric linkage analysis was performed. Whole-exome sequencing was done on the proband. Linkage analysis identified a locus on chromosome 7 where exome sequencing successfully identified a homozygous two base pair duplication (c.1947_48dupCT), leading to a truncated protein p.(Y650Sfs*22) in the STAG3 gene, confirming it as the cause of POI in this family. Exome sequencing combined with linkage analyses offers a powerful tool to efficiently find novel genetic causes of rare, heterogeneous disorders, even in small single families. This is only the second report of a STAG3 variant; the first STAG3 variant was recently described in a phenotypically similar family with extreme POI. Identification of an additional family highlights the importance of STAG3 in POI pathogenesis and suggests it should be evaluated in families affected with POI

OVAS: an open-source variant analysis suite with inheritance modelling

Abstract Background The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functionally important variants has now shifted towards identifying the critical differences between normal variants and disease-causing ones. The ever-increasing reliance on cloud-based services for sequence analysis and the non-transparent methods they utilize has prompted the need for more in-situ services that can provide a safer and more accessible environment to process patient data, especially in circumstances where continuous internet usage is limited. Results To address these issues, we herein propose our standalone Open-source Variant Analysis Sequencing (OVAS) pipeline; consisting of three key stages of processing that pertain to the separate modes of annotation, filtering, and interpretation. Core annotation performs variant-mapping to gene-isoforms at the exon/intron level, append functional data pertaining the type of variant mutation, and determine hetero/homozygosity. An extensive inheritance-modelling module in conjunction with 11 other filtering components can be used in sequence ranging from single quality control to multi-file penetrance model specifics such as X-linked recessive or mosaicism. Depending on the type of interpretation required, additional annotation is performed to identify organ specificity through gene expression and protein domains. In the course of this paper we analysed an autosomal recessive case study. OVAS made effective use of the filtering modules to recapitulate the results of the study by identifying the prescribed compound-heterozygous disease pattern from exome-capture sequence input samples. Conclusion OVAS is an offline open-source modular-driven analysis environment designed to annotate and extract useful variants from Variant Call Format (VCF) files, and process them under an inheritance context through a top-down filtering schema of swappable modules, run entirely off a live bootable medium and accessed locally through a web-browser

Additional file 1 of OVAS: an open-source variant analysis suite with inheritance modelling

Supplementary Data. (DOCX 104 kb

Qualitative and quantitative phytochemicals of essential oils and extracts of Thymbra spicata subsp. spicata L. as a spice for diabetes mellitus

The aim of this paper was to evaluate the antidiabetic and antioxidant activities of methanolic extracts, n-hexane, dichloromethane, ethyl acetate, butanol, aqueous subextracts and essential oils of flowers, roots, leaves and aerial parts of Thymbra spicata subsp. spicata, which has been utilized in the public medicine systems of Turkey, Greece, Egypt and Rome for the treatment of asthma and bronchitis, as well as for flavour and aroma in the food industry and protection. Quantitative determination of secondary metabolites in the most effective samples of the plant was also analysed by LC–MS/MS. Moreover, the chemical composition of essential oils of different parts of the plant was analysed via GC-FID and GC/MS. The main constituents in the flower, leaf and aerial part were found to be carvacrol (75.6%), γ-terpinene (10.5%), carvacrol (73.3%), γ-terpinene (9.5%), p-cymene (8.6%), carvacrol (76.1.8%) and p-cymene (7.3%), respectively. Quinic acid, caffeic acid, vanillic acid, naringin, hesperidin and rosmarinic acid were measured in four ethyl acetate subextracts, and rosmarinic acid was found to have the highest amount in the flower subextract with a value of 48095.1083 ng/mL. The ethyl acetate extract of flowers showed the best activity with a 326 ± 12 μg/mL IC50 value, while the standard acarbose IC50 value was 4143 ± 243 μg/mL. It was determined that the leaf ethyl acetate extract, in particular, had a very high % inhibition value on ABTS·+ (99.137 ± 0.011% inhibition) and DPPH• (41.068 ± 0.031% inhibition). It is thought that the plant, which has been used as a spice in the kitchen for centuries by the public, can be safely used due to its high antidiabetic and antioxidant effects