Project description:Classical-like Ehlers–Danlos syndrome (clEDS) is an autosomal recessive disorder caused by complete absence of tenascin-X resulting from biallelic variation in TNXB. Accurate detection of TNXB variants is challenging because of the presence of the pseudogene TNXA, which can undergo non-allelic homologous recombination. Therefore, we designed a genetic screening system that is performed using similar operations to other next-generation sequencing (NGS) panel analyses and can be applied to accurately detect TNXB variants and the recombination of TNXA-derived sequences into TNXB. We also analyzed the levels of serum form of TNX (sTNX) by Western bot and LC/MS/MS. Using this system, we identified biallelic TNXB variants in nine unrelated clEDS patients. This report is the first to apply an NGS-based screening for TNXB variants and represents the third largest cohort of clEDS.
Project description:The purpose of this study is to determine the proportion of patients diagnosed with Lynch syndrome in colorectal cancer patients with the loss of staining by immunohistochemistry (IHC) of any of the mismatch repair (MMR) proteins. Besides, this study aims to test the specificity and the sensitivity of detecting microsatellite instability (MSI) by next-generation sequencing, and to find out the consistency between IHC and MSI in colorectal cancer patients in China. In addition, researchers want to analyze the clinical characteristics and germline mutation of Lynch syndrome in Chinese population.
Project description:The method to analyze the microsatellite instability (MSI) status by next-generation sequencing (NGS) has been established to assess the deficiency of DNA mismatch repair (MMR) system. The aim of our study is to evaluate the feasibility and reliability of this NGS method by testing the circulating tumor DNA (ctDNA) in blood sample of advanced colorectal cancer patients. If the result is positive, the MSI status could be easily learned without the acquisition of tissue samples.
Project description:NGPS is a method for de-novo, full-length protein sequencing in high throughput. The method is based on cleavage of the protein at semi-random sites by microwave-assisted acid hydrolysis (MAAH), enrichment of LC-MS/MS amenable peptides from the hydrolysate by solid-phase-extraction, LC-MS/MS analysis, de-novo long peptide tag sequencing of resulting peptides and assembly of peptide tags into consensus contigs.
Project description:Despite relevant clinical and/or familial presentations suggesting a hereditary predisposition (early-onset, multiple primary tumors, familial aggregation), targeted genomic analysis based on the phenotype are often non contributive. As somatic cancer genes are limited, the hypothesis is that the targeted next-generation sequencing of 200 genes, selected for their implications in cancers may contribute to the understanding of many selected patients’ presentation by the identification of germline deleterious mutations, and may identified phenotype overlapping and/or mosaicisms. The focus will be put on early-onset breast, ovarian, colorectal cancer or pediatric cancers and multiple primary tumors.
Project description:We analyze the contribution of alternative splicing to the transcriptional complexity in adipose tissue and the development of diet-induced obesity. We use Next generation sequencing analysis of mice fed with a control chow diet or a high fat diet.
Project description:Development of an alternative method to ChIP for the identification of DNA bound by transcriptional complexes assayed using next-generation sequencing Next-generation sequencing data from sites identified by different Notch complexes using SpDamID-seq and compared against FAIRE and ChIP data
Project description:Next generation sequencing in a rat model of diabetic nephropathy was employed to study in depth the pathogenic alterations involved in progressive diabetic kidney damage. We employed the obese, diabetic ZS rat, a model that develops renal failure and fibrosis, the hallmarks of human disease. We then used RNA-seq to examine in a comprehensive manner the combined effects of renal cells and infiltrating inflammatory cells acting as a pathophysiological unit. 12 samples (4 independent samples for each of 3 groups, 1 control group)
Project description:We analyze the contribution of alternative splicing to the transcriptional complexity in adipose tissue and the development of diet-induced obesity. We use Next generation sequencing analysis of eWAT from control and Nova1 and Nova2-deficient mice fed with a control diet
Project description:We analyze the contribution of alternative splicing to the transcriptional complexity in adipose tissue and the development of diet-induced obesity. We use Next generation sequencing analysis of eWAT from control and Nova1 and Nova2-deficient mice fed with a high fat diet.