Project description:Most proteogenomic approaches for mapping single amino acid polymorphisms (SAPs) require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. We present a new strategy for direct SAP detection without relying on NGS data. Among the 348 putative SAP peptides identified in an industrial yeast strain, 85.6% of SAP sites were validated by genomic sequencing.
Project description:In this study, we performed a comparative analysis of gut microbiota composition and gut microbiome-derived bacterial extracellular vesicles (bEVs) isolated from patients with solid tumours and healthy controls. After isolating bEVs from the faeces of solid tumour patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of faeces from patientsand controls using 16S rRNA sequencing. Machine learning was used to classify the samples into patients and controls based on their bEVs and faecal microbiomes.
Project description:The objective of this study is to optimize the search by next-generation sequencing (NGS) mutations in the KRAS, BRAF and NRAS on circulating tumor DNA and compare the genetic profiles obtained with those from tumors embedded in paraffin
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:We have performed ChIP-sequencing analysis on human FOXN2 and RFX1 target sequences in human embryonic kidney HEK293T cells stably expressing Streptavidin-S-FLAG (SFB) triple-tagged proteins. The NGS sequencing were performed on Illumina MiSeq desktop sequencer.
Project description:We report a detailed characterization of the HPV16 genome in two brain metastases from OPSCC tumors. The use of a target enrichment strategy followed by next generation sequencing (NGS) provided an effective way to identify viral infection in tumor genome, including internal deletions and insertion sites into the host genome. Applying similar strategies to a larger cohort of HPV+ HNSCC brain metastases could help to identify biomarkers that can predict metastasis and/or identify novel therapeutic options.
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:Because gastric cancer cells already had genetic and epigenetic alterations which can affect the gastric carcinogenesis, we tried to characterize genetic and epigenetic changes during gastric carcinogenesis. To do this, we performed MBD sequencing and RRBS sequencing. MBD and RRBS sequencing of gastric mucosa, intestinal metaplasia, and gastric cancer cells from one patient were generated by NGS using Illumina GAII.
Project description:Because gastric cancer cells already had genetic and epigenetic alterations which can affect the gastric carcinogenesis, we tried to characterize genetic and epigenetic changes during gastric carcinogenesis. To do this, we performed MBD sequencing and RRBS sequencing. MBD and RRBS sequencing of gastric mucosa, intestinal metaplasia, and gastric cancer cells from one patient were generated by NGS using Illumina GAII.