Publications by authors named "Vincent Sater"
Follicular lymphoma (FL) course is highly variable, making its clinical management challenging. In this incurable and recurring pathology, the interval between relapses tends to decrease while aggressiveness increases, sometimes resulting in the transformation to higher-grade lymphoma. These evolutions are particularly difficult to anticipate, resulting from complex clonal evolutions where multiple subclones compete and thrive due to their capacity to proliferate and resist therapies.
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- The study focuses on the identification of specific gene fusions in salivary gland and sinonasal tumors, enhancing understanding of their molecular pathology and classification.
- A new multiplexed next-generation sequencing (NGS) method was developed to detect oncogenic fusion transcripts involving 116 genes, showing high sensitivity and specificity in analyzing 180 tumor samples.
- The results indicate that this NGS-based method is effective for diagnosing these tumors and can be adapted for future genetic discoveries, potentially improving patient treatment options.
Hyalinizing clear cell carcinoma (HCCC) is a rare salivary gland carcinoma with a generally indolent behavior, characterized by recurrent chromosomal translocation involving EWSR1 (22q12.2) leading to two fusion genes EWSR1::ATF1 or EWSR1::CREM. We report one case of HCCC with a novel SMARCA2::CREM fusion, identified by targeted RNA next generation sequencing by LD-RT-PCR, which has until now never been described in salivary glands.
View Article and Find Full Text PDFThe rapid transition from traditional sequencing methods to Next-Generation Sequencing (NGS) has allowed for a faster and more accurate detection of somatic variants (Single-Nucleotide Variant (SNV) and Copy Number Variation (CNV)) in tumor cells. NGS technologies require a succession of steps during which false variants can be silently added at low frequencies. Filtering these artifacts can be a rather difficult task especially when the experiments are designed to look for very low frequency variants.
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- A new molecular diagnostic assay has been developed for detecting gene fusions in sarcomas, leveraging a method called ligation dependent reverse-transcriptase polymerase chain reaction (LD-RT-PCR-NGS) that identifies oncogenic fusion transcripts from 137 genes.
- * The assay was tested on 158 bone and soft-tissue tumors, showing it can accurately detect in-frame fusion transcripts with a 98.1% success rate, aligning well with conventional methods like FISH and RT-PCR.
- * This assay offers a rapid and sensitive solution for diagnosing sarcomas, helping to pinpoint tumors with targetable gene fusions for better clinical management.
Article Synopsis
- The study examines the complex genetic factors behind peripheral T-cell lymphoma (PTCL) and introduces a new multiplex ligation-dependent RT-PCR assay for detecting 33 associated fusion transcripts simultaneously, which is crucial since current detection methods are costly and slow.
- The assay successfully identified anaplastic lymphoma kinase (ALK) fusions in most ALK-positive cases, and also revealed several non-ALK fusion transcripts mainly derived from follicular helper T-cells in various PTCL samples.
- The method's effectiveness was confirmed using traditional RT-PCR and Sanger sequencing, highlighting its potential as a reliable tool for analyzing these diverse lymphomas in clinical settings.
Article Synopsis
- Copy number variations (CNV) are crucial genetic alterations linked to cancer, affecting oncogenes and tumor suppressors; new sequencing techniques using unique molecular identifiers (UMI) enhance CNV detection.
- The study introduces a novel method called molecular Copy Number Alteration (mCNA), which employs UMI and a four-step algorithm to accurately identify copy number changes in cancer samples.
- mCNA has shown strong correlation with existing genomic methods and is made publicly available, promising improved accuracy in detecting CNV changes in cancer research.
Motivation: With Next Generation Sequencing becoming more affordable every year, NGS technologies asserted themselves as the fastest and most reliable way to detect Single Nucleotide Variants (SNV) and Copy Number Variations (CNV) in cancer patients. These technologies can be used to sequence DNA at very high depths thus allowing to detect abnormalities in tumor cells with very low frequencies. Multiple variant callers are publicly available and are usually efficient at calling out variants.
View Article and Find Full Text PDFNon-Hodgkin B-cell lymphomas (B-NHLs) are a highly heterogeneous group of mature B-cell malignancies. Their classification thus requires skillful evaluation by expert hematopathologists, but the risk of error remains higher in these tumors than in many other areas of pathology. To facilitate diagnosis, we have thus developed a gene expression assay able to discriminate the seven most frequent B-cell NHL categories.
View Article and Find Full Text PDFMotivation: Next-generation sequencing has become the go-to standard method for the detection of single-nucleotide variants in tumor cells. The use of such technologies requires a PCR amplification step and a sequencing step, steps in which artifacts are introduced at very low frequencies. These artifacts are often confused with true low-frequency variants that can be found in tumor cells and cell-free DNA.
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