278 results for "study_type:"exome sequencing" AND repository:ega"

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• VariantMedium: Sensitive and generalizable somatic point mutation calling with 3D DenseNets trained and evaluated on experimental confirmation data

  This study contains whole-exome sequencing (WES) and results of targeted deep-sequencing data of three matched tumor and normal cell lines, with two technical WES replicates each. The calls by Mutect2, Strelka2, and VariantMedium were confirmed using targeted deep sequencing on Illumina Miseq The targeted deep sequencing was performed in three runs and the results are summarized under VCF files.

  Study EGAS50000001661

• Genomic Data from Patients with Advanced Rare Cancers Treated with Pembrolizumab

  Rare cancers lack effective evidence-based treatments despite contributing substantially to cancer-related mortality. The goal of this study is to identify molecular biomarkers associated with response to pembrolizumab in patients with advanced rare cancers.This dataset includes genomic profiling generated from patients enrolled in an investigator-initiated phase II basket trial of pembrolizumab.

  Study EGAS50000001508

• Germline variants in patients with five cutaneous melanoma

  Skin melanoma arises from a complex interplay between UV radiation exposure and inherited genetic susceptibility. A subset of invidiuals experience multiple independent tumours, suggestingh a stronger underlying genetic component. In this study, we investigate the germline contribution to melanoma development in individuals diagnosed with five or more primary melanomas.

  Study EGAS50000001361

• Personalized ctDNA detection and genomic profiling in the NeoRHEA Study

  In the management of early hormone receptor (HR)+, HER2-negative breast cancer, circulating tumor DNA (ctDNA) detection is an evolving yet promising diagnostic approach. We evaluated ctDNA detection using the personalized RaDaR assay in plasma samples from patients enrolled in the NeoRHEA clinical trial (NCT03065621), a single-arm, phase II study of neoadjuvant palbociclib and endocrine therapy administered over 4 months (four 28‑day cycles). Plasma samples were collected pre-treatment, after the first treatment cycle, prior to surgery, and one month post-surgery. At baseline, ctDNA positivity was detected in 55% of patients; however, this dropped to 5% during treatment and ctDNA became undetectable in all patients by one month post-surgery. CtDNA detection at baseline was higher in histological grade 3 tumors, lower in multifocal/multicentric tumors and higher in residual cancer burden (RCB) 3 tumors. Genomic analysis revealed MYC gene gains or amplifications were more frequent in ultrasound (US) responders, while PIK3CA gains were more common in US non-responders. Additionally, FAT1 losses were more frequently observed in patients with RCB 3. Our findings suggest that baseline ctDNA presence predicts poor response to neoadjuvant palbociclib and endocrine therapy, underscoring its potential as a biomarker to guide tailored therapeutic approaches in HR+/HER2-negative breast cancer.

  Study EGAS50000001702

• Whole-exome sequencing data from a phase 2 trial of dasatinib for patients with relapsed or refractory nodal T follicular helper cell lymphomas

  Whole-exome sequencing (WES) analysis data from tumor tissues of 14 patients with T follicular helper cell lymphomas enrolled in a phase 2 trial of dasatinib for relapsed or refractory nodal disease.

  Study EGAS50000001239

• Germline WES of serrated polyposis syndrome

  The serrated polyposis syndrome (SPS) is a disease with a mainly unknown inherited genetic basis characterized by the presence of multiple and/or large serrated polyps in the colon and a higher associated risk for colorectal cancer (CRC). The objective of the present study was to identify new SPS/CRC germline predisposition genes by using whole-exome sequencing in two affected SPS patients from the same family.

  Study EGAS50000000765

• TRACERx NSCLC - Whole exome multiregion sequencing data

  Study EGAS00001006494

• Mechanisms of resistance to pembrolizumab treatment in classical Hodgkin Lymphoma

  In this project we are applying whole exome sequencing (WES) on plasma-derived ctDNA samples to identify mutations that drive resistance to pembrolizumab treatment in classical Hodgkin Lymphoma

  Study EGAS50000001985

• Familial Melanoma Sequencing

  In this experiment we have sequenced the exome of 15 individuals from eight families who have familial melanoma. By sequencing the exome we hope to be able to identify new genes that are associated with this disease.

  Study EGAS00001000017

• Spatial atlas of diffuse large B-cell lymphoma

  We leveraged highly multiplexed, single-cell–resolution spatial transcriptomics, bulk RNA sequencing, and tumor–germline paired whole-exome sequencing to profile 465 diffuse large B-cell lymphoma (DLBCL) tumors and define the assembly of 60 lymphoma microenvironment (LME) cell subsets and 5 tumor B cell states into conserved spatial niches and communities that resemble non-malignant lymphoid architecture. Three distinct LME-enriched communities were assembled from combinations of niches and reflected recently described LME archetypes with conserved spatial biology. Tumor B cells were enriched in three B communities harboring distinct, developmentally linked, transcriptional states associated with divergent cell-cell communication (CCC) pathways. Intratumoral heterogeneity in B communities was pervasive across patients and largely unlinked with molecular subtype. Combinations of B communities, rather than single states, were associated with patient outcome, implicating microenvironment-associated tumor B cell transcriptional plasticity in the biology and clinical behavior of DLBCL.

  Study EGAS50000002036