Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ena-DATASET-BCI-18-03-2015-12:48:54:303-380 - samples

ABSTRACT: Whole exome sequencing data of 5 patients diagnosed with FL that had undergone several relapse episodes without evidence of transformation

PROVIDER: EGAD00001001301 | EGA |

REPOSITORIES: EGA

ACCESS DATA

Json Xml

Publications

Recurrent mTORC1-activating RRAGC mutations in follicular lymphoma.

Okosun Jessica J Wolfson Rachel L RL Wang Jun J Araf Shamzah S Wilkins Lucy L Castellano Brian M BM Escudero-Ibarz Leire L Al Seraihi Ahad Fahad AF Richter Julia J Bernhart Stephan H SH Efeyan Alejo A Iqbal Sameena S Matthews Janet J Clear Andrew A Guerra-Assunção José Afonso JA Bödör Csaba C Quentmeier Hilmar H Mansbridge Christopher C Johnson Peter P Davies Andrew A Strefford Jonathan C JC Packham Graham G Barrans Sharon S Jack Andrew A Du Ming-Qing MQ Calaminici Maria M Lister T Andrew TA Auer Rebecca R Montoto Silvia S Gribben John G JG Siebert Reiner R Chelala Claude C Zoncu Roberto R Sabatini David M DM Fitzgibbon Jude J

Nature genetics 20151221 2

Follicular lymphoma is an incurable B cell malignancy characterized by the t(14;18) translocation and mutations affecting the epigenome. Although frequent gene mutations in key signaling pathways, including JAK-STAT, NOTCH and NF-κB, have also been defined, the spectrum of these mutations typically overlaps with that in the closely related diffuse large B cell lymphoma (DLBCL). Using a combination of discovery exome and extended targeted sequencing, we identified recurrent somatic mutations in R ...[more]

PMID: 26691987

Similar Datasets

ena-DATASET-BCI-07-08-2017-15:27:08:247-1498 - samples

Project description:Follicular lymphoma (FL) is an incurable B cell malignancy characterized by advanced stage disease and a heterogeneous clinical course. Recent genomic studies have focused on profiling Ã¢Â€ÂœsingleÃ¢Â€Â FL biopsies over several time-points, however, multi-site sampling in solid cancers has demonstrated profound spatial intra-tumor heterogeneity (ITH) with implications for precision medicine based initiatives. This study examined the extent of spatial heterogeneity in FL by whole exome sequencing 22 synchronously removed spatially separated biopsies from 9 patients. We observed significant differences in the extent of ITH across cases, with two distinct patterns of high and low spatial heterogeneity emerging. Site-specific alterations in genes with biological, prognostic or therapeutic relevance included, TNFRSF14, PIK3CD, TNFAIP3, PTEN, EP300 and XBP1. In depth characterization of these variants using deep-sequencing techniques confirmed their discordant nature, suggesting on-going genetic diversification driving evolution after widespread tumor dissemination. There was evidence of tumors comprising multiple competing subclones, with distinct clusters of mutations demonstrating differential expansions within spatially-separated sites. For cases where spatial tumors were examined at two time-points (FL and transformation to diffuse large B cell lymphoma (DLBCL)), the degree of heterogeneity increased with transformation. Collectively, our results demonstrate that spatial ITH is prevalent in FL. The existence of site-specific aberrations suggests that a single biopsy may not be sufficient in all patients to capture the full genomic complexity present and these spatial variations need to be considered in biomarker-led clinical studies.

| EGAD00001003553 | EGA

OXA-48-Like-Producing Klebsiella pneumoniae in Southern Spain in 2014-2015.

Project description: Not available

| S-EPMC6325174 | biostudies-literature

Molecular characterization of patient-derived Follicular Lymphoma and Chronic Lymphocytic Leukemia B cell receptor variable domain glycans

Project description:Follicular lymphoma (FL) is a systemic, lymphoid tissue-derived neoplasm of germinal center phenotype B cells that have undergone a t(14;18) chromosomal translocation. A remarkable feature of B cell receptors (BCRs) expressed by FL B cells is the presence of variable domain N-linked glycosylation sites, which are introduced during a process called somatic hypermutation. These novel glycosylation sites are preferentially located in specific ‘hotspot’ sites and are suggested to play a role in the survival of FL B cells, feasibly via the interactions between the N-glycans that occupy these sites and environmental lectins. Thus far, in-depth, molecular characterization of patient-derived, primary FL BCR variable domain glycans (VDGs) has not been performed. In this report, using liquid chromatography-mass spectrometry, we assess the glycosylation profiles of 14 VDG sites from 9 unique patient-derived tumors, and as a comparator, include 3 patient-derived chronic lymphocytic leukemia B cell clones, each harboring a VDG site. We show that FL BCR heavy chain VDG are enriched in oligomannose-type glycans and show using molecular dynamics simulations, that the level of glycan processing correlates with the accessibility of glycosidase ERManI to the glycosylation site and is additionally affected by steric hindrance from neighboring glycans.

2026-01-23 | PXD073349 | Pride

Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma [SNP arrays]

Project description:We studied 277 lymphoma samples (198 FL and 79 transformed FL [tFL]) using a single-nucleotide polymorphism array to identify the secondary chromosomal abnormalities that drive the development of FL and its transformation to diffuse large B-cell lymphoma.

2015-03-30 | GSE67385 | GEO

ena-DATASET-BCCA-11-05-2021-16:26:34:920-117 - samples

Project description:Follicular lymphoma (FL) is an indolent cancer of mature B-cells but carries increased risk of transformation to a more aggressive histology over time. We present here comprehensive profiling both tumor and immune compartments in 6 diagnostic FL biopsies by single-cell RNA sequencing. This confirmed results from 155 FL tumors characterized by mass cytometry (CyTOF) which revealed two distinct evolutionary trajectories with disparate risk of transformation and alternate biologies.

| EGAD00001007691 | EGA

Single-cell RNA sequencing of 6 follicular lymphoma tumors

| EGAS00001005257 | EGA

OXA-48-Producing Uropathogenic Escherichia coli Sequence Type 127, the Netherlands, 2015-2022.

Project description: Not available

| S-EPMC10683799 | biostudies-literature

Mus musculus

Project description:Oviductal vs. ovarian epithelial transformation yields very different tumor phenotypes in Apc fl/fl Pten fl/fl mice

| PRJNA317778 | ENA

siRNA smart pool silencing of master regulators of Follicular Lymphoma transformation to DLBCL

Project description:Follicular lymphoma (FL) is the most common indolent subtype of non-Hodgkin’s lymphoma, with relatively long overall survival rate ranging from 6 to 10 years from time of diagnosis. However, 20-60% of FL patients undergo transformation to aggressive diffuse large B cell lymphoma (DLBCL), with a reduced median survival of about 1.2 years. The specific functional and genetic determinants of FL transformation are still elusive and only a relatively small fraction of the cases is accounted for by established, recurrent alterations in TP53, MYC and BCL6, inactivation of CDKN2A and CDKN2B, or amplification of REL. We addressed this deficiency by performing systematic analysis of a B cell specific regulatory model with FL transformation signatures, using the Master Regulator Inference algorithm (MARINa). We show that the candidate master regulators inferred by the algorithm in FL induce synthetic lethality in DLBCL cells and lead to identification of specific compound combinations inducing synergistic loss of viability in transformed DLBCL cells

2015-11-11 | GSE66714 | GEO

BCI move: exploring pediatric BCI-controlled power mobility.

Project description: Not available

| S-EPMC12015940 | biostudies-literature