Search Results - EGA European Genome-Phenome Archive

Genome and transcriptome sequence data from a laryngeal squamous cell carcinoma patient

Genome and transcriptome sequence data from a laryngeal squamous cell carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001016127

Genome and transcriptome sequence data from a squamous cell carcinoma left mandible and extranodal extension patient

Genome and transcriptome sequence data from a squamous cell carcinoma left mandible and extranodal extension patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001016128

Genome and transcriptome sequence data from a keratinizing squamous cell carcinoma patient

Genome and transcriptome sequence data from a keratinizing squamous cell carcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001016131

Genome and transcriptome sequence data from a rectal adenocarcinoma patient

Genome and transcriptome sequence data from a rectal adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001016151

WGS files for paper titled "Sensitive detection of MYCN amplified neuroblastoma in blood samples with structural variants using whole genome sequencing"

This dataset contains one long read whole genome sequence tumor sample. 2.5µg of patient DNA was used to prepare SMRTbell sequencing library following the “Preparing whole genome and metagenome libraries using SMRTbell® prep kit 3.0” protocol (PacBio). Sequencing was conducted on PacBio Revio+SPRQ chemistry with 250pM loading concentration, generating 35x mean coverage for the whole genome. Reads were mapped to human genome assembly GRCh37 using pbmm2 v1.17.0 (https://github.com/PacificBiosciences/pbmm2)

Dataset EGAD00001016133

CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Angioleiomyoma_WES

Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

Dataset EGAD00001016134

CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Glomus tumour_WES

Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

Dataset EGAD00001016135

CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Angioleiomyoma_RNAseq

Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

Dataset EGAD00001016136

CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Myopericytoma_RNAseq

Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

Dataset EGAD00001016137

Genome and transcriptome sequence data from a esophageal adenocarcinoma patient

Genome and transcriptome sequence data from a esophageal adenocarcinoma patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001016152

CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Glomus tumour_RNAseq

Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

Dataset EGAD00001016138

CARMN fusions and PDGFRB mutations highlight key differences amongst cutaneous tumors with myopericytic differentiation - DERMATLAS: Myopericytoma_WES

Cutaneous tumors with myopericytic differentiation (PTs) are a family of soft tissue tumors arising from pericytes, encompassing myopericytoma (MPC), glomus tumor (GT) and angioleiomyoma (ALM). These tumors represent a morphological continuum, with some cases showing overlapping features. Molecular studies of PTs to date have focussed on either their mutational profile or gene fusions, however, it remains to be determined how these alterations overlap and if they can explain the subtle morphological differences between these subtypes. Thus, we collated an international cohort of formalin-fixed, paraffin-embedded PTs, comprised of MPC, GT and ALM cases. We performed tumor and normal DNA whole-exome sequencing and tumor RNA exome-capture transcriptome sequencing from cases for which both tumor and matched normal tissue were available (‘matched’ cohort) or which tumor-only tissue was available (‘unmatched’ cohort).

Dataset EGAD00001016139

Genome and transcriptome sequence data from a adenocarcinoma, non-small cell lung cancer patient

Genome and transcriptome sequence data from a adenocarcinoma, non-small cell lung cancer patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001016149

Genome and transcriptome sequence data from a adenocarcinoma of the duodenum patient

Genome and transcriptome sequence data from a adenocarcinoma of the duodenum patient,generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001016150

snRNA sequencing of high-grade pancreatic neuroendocrine carcinoma (panNEC)

High-grade pancreatic neuroendocrine carcinoma (panNEC) is a rare, aggressive cancer with limited tissue availability. Single-nucleus transcriptomics of five large-cell panNECs revealed two interesting neuroendocrine cell states: one highly proliferative with an aberrant brain-specific neuronal differentiation program and another stress-responsive state enriched for heat stress, hypoxia, and glycolysis. Our findings suggest potential therapeutic vulnerabilities, highlighting the need to evaluate the efficacy of combination therapies.

Dataset EGAD00001016154

GBM-Space: Whole Genome Sequencing of Laser Capture Microdissected Glioblastoma (LCM-WGS)

Cancer cells display heterogeneous and dynamic states in glioblastoma, but how these malignant states arise and whether they follow a tractable cellular trajectory across tumours is poorly understood. Here, we generate a deep single cell and spatial multi-region atlas of 12 isocitrate dehydrogenase wild-type (IDH-wt) primary glioblastomas that integrates transcriptomic, epigenomic and genomic analysis to comprehensively characterise their tumour heterogeneity. This dataset contains whole genome sequencing (WGS) data generated from regions of interest (ROIs) collected via laser capture microdissection (LCM), towards identifying copy number alterations and subclones directly at the DNA level.

Dataset EGAD00001016155

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