20200417_PNET_methylation_paper - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001006063 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:RNA-seq data characterising neuroendocrine (NE) and non-NE cells, cultured on plastic or Matrigel, extracted from small cell lung cancer circulating tumour cell derived explants.
2023-09-17 | E-MTAB-10950 | biostudies-arrayexpress
Project description:BAM outputs from RSEM (https://deweylab.github.io/RSEM/) analysis of RNASeq sequencing on HiSeq platform of tumour samples from 29 pancreatic neuroendocrine cases.
| EGAD00001003336 | EGA
Project description:Background and Aims Small intestinal neuroendocrine tumours (SINETs) are the commonest malignancy of the small intestine; however underlying pathogenic mechanisms remain poorly characterised. Whole genome and exome sequencing has demonstrated that SINETs are mutationally quiet with the most frequent known mutation in the cyclin dependent kinase inhibitor 1B gene (CDKN1B) occurring in only ~8% of tumours, suggesting that alternative mechanisms may drive tumourigenesis. The aim of this study is to perform genome-wide molecular profiling of SINETs in order to identify pathogenic drivers based on molecular profiling. This study represents the largest unbiased integrated genomic, epigenomic, and transcriptomic analysis undertaken in this tumour type. Methods Here we present data from integrated molecular analysis of SINETs (n=97) including whole exome or targeted CDKN1B sequencing (n=29), HumanMethylation450 BeadChip (Illumina) array profiling (n=69), methylated DNA immunoprecipitation sequencing (n=16), copy number variance analysis (n=47) and Whole Genome-DASL (Illumina) expression array profiling (n=43). Results Based on molecular profiling SINETs can be classified in to three groups which demonstrate significantly different progression-free survival after resection of primary tumour (not reached at 10 years vs 56 months vs 21 months, p=0.04). Epimutations were found at a recurrence rate of up to 85% and 21 epigenetically dysregulated genes were identified, including CDX1 (86%), CELSR3 (84%), FBP1 (84%) and GIPR (74%). Conclusions This is the first comprehensive integrated molecular analysis of SINETs. We have demonstrated that these tumours are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression free survival. Background and Aims Small intestinal neuroendocrine tumours (SINETs) are the commonest malignancy of the small intestine; however underlying pathogenic mechanisms remain poorly characterised. Whole genome and exome sequencing has demonstrated that SINETs are mutationally quiet with the most frequent known mutation in the cyclin dependent kinase inhibitor 1B gene (CDKN1B) occurring in only ~8% of tumours, suggesting that alternative mechanisms may drive tumourigenesis. The aim of this study is to perform genome-wide molecular profiling of SINETs in order to identify pathogenic drivers based on molecular profiling. This study represents the largest unbiased integrated genomic, epigenomic, and transcriptomic analysis undertaken in this tumour type. Methods Here we present data from integrated molecular analysis of SINETs (n=97) including whole exome or targeted CDKN1B sequencing (n=29), HumanMethylation450 BeadChip (Illumina) array profiling (n=69), methylated DNA immunoprecipitation sequencing (n=16), copy number variance analysis (n=47) and Whole Genome-DASL (Illumina) expression array profiling (n=43). Results Based on molecular profiling SINETs can be classified in to three groups which demonstrate significantly different progression-free survival after resection of primary tumour (not reached at 10 years vs 56 months vs 21 months, p=0.04). Epimutations were found at a recurrence rate of up to 85% and 21 epigenetically dysregulated genes were identified, including CDX1 (86%), CELSR3 (84%), FBP1 (84%) and GIPR (74%). Conclusions This is the first comprehensive integrated molecular analysis of SINETs. We have demonstrated that these tumours are highly epigenetically dysregulated. Furthermore, we have identified novel molecular subtypes with significant impact on progression free survival. This study included 97 tumour samples from 85 individuals, this included both primary and metastatic tumour samples. 25 normal small intestinal samples were analysed.
2016-07-03 | E-GEOD-73832 | biostudies-arrayexpress
Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from placental samples from two species: human and mouse. n=47 samples (n=24 placental samples from humans, 23 placental samples from mice).
2023-08-05 | GSE184220 | GEO
Project description:<p>Most pancreatic neuroendocrine tumors (PNETs) do not produce symptoms of hormonal excess and are hence considered “non-functional”. Their clinical behaviors vary widely, emphasizing the need for a robust classification with prognostic power. Using enhancer maps to infer regulatory programs, we find that the large majority of non-functional PNETs fall into two major sub-types that reflect alpha and beta endocrine cell ontogeny, respectively. Tumors of the different subtypes have similar clinical presentations and histology, but express distinct lineage-specifying transcription factors, ARX or PDX1. Here we provide the raw ChIP-seq and RNA-seq data of the PNET cohort in this study, as well as ChIP-seq data of ileal carcinoids.</p>
| phs001910 | dbGaP
Project description:STAR outputs from RNA-seq of 84 pancreatic neuroendocrine neoplasms, 10 normal islet samples and 4 cell line samples.
| EGAD00001006991 | EGA
Project description:Set7: ERCC bulk short-read RNA-seq by Illumina NextSeq platform, additional samples
| PRJNA1123717 | ENA
Project description:Purpose: Molecular characterization of ECRT-SMARCA4 tumours and their place within the constellation of ECRT-SMARCB1, ATRT and SCCOHT Methods: Total RNA was obtained from 72 fresh-frozen tumour samples using the Qiagen RNAeasy kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s procedure. Barcode Illumina compatible libraries were generated from 750 ng of total RNA for each sample using the TruSeq Stranded mRNA Library Preparation Kit (Illumina). Libraries were sequenced using the Illumina HiSeq 2500 platform. RNA-seq data pre-processing was performed using an in-house pipeline developed at the Curie Institute Bioinformatics Core Facility. Read mapping and counting were performed using STAR, version 2.5.3) and the hg19 version of the human reference genome. Results: Dimensionality reduction and hierarchical clustering algorithms applied to the transcriptomics dataset show that ECRT-SMARCA4 display molecular features intermediate between SCCOHT and ECRTS-MARCB1.
2021-06-02 | GSE175891 | GEO
Project description:Genome wide DNA methylation profiling of drinkers and non-drinkers in WB samples. The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across 485,577 CpGs in WB samples that oevrlapped with CpGs from Illumina Infinium450k Human DNA methylation Beadchip. Samples included 47 drinkers (cases) and 47 non-drinkers (controls).
2018-04-01 | GSE110043 | GEO
Project description:JAGuaR outputs from RNA-seq of 35 pancreatic neuroendocrine neoplasms.
| EGAD00001006990 | EGA