Project description:The fallopian tube (FT) has been proposed as a potential site of origin for high-grade serous ovarian cancer (HGSOC), supporting investigation of genomic alterations across matched tissues. This dataset includes whole-genome sequencing (WGS) and DigiPico data from matched samples, including peripheral blood mononuclear cells (PBMCs), fallopian tube tissue, and tumor tissue from HGSOC patients. The data support analysis of germline and somatic variants, copy number alterations (CNAs), and neoantigen prediction across matched sample types. This submission contains the WGS data DigiPico data associated with this study.
Project description:This dataset includes gene expression data from 103 primary tumour samples. 86 samples from this dataset have already been deposited into GEO (GSE36924), and has been duplicated here since the data has been processed differently. This data is also available through the International Cancer Genome Consortium (ICGC) Data Portal (http://dcc/icgc.org), under the project code: Pancreatic Cancer (QCMG, AU). Access to the restricted clinical data must be made through the ICGC Data Access Compliance Office (http://www.icgc.org/daco).
Project description:This dataset includes both whole transcriptome (WT) and mRNA-seq data for interferon-treated mouse samples. This is part of a larger study (GSE52405), where these interferon datasets were used as validation.
Project description:We sequenced two tumor/normal pairs obtained from two paediatric medulloblastoma patients (MB14 and MB24) with at least 30x coverage on all commonly used next-generation sequencing platforms for whole genome sequencing (SOLiD 4, 5500xl SOLiD, Illumina's HiSeq2000, and Complete Genomic' technology). The normal tissue samples came from venous blood. We compared their ability to call single nucleotide variations (SNVs) in whole-genome sequencing data with high confidence. As gold standard for SNV calling, we used genotypes determined by Affymetrix SNP 6.0 Array Technology (total of 907,551 SNPs after quality filtering).
Project description:This dataset was applied to evaluate the performance of a deep learning framework, FFPERescuer, specifically designed to reconstruct gene expression profiles from RNA sequencing data derived from FFPE (formalin-fixed, paraffin-embedded) tumor tissues. The dataset includes a total of 12 RNA-Seq samples, comprising 10 FFPE tumor tissue samples from colorectal cancer (CRC) cases collected in Amsterdam, the Netherlands, with 2 duplicate samples included for reproducibility assessment. The corresponding gene expression profiles from fresh-frozen tumor tissues for these 10 cases are available in the dataset GSE33113, generated using microarray technology.
Project description:Genome wide DNA methylation profiling of normal whole blood samples. The data consist of 43 samples with Illumina HumanMethylation450 BeadChip data.
Project description:The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. In addition, the genes CSPG2, FLT4, SFRP1, DLK1, and GAS7 were frequently involved in regions of UPDs/UPPs and showed high levels of methylation revealing that UPDs/UPPs can result in the duplication of hypermethylated inactive genes. This dataset includes the array CGH of 30 colorectal cancers.
Project description:The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs, CNAs and genome-wide methylation status in sporadic CRC. Our results indicate that regions showing high frequencies of UPDs/UPPs mostly coincide with regions typically involved in genomic losses such as chromosome arms 1p, 5q, 8p, 14q, 17p, 18q, 20p, and 22q. Of these, chromosome arms 5q, 14q, 17p, and 20p preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. In addition, the genes CSPG2, FLT4, SFRP1, DLK1, and GAS7 were frequently involved in regions of UPDs/UPPs and showed high levels of methylation revealing that UPDs/UPPs can result in the duplication of hypermethylated inactive genes. This dataset includes the array CGH of 30 colorectal cancers.
Project description:This dataset includes RNA-seq data from ileal and colonic biopsies at time of diagnosis for treatment-naive, uncomplicated Crohn's disease (CD) patients and matched controls. This is includes 56 CD patients each for ileal and colonic tissue and for controls, 46 colonic samples and 45 ileal samples. Clinical characteristics such as development of complications, disease remission, or progression to surgery were recorded with a mean follow-up of 6 years.