7296 results for "canc*"

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• The University of Hong Kong Gastric Cancer RHOA Study RNASeq Data

  RNAseq data generated from paired tumor frozen tissues in which the tumor organoids were established for cell-cell or cell-matrix adhesion dependency assay.

  Dataset EGAD00001008830

• RNA-seq for identification of neotranscripts

  This dataset contains RNA-seq data (Fastq files of paired-end data) of 18 patient tumors used for identification of neotranscripts in 18 different types of fusion-driven sarcomas and other cancers as described in Vibert et al., Mol Cell 2022 (PMID: 35550257)

  Dataset EGAD00001008832

• Genomic determination for Homologous Recombination Deficiency (HRD) by shallow Whole Genome Sequencing (sWGS)

  Homologous recombination deficiency (HRD) score in a large cohort of 55 triple-negative breast cancer PDX

  Dataset EGAD00001008839

• Dataset for synovial_sarcoma-RNA

  Rare cancer sequencing data of 23 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008844

• Dataset for Ewing_sarcoma_PNET-RNA

  Rare cancer sequencing data of 28 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008845

• Dataset for NSCLC-RNA

  Rare cancer sequencing data of 45 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008846

• Dataset for other_cancer-RNA

  Rare cancer sequencing data of 95 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008847

• Dataset for bone_cancer-RNA

  Rare cancer sequencing data of 55 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008848

• Dataset for leiomyosarcoma-RNA

  Rare cancer sequencing data of 87 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008849

• Dataset for breast_cancer-RNA

  Rare cancer sequencing data of 59 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008850

• Cholangiocarcinoma

  Arcagen is an EORTC/SPECTA pan-European project that aims to recruit 1000 rare cancer patients from different tumour domains of EURACAN. This study collected samples from advanced or metastatic rare cancer from patients older than 12, and analysed them using Foundation Medicine next-generation sequencing (NGS) panels (FoundationOne CDx for FFPE samples or FoundationOne Liquid CDx for blood samples). Here we are submitting two datasets that contain NGS files from gastrointestinal rare cancers (n=119): - Dataset 2 (87 patients): Intra-hepatic cholangiocarcinoma (n=47), Extra-hepatic, cholangiocarcinoma (n=16), Not specified Cholangiocarcinoma (n=9), Small bowel adenocarcinoma (n=6) and other rare GI cancer (n=9)

  Dataset EGAD00001008968

• Ovarian cancer EV RNA-seq

  Ovarian cancer EV RNA-seq

  Dataset EGAD00001008972

• RNA-seq derived from metastatic Castration-Resistant Prostate Cancer

  Patients with progressive, metastatic castration-resistant prostate cancer (mCRPC) underwent metastatic tumor biopsy. 118 total samples including 14 paired samples (baseline and later progression). Various organ sites including soft tissue & bone were present. Published in DOI: 10.1200/JCO.2017.77.6880 Journal of Clinical Oncology 36, no. 24 (August 20, 2018) 2492-2503.

  Dataset EGAD00001008991

• Plasma whole genome sequencing from patients with stage IV colorectal cancer and microsatellite instability

  This dataset contains plasma WGS data from patients with stage IV colorectal cancer (CRC, n = 16) and healthy individuals (n = 21) used in the Pointy manuscript. Patients with CRC provided written consent and samples were collected as performed as described previously (Clinical-Trials.gov number NCT01876511; Georgiadis et al., 2019, Le et al., 2017). Plasma samples from 21 healthy control individuals were procured through BioIVT. Cell-free DNA (cfDNA) was extracted from plasma using the QIAamp Circulating Nucleic Acid Kit. Libraries were prepared with 5 to 250 ng of cfDNA using the NEBNext DNA Library Prep Kit. Libraries were sequenced on HiSeq2000/2500.

  Dataset EGAD00001008999

• Detection of cancer cell transcriptomes

  Single cell transcriptomes, generated using chromium 10X 3' sequencing, for two tumour types (AT/RT, and Ewing's sarcoma). For each individual, tumour and normal whole genome sequencing was also obtained using Illumina short read sequencing to an average depth of 30X. These data were used to validate the accuracy of a method for identifying cancer cell transcriptomes based on the allelic shift produced by copy number changes.

  Dataset EGAD00001009005

• Diagnostic utility of whole genome sequencing in adults with B-other acute lymphoblastic leukemia - RNA

  Genomic profiling at diagnosis of B-cell precursor Acute Lymphoblastic Leukemia (BCP-ALL) in adults is used to guide disease classification, risk stratification and treatment decisions. Patients for which diagnostic screening fails to identify disease defining or risk stratifying lesions are classified as B-other ALL. We screened a cohort of 652 BCP-ALL cases enrolled in UKALL14 to identify and perform whole genome sequencing (WGS) on paired tumor-normal samples. For 52 B-other patients we compared WGS findings to data from clinical and research cytogenetics. WGS identifies a cancer associated event in 51/52 cases, this includes an established subtype defining genetic alteration in 5/52 that were previously missed by standard-of-care genetics. Of the 47 true B-other ALL we identified a recurrent driver in 87% (41).  Complex karyotype by cytogenetics emerges as a heterogeneous group, underlied by distinct genetic alterations associated with either favorable (DUX4-r) or poor outcomes (MEF2D-r, IGK::BCL2). For a subset of 31 cases, we integrate findings from RNA-sequencing (RNA-seq) analysis to include fusion gene detection, and classification by gene expression. Compared to RNA-seq, WGS was sufficient to detect and resolve recurrent genetic subtypes, however RNA-seq can provide orthogonal validation of findings. In conclusion, we demonstrate that WGS can identify clinically relevant genetic abnormalities missed by standard-of-care testing and identify leukemia driver events in virtually all cases of B-other ALL.

  Dataset EGAD00001009305

• WGS of cell-free DNA derived from plasma of CRC patients and healthy controls, and WGS of matched tumor tissue and saliva

  This dataset contains: 1.) Whole-genome sequencing (WGS) data (~6x) of 259 cfDNA samples obtained from 50 colorectal cancer (CRC) patients and 61 healthy controls. Paired-end sequencing was performed with 2x101 bp reads on the NovaSeq 6000 system. Data is provided as mapped .bam files (aligned to GRCh38/hg38). 2.) WGS data (~1x) of 50 tumor biopsy and 45 saliva samples from CRC patients. Paired-end sequencing was performed with 2x101 bp reads on the NovaSeq 6000 system. Data is provided as mapped .bam files (aligned to GRCh38/hg38).

  Dataset EGAD00001009309

• WES and RNA-seq of triple-negative breast cancers from the MyBrCa cohort

  The dataset contains a genomics characterization of 35 triple-negative Asian breast tumours from the Malaysian Breast Cancer cohort. This includes whole-exome sequencing of tumour tissue at 80X, whole-exome sequencing of matched normal (blood) tissue at 40X, and RNA-seq of tumour tissue at 40X coverage (>15 million reads). Whole-exome libraries were prepared using the Nextera Rapid Capture Exome Kit; exome capture was performed in pools of 3 and subjected to paired end 75 sequencing on a NovaSeq 6000 platform. RNA libraries were prepared using the TruSeq Stranded Total RNA HT kit with Ribo-Zero Gold as per manufacturer’s instructions and also subjected to paired end 75 sequencing on a NovaSeq 6000 platform. Uploaded bam files have been mapped to the hs37d5 human genome and processed using the standard GATK pipelines. Paired clinical, demographic, genotyping, and overall survival data for these patients are available from the associated publications or by request.

  Dataset EGAD00001009311

• Single Cell Genome Sequence for DLP+ library A95618B

  Single Cell Genome Sequence for Triple negative breast cancer patient-derived xenograft SA609 passage 3 on DLP+ library A95618B

  Dataset EGAD00001009316

• Single Cell Genome Sequence for DLP+ library A95628A

  Single Cell Genome Sequence for triple negative breast cancer patient SA1162SB on DLP+ library A95628A

  Dataset EGAD00001009319

• Single Cell Genome Sequence for DLP+ library A95632C

  Single Cell Genome Sequence for triple negative breast cancer patient-derived xenograft SA609 passage 6 on DLP+ library A95632C

  Dataset EGAD00001009322

• cell-free DNA Whole Genome Sequencing of 3784 samples on MGI and Illumina platform

  The dataset of Integrative modeling of tumor genomes and epigenomes for enhanced cancer diagnosis by cell-free DNA includes 3784 whole genome sequencing bam files on the MGI and Illumina platform. The analyzed samples include plasma samples from normal individuals and patients with cancer.

  Dataset EGAD00001009335

• NLG-LBC-05 ctDNA project sequencing data

  Low-pass whole-genome sequencing of pretherapy lymphoma cfDNA and targeted sequencing of cfDNA, tumor tissue and whole-blood samples of NLG-LBC-05 patient samples and cfDNA of nine subjects with no known cancer. Hybrid capture target enrichment; panel target and sequencing information provided in PMID:34932792. FASTQ files provided for targeted sequencing, separate sequencing runs per sample noted with prefix "run" if applicable. Sequences from DTX1 and KLHL6 targets are advised to be excluded from analyses due to PCR/plasmid contaminants of in-house origin.

  Dataset EGAD00001009337

• Normal sample for patient SA238

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA238

  Dataset EGAD00001009363

• Normal sample for patient SA221

  Whole genome sequencing of normal sample for triple negative breast cancer patient SA221

  Dataset EGAD00001009362