8215 results for "canc*"

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• Angiopredict Whole genome Shallow Sequencing

  Shallow sequencing of metastatic colorectal cancer samples for the Angiopredict and Nobev cohorts described in: van Dijk et al., JCO, in revision

  Dataset EGAD00001003990

• RNA-seq of Liver Cancer

  The present series corresponds to 161 RNA-seq samples from tumors with matched WES or WGS. Hepatocellular carcinoma (HCC) accounts for more than 90% of liver cancers, and is a major health problem. It is the 3rd cause of cancer-related mortality. Advances in genomic analyses have formed a comprehensive understanding of different underlying pathobiological layers resulting in hepatocarcinogenesis. Thus, the development of next-generation sequencing technologies has made it possible to generate more comprehensive catalogues of somatic alteration events (single nucleotide substitutions, structural variations, and epigenetic changes) in liver cancer genome than ever before.

  Dataset EGAD00001003993

• 20180221_EGA_OESO

  Illumina platform sequencing of whole genome libraries prepared from normal, Barrett's oesophagus and oesophageal cancer samples from 44 donors

  Dataset EGAD00001003996

• Single-cell RNA sequencing on 12346 single T cells from 14 non-small cell lung cancer (NSCLC) patients

  Deep single-cell RNA sequencing data for 12346 T cells from tumour, adjacent normal tissue and peripheral blood of treatment-naïve NSCLC patients

  Dataset EGAD00001003999

• Lung cancer organoids

  Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term culture conditions of human airway epithelial organoids that contain all major cell populations and allow personalized human disease modelling. We collected macroscopically inconspicuous lung tissue from non-small-cell lung cancer (NSCLC) patients undergoing medically indicated surgery and isolated epithelial cells to engineer 3D organoids. We exploit the potential to derive sub-clones from AOs to demonstrate the feasibility of CRISPR gene editing. Finally, we show that AOs readily allow modelling of viral infections such as RSV and for the first time demonstrate the possibility to study neutrophil-epithelium interaction in an organoid model. Taken together, we anticipate that human AOs will find broad applications in the study of adult human airway epithelium in health and disease.

  Dataset EGAD00001004013

• Sebaceous carcinoma tumor/normal exome sequencing and transcriptome sequencing. Transcriptome sequencing of

  Sebaceous carcinomas (SeC) are cutaneous malignancies that, in rare cases, metastasize and prove fatal. Here we report whole exome sequencing on 32 SeC, revealing distinct mutational classes that explain both cancer ontogeny and clinical course. A UV-damage signature predominated 10/32 samples, while 9 were instead defined by microsatellite instability (MSI) mutations. UV-damage SeC exhibited poorly differentiated, infiltrative histopathologycompared to MSI signature SeC (p = 0.003), features previously associated with dissemination. Strikingly, UV-damage SeC transcriptomes and anatomic distributionclosely resembling those of cutaneous squamous cell carcinomas (SCC), implicating sun-exposed keratinocytes as a cell of origin. Like SCC, this UV-damage subclass harbors a high somatic mutation burden with >50 mutations/Mb, predicting immunotherapeutic response. In contrast, ocular SeC acquire far fewer mutations without a dominant signature, but show frequent truncating mutations in the ZNF750 epidermal differentiation regulator. Our data exemplify how different mutational processes convergently drive histopathologically related but clinically distinct cancers.

  Dataset EGAD00001004016

• Amplicon sequencing data from organoids of colorectal cancer patients.

  The dataset includes 13 bam files. Each bam file is a different colorectal cancer patient organoid.

  Dataset EGAD00001004313

• WGBS data of solid liver tumor DNA, and WGBS data of cell-free DNA derived from human blood, for CancerDetector study

  The blood samples of four liver cancer patients and four healthy people, and the solid liver tumor samples of two liver cancer patients are collected for this dataset. Blood samples were centrifuged first at 1,600 × g for 10 minutes, and then the plasma was transferred into new micro tubes and centrifuged at 16,000 × g for another 10 minutes. The plasma was collected and stored at -80⁰C. CfDNA was extracted from 5 ml plasma using the Qiagen QIAamp Circulating Nucleic Acids Kit and quantified by Qubit 3.0 Fluoromter (Thermo Fisher Scientific). Bisulfite conversion of cfDNA was performed by using EZ-DNA-Methylation-GOLD kit (Zymo Research). After that, Accel-NGS Methy-Seq DNA library kit (Swift Bioscience) was used to prepare the sequencing libraries. The DNA libraries were then sequenced with 150bp paired-end reads.

  Dataset EGAD00001004317

• Somatic mutations of 256 whole-genome sequenced colorectal cancer tumors.

  Somatic mutations of 256 whole-genome sequenced colorectal tumors. 234 MSS, 19 MSI and 3 POLE mutants. See Katainen R. et al. CTCF/cohesin-binding sites are frequently mutated in cancer, Nature Genetics 2015. doi:10.1038/ng.3335

  Dataset EGAD00001004329

• Adenoma development in familial adenomatous polyposis and MUTYH‐associated polyposis: somatic landscape and driver genes

  Familial adenomatous polyposis (FAP) and MUTYH‐associated polyposis (MAP) are inherited disorders associated with multiple colorectal adenomas that lead to a very high risk of colorectal cancer. The somatic mutations that drive adenoma development in these conditions have not been investigated comprehensively. In this study we performed analysis of paired colorectal adenoma and normal tissue DNA from individuals with FAP or MAP, sequencing 14 adenoma whole exomes (eight MAP, six FAP), 55 adenoma targeted exomes (33 MAP, 22 FAP) and germline DNA from each patient.

  Dataset EGAD00001004332

• Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer

  The dataset for Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer includes 17 bam files from next-generation sequencing on the Illumina HiSeq2500. The biospecimens analyzed include matched tumor pre-treatment, post-progression and normal samples.

  Dataset EGAD00001004336

• Dataset for "Genomic landscape of oral cancers" (CGI WGS)

  Dataset for "Genomic landscape of oral cancers" (CGI WGS)

  Dataset EGAD00001004339

• NKI-AvL CRC-OVC RNA-seq

  The dataset “NKI-AvL CRC-OVC RNA-seq" includes 4 FASTQ files from single-end total RNA sequencing on Illumina HiSeq2500 for 2 colorectal cancer and 2 ovarian cancer patients.

  Dataset EGAD00001004341

• NKI-AvL CRC-OVC DNA-seq

  The dataset “NKI-AvL CRC-OVC DNA-seq" includes 4 normal and 4 tumor BAM files from paired-end whole exome sequencing on Illumina HiSeq2500 and Illumina NovaSeq6000 for 2 colorectal cancer and 2 ovarian cancer patients.

  Dataset EGAD00001004340

• NKI-AvL CRC-OVC scTCR RNA-seq

  The dataset “NKI-AvL CRC-OVC scTCR RNA-seq" includes 368 BAM files from paired-end RNA sequencing on Illumina MiSeq for 2 colorectal cancer and 2 ovarian cancer patients.

  Dataset EGAD00001004342

• Germline whole exome sequencing in testicular cancer

  This dataset contains variant call format files generated from whole exome sequencing of germline DNA from indiviudals with diagnosed with testicualr germ cell cancer.

  Dataset EGAD00001004345

• microRNA-seq of human serum from a longitudinal study of 66 women with no history of cancer

  This dataset includes microRNA sequencing data from 198 human serum samples, representing a subset of 66 women with no history of cancer who participated in the UKCTOCS study and with serum samples collected at three timepoints over a period of up to 5 years. Small RNA libraries prepared from the serum samples were sequenced with 50-bp single end reads on an Illumina HiSeq 2000 instrument. Data is provided as FASTQ files.

  Dataset EGAD00001004348

• Exome sequencing to evaluate HER2/ERBB2 mutations in cancer

  ERBB2/HER2 transmembrane and juxtamembrane domain mutations in cancer. Exome sequencing of tumor and matched blood and 2 blood samples from relatives.

  Dataset EGAD00001004351

• Whole Exome Sequencing

  The Whole Exome Sequencing dataset contains 30 whole exome sequencing files (tumor, germ line DNA) and phenotype metadata for 15 patients on the phase II clinical trial of neoadjuvant immune checkpoint blockade in high-risk resectable melanoma at MD Anderson Cancer Center (NCT02519322). Included are data from baseline samples.

  Dataset EGAD00001004352

• Molecular portraits of breast cancer diagnosed during pregnancy

  The aim of this study was to compare the mutational landscape of breast cancer diagnosed during pregnancy (BCP) and breast cancer from age/stage non-pregnant patients (controls). We present whole genome sequencing data (Illumina HiSeq X ten platform) of tumor and matched normal tissues from 35 BCP patients and 20 controls. This work provides important novel biological insights and a unique resource to study the biology of breast cancer in young women and how pregnancy could modulate tumor biology.

  Dataset EGAD00001004353

• Dataset for "Genomic landscape of oral cancers" (Illumina WGS)

  Dataset for "Genomic landscape of oral cancers" (Illumina WGS)

  Dataset EGAD00001004356

• Summary statistics for cervical cancer GWAS

  Summary statistics from GWAS meta-analysis of cervical cancer

  Dataset EGAD00001004361

• DNA sequencing for gastric cancer ascites

  Whole-exome sequencing (WES) was performed on a total of 34 PC specimens, with 15 cases having matched gDNAs extracted from blood.

  Dataset EGAD00001004364

• RNA sequencing for gastric cancer ascites

  Whole transcriptome sequencing (RNA-seq) was performed on 39 PC specimens. Among them, 21 specimens also had WES data.

  Dataset EGAD00001004365

• Dataset for "Genomic landscape of oral cancers" (Illumina RNA)

  Dataset for "Genomic landscape of oral cancers" (Illumina RNA)

  Dataset EGAD00001004366