9295 results for "cancer rna-seq"

in 32.81 milliseconds.

• ICR96 exon CNV validation series

  A resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in BRCA1, BRCA2, TP53, MLH1, MSH2, MSH6, PMS2, EPCAM and PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs the most difficult exon CNV to detect.

  Dataset EGAD00001003335

• Normal prostatectomy project analysis and leftovers

  Data collected as part of the Normal prostatectomy project analysis. Whole genome sequencing (WGS, targeted at 30X for normal tissue and 50X for tumour tissue) was performed on morphologically normal tissue samples from 30 patients with prostate cancer. In addition, seven prostate tissue samples were sequenced from 7 non-cancer patients: two collected after a cystoprostatectomy and five from samples collected at autopsy. Matched blood controls were included for all patients. An extra five samples were sequenced from the stroma of cell cultured fibroblasts. In addition a few tumour samples obtained at prostatectomy and their blood matched controls are included in this dataset from the main study that are not included elsewhere.

  Dataset EGAD00001004125

• sWGS on cfDNA and matching tumor DNA in pediatric cancer

  This dataset contains shallow whole genome sequencing data from paired cfDNA - tumor DNA samples of various pediatric cancer entities (total 215 samples). Files are provided in fastq format. Samples were sequenced on an Ion Proton sequencer (Thermo Fisher Scientific) or a Hiseq3000 (Illumina). Data analysis is available at https://github.com/rmvpaeme/sWGS_pediatric_cancer.

  Dataset EGAD00001007508

• EPICC: Evolutionary Predictions in Colorectal Cancer

  661 bam files generated from high-throughput RNAseq of tumour biopsies from colorectal cancer patients

  Dataset EGAD00001007828

• 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

• WES and RNAseq of Simultaneous Bilateral Breast Cancer

  This dataset includes NGS profiling of 13 women with simultaneous bilateral breast cancer. Seven women have WES of untreated surgical resections and matched healthy tissue. The six other women have WES of healthy tissue, WES+RNAseq of pre-neoadjuvant tumor biopsies, and when residual disease was present (6 tumors in 4 patients), WES+RNAseq of residual disease from post-neoadjuvant therapy surgery. One patient from the WES+RNAseq cohort had multifocal bilateral disease at diagnosis so there are 2 pre-neoadjuvant biopsy samples from each breast.

  Dataset EGAD00001009987

• Diverse modes of genomic alterations in hepatocellular carcinoma

  Hepatocellular carcinoma is the most prevalent type of liver cancer. We intended to study the genomic landscape of this disease. We conducted whole-genome, exome and transcriptome sequencing for 42 patients. We show diverse modes in which the HCC genome is affected in these patients, including well-known and novel mutations, structural variations, and Hepatitis B-virus integration into the genome.

  Study EGAS00001000824

• Myelodysplastic_Syndrome_Exome_Sequnecing

  Cancer is driven by mutation. Illumina GA massively parallel sequencing technology will be applied to Agilent exome hybridisation capture libraries and total genomic paired-end libraries. Bespoke algorithms are being developed to identify the somatically acquired structural variants, point mutations, insertions and deletions in these samples. This project will give unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with Myelodysplastic Syndrome development.

  Study EGAS00001000089

• Whole-exome sequencing of Fanconi anemia-like inherited bone marrow failure syndrome

  We identified three fibroblast cultures derived from aplastic anemia patients in the Japanese Cancer Research Resources Bank (JCRB) Cell Bank that showed high levels of sister chromatid exchanges (SCEs) in PHA-stimulated lymphoblasts. To elucidate the genetic basis of the high SCE, we carried out whole exome sequencing of these samples. Subsequently, germline variants were analysed for these patients.

  Study EGAS00001003809

• Whole-exome sequencing performed on a patient with chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia

  We studied the rare case of a patient who underwent transformation of myelodysplastic syndrome to chronic myelomonocytic leukemia and B cell acute lymphoblastic leukemia. We used fluorescence-activated cell sorting and whole-exome sequencing to identify driver mutations in the various clones. This allowed us to propose a model of branching clonal evolution with a possible germline predisposition to cancer.

  Study EGAS00001005117