5525 results for "*oma"

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• WGS data from 20 cholangiocarcinoma cases

  WGS data from biliary tract cancer samples (Holzapfel, et al., J Gastrointest Oncol,14(1):379-389, 2023). The dataset includes tumour and normal BAM files sequenced on Illumina HiSeq/NovaSeq and aligned against GRCh38 (n=20 tumour/normal pairs).

  Dataset EGAD50000002307

• RRBS of 58 pleural mesothelioma samples (Paired-end)

  The dataset contains RRBS data (bam files) for 58 pleural mesothelioma samples. The samples were sequenced on NovaSeq6000 (Illumina, San Diego, CA) in paired-end 150bp mode. RRBS raw reads were trimmed for adaptor sequences using trim galore (v. 0.6.5) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and filtered for low-quality sequences using fastQC (v. 0.11.8) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). High quality trimmed reads were mapped to the Human reference genome (UCSC genome assembly GRCh38/hg38) using Bismark (v. 0.22.3) with default parameters.

  Dataset EGAD50000002129

• WES for 45 patients with pleural mesothelioma (Matched)

  The dataset contains WES data (bam files) for 45 pleural mesothelioma samples. Nextera Flex for Enrichment solution (Illumina, San Diego, CA) in combination with SureSelect Human All Exon V7 probes (Agilent, Santa Clara, CA) was used for library preparation and generated libraries were sequenced on NovaSeq 6000 (Illumina, San Diego, CA) in 150 pair-end mode. Quality control of the raw data was conducted using fastQC (v. 0.11.8) (https://www.bioinformatics. babraham.ac.uk/projects/fastqc/). WES data were then analyzed with the DRAGEN Bio IT platform 49 (version 4.2.4) and the human GRCh38 as reference genome.

  Dataset EGAD50000002128

• WES for 42 patients with pleural mesothelioma (Not matched)

  The dataset contains WES data (bam files) for 42 pleural mesothelioma samples. Nextera Flex for Enrichment solution (Illumina, San Diego, CA) in combination with SureSelect Human All Exon V7 probes (Agilent, Santa Clara, CA) was used for library preparation and generated libraries were sequenced on NovaSeq 6000 (Illumina, San Diego, CA) in 150 pair-end mode. Quality control of the raw data was conducted using fastQC (v. 0.11.8) (https://www.bioinformatics. babraham.ac.uk/projects/fastqc/). WES data were then analyzed with the DRAGEN Bio IT platform 49 (version 4.2.4) and the human GRCh38 as reference genome.

  Dataset EGAD50000002127

• cfMeDIP-seq for 18 patients with pleural mesothelioma

  The dataset contains cfMeDIP-sequencing data (bam files) for 18 plasma samples from pleural mesothelioma patients. The libraries were prepared according to the published protocol (Shen, S. Y., Burgener, J. M., Bratman, S. V. & De Carvalho, D. D. Preparation of cfMeDIP- seq libraries for methylome profiling of plasma cell-free DNA. Nat. Protoc. 14, 2749–2780 (2019)). Whole genome sequencing (WGS) was performed for pre-made libraries on NovaSeq X Plus with a 150 paired-end strategy. Low-quality reads and adapters were removed with Trim Galore version 0.6.6 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore). The trimmed reads were aligned to hg38 with Bowtie2 version 2.3.4.3. SAMTools version 1.9 was used to convert the SAM alignment files to BAM files, sort and index reads, and remove duplicates.

  Dataset EGAD50000002126

• RNAseq of 704 patients with soft tissue tumors

  The dataset contains transcriptome sequencing (RNA-seq) data of 704 soft tissue tumors (STT) from 704 patients. The sequencing data comes in FASTQ format and contains 1408 files. A total of 56 different STT types were included in the present study and each tumor type was represented by >2 samples. The vast majority of the patients had been diagnosed and treated at the sarcoma centers in Lund (Sweden) or Stockholm (Sweden) during the period 1988-2020, but also a few samples from other centers, obtained through previous collaborative projects, were included. RNA was extracted from fresh frozen tumor material and samples were primary lesions unless otherwise indicated. The sequencing was performed using 2x150 bp paired-end chemistry on a series of Illumina instruments at various facilities during the period 2013-2023.Samples were obtained after informed consent from the patients and the study was approved by the regional ethics committee (Etikprövningsmyndigheten, Uppsala, dnr 2023-01550-01, dnr 2025-02997-02).

  Dataset EGAD50000002120

• Targeted DNA sequencing of TTFields-treated glioblastoma, IDH wildtype

  This dataset contains raw paired-end FASTQ files from targeted DNA sequencing using the TruSight Oncology 500 panel in patients with glioblastoma, IDH wildtype, treated with surgery, standard chemoradiotherapy and Tumor Treating Fields at Charité – Universitätsmedizin Berlin. Tumour samples were collected at first surgery and are linked to pseudonymised clinical and molecular annotations described in the associated EGA study.

  Dataset EGAD50000002117

• HOVON152 Trial shallow Whole Genome Sequencing

  Associated with Molecular profiling of HGBCL-DH-BCL2 patients treated in the HOVON-152 triaL. Targeted sequencing of 30 samples from 30 High-grade B-cell lymphoma patients. Targeted sequencing was used for identify genomic alterations associated with patient outcome.

  Dataset EGAD50000002094

• HOVON152 Trial Targetted Sequencing

  Associated with Molecular profiling of HGBCL-DH-BCL2 patients treated in the HOVON-152 triaL. Targeted sequencing of 30 samples from 30 High-grade B-cell lymphoma patients. Targeted sequencing was used for identify genomic alterations associated with patient outcome.

  Dataset EGAD50000002093

• Targeted sequencing data of cfDNA, archival tissue, and WBC from 208 patients with mUC

  Targeted tissue (n=81), cfDNA (n=319), and WBC (n=208) Illumina sequencing of metastatic urothelial carcinoma patients. All cfDNA is collected in the metastatic setting, while archival tissue is from across the disease course. White blood cell (WBC) samples are used as patient matched germline samples. All files are in paired-end fastq format.

  Dataset EGAD50000002089