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• HERBY trial WES

  Whole exome sequencing of non-brainstem paediatric high grade glioma from the HERBY phase II randomised trial. DNA from 86 cases was subjected to Illumina paired end whole exome sequencing using a customised SureSelect Human All Exon V6 capture set. Germline DNA from whole blood was sequenced for 83 cases. 26 cases were sequenced from both fresh frozen tissue and FFPE material, 10 were sequenced from only fresh frozen material and 50 from only FFPE. Data is provided as bwa aligned BAM files

  Dataset EGAD00001004036

• Case Study of Acquired Resistance to FGFR Inhibition in Cholangiocarcinoma using Targeted DNA and RNA Sequencing

  Targeted sequencing was performed on blood, tumor, and cell free DNA samples from an FGFR2-fusion positive cholangiocarcinoma patient before and after treatment with an FGFR targeted therapy.

  Study phs001924

• Genome-Wide Bisulfite Sequencing of Urinary Cell-Free DNA

  The current sequencing dataset consists of 85 bisulfite sequencing data files (Fastq files) of human cell-free urine DNA samples. These extracted cfDNA samples were then constructed into DNA libraries using the KAPA HTP Library Preparation Kit (Kapa Biosystems) with bisulfite modification using the EpiTect Bisulfite Kit (Qiagen) and subsequently sequenced on the Nextseq500 platform (Illumina).

  Dataset EGAD50000001902

• Tumor Profiler Project - OV cell-free DNA data

  The dataset contains amplicon sequencing data from 48 samples from 35 different patients with ovarian cancers. Cell free DNA was collected from plasma. Sequencing was performed on an Ion Torrent platform and the sequencing data is provided in bam format.

  Dataset EGAD50000001410

• The dataset for Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers

  The dataset for “Early detection of ovarian cancer using cell-free DNA fragmentomes and protein biomarkers” includes 409 cram files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD50000000695

• The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer

  The dataset for Genome-wide cell-free DNA fragmentation in patients with cancer includes 538 bam files from whole genome next-generation sequencing on the Illumina HiSeq2500. The samples analyzed include plasma samples from healthy individuals and patients with cancer.

  Dataset EGAD00001005339

• Circulating tumor DNA in urine and plasma of glioma patients - sequencing data

  Dataset consisting of sequence data from 36 glioma patients. Data includes; -Whole exome sequencing of tumour tissue and matched germline -Shallow whole genome sequencing of urine cell-free DNA -Targeted capture sequencing of plasma and CSF cell-free DNA Additional sequencing data are provided from non-glioma and healthy controls

  Dataset EGAD00001006156

• Single-cell T-cell receptor sequencing of intraepithelial CD8+ αβ T-cells in celiac disease

  Single-cell paired TCR sequencing of intraepithelial CD8+ αβ T-cells in gluten-free diet treated and untreated celiac disease patients and in controls. (Paired end, amplicon sequencing).

  Study EGAS00001004989

• A dataset compiled as a resource a for orthogonal assessment of exon CNV calling in NGS data

  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. The full dataset includes FASTQ files, target BED file, and MLPA results.

  Study EGAS00001002428

• Mitochondrial DNA sequencing of iPSC, parental cells, and iPSC derived cardiomyocytes

  The aim of this work was to analyze to which extent mitochondrial DNA (mtDNA) variants in human induced pluripotent stem cells (iPSC) originate from their parental cells or from de novo mutagenesis, and whether dynamics in variant heteroplasmy levels during prolonged expansion culture of iPSC are caused by inter- or intra-cellular selection or genetic drift. Hence, mtDNA of 26 early passage iPSC clones from, in total, 10 donors and the corresponding parental cell populations (here endothelial cells) were sequenced. Furthermore, 7 iPSC clones were expanded up to passage 50 and the change in variant heteroplasmy levels was monitored. Lastly, the effect of differentiation on the variant heteroplasmy levels was investigated during directed cardiomyocyte differentiation of 4 iPSC clones.

  Study EGAS00001005560