Search Results - EGA European Genome-Phenome Archive

Whole genome sequencing of matched esophageal tumor-normal samples

The dataset includes whole genome sequencing (WGS) data on ten matched esophageal tumor-normal pairs. WGS was performed by the cancer sequencing service of CG with an average read coverage of approximately 50-fold. Illumina HiSeq2000 instrument was used to perform the sequencing.

Dataset EGAD00001004832

Whole exome and targeted DNA sequencing data for formalin-fixed paraffin embedded tissue from de novo small cell prostatic carcinoma cases

This dataset consists of 44 compressed paired fastq files, 15 of which are generated from whole exome sequencing, and 29 of which are generated from DNA sequencing using a targeted gene panel capturing the exonic regions of 73 prostate cancer driver genes. Targeted DNA sequencing was performed on an Illumina MiSeq (v3 600 cycle kit), and exome sequencing was done using an Illumina HiSeq 2500 (v4 250 cycle kit) machine. The fastq files are named in accordance with the sample aliases provided, which reflect the pathology of interest to this study (small cell prostatic carcinoma--SCPC), whether it was sequenced using an exome or targeted gene panel, whether the FFPE sample was sourced from tumor or benign tissue (labeled T or B, respectively), and whether there exists multiple samples belonging to a single patient.

Dataset EGAD00001004139

Whole Exome Sequencing of Localized Prostate Cancer Patients

Whole exome sequencing of localized prostate cancer patients in this study contained pair tumor-normal samples and validated tumor content.

Dataset EGAD00001008274

Chromosome Segregation Errors Promote a Diverse Spectrum of Simple and Complex Genomic Rearrangements

Cancer genomes are frequently characterized by numerical and structural karyotypic abnormalities. Here we combined an inducible centromere-specific inactivation approach with selection for a conditionally essential gene, a strategy we term ‘CEN-SELECT’, and show that single-chromosome missegregation during cell division can directly drive a broad spectrum of structural rearrangement types. Cytogenetic profiling revealed that missegregated chromosomes are 120-fold more susceptible to developing seven major categories of structural variants, including translocations, insertions, deletions, and reassembly into chromothriptically rearranged chromosomes. Whole-genome sequencing of clones with genetically propagatable derivative chromosomes identified complex rearrangements and copy-number alterations that can result in gene inactivation or extrachromosomal gene amplification. We conclude that chromosome segregation errors are sufficient to drive extensive structural variation that recapitulates those commonly associated with human cancers.

Dataset EGAD00001004163

Genome and transcriptome sequence data from a metastatic choroid melanoma patient

Genome and transcriptome sequence data from a metastatic choroid melanoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001005839

Genome and transcriptome sequence data from a metastatic rectal carcinoma patient

Genome and transcriptome sequence data from a metastatic rectal carcinoma patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

Dataset EGAD00001005825

Healthy control and lung cancer plasma cfDNA samples from various collection tubes

The dataset contains 6 lung cancer and 60 healthy control plasma cfDNA samples collected in EDTA, PAXGene and Norgen blood collection tubes at various locations. Shallow WGS was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

Dataset EGAD00001008322

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