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• Genome and transcriptome sequence data from a metastatic colon cancer patient

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

  Dataset EGAD00001002977

• Genome and transcriptome sequence data from a metastatic colon cancer patient

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

  Dataset EGAD00001002978

• Genome and transcriptome sequence data from a GI primary (prev breast cancer) patient

  Genome and transcriptome sequence data from a GI primary (prev breast cancer) patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001002979

• Genome and transcriptome sequence data from a metastatic fibrolamellar hepatocelluar carcinoma patient

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

  Dataset EGAD00001002980

• Genome and transcriptome sequence data from a metastatic pancreatic carcinoma patient

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

  Dataset EGAD00001002981

• Genome and transcriptome sequence data from a metastatic rectosigmoid adenocarcinoma patient

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

  Dataset EGAD00001002982

• Genome and transcriptome sequence data from a metastatic carcinoma of the lung patient

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

  Dataset EGAD00001002983

• Genome and transcriptome sequence data from a metastatic pancreatic carcinoma patient

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

  Dataset EGAD00001002984

• Genome and transcriptome sequence data from a adenocarcinoma of the lung patient

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

  Dataset EGAD00001002985

• Genome and transcriptome sequence data from a metastatic breast cancer patient

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

  Dataset EGAD00001002986

• Genome and transcriptome sequence data from a metastatic endocervical adenocarcinoma patient

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

  Dataset EGAD00001002987

• Genome and transcriptome sequence data from a metastatic breast cancer patient

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

  Dataset EGAD00001002988

• Genome and transcriptome sequence data from a medullary thyroid cancer patient

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

  Dataset EGAD00001002989

• Genome and transcriptome sequence data from a metastatic colorectal cancer patient

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

  Dataset EGAD00001002990

• Genome and transcriptome sequence data from a metastatic breast cancer patient

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

  Dataset EGAD00001002992

• Genome and transcriptome sequence data from a metastatic carcinoma of primary unknown patient

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

  Dataset EGAD00001002993

• Genome and transcriptome sequence data from a metastatic squamous cell carcinoma of anus patient

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

  Dataset EGAD00001002994

• Genome and transcriptome sequence data from a carcinosarcoma of the uterus patient

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

  Dataset EGAD00001002995

• Genome and transcriptome sequence data from a metastatic breast cancer patient

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

  Dataset EGAD00001002997

• Autozygosity pilot - Born in Bradford (2017-05-11)

  The offspring of first cousin marriages have ~6% of their genome autozygous, i.e. homozygous identical by descent, or even more if there was further consanguinity in their ancestry. In the UK there are large populations with very high first cousin marriage rates of 20-50%. Sequencing the exomes of a sample of these individuals has the potential both to support genetic health programmes in these populations, and to provide genetic research information about rare loss of function mutations. This pilot study based on existing cohort samples from the Born In Bradford study will identify homozygous individuals for almost all variants down to an allele frequency around 1%, plus individuals carrying hundreds of new homozygous rare loss-of-function variants, and will support development of community relations and ethics for a wider study currently being designed. The data deposited in the EGA consist of low coverage whole exome sequencing on these samples. This dataset contains all the data available for this study on 2017-05-11.

  Dataset EGAD00001003329

• Targeted resequencing of Cardiomyopathies associated genes

  In this study, we present the results of a custom “pan-cardiomyopathy panel” in a molecular screening of 38 unrelated patients, 16 affected by DCM, 14 by HCM, and 8 by ARVC. The panel was designed using the Design Studio Tool (Illumina, San Diego, CA,USA). Coding regions and intron–exon boundaries of 115 genes, known to be associated with 7 DCM, HCM, and ARVC as well as channelopathies, were selected for targeted gene enrichment. For genes with multiple transcripts, all exons included in transcripts expressed in cardiac muscle were considered in the gene panel design. Total DNA was extracted from peripheral blood samples using the Wizard Genomic DNA Purification Kit (Promega, Mannheim, Germany) according to the manufacturer’s instructions, quantified, and qualitatively checked using NanoDrop 2000c (Thermo Fisher Scientific, Waltham, MA, USA). Custom targeted gene enrichment and DNA library preparation were performed using the Nextera Capture Custom Enrichment kit (Illumina) according to the manufacturer’s instructions. Targeted regions were sequenced using the Illumina MiSeq platform, generating approximately two millions of 150-bp paired-end reads for each sample (Q30 ≥90%).

  Dataset EGAD00001003359

• Leiomyosarcoma Cancer Transcriptome Sequencing

  RNA-Seq data (fastq raw read sequences) for French ICGC leiomyosarcoma cancer sequencing project, 78 samples representing 67 donors. Sequencing was performed on Illumina HiSeq. The libraries were then sequenced with a 2 x 75bp paired-end protocol to a minimum mean reads of 50 million.

  Dataset EGAD00001003192

• GoNL release 5 haplotype panel

  The samples in this panel come from 250 families: 248 parents-child trios and 2 parent-child duos. As the children do not provide additional haplotypes or population information, they were excluded from the panel. The samples present in the release are composed of 248 couples, 2 single individuals and 1 sample composed from the 2 haplotypes from the duo's children transmitted by their missing parent. The composed sample is named gonl-220c_223c.The files contain a total of 18.9M SNVs and 1.1M INDELs in autosomal chromosomes. They were generated by phasing/imputing the SNVs (a) and INDELs (b) using MVNCall. Only sites passing filters are reported. Sites filtered as part of the GoNL inaccessible genome were kept (but flagged as filtered) and still may contain true positive calls but should be used with care as they are located in parts of the genome that are less well captured (systematic under or over-covered or low-mapping quality)

  Dataset EGAD00001000744

• Integrated genomic characterization of adrenocortical carcinoma

  Adrenocortical carcinomas (ACC) are aggressive cancers originating in the cortex of the adrenal glands. Despite the overall poor prognosis, ACC outcome is heterogeneous. CTNNB1 and TP53 mutations are frequent in these tumors, but the complete spectrum of genetic changes remains undefined. Exome sequencing and SNP array analysis of 45 ACC revealed recurrent alterations in known drivers (CTNNB1, TP53, CDKN2A, RB1, MEN1) and genes not previously reported to be altered in ACC (ZNRF3, DAXX, TERT and MED12), which were validated in an independent cohort of 77 ACC. The cell-surface transmembrane E3 ubiquitin ligase ZNRF36 was the gene the most frequently altered (21%), and appears as a potential novel tumor suppressor gene related to the ß-catenin pathway.Our integrated genomic analyses led to the identification of two distinct molecular subgroups with opposite outcome. The C1A group of poor outcome ACC was characterized by numerous mutations and DNA methylation alterations, whereas the C1B group with good prognosis displayed a specific deregulation of two miRNA clusters. Thus, aggressive and indolent ACC correspond to two distinct molecular entities, driven by different oncogenic alterations.

  Dataset EGAD00001000764

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002048

• Genome and transcriptome sequence data from a liposarcoma patient

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

  Dataset EGAD00001002046

• Genome and transcriptome sequence data from a lung cancer patient

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

  Dataset EGAD00001002045

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002044

• Genome and transcriptome sequence data from a recurrent glioma patient

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

  Dataset EGAD00001002043

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002041

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002036

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002035

• Genome and transcriptome sequence data from a pancreatic cancer patient

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

  Dataset EGAD00001002034

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002033

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002031

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002030

• Genome and transcriptome sequence data from a pancreatic cancer patient

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

  Dataset EGAD00001002028

• Genome and transcriptome sequence data from a colorectal cancer patient

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

  Dataset EGAD00001002027

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002026

• Genome and transcriptome sequence data from a colorectal cancer patient

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

  Dataset EGAD00001002025

• Genome and transcriptome sequence data from a lung cancer patient

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

  Dataset EGAD00001002023

• Genome and transcriptome sequence data from a colorectal cancer patient

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

  Dataset EGAD00001002022

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002021

• Genome and transcriptome sequence data from a metastatic NPC patient

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

  Dataset EGAD00001002020

• RNA-seq FASTQ files from newborn screening dried blood spot samples

  Paired-end RNA-seq FASTQ files from 21 newborn screening dried blood spot (DBS) samples. These DBS samples were obtained from extremely low gestional age newborns, where 10 of them were affected by a fetal inflammatory response (FIR) before birth, and 11 were unaffected. Total RNA was sequenced using an Illumina NextSeq-500 instrument. The sample preparation protocol included the depletion of rRNA and globin mRNA using the Globin Zero Gold rRNA Removal Kit from Illumina. Libraries were prepared using the NebNext Ultra TM II Directionl RNA LIbrary Prep Kit (New England Biolabs). Each sample was sequenced in 4 lanes, leading to 8 FASTQ files per sample and a total of 21x8=168 FASTQ files. There is an additional number of 8 FASTQ files corresponding to sample BS13, which was downsampled to 1/4 of its original depth (see BS13_README file for details).

  Dataset EGAD00001004991

• UCSF Pediatric Bithalamic Glioma Genome Project

  Targeted next-generation sequencing of 13 pediatric bithalamic diffuse gliomas. BAM files of targeted next-generation DNA sequencing data of 13 pediatric gliomas, with multi-region sequencing data from 2 of these cases (17 total tumor samples). Genomic DNA was extracted from formalin-fixed, paraffin-embedded blocks of tumor tissue from using the QIAamp DNA FFPE Tissue Kit (Qiagen). Capture-based next-generation DNA sequencing was performed at the University of California, San Francisco Clinical Cancer Genomics Laboratory, using an assay that targets all coding exons of 480 cancer-related genes, select introns of 47 genes, and TERT promoter with a total sequencing footprint of 2.8 Mb (UCSF500 Cancer Panel). Sequencing libraries were prepared from genomic DNA, and target enrichment was performed by hybrid capture using a custom oligonucleotide library (Nimblegen SeqCap EZ Choice). Captured libraries were sequenced as paired-end 100 bp reads on an Illumina HiSeq 2500 instrument. Duplicate sequencing reads were removed computationally to allow for accurate allele frequency determination and copy number calling.

  Dataset EGAD00001005499

• MutWP5: CRUK Mutographs of Cancer: Breast: Cancer Mastectomy (Exome) (2020-01-29)

  Sequencing of LCM-derived microbiopsies from 30 women who underwent mastectomies due to a breast cancer diagnosis. Goal to assess the mutational burden, spectrum, and clonal dynamics within the tissue. Exome data will be used as a driver and clonality screen, highly clonal or driver-containing samples will subsequently be sent for whole-genome sequencing. Results from this portion of the study will be compared to women who had cosmetic breast reduction surgeries and those with germline BRCA 1/2 mutations. . This dataset contains all the data available for this study on 2020-01-29.

  Dataset EGAD00001005924

• Genome and transcriptome sequence data from a colon cancer patient

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

  Dataset EGAD00001005826

• Genome and transcriptome sequence data from a metastatic melanoma patient

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

  Dataset EGAD00001005852

• Genome and transcriptome sequence data from a cholangiocarcinoma patient

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

  Dataset EGAD00001005838