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• Whole genome sequence of third generation family member (SFHS)

  Previously we performed deep WGS on 6 parents and 13 children from 3 large families from the Scottish Family Health Study to identify de novo mutations. This prelim is cover the additional sequencing of one grandchild from one of these three families. The inclusion of a third generation individual will provide additional experimental validation for the de novo mutations found in the initial trio. As in the previous study, the DNA will be WGS to a depth of approximately 25X to achieve this purpose.These data can only be used for the investigation of the genetic causes of the reported clinical phenotypes in these patients

  Dataset EGAD00001001454

• 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 EGAD00001001961

• 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 EGAD00001001962

• 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 EGAD00001001965

• Genome and transcriptome sequence data from a breast cancer patient

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

  Dataset EGAD00001002019

• Genome and transcriptome sequence data from a breast primary patient

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

  Dataset EGAD00001002017

• A somatic reference standard for cancer genome sequencing.

  Paired PCR-free whole genome sequencing data of a matched metastatic melanoma cell line (COLO829) and normal across three lineages and across separate institutions, with independent library preparations, sequencing, and analysis. The data was generated with mean mapped coverages of 99X for COLO829 and 103X for the paired normal across three institutions. Overall, common events include >35,000 point mutations, 446 small insertion/deletions, and >6,000 genes affected by copy number changes. We present this reference to the community as an initial standard for enabling quantitative evaluation of somatic mutation pipelines across institutions.

  Dataset EGAD00001002142

• Native American Ancient DNA sequencing

  The morphology of the first humans in the Americas (Paleoamericans) differs from that of Native Americans, and has raised the question of whether or not there are also differences in origin or genetics. A few populations who survived until relatively recently have been suggested to retain Paleoamerican morphology. One of these populations is from La Jolla. Here, we have generated genome sequence data from four La Jolla individuals in order to investigate these questions This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

  Dataset EGAD00001002144

• Genome and transcriptome sequence data from a multifocal hepatocellular carcinoma patient

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

  Dataset EGAD00001002644

• 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 EGAD00001002643

• 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 EGAD00001002639

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

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

  Dataset EGAD00001002648

• 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 EGAD00001002647

• 24 Chordoma samples (WES,WGS)

  Case series of the rare tumor entity chordoma. 9 cases sequenced with Whole Exome Sequencing (WES) and 2 cases sequenced with Whole Genome Sequencing (WGS) were recruited from the personalized oncology program NCT-MASTER/DKTK-MASTER at the German Cancer Research Center. One of the WES patients was re-sequenced at a later time point when he relapsed, this resequencing was done by WGS. Therefore there are 11 patients, one of which with two samples, all of which were sequenced with matched normal controls, amounting to a total number of 24 NGS samples.

  Dataset EGAD00001004825

• Whole Genome Sequencing of CRLF2/IL7RA transduced cells

  There are two samples, 42 (control) and 49 To test the role of activated CRLF2/IL7RA in leukemia initiation we expressed CRLF2 together with IL7RA in human CB hematopoietic progenitors. Human CRLF2 and wild type and/or activated mutant form of human IL7RA (IL7RAwt/ins) were cloned into a lentiviral vector with a bi-cistronic cassette under the expression control of an Eμ-B29 promoter/enhancer to augment expression in B-cell precursors. Backbone vector expressing GFP (BB). Whole genome sequencing Leukemic (49) and BB transduced (42) corresponding CB cells were collected from transplanted mice. Sequencing libraries were prepared from these samples

  Dataset EGAD00001005456

• Tumor and normal exomes for 95 PMBCL cases

  Whole-exome sequencing for 95 PMBCL cases (including 21 with matching normal DNA) was performed using a targeted capture approach with the SureSelect Human All Exon V6+UTR bait (Agilent Technologies) followed by massively parallel sequencing of enriched fragments on the HiSeq2500 platform (Illumina). Five libraries were pooled per lane and a 125bp paired-end mode was used. Tumor and normal DNA samples were sequenced to an average of 115X (SD 24X). All reads were aligned to the human reference genome (hg19) using bwa-mem version 0.7.5a29 with optical and PCR duplicates removed using the Picard tool.

  Dataset EGAD00001005780

• Genome and transcriptome sequence data from a gastroesophageal junction adenocarcinoma patient

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

  Dataset EGAD00001005910

• Genome and transcriptome sequence data from a colon adenocarcinoma patient

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

  Dataset EGAD00001005911

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

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

  Dataset EGAD00001005908

• Genome and transcriptome sequence data from a pancreatic adenocarcinoma patient

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

  Dataset EGAD00001005907

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

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

  Dataset EGAD00001005903

• Genome and transcriptome sequence data from a pancreatic ductal adenocarcinoma patient

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

  Dataset EGAD00001005904

• Lymphocyte LCM WGS (2020-02-20)

  Using whole genome sequencing of lymphocytes excised from human tissue using laser capture microscopy (LCM), we identify the mutations arising in these microenvironments. This work will contribute towards developing a catalogue of mutations present in tissue resident lymphocytes across a range of tissues, and will characterize the mutational signatures that result from each microenvironment. . This dataset contains all the data available for this study on 2020-02-20.

  Dataset EGAD00001005992

• Whole genome sequencing data for Molecular Characterization of ETMRs

  This dataset contains whole genome sequencing data from 59 samples. WGS libraries were prepared using the Illumina TruSeq Nano DNA LT Library Prep or TruSeq Nano DNA HT Library Prep Kit following the manufacturer’s instructions. In brief, 100 ng of genomic DNA was fragmented to approximately 350 bp using a Covaris ultrasonicator (Covaris). The fragmented DNA was then end-repaired, size-selected using magnetic beads, extended with an ‘A’ base on the 3′ end and ligated with TruSeq paired-end indexing adapters. Up to four lanes per sample have been sequenced resulting in 222 Fastq files (paired end).

  Dataset EGAD00001006211

• AVENIO Expanded ctDNA panel sequence alignments (BAMs) from plasma DNA of BC, CRC and NSCLC patients

  The AVENIO ctDNA Expanded Kit is a next-generation sequencing (NGS) liquid biopsy assay with a 77 gene panel (192 kb) containing genes in U.S. National Comprehensive Cancer Network (NCCN) Guidelines and emerging cancer biomarkers. This pan-cancer assay was applied to 48 plasma samples from patients with breast, colorectal and non-small cell lung cancer. After sequencing 150bp paired-end, reads were aligned to the hg38 genome with the AVENIO Oncology Analysis Software (version 2.0). These files are the deduplicated alignments generated by the analysis software used for subsequent variant, indel and CNV calling.

  Dataset EGAD00001006301