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• GenomeEUtwin Data Access Committee

  Access to data generated by the GenomeEUtwin is available by emailing application to the data access committee and will be granted to qualified investigators for appropriate use.

  Dac EGAC00000000007

• New classification of occlusive cerebrovascular diseases by combining diagnostic imaging and genetic analysis of RNF213

  The aim of the study is to unravel the genetic and environmental background of moyamoya disease and to understand the pathophysiology of the disease by utilizing radiological evaluations. We will identify susceptibility genes other than RNF213. We also assess whether genetics affects radiological characteristics including collateral development, tortuosity of the main trunk of the arteries and the extent of stenosis. Environmental factors will be evaluated such as feces, urea, and cerebrospinal fluid.

  Study JGAS000540

• Placental_genomics

  The aim of this study is to define the mutational landscape of placentas.

  Study EGAS00001003297

• Whole_Genome_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008280

• Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008281

• Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008283

• Bulk_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008278

• Bulk_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008282

• Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008279

• Whole exome sequencing of normal CD34+ cells

  The Genomic DNA Clean & Concentrator kit (ZYMO Research) was used to remove EDTA from the DNA samples. Sample libraries were prepared using 100 ng of input according to the KAPA HyperPlus Kit (Roche) using Unique Dual Index adapters (Integrated DNA Technologies, Inc.). Exomes were captured using the SeqCap EZ MedExome (Roche Nimblegen) according to SeqCap EZ HyperCap Library v1.0 Guide (Roche) with the xGen Universal blockers – TS Mix (Integrated DNA Technologies, Inc.). The amplified captured sample libraries were paired-end sequenced (2x100 bp) on the Novaseq 6000 platform (Illumina) and aligned to the hg19 reference genome using the Burrows-Wheeler Aligner (BWA)3, v0.7.15-r1140.

  Dataset EGAD00001007645

• Identification of potential blood biomarkers for early diagnosis of Alzheimer���s disease through immune landscape analysis

  Mild cognitive impairment (MCI) is a clinical precursor of Alzheimer���s disease (AD). Recent genetic studies have reported on associations between AD risk genes and immunity. Here, we obtained samples and data from 317 AD, 432 MCI, and 107 cognitively normal (CN) subjects and investigated immune-cell type composition and immune clonal diversity of T-cell receptor (TRA, TRB, TRG, and TRD) and B-cell receptor (IGH, IGK, and IGL) repertoires through bulk RNA sequencing. Our prognosis prediction model using the potential blood-based biomarkers for early AD diagnosis, which combined two immune repertoires (IGK and TRA), WDR37, and clinical information, successfully classified MCI patients into two groups, low and high, in terms of risk of MCI-to-AD conversion.

  Study JGAS000532

• Molecular characterization of NASH-HCC

  We collected 80 NASH-HCCs formalin fixed paraffin-embedded (FFPE) samples from 5 different institutions. NASH was diagnosed in FFPE samples by at least two expert pathologists following a described histological algorithm (Bedossa et al., Hepatology, 2012). All NASH patients included in the study were HBV- and HCV-negative. Patients reporting alcohol consumption ≥ 20 g/day for women and 30 g/day for men, as well as patients with a known liver disease superimposed to NASH were excluded. Tumour and paired non-tumour gDNA of NASH-HCC FFPE samples was submitted to Whole Exome Sequencing (WES). Exome capture and sequencing library preparation were performed using the SureSelect Human All Exon V5, no UTR hybridization capture kit from Agilent (Target Size 50 Mb). Libraries were sequenced on an Illumina HiSeq 4000 instrument with 100-bp paired-end reads.

  Dataset EGAD00001007524

• BRAF_and_MEK_resistant_cell_line_clones

  The Sanger Institute has the largest collection of genetically-characterised cancer cell lines world-wide (we have collected >1000 human cancer cell lines which are being screened against >400 cancer therapeutics (http://www.sanger.ac.uk/genetics/CGP/translation). These lines have been characterized to the level of gene copy number, gene expression and cancer gene mutation sequence data. This has enabled us to select melanoma lines with varying BRAF mutational status and that show sensitivity to a range of BRAF inhibitors. Sensitive lines are being used to generate resistant clones by serial exposure to increasing concentrations of BRAF and MEK inhibitors and these are being characterised by genome-wide copy number analysis as well as by whole exome sequencing.

  Study EGAS00001000172

• Whole transcriptome sequencing of pediatric T-cell acute lymphoblastic leukemia

  Pediatric T-cell acute lymphoblastic leukemia (T-ALL) is rare and its pathogenesis is poorly understood. To investigate molecular basis of pediatric T-ALL, we performed whole transcriptome sequencing in 123 cases of pediatric T-ALL.

  Study JGAS000090

• MEMORI WES bams

  This project stores bam files from deep whole exome sequencing from oesophageal adenocarcinoma at different timepoints during neoadjuvant treatment (prior, during, post treatment), which were used to analyse evolutionary and phenotype dynamics in oesophageal adenocarcinoma during neoadjuvant treatment.

  Study EGAS50000000240

• Whole exome and whole genome sequencing of juvenile myelomonocytic leukemia (JMML)

  To obtain a complete registry of gene mutations in JMML, whole-exome sequencing was performed for paired tumor-normal DNA from 13 JMML cases, of which 2 cases were also analyzed by whole genome sequencing.

  Study EGAS00001000521

• Access to shallow whole genome sequencing data from DETECT

  Access to this dataset is subject to aceptance of the terms and conditions. Please summarise your project and sign the following document:

  Dac EGAC50000000553

• Genomic Characterization of Brain Metastases from Lung Cancer

  Metastatic disease to the brain is associated with a poor prognosis. Our understanding of the genetic drivers of metastasis remain limited. Whole-exome sequencing was performed from brain metastases from lung adenocarcinoma to identify putative drivers of metastatic progression.

  Study phs001920

• Comprehensive sequencing analyses of uterine and ovarian carcinosarcoma

  We collected 109 primary tumor and mached normal samples of uterine and ovarian carcinosarcoma. The purpose of this study is to find novel therapeutic options for carcinosarcoma as well as a clue to understand the molecular histogenic mechanism.

  Study JGAS000172

• De novo mutations in cell-free foetal DNA (cffDNA)

  This project is to develop and validate a method to detect de novo mutations in a foetal genome through deep sequencing of cell-free DNA from the plasma of pregnant women. 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 EGAD00001000596

• Childhood_arthritis_DNA

  The aim of this study is to describe the transcriptome of single arthritic cells.

  Study EGAS00001002652

• Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumouroids

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008273

• Single_cell_RNA_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008275

• Single_cell_ATAC_sequencing_of_rhabdomyosarcoma_tumour_tissue

  The aim of this study is to investigate the genomic landscape of human cancer.

  Study EGAS00001008276

• Total RNA sequencing of 32 chronic lymphocytic leukemia (CLL) patients

  Peripheral blood mononuclear cells (PBMC) of CLL patients were isolated by density-gradient centrifugation over Linfosep (Biomedics, Madrid, Spain). B cells were purified with a CD19+ magnetic-bead system (MidiMACS, Miltenyi Biotec, Bergish Gladbash, Germany) according to the manufacturers’ instructions. Mean B-cell purity was >99% and the mean percentage of CD5+/CD19+ cells after purification was >98%, as measured by flow cytometry. Total RNA was extracted from purified cells in a single step using TriPure Isolation Reagent (Roche Applied Science, Vilvoorde, Belgium).Whole transcriptome sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina). Libraries underwent 2 × 76 bp paired-end sequencing on a HiSeq 2500 instrument (Illumina). The median number of paired-end reads was 60.5 million (range, 49.7-79.7 million).

  Dataset EGAD00001004047