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• Whole-exome sequencing of meningiomas for integrative molecular classification.

  Exome libraries were prepared using 100ng DNA of tumor tissue or matched normal DNA. Exome capture was performed using Agilent SureSelect Human Exome Library Preparation V5 or V6 COSIMC + kits.

  Dataset EGAD00001007051

• Alpha synucleinopathy spectrum - single nucleus RNA seq of prefrontal cortex

  Single nucleus RNA seq dataset from prefrontal cortex of a total of N=46 individuals with alpha synucleinopathies and healthy controls. Tissue samples correspond to patients with Parkinson's disease (PD, N=20) monogenic PD caused by LRRK2 mutations (LRRK2-PD, N=7), multiple system atrophy (MSA, N=6) and neurologically healthy controls (N=13). RNA seq was carried out employing 10X Genomics Chromium. These samples were also sequenced using conventional bulk tissue RNA seq, and available within the same study as a separate dataset.

  Dataset EGAD50000000431

• pe_meta_20170131

  Inverse variance weighted fixed effect meta-analysis of three European GWAS studies of the offspring of Pre-eclampsia affected births (2658 Cases and 308267 Controls).

  Dataset EGAD00010001211

• egyptgp-G-1

  Illumina Omni 2.5M SNPchip data (build37) of Egyptian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019)

  Dataset EGAD00010001223

• Single cell RNA sequencing of colorectal cancer patients (CRC-SG1)

  Raw sequencing reads were processed as single end sequencing, aligned to the human reference genome GRCh38 and processed using CellRanger 3.1.

  Dataset EGAD00001008555

• Lung cancer, healthy control and non-cancerous plasma cfDNA samples

  The dataset contains 106 lung cancer, 12 healthy control and 11 non-cancerous lesion plasma cfDNA sample. Shallow WGS was performed on an Illumina Novaseq S4 PE150bp. Samples are provided as raw reads without any prior processing.

  Dataset EGAD00001008321

• The natural history of clonal haematopoiesis: time-series (phase 1-5) targeted

  Deep targeted sequencing of 56 genes associated with clonal haematopoiesis and haematological malignancy in peripheral blood-derived DNA from 385 older adults, each sampled 2-5 times over ~13 years.

  Dataset EGAD00001007682

• Exome sequences of AL amyloidosis (ALA), multiple myeloma (MM) and ALA+MM hematological malignancies

  DNA was isolated from aberrant plasma cells (aPCs) and peripheral blood of 12 ALA, 10 ALA+MM and 29 MM individuals. DNA from aPCs was amplified using REPLI-g Mini Kit (Qiagen). Totally, we analyzed 51 patients, 102 samples. One batch of exome libraries (paired tumor-normal samples from 12 ALA, 10 ALA+MM and 6 MM) was prepared using SureSelect Human All Exon V5 Kit (Agilent Technologies) and sequenced on Illumina HiSeq 4000 platform, 100 cycles. Second batch (23 MM samples; IDs ARK01-ARK26) was prepared using SureSelect Human All Exon V5 + IGH, IGK, IGL, MYC (Agilent Technologies) library preparation kit and sequenced on Illumina HiSeq 2000 platform in paired-end settings, 75 cycles. The reads were mapped using BWA-MEM on human genome GRCh38 without alternate loci.

  Dataset EGAD00001006047

• Feasibility of targeted capture sequencing in FFPE cancer specimens 2

  Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Dataset EGAD00001001448

• Ewings Sarcoma RNA-seq drug sensitivity

  Illumina RNA-Seq will be performed on four Ewing's sarcoma cell lines and two control cell lines. RNA was extracted from all the lines using a basic Trizol extraction protocol.

  Dataset EGAD00001000337

• Breast Cancer FRT RNA seq

  We propose to definitively characterise the somatic genetics of ER+ve, HER2-ve breast cancer through generation of comprehensive catalogues of somatic mutations in breast cancer cases by high coverage genome sequencing coupled with integrated transcriptomic and methylation analyses.

  Dataset EGAD00001000338

• Balanced Ependymoma

  We propose to definitively characterise the somatic genetics of a number of pediatric malignant tumours including ependymoma, high grade glioma and central nervous system primitive neurectodermal tumours through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing.

  Dataset EGAD00001000350

• Feasibility of targeted capture sequencing in routinely collected FFPE cancer specimens

  Testing the feasibility of genome-scale sequencing in routinely collected formalin-fixed paraffin-embedded (FFPE) cancer specimens versus matched fresh-frozen samples using targeted pulldown capture prior to Illumina sequencing.

  Dataset EGAD00001000354

• The BC Cancer Agency's Personalized Onco-Genomics Project

  The BC Cancer Agency's Personalized Onco-Genomics (POG) Project involves molecular and clinical characterization of individual cancer patients to guide their treatment. The project aims to use whole genome and transcriptome data together with patient information to match treatments to cancer driver alterations and support clinical decision-making. Incorporating genomic data into decision-making should enable more rational development of treatment plans, facilitate enrollment into appropriate clinical trials and potentially identify less toxic and more effective therapeutic options.

  Study EGAS00001001159

• Single cell genomic variation induced by mutational processes in cancer

  How cell-to-cell copy number alterations that underpin genomic instability in human cancers drive genomic and phenotypic variation, and consequently cancer evolution, remains understudied. Here, applying scaled single cell whole genome sequencing to wildtype, TP53-deficient and TP53/BRCA1/2-deficient mammary epithelial cells (n=13,818 genomes) and primary triple negative breast (TNBC) and high grade serous ovarian cancers (HGSC) (n=22,057 genomes), we identified three distinct ‘foreground’ mutational patterns defined by cell-to-cell copy number and structural variation properties occurring in the ‘background’ of cancer-associated genomic instability. Cell and clone-specific high level amplifications (HLAMPs), parallel allele-specific copy number alterations and copy number segment length variation (serrate structural variations) exhibited measurable phenotypic and evolutionary consequences. Clone-specific HLAMPs in known oncogenes were highly prevalent in fold back inversion (FBI)-bearing tumors and associated with increased clone-to-clone phenotypic variation in gene expression inferred from matched single cell RNASeq. Parallel allele-specific alterations were linked with phylogenetically determined evolutionary diversity and clone-specific mono-allelic expression. Serrate patterns present across all clones were increased in FBI tumors, most prominently on a tetraploid background and were highly correlated with increased genomic diversity of cellular populations. Taken together, we show that cell-to-cell structural-copy number variation significantly impacts the phenotypes and evolutionary diversity of TNBC and HGSC, revealing previously hidden genomic states of cancer cells.

  Study EGAS00001006343

• Gut microbiota of the Pinggu cohort

  Shotgun metagenomic sequencing data of a total 2,338 fecal DNA samples from adults of the Pinggu cohort.

  Dataset EGAD00001007064

• The Genetics of Lung Cancer Susceptibility in Smokers

  Over 85% of all patients diagnosed with lung cancer report a history of tobacco use, though only 10% of tobacco smokers eventually develop lung cancer. Epidemiologic studies have shown that family members of patients with lung cancer have a higher risk of developing lung cancer than controls. In an effort to identify variants associated with tobacco induced lung cancer, we have sequenced germline DNA from affected and unaffected members of families with strong histories of tobacco related lung cancer.

  Study phs000728

• egpg-G-1

  Illumina Omni 2.5M SNPchip data (build37) of Ethiopian samples from the Pagani et al. 2015 AJHG paper (doi: http://dx.doi.org/10.1016/j. ajhg.2015.04.019)

  Dataset EGAD00010001221

• EGAD00010000632

  WTCCC2 People of the British Isles (POBI) samples using Illumina 1.2M array

  Dataset EGAD00010000632

• EGAD00010000634

  WTCCC2 People of the British Isles (POBI) samples using Affymetrix 6.0 array

  Dataset EGAD00010000634

• EGAD00010000730

  WTCCC2 Psychosis Endophenotype samples from UK, Germany, Holland, Spain and Australia using the Affymetrix 6.0 array

  Dataset EGAD00010000730

• EGAD00010000740

  Osteoarthritis cases genotyped on Illumina HumanOmniExpress from the arcOGEN Consortium (http://www.arcogen.org.uk/) with broader consent.

  Dataset EGAD00010000740

• EGAD00010000742

  Subset 1 of osteoarthritis cases genotyped on Illumina610k from the arcOGEN Consortium (http://www.arcogen.org.uk/) with broader consent.

  Dataset EGAD00010000742

• 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 EGAD00001008948

• Genome and transcriptome sequence data from a multiple myeloma patient

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

  Dataset EGAD00001008947

• Genome and transcriptome sequence data from a neuroendocrine carcinoma patient

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

  Dataset EGAD00001008946

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

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

  Dataset EGAD00001008945

• Genome and transcriptome sequence data from a hematopoietic or lymphoreticular systems myeloma-multiple patient

  Genome and transcriptome sequence data from a hematopoietic or lymphoreticular systems myeloma-multiple patient, generated as part of the BC Cancer Agency's Personalized OncoGenomics (POG) study

  Dataset EGAD00001008944

• Genome and transcriptome sequence data from a melanoma patient

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

  Dataset EGAD00001008943

• Genome and transcriptome sequence data from a breast carcinoma patient

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

  Dataset EGAD00001008942

• 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 EGAD00001008941

• Genome and transcriptome sequence data from a neuroendocrine tumor patient

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

  Dataset EGAD00001008939

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

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

  Dataset EGAD00001008938

• Genome and transcriptome sequence data from a salivary gland carcinoma patient

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

  Dataset EGAD00001008937

• Genome and transcriptome sequence data from a thoracic cancer patient

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

  Dataset EGAD00001008936

• Genome and transcriptome sequence data from a clear cell adenocarcinoma patient

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

  Dataset EGAD00001008940

• Genome and transcriptome sequence data from a paraganglioma patient

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

  Dataset EGAD00001008935

• Genome and transcriptome sequence data from a pancreatic acinar cell adenocarcinoma patient

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

  Dataset EGAD00001008934

• 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 EGAD00001008933

• Genome and transcriptome sequence data from a mucosal melanoma patient

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

  Dataset EGAD00001008932

• 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 EGAD00001008931

• Genome and transcriptome sequence data from a adrenocortical carcinoma patient

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

  Dataset EGAD00001008930

• Genome and transcriptome sequence data from a hepatocellular carcinoma patient

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

  Dataset EGAD00001008929

• 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 EGAD00001008928

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

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

  Dataset EGAD00001008927

• Genome and transcriptome sequence data from a lung adenocarcinoma patient

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

  Dataset EGAD00001008926

• 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 EGAD00001008925

• RNA sequencing of 499 Greenlanders

  The data contain whole transcriptome sequencing of 499 Greenlanders.

  Dataset EGAD00001007717

• RNA-sequencing of primary urothelial bladder cancer samples

  Paired-end RNA-sequencing of tumour tissue samples (n=85) from primary urothelial bladder cancer patients. Sequencing was performed using either HiSeq (n=27) or NextSeq (n=58) Illumina platforms. Of the 85 samples, 78 are Non-muscle invasive (NMIBC) and 7 are Muscle invasive (MIBC).

  Dataset EGAD00001007005

• Genome and transcriptome sequence data from a retroperitoneal mucinous cystic adenocarcinoma patient

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

  Dataset EGAD00001003626