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• Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

  Development of a novel machine learning guided ctDNA detection platform for use in liquid biopsy detection and therapeutic monitoring of solid tumors in several clinical contexts. Included are WGS alignments from our study.

  Study EGAS00001007306

• BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 Full Summary Statistics

  BLUEPRINT WP10 Quantitative Trait Loci (QTLs) Phase 2 full summary statistics data include five molecular traits (eQTL, hQTL(H3K27ac), hQTL(H3K4me1), mQTL, and psiQTL) for three primary blood cells (Monocytes, Neutrophils, and T-cells). Each full summary statistics file contains the associations for all tested variants for each phenotype ID.

  Dataset EGAD00001005199

• Metadata and count matrix

  The dataset contains metadata for all cells before scRNA-seq quality control and for cells passing quality control. It also contains a count matrix with Salmon gene counts for all cells passing quality control, and reconstructed B-cell receptor sequences using the computational tool BraCeR. The scRNA-seq data was generated using the Smart-seq2 protocol and sequenced on Illumina NextSeq500.

  Dataset EGAD00001006435

• Sequencing data for the Genomic Autopsy Study

  The .cram files of the Trio or Quad sequencing data used for generation of the genomic autopsy study. This contains a mix of genome sequencing and exome sequencing data for probands and their parents. A subset of families (n=32) did not provide consent to publicly sharing their data.

  Dataset EGAD00001009737

• Dataset of transcriptomic, whole genome and whole exome sequencing to identify predictive biomarkers in pediatric solid tumors

  This Dataset contains whole genome sequencing data for 148 sample, transcriptome sequencing for 66 samples and exome sequencing for 123 samples from pediatric solid tumors. Sequencing was performed on Illumina NovaSeq 6000 and Illumina HiSeq 4000. The sequencing was paired.

  Dataset EGAD00001015701

• cfDNA methylation dataset for colon cancer

  Enzymatic conversion-based methylation sequencing data (EM-seq) for colon cancer used in the MESA study

  Dataset EGAD50000000075

• PASCAL-MID Data Access Committee

  DAC for the center of Personalized Approach to Genome Editing of Stem Cells for Autotransplantation of Monogenic Immunodeficiencies (PASCAL-MID) at Aarhus University and Aarhus University Hospital

  Dac EGAC50000000680

• Pancreatic Cancer NGS WGS data

  Whole genome sequencing data for Pancreatic Cancer Samples exploring the tandem duplicator phenotype

  Study EGAS50000001078

• V4_Colorectal_panel_test

  Targeted gene screen of cell line tumours for testing the new V4 Colorectal gene panel.

  Study EGAS00001001807

• Dataset for B-ALL scRNA-seq

  10x Genomics 5' library scRNA-seq data for 85 B-ALL patients with different subtypes

  Dataset EGAD00001011327

• WGBS data for Glioblastoma (EGAS00001003953, H016)

  Whole Genome Bisulfite data for human glioblastoma patients, EGAS00001003953. 68 human samples

  Dataset EGAD00001006546

• A98269B

  Whole genome sequencing for single cells for library A98269B 1609 cells; filetype=bam

  Dataset EGAD00001006947

• A96217B

  Whole genome sequencing for single cells for library A96217B 1616 cells; filetype=bam

  Dataset EGAD00001006945

• ChIP-Seq files for PCGP ATRX study

  ChIP-Seq files for PCGP ATRX study paper titled "MYCN Amplification and ATRX Mutations are Incompatible in Neuroblastoma"

  Dataset EGAD00001004429

• PACA-CA RNASeq fastq files

  Fastq files for PACA-CA RNA Seq analysis, for DCC release 27

  Dataset EGAD00001003972

• Covacta RNAseq merged EGA metadata

  Sample metadata for the RNA-seq dataset. This dataset includes subject-level data and longitudinal visit day information for the corresponding samples.

  Dataset EGAD00001011162

• KiCS cancer panel academic only data

  This data set contains KiCS cancer panel data for academic and for-profit use.

  Dataset EGAD00001009733

• Whole exome sequencing (bam files) of 55 samples of myxofibrosarcoma and 44 matched pairs

  Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the whole exome sequence was performed.

  Study EGAS00001005442

• Genomic landscape of Chordoid Glioma

  Chordoid glioma (ChG) is a characteristic, slow growing and well-circumscribed diencephalic tumor, whose mutational landscape is unknown. We analyzed primary chordoid glioma samples by whole exome sequencing, RNAseq

  Study EGAS00001002433

• Targeted_gene_fusion_sequencing__Fus_seq__in_mesothelioma

  This is a small pilot data set to test the feasibility of cDNA exomes across 1200 cancer cell line panel. cDNA exomes or Fus-seq is further explained in this studies Abstract.

  Study EGAS00001000390

• Whole genome sequencing (bam files) of 5 samples of myxofibrosarcoma and 5 matched pairs

  Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the whole genome sequence was performed.

  Study EGAS00001005444

• Targeted-capture sequencing (bam files) of 81 samples of myxofibrosarcoma and 44 matched pairs

  Myxofibrosarcoma (MFS) is a rare subtype of sarcomas in the elderly, whose genetic basis is poorly understood. To elucidate it, the Targeted-capture sequencing was performed.

  Study EGAS00001005443

• Smoking and the Vaginal Microbiome

  The focus of this study was to better understand the effects of cigarette smoking on the vaginal microbiome. There were two phases of the study, cross-sectional and longitudinal, conducted at the Center for Health Behavior Research at the University of Maryland School of Public Health. In the cross-sectional phase, 20 smokers and 20 non-smokers collected mid-vaginal swabs, measured their vaginal pH, prepared a vaginal smear on a slide for Nugent Gram stain analysis, and completed questionnaires about demographics, tobacco use, and reproductive and sexual health history. Smoking status was confirmed through self-report, carbon monoxide exhalation and saliva cotinine measures. Secretions from the mid-vaginal swabs were tested for presence/absence of HPV strains and GC-MS was used to quantify the levels of over 600 metabolites. In the longitudinal phase, 7 participants who were current smokers and motivated to quit smoking were recruited and followed for up to 12 weeks. On a daily basis, participants collected mid-vaginal swabs, measured their vaginal pH, and prepared a mid-vaginal smear on a slide for Nugent Gram stain analysis, and completed daily diaries on tobacco use and reproductive health. Carbon monoxide exhalation and saliva cotinine measures were collected at weekly clinical visits. In addition, participants had weekly behavioral counseling sessions about smoking cessation and used Nicoderm CQ patches to aid in quitting smoking. The self-collected vaginal swabs were used for DNA extractions,16s rRNA sequencing and measurement of metabolites in vaginal fluid.

  Study phs001386

• Whole Exome Sequencing for Colorectal Cancer

  This project was designed to use next generation sequencing technology to screen the protein coding regions of the genome for low frequency variants in a panel of high-risk colorectal adenocarcinoma cases. Blood and cell-line DNA for colorectal cancer patients and a subset of quality control samples that had existing whole exome sequence data were analyzed using Illumina HiSeq sequencers. Samples from this project were from participants in the Women's Health Initiative (WHI) and the Diet, Activity, and Lifestyle Study (DALS).

  Study phs000410

• Investigation of different library preparation and tissue of origin deconvolution methods for urine and plasma cfDNA methylome analysis

  In this study, a single- and a double-stranded library preparation approach was evaluated with respect to their technical biases when applied on cfDNA from plasma and urine. This study thus outlines potential limitations of double-stranded library preparation for methylation analysis of cfDNA especially for urinary cfDNA. While the double-stranded method allows jagged end analysis in addition to TOO analysis, it leads to significant methylation bias in urinary cfDNA, which single-stranded methods can overcome.

  Study EGAS00001007314

• A GWAS for cutaneous leishmaniasis in Brazil

  Our goal was to identify genetic risk factors for cutaneous leishmaniasis (CL) caused by Leishmania braziliensis. Genotyping 2066 CL cases and 2046 controls using Illumina HumanCoreExomeBeadChips provided data for 4,498,586 imputed single nucleotide variants (SNVs). Genome-wide association testing using linear mixed models took account of genetic diversity/ethnicity/admixture. Post-GWAS positional, expression quantitative trait locus (eQTL), and chromatin interaction mapping was performed in FUMA. Transcriptional data were compared between lesions and normal skin, and cytokines measured using flow cytometry and Bioplex assay.

  Study EGAS00001004596

• Annotated VCF Files for WGS of ASD Cohort with 68 Individuals from 22 families, enriched for recent shared ancestry

  We performed whole genome sequencing (WGS) in an ASD cohort of 68 individuals from 22 families enriched for recent shared ancestry. Samples were sequenced using Illumina HiSeq X platform, and Variants (single nucleotide variants (SNVs) and insertions or deletions (indels)) were detected using GATK with HaplotypeCaller. Quality control checks for (i) duplicate samples, (ii) samples per platform, (iii) genome call rate, (iv) missingness rate, (v) singleton rate, (vi) heterozygosity rate, (vii) homozygosity rate, (viii) Ti/Tv ratio, (ix) inbreeding coefficient, and (x) sex inference were performed as previously described. Variant call format (VCF) files for SNVs and indels were annotated with ANNOVAR using allele frequencies from the 1000 Genomes project (2015; 1000G), the Genome Aggregation Database (gnomAD), and the Greater Middle East Variome Project (GME).

  Dataset EGAD00001008634

• ctDNA multigenic panel for non-small cell lung cancer

  Detection of actionable mutations in liquid biopsies constitute an important tool for management of non-small cell lung cancer (NSCLC) patients in the era of oncology precision medicine. We aimed to evaluate the actionable alterations using a commercial multi-gene panel in circulating tumor DNA (ctDNA) derived from plasma samples of treatment naïve and prior-treated non-small cell lung cancer (NSCLC) patients. For this, we analyze plasma samples of 30 subjects with non-small cell lung cancer.

  Study EGAS50000000643

• The Gut Microbiome of renal transplant recipients – Cross-sectional

  TransplantLines is designed as a single-center, prospective cohort study and biobank including all different types of solid organ transplant recipients as well as living organ donors. In the TransplantLines gut microbiome study the gut microbiome of solid organ transplant recipients is characterized and linked to clinical phenotypes. This batch contains the cross-sectional data from renal transplant recipients is.

  Study EGAS00001006257

• Additional Methylation files for Roussel-ATRT-TM

  Additional Methylation files for Roussel-ATRT-TM paper titled "Atypical teratoid/ rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities"

  Dataset EGAD00010002495

• DAC for TFHL single-cell analysis project at Department of Hematology, University of Tsukuba

  DAC for study of tumor heterogeneity and immune-evasive microenvironment in T follicular helper cell lymphomas

  Dac EGAC50000000201

• COMPASS Next Generation Sequencing WGS data

  Whole genome sequencing data for Pancreatic Cancer Samples from the COMPASS clinical trial

  Study EGAS50000001091

• Mucosal 16S metadata

  Metadata for 16S-V4 rRNA gene sequence data for intestinal biopsies from NCT02749630 trial participants.

  Dataset EGAD00001008823

• A95673A

  Whole genome sequencing for single cells for library A95673A 1446 cells; filetype=bam

  Dataset EGAD00001006941

• Data files for CONSERTING

  Data files for CONSERTING (WGS)

  Dataset EGAD00001001352

• Targeted sequencing analysis for MDS with HSCT

  Targeted capture sequencing for cases with MDS who were subjected to unrelated bone marrow transplantation via Japan marrow donor program

  Dataset EGAD00001003118

• RNA data for MMML (EGAS00001002422)

  RNA sequencing data for MMML (3 tumor samples and 1 gcbcell)

  Dataset EGAD00001003285

• CUTRUN files for Klco-NUP98 data

  CUTRUN files for paper titled "Fusion oncoproteins and cooperating mutations define disease phenotypes in NUP98-rearranged leukemia"

  Dataset EGAD00001015478

• WGS files for Mullighan_GL_reALL

  WGS files for Mullighan_GL_reALL paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001005506

• WXS files for Mullighan_GL_reALL

  WXS files for Mullighan_GL_reALL paper titled "Mutational landscape and patterns of clonal evolution in relapsed pediatric acute lymphoblastic leukemia"

  Dataset EGAD00001005509

• Genome-wide analyses of cell-free DNA for therapeutic monitoring of patients with pancreatic cancer

  Determining response to therapy for patients with pancreatic cancer can be challenging. We evaluated methods for assessing therapeutic response using cell-free DNA (cfDNA) in plasma samples from 40 patients with metastatic pancreatic cancer as part of the CheckPAC trial (NCT02866383). Patients were evaluated before and after initiation of therapy using tumor-informed plasma whole-genome sequencing (WGMAF), and genome-wide cfDNA fragmentation profiles and repeat landscapes (ARTEMIS-DELFI). Of those assessed with WGMAF, molecular responders had a median overall survival (OS) of 319 days compared to 126 days for non-responders (HR=0.29, 95% CI=0.11–0.79, p=0.011). For ARTEMIS-DELFI, patients with low scores after therapy initiation had a longer median OS than patients with high scores (233 days versus 172 days, HR=0.12, 95% CI=0.046-0.31, p<0.0001). We validated ARTEMIS-DELFI in a separate cohort of 40 patients with pancreatic cancer who were part of the PACTO trial (NCT02767557). These analyses suggest that non-invasive mutation and fragmentation-based cfDNA approaches can identify therapeutic response of individuals with pancreatic cancer.

  Study EGAS50000000923

• An Isogenic Cell Line Panel for Sequence-based Screening of Targeted Anti-cancer Drugs

  We describe the creation and characterization of an isogenic cell line panel representing common cancer pathways, with multiple features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cells were generated using CRISPR-technologies. Surprisingly, we discovered most of these lines did not result in complete gene inactivation, despite integration of sgRNA at the desired genomic site. However, a subset of the lines harbored true, biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterize lines covering 19 pathways frequently subject to loss of function in cancers. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a multiplexed high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena

  Study EGAS00001005974

• WES data for Heterogeneity of IKZF1 genomic alterations and risk of relapse in childhood BALL

  Whole exome sequencing data for 425 samples with B-cell acute lymphoblastic leukemia

  Dataset EGAD50000000150

• ASD WGS DAC

  This data access committee will oversee the request for applications to whole genome sequencing data (WGS) generated at The Centre for Applied Genomics (TCAG), as part of our Autism Genome Project.

  Dac EGAC50000000279

• Japanese population-specific reference panels (BioBank Japan genotype data)

  Develop Japanese population-specific reference panels to improve imputation quality for GWAS

  Study JGAS000738

• V2_Colorectal_panel_test

  Targeted gene screen of cell line tumour samples for testing the new V2 Colorectal gene panel.

  Study EGAS00001001806

• A96219B

  Whole genome sequencing for single cells for library A96219B 1743 cells; filetype=bam

  Dataset EGAD00001006946

• Additional data for 01_HepG2_LiHG_Ct1, H3K122ac

  Additional histone modification data, not yet released as part of IHEC, for cell line 01_HepG2_LiHG_Ct1, H3K122ac.

  Dataset EGAD00001005954

• A95629A

  Whole genome sequencing for single cells for library A95629A 1023 cells; filetype=bam

  Dataset EGAD00001006939

• ATAC data for Glioblastoma (EGAS00001003953, H016)

  ATAC-seq data for 2 glioblastoma cell lines (LN229, ZH487), NT and SOX10KD.

  Dataset EGAD00001006544

• WGS data (19 tumor/control pairs) for EGAS00001000383

  Part of WGS data for Prostate (ICGC)

  Dataset EGAD00001002669

• A96192B

  Whole genome sequencing for single cells for library A96192B 1304 cells; filetype=bam

  Dataset EGAD00001006944

• A95703B

  Whole genome sequencing for single cells for library A95703B 1267 cells; filetype=bam

  Dataset EGAD00001006942

• SNP data for Ovarian cancer PRS (controls)

  SNP data of 28 sites required for the Ovarian cancer PRS (controls)

  Dataset EGAD00001008145

• WXS files for Roussel-ATRT-TM

  WXS files for Roussel-ATRT-TM paper titled "Atypical teratoid/ rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities"

  Dataset EGAD00001009164

• Additional WXS files for Roussel-ATRT-TM

  Additional WXS files for Roussel-ATRT-TM paper titled "Atypical teratoid/ rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities"

  Dataset EGAD00001010265

• Additional WGS files for Roussel-ATRT-TM

  Additional WGS files for Roussel-ATRT-TM paper titled "Atypical teratoid/ rhabdoid tumoroids reveal subgroup-specific drug vulnerabilities"

  Dataset EGAD00001010264

• McGill EMC Release 4 for assay "smRNA-seq"

  McGill EMC Release 4 for assay "smRNA-seq": Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001001292

• McGill EMC Release 4 for cell type "induced pluripotent stem cell"

  McGill EMC Release 4 for cell type "induced pluripotent stem cell"

  Dataset EGAD00001001276

• McGill EMC Release 4 for assay "Bisulfite-seq"

  McGill EMC Release 4 for assay "Bisulfite-seq": Methylation profiling by high-throughput sequencing

  Dataset EGAD00001001289

• McGill EMC Release 4 for assay "RNA-seq"

  McGill EMC Release 4 for assay "RNA-seq": Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001001290

• McGill EMC Release 4 for assay "mRNA-seq"

  McGill EMC Release 4 for assay "mRNA-seq": Transcriptome profiling by high-throughput sequencing

  Dataset EGAD00001001291

• A95728A

  Whole genome sequencing for single cells for library A95728A 876 cells; filetype=bam

  Dataset EGAD00001006943

• Genome-wide characterization of Kuwaiti Arab Population

  All the 620 individuals were genotyped using Illumina HumanOmniExpress arrays for 730,525 SNPs.

  Study EGAS00001005034

• Gene Expression Signatures in CATHGEN

  Case control cohort: The details have been previously published: American Heart Journal. 2010;160:371-379 e372. Briefly, a nested case:control cohort of CATHGEN participants who had experienced death or MI (n = 250) after their index catheterization and age-, sex-, and race-matched controls (n = 250) who were free of death/MI &#62; 2 years after cardiac catheterization was identified as part of the MURDOCK Horizon 1 Cardiovascular Disease Study.21 Sufficient RNA for microarray analysis was available in 447 members of this cohort. Observational cohort: 224 sequential CATHGEN samples were selected for whole blood RNA analysis, of which, 191 had sufficient RNA for microarray analysis.

  Study phs000551

• Genetics of Pigmentation in Eastern and Southern African Populations Study

  The goal of this study was to identify genes and loci associated with pigmentation in African populations. It comprises 1,593 participants from Ethiopia, Tanzania, and Botswana. Sexes are evenly represented (768 males and 825 females) and self reported ages ranged from 18 to 103. Mean age was used for individuals without ages. For each participant, a DSM II color meter was used to measure underarm skin reflectance in triplicate. These measures averaged and converted to a melanin index (MI = 100 x log10(1/(x/255)). All individuals were included in a genome wide scan that accounted for age, sex, and genetic relatedness.

  Study phs001396

• Multi-omics analysis of treated cancer samples

  We treated patient-derived cell lines with effective drug inhibitors that we discovered. To understand the mechanisms behind how the inhibitor can effectively inhibit tumor growth, we performed a series of RNA-Seq, Histone ChIP-Seq, TF ChIP-Seq and ATAC-Seq profiling for samples with and without treatment with the inhibitor. There are 18 RNA-Seq, 20 ATAC-Seq and 182 ChIP-Seq experiments performed. This includes 2 biological replicates. Novaseq 6000 was used to sequence the samples. Library preparation was performed in house for ChIP-Seq and ATAC-Seq, using NEB indexes, while libraries for RNA-Seq were constructed by the sequencing company hired. Total RNA was sequenced. Sequencing parameters used are PE150, bi-directional sequencing. For ATAC-Seq, sequencing was performed up to 40M reads, for ChIP-Seq, sequencing was performed up to 20M reads and for RNA-Seq, sequencing was performed up to 20M to 40M reads. Fastq files are uploaded here.

  Dataset EGAD50000000349

• CONSERTING: integrating copy number analysis with structural variation detection

  We developed Copy Number Segmentation by Regression Tree in Next Generation Sequencing (CONSERTING), a novel algorithm for detecting somatic copy number alteration (CNA) using whole-genome sequencing (WGS) data. CONSERTING performs iterative analysis of segmentation by read depth change and localized structural variation detection to achieve high accuracy and sensitivity. Analysis of 43 pediatric and adult cancer genomes revealed novel oncogenic CNAs, complex re-arrangements and subclonal CNAs missed by alternative approaches. This study contains all data for "CONSERTING: an accurate method for detecting somatic DNA copy number alterations in whole genome sequencing data", which was previously split between EGAS00001001202 and EGAS00001001050.

  Study EGAS00001001202

• WGS___Exploration_of__mutational_processes_in_human_cancer_cell_lines

  Approximately 25 cell lines representative of 11 mutation signatures have been selected and will be grown from a single cell, referred to as parental clone, for a period of 3 months to allow accumulation of mutations. Following that period, we will obtain 2 subclones from each of the parental clone for analysis by exome-sequencing . In total we will therefore be sequencing 2 parental clones and 4 subclones per cell line for approximately 25 cell lines. Once the data has been analysed and the potential ongoing mutation processes determined, we will perform whole-genome sequencing of the parental clones and subclones of the candidate cell lines.

  Study EGAS00001002680

• Enhanced cortical neural stem cell identity through SMAD/WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells

  For scRNA-Seq, single live cells were suspended in 0.4% BSA in DPBS buffer (1000 cells/µL) and subjected for GEM generation and barcoding. Library preparation was performed according to the recommended procedures of the manufacture Chromium Single Cell 3’ reagent Kit V3.1 chemistry. 10,000 cells were targeted for capturing and 9 cycles were used for cDNA amplification, while 12 cycles were performed for library formation, and sequencing was performed on an Illumina NovaSeq 6000 sequencer. For bulk RNA-Seq, RNA was purified using the miRNeasy™ RNA MiniPrep (Qiagene) and RNA-seq libraries were generated either using the Illumina TruSeq RNA Library Preparation Kits and sequenced on the Illumina HiSeq 2500 sequencer as 76 bp paired-end reads, or using the NEBnext UltraDirectional RNA Library Preparation Kits after rRNA depletion using the NEBNext rRNA depletion kit and sequenced on an Illumina HiSeq 2500 sequencer using 50 cycles of single-end sequencing.

  Dataset EGAD00001008609

• Targeted panel somatic variant sequencing dataset for "Molecular counting enables accurate and precise quantification of methylated ctDNA"

  Targeted panel somatic variant sequencing dataset for "Molecular counting enables accurate and precise quantification of methylated ctDNA." This dataset was created by running 60 cfDNA samples from patients with metastatic cancer to the lung through a research-use, tumor-naive, targeted-panel assay for measuring somatic mutations across a panel of 80 genes. All samples were sequenced on Illumina NextSeq 2000 with 150x2 paired end sequencing; files are in fastq.gz format. For the original study, the variant allele fractions of these somatic mutations were compared with the Tumor Methylation Scores calculated from Northstar Response in the same samples.

  Dataset EGAD50000001016

• Labcorp® Plasma Detect™ assay: whole genome sequencing analyses of plasma cfDNA, white blood cells and FFPE tumor tissue

  The dataset "Labcorp® Plasma Detect™ assay: whole genome sequencing analyses of plasma cfDNA, white blood cells and FFPE tumor tissue" includes CRAM and CRAI files derived from WGS of 555x plasma cfDNA, 209x white blood cells (normal DNA) and 209x FFPE tumor tissue (tumor DNA) samples for 209 stage III colorectal cancer patients. WGS (150bp PE) was performed on a NovaSeq 6000 with a target depth of coverage of 80x for tumor DNA, 40x for normal DNA and 30x for cfDNA. Reads were aligned to GRCh37 (plasma cfDNA) or GRCh38 (tumor/normal DNA).

  Dataset EGAD50000001180

• Functional_characterisation_of_CpG_islands_in_human_and_mouse_tissues

  Tissue-specific methylation patterns suggest a role for CpG island (CGI) methylation in differentiation and cell-type-specific gene regulation. We have applied CXXC affinity purification (CAP), MBD affinity purification (MAP) and chromatin immunoprecipitation (ChIP) in combination with solexa sequencing to investigate the extent and functional significance of CGI methylation in sperm, blood, cerebellum and ES cells for both human and mouse.

  Study EGAS00001000075

• Whole genome sequencing of adult glioblastoma nuclei

  Nuclei were extracted from three primary adult glioblastoma samples and processed for scATAC-seq, and residual nuclei left over from these same samples were used to extract DNA and processed and sequenced for WGS. This WGS data was then used to cross-validate assessment of large-scale copy number alterations with scATAC-seq using the Copy-scAT tool.

  Study EGAS00001005256

• Genomic landscape of signals of positive natural selection in North Eurasia

  We searched for the genomic signatures of positive selection in the genome-wide data of 432 people from eight different northern Russian populations (Russians from the Archangelsky and Vologdsky regions, Izhemski Komi, Priluzski Komi, Veps, Khanty, Mansi and Nenets) who were genotyped using microarrays for 700,000 SNPs (InfiniumOmniExpress-24v1-2_A1) through testing the extended haplotype homozigosity (EHH).

  Study EGAS00001003955

• RNA-seq on neuroblastoma PDX model COG-N-519 treated with control miR-1283 and test miR-99b-5p mimics

  COG-N-519 primary neuroblastoma cells were innoculated by subcutaneous injection into NSG mice. When tumours reached a size of 100-200mm3 miRNAs conjugated to nanoparticles were injected intratumourally every 2 days for 1 week. 24 hr after the last injection, snap frozen tumour tissue was harvested for RNA extraction and RNA-seq analysis.

  Study EGAS00001005581

• DNA methylation of peripheral blood leukocytes from patients with Li-Fraumeni syndrome

  Genomic DNA (~ 1 μg) from LFS patients was treated using sodium bisulfite (Qiagen) converting unmethylated cytosine to uracil but leaving methylated cytosine intact. These samples were then hybridized to the HumanMethylation450 BeadChip or HumanMethylationEPIC BeadChip from Illumina at the Centre for Applied Genomics (TCAG) at the Hospital for Sick Children using the manufacturer’s recommended protocol.

  Study EGAS00001007075

• March 2018 cumulative data release for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium.

  March 2018 cumulative data release (bams,fastqs) for reference epigenomes generated at Centre for Epigenome Mapping Technologies, Genome Sciences Center, B.C. Cancer Agency as part of the International Human Epigenome Consortium

  Dataset EGAD00001003963

• The Causes of Clonal Blood Cell Disorders Study - SCOR_Custom (2018-04-19)

  We took a bone marrow aspirate and peripheral blood samples from a healthy patient aged around 60, and use flow cytometry to isolate 100 HSCs, 50 MEPs, and 50 GMPs. We grew these up into colonies, then whole genome sequenced each colony. Somatic mutations act as a unique barcode for each clone. We have designed a panel for targeted resequencing of the mutations that we find. We are now looking for these mutations in the peripheral blood, to see the dynamics of how HSCs contribute to the peripheral blood in health. This dataset contains all the data available for this study on 2018-04-19.

  Dataset EGAD00001004087

• Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML

  Our aim was to identify regulators of the EVI1/MECOM gene, which is the most lethal oncogenic TF and is highly expressed in AML with chromosome 3q26 abnormalities.

  Study EGAS50000000347

• Control human putamen and Substantia Nigra

  The study is affiliated to the UKBEC sample of healthy human putamen and substantia nigra phenotype. The gender is from both male and female samples of the the phenotype.

  Study EGAS00001003065

• Mesothelioma_Whole_Genomes

  Genomic architecture of mesothelioma parent study is project 925. This project is set up in parallel to project 925 in order to Whole genome sequence ten of the 59 tumours in that project.

  Study EGAS00001000830

• Bacterial SNPs in the human gut microbiome associate with host BMI

  Genome-wide association studies (GWAS) have revolutionized the field of genetics, providing numerous associations between human SNPs and health traits. Likewise, metagenome-wide association studies (MWAS) between bacterial SNPs and human traits can suggest mechanistic links between the microbiota and its host. However, very few such studies have been done to date, in part due to the large number of samples required to address the variable coverage of bacteria across samples and the fact that most bacteria are present in only a subset of the population. Here, we devised an MWAS framework to detect SNPs and associate them with host phenotypes systematically. We recruited and obtained gut metagenomic samples from a cohort of 7,190 healthy individuals and discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI). To address the possible effects of population structure and linkage disequilibrium, we applied a clumping procedure, and found 40 independent associations between SNPs and host BMI. We uncovered BMI-associated SNPs in the genomes of 27 bacterial species, even though the relative abundance of 12 of these species was not associated with the phenotype. We separated genome-wide sub-species variations from local associations in individual SNPs, and demonstrated how this framework can highlight specific bacterial functions of interest. Our results demonstrate the importance of considering nucleotide-level diversity in microbiome studies and pave the way toward a better understanding of interpersonal gut microbiome differences and their health implications.

  Study EGAS00001007204

• RNA sequencing of baseline HCC PDX models

  To establish the baseline transcriptional profiles, we performed bulk RNA-seq for 36 of our HCC PDX models. 2-6 samples were collected for each model resulting in a total of 68 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

  Dataset EGAD50000000736

• BLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples

  BLLUEPRINT ATAC-seq data for cells in the haematopoietic lineages, from adult and cord blood samples.

  Study EGAS00001001596

• RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 or vehicle

  This experiment consists of RNAseq of liver harvested from CDAHFD mice treated for 8 weeks with either the MGAT2 inhibitor compound BMS-963272 (N = 10) or with vehicle (N = 10).

  Study EGAS00001006583

• Reference single cell SNP array dataset from Coriell for training and validation of method for accurate single cell genotyping

  This dataset contains DNA from B-lymphocytes from 2 Coriell families and 4 individuals hybridized to HumanKaryomap BeadChip Array. Single cells from subjects GM12878 and GM7228 were amplified using multiple displacement amplification (SureMDA) according to Infium Karyomapping Assay Guide. Bulk DNA was processed and hybridized to an array for subject GM12878, GM07224 and GM07225.

  Dataset EGAD00001006376

• WES and WGS data for HGSC patient derived cell lines and fresh frozen tumor samples from same patients

  Sequencing data for three HGSC patients with patient derived cell lines. WES data for two patient derived cell line samples and matched blood control samples. Fresh frozen tumor samples of two patients with WES or WGS sequencing data.

  Dataset EGAD00001009330

• ESGI - Molecular diagnosis for mitochondrial disorders (2017-08-29)

  The MITOEXME project aims to improve protocols for molecular diagnosis of patients with OXPHOS disorders with a focus on a next generation sequencing methods and to increase the knowledge of pahtophysiological mechanisms by identification of new targets and cellular studies. In this project we will sequence the exomes fo 120 patients. This dataset contains all the data available for this study on 2017-08-29.

  Dataset EGAD00001003596

• Paired-end Whole Exome-seq analysis of multi-centric lower grade glioma

  This dataset includes Nimblegen SeqCap EZ Exome v3 data for each lesion of three patients with multicentric glioma. For two patients, each lesion was sequenced along with whole blood. For a third patient, 3 pieces from the right lesion and 4 pieces from the left were sequenced along with whole blood. In each case BAM files that have been aligned with BWA mem alignment are available.

  Dataset EGAD00001003795

• RNA-Seq of novel miR (nmiR-1 and nmiR-2) overexpression and knockdown in BL

  After overexpression and knockdown of both described novel miRs nmiR-1 and nmiR-2 in BL cell lines (SU-DHL4 for nmiR-1 and Raji for nmiR-2), we performed regular RNA-Seq (including Mock controls for all cell lines) to identify their direct and indirect downstream mRNA targets.

  Dataset EGAD00001001612

• Coding and small non-coding transcriptional landscape of tuberous sclerosis complex cortical tubers: implications for pathophysiology and treatment

  Tuberous Sclerosis Complex (TSC) is a rare genetic disorder that results from a mutation in the TSC1 or TSC2 genes leading to constitutive activation of the mechanistic target of rapamycin complex 1 (mTORC1). TSC is associated with autism, intellectual disability and severe epilepsy. Cortical tubers are believed to represent the neuropathological substrates of these disabling manifestations in TSC. In the presented study we used high-throughput RNA sequencing in combination with systems-based computational approaches to investigate the complexity of the TSC molecular network. Overall we detected 438 differentially expressed genes and 991 differentially expressed small non-coding RNAs in cortical tubers compared to autopsy control brain tissue. We observed increased expression of genes associated with inflammatory, innate and adaptive immune responses. In contrast, we observed a down-regulation of genes associated with neurogenesis and glutamate receptor signaling. MicroRNAs represented the largest class of over-expressed small non-coding RNA species in tubers. In particular, our analysis revealed that the miR-34 family (including miR-34a, miR-34b and miR-34c) was significantly over-expressed. Functional studies demonstrated the ability of miR-34b to modulate neurite outgrowth in mouse primary hippocampal neuronal cultures. This study provides new insights into the TSC transcriptomic network along with the identification of potential new treatment targets.

  Study EGAS00001002485

• Sequencing data for Australian Ovarian Cancer study submitted 20121116

  Sequencing data for Australian Ovarian Cancer study submitted 20121116

  Dataset EGAD00001000293

• Sequencing data for Australian Pancreatic Cancer study submitted 20130102

  Sequencing data for Australian Pancreatic Cancer study submitted 20130102

  Dataset EGAD00001000323

• HiSeq sequencing data for PDAC cell lines generated by QCMG

  Sequencing data for PDAC cell lines generated by QCMG

  Dataset EGAD00001000371

• Array data for oesophageal and related samples – sj_paper_methyl_tumour_release

  Array data for oesophageal and related samples – sj_paper_methyl_tumour_release

  Dataset EGAD00010001822

• Colorectal cancer functional annotation - ChIP

  ChIP-seq data for multiple colorectal cancer cell lines (H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me3, CTCF)

  Study EGAS50000000207

• Roifman DAC

  This Data Access Committee will oversee all requests for data submitted by Dr. Chaim Roifman at the Hospital for Sick Children in Toronto, Canada. Requests should be directed by email to chaim.roifman@sickkids.ca.

  Dac EGAC50000000396

• EM-seq converted WGS for CSF-derived cfDNA from pediatric brain tumor patients

  EM-seq converted WGS for CSF-derived cfDNA from pediatric brain tumor patients

  Dataset EGAD50000001975

• GBM cancer stem cell lines -RNA-seq and WGS data

  Glioblastoma stem cell lines have been profiled for RNA-seq and WGS

  Study EGAS00001003700