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• Development of hunanized mice for human hematopoisis and immunity research

  We obtained peripheral blood or bone marrow samples from 112 acute myeloid leukemia patients and examined sensitivity and resistance of the AML samples to molecular targeting drugs. By doing RNA sequencing using AML cells, we found heterogenous gene expression patterns in AML with different mutational landscapes. From the RNA sequencing, we identified anti-apoptosis, cell cycle progression, and immune-related signals as pathways up-regulated in AML cells as compared with normal CD34+ cells. From the pathway analyses, we further setup in vitro experiments to find vulnerability genes in clinically-aggressive AML. BIRC, BCL2, MCL1, AURKB, and KIF10 may be essential molecules for AML cell survival and proliferation.

  Study JGAS000253

• Sequencing data of multiple sarcoma samples for personalized medicine and endotype identification

  Sequencing data derived from multiple patient samples was used to guide multiple patient-specific experiments and identify potential therapeutic options. These diseases are rare and high-risk (undifferentiated pleomorphic sarcoma, rhabdomyosarcoma) and thus have few available validated clinical options. This leaves the population of patients with few options if, and when, standard therapy fails to cure or control disease. An aspect of the personalize therapy design included the identification of broader disease endotypes (a combination of genetic and clinical data describing patient status) to identify subgroups of the individual disease that could better define treatments and could segment patient populations for deeper preclinical research.

  Study EGAS00001003981

• A personalised medicine approach for ponatinib-resistant chronic myeloid leukaemia

  Chronic myeloid leukaemia (CML) is characterised by the presence of a fusion driver oncogene, BCR-ABL1, which is a constitutive tyrosine kinase. Tyrosine kinase inhibitors (TKIs) are the central treatment strategy for CML patients and have significantly improved survival rates, but the T315I mutation in the kinase domain of BCR-ABL1 confers resistance to all clinically approved TKIs, except ponatinib. However, compound mutations can mediate resistance even to ponatinib and remain a clinical challenge in CML therapy. Here, we investigated a ponatinib-resistant CML patient through whole genome sequencing (WGS) to identify the cause of resistance and to find alternative therapeutic targets.

  Study EGAS00001001150

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

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

  Study EGAS00001000327

• How are we funded?

  How are we funded? The EGA is provided infrastructure, administrative support, advisory input, and other relevant and necessary aspects by: CRG The EGA at the CRG is funded and supported by “La Caixa Foundation”, The Generalitat de Catalunya (Catalan Government), the Spanish Ministerio de Asuntos Económicos y Transformación Digital (Spanish Government) and the Instituto de Salud Carlos III. The Generalitat de Catalunya contributes with funding to the CRG and to the Barcelona Supercomputing Centre (BSC). The Barcelona Supercomputing Center is decisively contributing to EGA by providing the required compute, storage and networking resources, as well as key personnel for shared operations of EGA infrastructure. EMBL-EBI As part of the European Molecular Biology Laboratory (EMBL), the EGA at EMBL’s European Bioinformatics Institute receives funding from the governments of EMBL’s member states. The UK government, via UK Research and Innovation, also continues to support EMBL-EBI technical infrastructure, with EMBL supporting operational costs. A major source of funding for the EGA both at CRG and EMBL-EBI are competitive projects.The EGA resource continues to be funded through strategic engagement in collaborative partnerships and projects. Please see our projects page for more information. Other funders include the European Commission, the US National Institutes of Health, the Wellcome Trust, UK Research Councils, and our Industry Programme partners. Last updated on October, 2024.

  Documentation about/projects-and-funders/funders

• Peripheral blood RNA sequencing of samples for a healthy cohort and a cohort with cancer patients

  RNA sequencing (fastq files) of white blood cells (WBCs) from healthy donors (n=376) and cancer patients (n=421) with different diagnoses, stages of disease and previously administered treatments, was performed. Samples from cancer patients were collected from the BostonGene clinical program; all patients provided written consent per IRB-approved protocols. Blood samples from healthy donors were purchased from multiple collection centers throughout the United States. Whole blood samples (3 ml) in K2-EDTA tubes received within 24 hours of collection at RT underwent red blood cell (RBC) lysis to isolate WBCs. Isolated WBCs for RNA sequencing were centrifuged at 300 x g for 5 minutes with a maximum of 10^6 cells per vial. The supernatant was removed, and the cells were resuspended in cold Homogenization Buffer (2% 1-Thioglycerol, Promega). Samples were then frozen at -80°C until extraction. RNA extraction was performed from frozen samples with Maxwell RSC simplyRNA Cells Kit (Promega) using the benchtop automated Maxwell RSC Instrument (Promega). Libraries were prepared with Illumina TruSeq® Stranded mRNA Library Prep (Poly-A mRNA; stranded). Libraries were sequenced on NovaSeq 6000 as Paired-End Reads (2x150) with targeted coverage of 50 mln reads.

  Dataset EGAD50000000414

• Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

  CRISPR-Cas9 genome editing is widely used to study gene function, from basic biology to biomedical research. Structural rearrangements are a ubiquitous feature of cancer cells and their impact on the functional consequences of CRISPR-Cas9 gene-editing has not yet been assessed. Utilizing CRISPR-Cas9 knockout screens for 250 cancer cell lines, we demonstrate that targeting structurally rearranged regions, in particular tandem or interspersed amplifications, is highly detrimental to cellular fitness in a gene independent manner. In contrast, amplifications caused by whole chromosomal duplications have little to no impact on fitness. This effect is cell line specific and dependent on the ploidy status. We devise a copy-number ratio metric that substantially improves the detection of gene-independent cell fitness effects in CRISPR-Cas9 screens. Furthermore, we develop a computational tool, called Crispy, to account for these effects on a single sample basis and provide corrected gene fitness effects. Our analysis demonstrates the importance of structural rearrangements in mediating the effect of CRISPR-Cas9-induced DNA damage, with implications for the use of CRISPR-Cas9 gene-editing in cancer cells.

  Dataset EGAD00001004124

• BLUEPRINT EpiVar ChIP-seq in lineage specifying transcription factors

  The BLUEPRINT project is a large-scale project investigating epigenetic mechanisms involved in blood formation, in health and disease. The human variation workpackage (WP10) of the project seeks to characterize the effect of common sequence variation on the epigenome status of a cell. To do this, the project will use highly purified blood cells to minimise "experimental noise" and therefore enhance the power to discover modest effects. Two peripheral blood cell types, the CD14+CD16- monocyte (an important central orchestrator of adaptive immunity and a bridge between innate and adaptive immunity) and the CD65+CD9- neutrophilic granulocyte (the frontline cell for innate immunity) have been selected for this purpose. The two types of cells will be obtained at high purity from adult blood (AB) of 200 healthy males and females, respectively. Cells will be purified by using already validated and fully operational protocols that are based on density gradient centrifugation of the buffy coat obtained from whole blood, followed by magnetic bead-based purification using monoclonal antibodies against Cluster of Differentiation (CD) lineage-specific cell surface markers. This data set contains functional genomics data for gene expression and chromatin state.

  Dataset EGAD00001004571

• Field effect of healthy and diseased livers (2019-04-08)

  Recent work in the Campbell group has revealed somatic mutations present in normal, non-cancerous human skin. A subset of the mutations conferred selective advantages to the host cells, leading to clonal expansions and raising the risk for future cancer development. Capturing such somatic mutations in normal tissue is important to advance our understanding about carcinogenesis and could provide prospective medical insights. In this project, our goal is to detect somatic mutations in normal (pre-cancerous) liver tissue. Using Laser Microdissection technology, we will dissect individual liver lobules from patient samples and submit these to sequencing. For each patient sample, we aim to sequence multiple lobules to characterise the mutagenic burden. Samples will be taken from patients with different liver disease aetiologies, including alcoholism and obesity, with a view on distinguishing the prevalent mutation types occurring in each disease context. We will perform targeted sequencing, initially using the WTSI cancer panel. Later we aim to use a novel bait set that captures both cancer genes as well as genes relevant to the non-cancerous samples (ie. genes implicated in hereditary disorders, immune sequences). . This dataset contains all the data available for this study on 2019-04-08.

  Dataset EGAD00001004941

• Understanding Self- Organising Capacity of Stem Cells during Implantation and Early Post-implantation Development in vitro and in vivo: Implications for Human Development (2020-04-20)

  The aim of this project is to differentiate human embryonic stem cells to an extra-embryonic fate, specifically the hypoblast. This is of uttermost importance given the current lack of human hypoblast stem cells. We hypothesized that the pluripotent characteristics of the starting human embryonic stem cell population may dictate the competency for extra-embryonic cell fate specification. Based on this hypothesis and using human embryonic stem cells maintained in different naïve-like culture regimes, we have now developed conditions that allow the differentiation of human embryonic stem cells to a stable GATA6+ SOX2- population. This suggests that these cells may be putative human hypoblast stem cells. To validate this finding here we propose to perform RNA sequencing experiments of the differentiated human embryonic stem cells. By comparing their RNA expression profile to the single cell sequencing data of the human embryo that we are currently generating, we will be able to determine the identity of our GATA6+ SOX2- cells, and establish whether they represent the in vivo human hypoblast. This dataset contains all the data available for this study on 2020-04-20.

  Dataset EGAD00001006056

• A spatial human thymus cell atlas mapped to a continuous tissue axis

  T cells develop from circulating precursor cells, which enter the thymus and migrate through specialised sub-compartments that support their maturation and selection. In humans, this process starts in early fetal development and is highly active until thymic involution in adolescence. To map the micro-anatomical underpinnings of this process in pre- and early postnatal stages, we established a novel quantitative morphological framework for the thymus, the Cortico-Medullary Axis, and used it to perform a spatially resolved analysis. By applying this framework to a curated multimodal single-cell atlas, spatial transcriptomics, and high-resolution multiplex imaging data, we demonstrate establishment of the lobular cytokine network, canonical thymocyte trajectories and thymic epithelial cell distributions within the first trimester of fetal development. We pinpoint tissue niches of thymic epithelial cell progenitors and distinct subtypes associated with Hassall’s corpuscles and uncover divergence in the timing of medullary entry between CD4 vs. CD8 T cell lineages. These findings provide a basis for a detailed understanding of T lymphocyte development and are complemented with a holistic toolkit for cross-platform imaging data analysis, annotation, and Organ Axis construction (TissueTag), which can be applied to any tissue.

  Dataset EGAD00001015384

• Single-cell level characterization of B cell depletion and repopulation following rituximab in systemic lupus erythematosus

  Rituximab, a CD20+ B cell depletion therapy, is frequently used in the treatment of systemic lupus erythematosus (SLE). However, variability in patient response highlights the need for a deeper understanding of the underlying immune cell dynamics of B cell depletion and repopulation. In this study, we conducted longitudinal single-cell profiling of nine SLE patients treated with rituximab from pretreatment to up to 15 months post-treatment. These were compared to eight healthy controls. We profiled PBMCs via 10X Genomics single-cell RNA, surface protein (CITE-seq), B cell receptor (BCR), and T cell receptor (TCR) sequencing and sequenced bulk BCR repertoires in parallel. For single cell sequencing, 10 pools were created with an equal number of cells from 4 samples each. Samples collected at different timepoints from the same patient were distributed across different pools to allow demultiplexing of individuals using genotypes captured from the scRNA-seq data. Libraries were pooled using a ratio of GEX:CITE:TCR:BCR=9:2:1:1 and were sequenced across two lanes of the NovaSeq 6000. For bulk BCR sequencing, individual samples were demultiplexed using primer barcodes and paired-end BCR amplicon reads were merged prior to submission; data are provided as unmapped single-end reads.

  Dataset EGAD00001015817

• ONGOING CHROMOSOMAL INSTABILITY ACROSS ANEUPLOID SUBTYPES OF CHILDHOOD B-CELL ACUTE LYMPHOBLASTIC LEUKEMIA ASSOCIATES WITH DISEASE PROGRESSION

  This is the DAC for the scDNA data on the c-B-ALL datasets

  Dac EGAC50000000005

• Cancer Genomics, ICR, cell line data

  DAC for cell line (non patient) data from the Cancer Genomics group, Division of Genetics and Epidemiology at the Institute of Cancer Research, Sutton, UK.

  Dac EGAC50000000023

• DAC Ghent University - Department of Movement and Sports Sciences

  DAC of Ghent University for RNA-seq data of human skeletal muscle biopsies collected at the Department of Movement and Sports Sciences

  Dac EGAC50000000263

• Michigan-Georgetown Cancer DAC

  Genomics data from cancers and/or dysplasias for the collaborations between Maureen Sartor and Nisha D'Silva at the University of Michigan and Laura Rozek at Georgetown University

  Dac EGAC50000000397

• CTOS colorectal cancer organoids – WES and RNA-seq

  Runs for WES and RNA-seq (excluding C138_WES pending file replacement).

  Dataset EGAD50000002401

• Small RNA and MicroRNA sequencing data

  Small RNA and MicroRNA sequencing data was generated for the multiomics analysis of Eurotarget

  Dataset EGAD50000002294

• Targeted PacBio long-read scRNA-seq

  Twist custom capture–based targeted PacBio long-read scRNA-seq datasets for human adrenal sampleA and sampleB

  Dataset EGAD50000002212

• Short-read scRNA-seq

  10x Chromium Single Cell 3′ single-cell cDNA sequencing data for adrenal tissue sampleA and sampleB.

  Dataset EGAD50000002210

• RNAseq for 208 patients with medulloblastoma cancer (MB_COMICS cohort)

  This dataset contains 208 paired fastq files sequenced with Illumina HiSeq 2500.

  Dataset EGAD50000000600

• Taste Receptor Genotypes_Centenarians and Young

  This dataset includes targeted genotyping data for six BMI-associated polymorphisms across four candidate genes in young and centenarian individuals.

  Dataset EGAD00010002829

• SAFIR02_Oncoscan

  Genomics to select patients with metastatic breast cancer for targeted therapy (microarray_oncoscan)

  Dataset EGAD00010002241

• INMUNGEN_CoV2_genotype

  Cohort: Raw genotype files for INMUNGEN_CoV2 cohort. Genotype Chip: HumanCore Exome Chip (Illumina) and Axiom Spanish Biobank Array (Thermofisher) genomic build: b37

  Dataset EGAD00010002174

• stilts-G-1

  Human Core Exome Genotyping for 1471 samples from the STudy Into Lean and Thin Subjects (STILTS) cohort

  Dataset EGAD00010001622

• Gencode_741K

  The individuals were genotyped for the Illumina Human Omni Express Bead Chip (OmniExpress), containing 741,000 SNPs. 22 samples were excluded with more than 10% missing genotypes

  Dataset EGAD00010001640

• Imputation analysis file

  This data set includes the following summary level data file used for the imputation data: imputation.sv.assoc.txt: results from single variant association analysis in imputed samples

  Dataset EGAD00010001184

• RNA-sequencing of SYSCOL colorectal adenoma-carcinoma samples

  RNA-sequencing alignment for SYSCOL colorectal adenoma-carcinoma samples

  Dataset EGAD00001003318

• Reference epigenome CKD23_C_Mesan_mRNA-Seq data generated from KEP study

  A CKD23_C_Mesan_mRNA-Seq paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003481

• Reference epigenome CKD27_C_Mesan_mRNA-Seq data generated from KEP study

  A CKD27_C_Mesan_mRNA-Seq paired end data for Mesangial cells(kidney)

  Dataset EGAD00001003484

• Reference epigenome CKD23_C_Mesan_smRNA-Seq data generated from KEP study

  A CKD23_C_Mesan_smRNA-Seq single end data for Mesangial cells(kidney)

  Dataset EGAD00001003497

• Reference epigenome CKD27_C_Mesan_smRNA-Seq data generated from KEP study

  A CKD27_C_Mesan_smRNA-Seq single end data for Mesangial cells(kidney)

  Dataset EGAD00001003500

• Reference epigenome SMC05_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC05_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003849

• Reference epigenome SMC06_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC06_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003850

• Reference epigenome SMC01_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC01_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003845

• Reference epigenome SMC02_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC02_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003846

• Reference epigenome SMC03_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC03_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003847

• Reference epigenome SMC04_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC04_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003848

• Reference epigenome SMC07_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC07_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003851

• Reference epigenome SMC08_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC08_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003852

• Reference epigenome SMC09_ChIP-Seq(H3K27me3) data generated from KEP study

  A SMC09_ChIP-Seq(H3K27me3) paired end data for skeletal muscle cells

  Dataset EGAD00001003853

• Reference epigenome SMC07_WGBS data generated from KEP study

  A SMC07_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003875

• Reference epigenome SMC01_WGBS data generated from KEP study

  A SMC01_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003871

• Reference epigenome SMC02_WGBS data generated from KEP study

  A SMC02_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003872

• Reference epigenome SMC05_WGBS data generated from KEP study

  A SMC05_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003873

• Reference epigenome SMC06_WGBS data generated from KEP study

  A SMC06_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003874

• Reference epigenome SMC08_WGBS data generated from KEP study

  A SMC08_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003876

• Reference epigenome SMC09_WGBS data generated from KEP study

  A SMC09_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003877

• Reference epigenome SMC03_WGBS data generated from KEP study

  A SMC03_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003888

• Reference epigenome SMC04_WGBS data generated from KEP study

  A SMC04_WGBS paired end data for skeletal muscle cells

  Dataset EGAD00001003889

• Reference epigenome KNIH010 mRNA-seq data generated from KEP study

  A KNIH010 mRNA-seq paired end data for podocytes

  Dataset EGAD00001002176

• Reference epigenome KNIH011 mRNA-seq data generated from KEP study

  A KNIH011 mRNA-seq paired end data for podocytes

  Dataset EGAD00001002177

• Reference epigenome KNIH010 miRNA-seq data generated from KEP study

  A KNIH010 miRNA-seq single end data for podocytes

  Dataset EGAD00001002769

• Reference epigenome KNIH011 miRNA-seq data generated from KEP study

  A KNIH011 miRNA-seq single end data for podocytes

  Dataset EGAD00001002770

• Brain mets external validation cohort targeted panel sequencing raw sequencing files

  Raw sequencing files for the 18 (brain tumour-only) samples within the external validation cohort.

  Dataset EGAD00001005984

• Brain mets discovery cohort, orthogonal validation raw sequencing files

  These are the raw sequencing files for the orthogonal validation brain tumour samples in the discovery cohort.

  Dataset EGAD00001005985

• RNA-seq for IgA BMPC project

  7 RNA-seq samples in total: CD19n_IgAn (x2) , CD19n_IgAp (x2) , CD19p_IgAn (x1), CD19p_IgAp (x2)

  Dataset EGAD00001006862

• Methylation tumour profiles for EGAS00001004572

  Bulk methylation tumour profiles from infinium methylation epic bead kit in EGAS00001004572

  Dataset EGAD00001006909

• KCL PRECSION SNP

  KCL SNP array samples for copy number analysis

  Dataset EGAD00001008379

• Birth Defects: Moebius Syndrome and Related Congenital Facial Weakness Disorders

  It is estimated that about 1 in every 33 infants in the United States is born with a birth defect. Among these, the subset of birth defect syndromes associated with facial weakness and lack of facial expression can have profound implications for social interactions and psychosocial development. Moebius syndrome is defined by congenital and non-progressive facial weakness and limited eye abduction, and most cases are believed to result from dysfunction of cranial nuclei/nerves VI and VII. Although rare, this syndrome causes significant impairment because of facial weakness and associated intellectual disabilities, autism, hearing loss, difficulty swallowing and breathing, peripheral neuropathy, muscle hypotonia, heart defects, chest wall abnormalities, and limb malformations. The phenotypic spectrum and the associated genetic and environmental factors underlying Moebius syndrome are poorly understood. The goal of this research is to identify causative gene mutations for Moebius syndrome and related conditions, such as Moebius-Poland or -Robin sequence, hereditary congenital facial paresis (HCFP), and oculoauriculovertebral dysplasia (Goldenhar syndrome). This proposal builds on an ongoing collaboration among researchers at Mount Sinai Medical Center, Boston Children's Hospital, NHGRI intramural program, and the Moebius Syndrome Foundation, but aims to greatly extend that work by collaboration with investigators in the NIH Clinical Center (CC). Our groups have already defined a new autosomal dominant syndrome with Moebius syndrome, Kallmann syndrome, cyclic vomiting resulting from a TUBB3 E410K substitution. We have also identified a new autosomal recessive Moebius-related syndrome with bilateral facial palsy, hearing loss, and strabismus resulting from a HOXB1 R207C substitution. Through collaborative efforts of these extramural teams with intramural investigators, whole exome sequencing (WES) has been conducted for four families with Moebius-like features, and data analyses are ongoing. The overall goal of this new grant application will be to conduct extensive phenotype analysis on approximately 24 families per year with Moebius and other undefined syndromes with facial weakness. Studies to be conducted at the CC include neurology, psychiatry, neurocognitive, rehabilitation medicine (muscle strength, speech/language pathology), ophthalmology, audiology, and genetics evaluations; autism screening; electromyography, nerve conduction, and blink reflex studies; videoscopy of quantitative eye movement recordings; 3D-CT craniofacial imaging; MRI of the brain, orbit, internal auditory canals, posterior fossa including brain diffusion tensor imaging for tractography; and genetic counseling. Jointly with the extramural teams, WES analysis and variant confirmation will be performed. A more comprehensive definition of the phenotypic and genotypic spectrum of these birth defects will have a significant impact on our understanding of the molecular pathways underlying dysmorphologies, cranial nerve development, and more common childhood disorders such as autism. Thus, this project will lead to strategies for prevention and treatment of birth defects.

  Study phs001383

• Human Microbiome Project Demonstration Study of Cutaneous Microbiome in Psoriasis

  Psoriasis, a highly prevalent disease of humans of unknown cause, is a chronic inflammatory disorder primarily involving skin, with distinctive clinical characteristics. With the newly developed tools that facilitate microbiome research, it now is possible to assess whether the cutaneous microbiome plays a role in the pathogenesis of this disorder. Preliminary data from our studies suggest that the cutaneous microbiome in psoriasis is complex and possibly different from normal. To deal with this complexity, we propose to examine the cutaneous microbiome in relation to psoriasis with explorations at several taxonomic and informatic levels. Our overall objective is to examine how changes in the normal cutaneous microbiome contribute to the pathogenesis of psoriasis. Since causality is complex and often difficult to prove, and beyond the scope of this RFP, our overall hypothesis is that there are alterations in the cutaneous microbiome in areas of skin affected by psoriasis in comparison with the range observed in clinically unaffected areas, or in healthy persons. We also hypothesize that the characteristics of the microbiome may affect clinical responses to the immunomodulatory agents used to treat psoriasis. An alternative hypothesis is that effective treatment of psoriasis with systemic immunomodulatory agents will not substantially affect the disordered microbial ecosystem. Such observations would provide evidence for the roles of the microbiota in this disorder. Since an important consideration in microbiome research is the optimal level (e.g. phylum, genus, species, strain, gene) at which to examine a scientific question, and we are not yet certain what are the optimal levels for psoriasis, this also will be examined. Our studies of psoriasis should allow development of both approaches and tools that will have general utility for Microbiome research. To test our hypothesis, we propose the following specific aims: 1) To understand the cutaneous microbiome species composition overlaying psoriatic lesions; 2)To investigate differences in metagenome content for psoriatic lesions compared to normal skin; 3) To identify differences in the transcriptional profiles of the microbiome and the host between normal skin and psoriatic lesions using high-throughput sequencing; and 4) To estimate the effects of systemic immunomodulatory therapy for psoriasis on microbiome composition. In total, these studies should help us understand the role of the microbiome in psoriasis pathogenesis. We sought to characterize and compare the cutaneous microbiota of psoriatic lesions (lesion), unaffected contralateral skin from psoriatic patients (normal), and similar skin loci in matched healthy controls (control) in order to discern patterns that govern skin colonization and their relationship to clinical diagnosis. Using high-throughput 16S rRNA sequencing, we assayed the cutaneous bacterial communities of 51 matched triplets and characterized these samples using community data analysis techniques.

  Study phs000251

• Analyzing Somatic Mutagenesis in Systemic Sclerosis

  The study was undertaken with the aim of estimating differences in the mutational burden in lung tissues from healthy vs systemic sclerosis (SSc) patients. SSc is an auto-immune disease, with patients often developing cancer. However, the etiology of this phenomenon is poorly understood. As such we sought to uncover potential molecular mechanisms prevalent within SSc tissues that might be potentiating cancer. Samples were randomly collected from individuals from two broad ethnic groups, European (EA) and African American (AA). In total, samples were obtained from 7 individuals belonging to the EA group and 4 individuals from the AA group. For this study, ethnicity was not included as a confounding variable, given that the data set has roughly comparable number of individuals from both ethnicities for the healthy and SSc cohorts. Study participants ranged in age from 37-63 years old. Median age (52 years old) of healthy individuals was comparable to the SSc cohort (~48 years old). Participants were self-described as current/former smokers or non-smokers. Lung tissues were obtained under a protocol approved by the University of Pittsburgh Institutional Review Board. Written informed consent statements were provided to the University of Pittsburgh IRB by the study participants/patients. Sample sizes were determined by the ability of bulk lung fibroblast tissues to stably propagate in culture until single cell clones could be obtained. Samples for which sufficient cell density could not be achieved for downstream high-depth sequencing analysis were excluded from the study and are not reported. Five or greater than 5 samples are collected from each cohort including healthy and SSc patients. Subjects were allocated to two basic cohorts based on diagnosis at the time of explant. Participants with no reported lung anomalies were allocated to the "healthy" cohort, whereas individuals with reported lung abnormalities, primarily SSc with pulmonary fibrosis and/or hypertension were allocated to the "SSc" cohort. All tissue samples were cultured, propagated and processed in identical fashion without requiring individual-specific protocols. Additionally, equivalent amounts of DNA were used for preparing sequencing libraries from both cohorts, and all samples were sequenced using Illumina whole genome sequencing (WGS) and analyzed using identical computational pipelines. Our study primarily discovered that there is a significantly higher burden of somatic mutations in SSc samples, compared to healthy samples. We observed an overall increase in a range of mutations in genomes of SSc patients, including single base substitutions, indels, structural variants and copy number alterations. Additionally, we uncovered a novel mutation signature associated with SSc samples, hinting at the activity of POLH in these samples, and highlighting the potential nexus between inflammation, DNA damage, and cancer.

  Study phs003700

• Prevention and Early Treatment of Acute Lung Injury (PETAL) Acetaminophen in Sepsis: Targeted Therapy to Enhance Recovery (ASTER) (PETAL ASTER-BioLINCC)

  Data Access NOTE: Please refer to the “Authorized Access” section below for information about how access to the data from this accession differs from many other dbGaP accessions. Access to Biospecimens is through the NHLBI Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC). Biospecimens from PETAL ASTER include plasma, urine and whole blood. Please note that use of biospecimens in genetic research is subject to a tiered consent. Objectives: To determine whether acetaminophen increases days alive and free of organ dysfunction in sepsis participants compared with placebo.Background: Acetaminophen (paracetamol) has many effects that can be beneficial in sepsis treatment, including analgesia, antipyresis, cyclooxygenase-2 inhibition, as well as a potent and specific hemoprotein reduction that can block hemoglobin-induced oxidation of lipids and other substrates. The majority of sepsis participants experience elevated circulating cell-free hemoglobin levels, which is associated with development of organ dysfunction including acute respiratory distress syndrome (ARDS) and death.Acetaminophen has been found in observational studies to be associated with improved survival in critically ill sepsis participants with elevated plasma cell-free hemoglobin, and small clinical trials have had positive sepsis participant outcomes such as reduced plasma biomarkers of lipid peroxidation and improved kidney function. However, a large, randomized trial of acetaminophen administration for treatment of fever in participants with suspected infection did not show a mortality benefit. The NHLBI PETAL Network initiated ASTER as a larger phase trial to examine the utility of plasma cell-free hemoglobin level as a biomarker for future sepsis trials and whether acetaminophen would increase the number of days alive and free of organ support for participants with sepsis and respiratory or circulatory organ dysfunction. Participants: A total of 447 participants were enrolled and randomized, 227 to the acetaminophen arm and 220 to the placebo arm. Data from 40 participants who were randomized to the Vitamin C arm, which was stopped early (see Design section below), is also included.Design: ASTER was a phase 2b multicenter, randomized, double-blind trial. The study originally had a 3-arm platform trial in which participants were randomized 1:1:1 to treatment with intravenous acetaminophen, vitamin C, or a common placebo. The vitamin C arm of the trial was stopped after enrolling 79 participants due to external clinical trial data for vitamin C.Participants randomized to the acetaminophen arm received acetaminophen at the dose of 1 g in 100 mL diluent (or 15 mg/kg if actual body weight was Conclusions: Intravenous acetaminophen was considered to be safe but did not significantly improve days alive and free of organ support in critically ill sepsis participants. There was no significant interaction between cell-free hemoglobin levels and acetaminophen.

  Study phs003900

• Exploratory novel biomarker and resistance mechanism of milademetan, an MDM2 inhibitor, in MDM2 amplified intimal sarcoma from an open-label phase 1b/2 trial ���NCCH1806/MK004���

  Amplified Murine double minute 2 (MDM2) is found in > 70% of intimal sarcoma, known as one of the ultra-rare sarcomas. Milademetan (DS3032, RAIN-32) is a novel, specific, small-molecule MDM2 inhibitor that disrupts MDM2 and the tumor suppressor protein p53 interactions in tumor cells. We conducted a phase 1b/2 trial (Trial registration No: JMA-IIA00402) in patients with amplified MDM2 wild-type TP53 intimal sarcoma as a sub-study under the nationwide large registry for rare cancers in Japan (MASTERKEY Project). Eleven patients were enrolled, and ten were included in the efficacy analysis. Two (20%) patients had durable responses for > 15 months. Milademetan provided clinical benefits in patients with amplified MDM2 intimal sarcoma. Predictive biomarkers other than amplified MDM2 and acquired resistance mechanisms for milademetan are unknown. Whole-exome and RNA sequencing analyses of pre-treatment tissue samples were conducted to identify determinants of response. Genomic alterations were analyzed for 10 patients, and gene expression was analyzed for 9 patients using their pre-treatment tissue samples. Targeted sequencing of cell-free DNA (cfDNA) samples (liquid biopsy) was also conducted sequentially at three points [before treatment with milademetan (baseline), at Cycle 2 Day1, and at the time of disease progression] to identify determinants of response and resistance. From whole-exome and RNA sequencing analyses of pre-treatment tissue samples, we could not find any molecular pathways associated with the anti-tumor activity of milademetan. Focusing on 8 genes (CDK4, CDKN2A, CDKN2B, EGFR, ERBB3, MDM2, PDGFRA, TP53) known to be frequently affected in intimal sarcoma and 10 genes (AKT1, ATM, BBC3, CDKN1A, CDKN1C, CHEK2, MDM4, PMAIP1, PPM1D, TWIST1) reported to be associated with MDM2 inhibitor responses; we found that anti-tumor activity correlated with amplified TWIST1 (p-value = 0.028) and negatively with CDKN2A loss (p-value = 0.071). Eight of the 10 patients had their cfDNA collected sequentially at baseline, at Cycle 2 Day1 and disease progression; however, one did not consent to the exploratory analysis study using cfDNA, and one had cfDNA collected at baseline but not at disease progression due to ongoing treatment. Of the eight patients, TP53 mutations in cfDNA were detected in one and five patients at baseline and disease progression, respectively. The cfDNA allele frequency of TP53 mutations increased with disease progression. CDKN2A loss and amplified TWIST1 could be associated with the anti-tumor activity of milademetan in patients with MDM2 amplified intimal sarcoma. Acquired TP53 mutations were detected in sequential liquid biopsies as loss-of-function mutations, and these TP53 mutations might compromise the anti-tumor activity.

  Study JGAS000619

• Geisinger Health System - MyCode, eMERGE III Exome Chip

  DNA samples were obtained from participants of the Geisinger MyCode biobank. Phenotype data to determine case or control status for abdominal aortic aneurysm or extreme obesity were derived from Geisinger electronic medical record data through an enterprise data warehouse. Samples were genotyped using the Illumina Human CoreExome-12 v1.0 Array. Genotype data were filtered using standard quality control measures.

  Study phs000957

• High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics

  We developed a novel microfluidic platform to automatically barcode genomic DNA from individual cancer cells. Using this approach, we sequenced acute myeloid leukemia (AML) tumors targeting up to 62 loci relevant for the disease from thousands of cells. We predict that our platform will enable analysis of heterogeneity in AML and improve stratification and therapy selection.

  Study phs001627

• Substance Dependence GWAS in European- and African - Americans

  This study includes SSADDA (Semi Structured Assessment for Drug Dependence and Alcoholism) assessed subjects (mostly unrelated, but including some affected sibling pairs) recruited in the course of several substance dependence genetics projects. The sample includes 1,531 self-reported African-American (AA) subjects, 1,339 self-reported European-American (EA) subjects, and 2 who reported race as "unknown" or "missing".

  Study phs000952

• Feasibility and Clinical Utility of Whole Genome Profiling in Pediatric and Young Adult Cancers

  Comprehensive Whole Genome Sequencing and Whole Transcriptome (RNASeq) analyses from 114 pediatric patients at Memorial Sloan Kettering. This dataset was used as a prospective clinical utility and feasibility study. By using our Isabl infrastructure for precision medicine, we developed a 2-week end-to-end pipeline to analyze cfDNA, WGS and WTS, which we refer to as cWGTS.

  Study phs002620

• Kids First: Pediatric Research Project on Adolescent Idiopathic Scoliosis

  Both childhood cancers and structural birth defects are critical and costly conditions associated with substantial morbidity and mortality. Elucidating the underlying genetic etiology of these diseases has the potential to profoundly improve preventative measures, diagnostics, and therapeutic interventions. For the current study, families with inherited adolescent idiopathic scoliosis were included. Both affected and unaffected family members were included.

  Study phs001410

• The Genomic Complexity of Primary Human Prostate Cancer

  Seven primary prostate cancers and their paired normal counterparts were DNA-sequenced on a massively parallel sequencing platform. This approach was taken to investigate the genomes for mutations and genomic alterations that would be undetectable by lower-resolution methods. As result, tumors containing chains of balanced rearrangements that occurred within or adjacent to known cancer genes were discovered.

  Study phs000330

• Genotyping Data From Subjects With Brain Lesions

  These data are from subjects with adult diffuse glioma (IDH wildtype, IDH mutant/1p19q intact, and IDH mutant/1p19q co-deleted), brain lesions, tumefactive multiple sclerosis, brain metastases, central nervous system lymphoma and controls genotyped on the Affymetrix Axiom Precision Medicine array. Data from this study were used for case/control association studies and developing polygenic risk scores.

  Study phs003806

• COVID Response Study 2 (COVRES-2)

  COVID Response Study 2 (COVRES-2) - is a collaborative effort between researchers at Ulster University and the Western Health and Social Care Trust. The study aims to identify temporal immune responses associated with COVID-19 severity. A total of n=20 individuals (10=Hospitalised/10=Non-hospitalised) were recruited following a positive PCR result for COVID-19. Current studies 1. Distinct Omicron longitudinal memory T cell profile and T cell receptor repertoire associated with COVID-19 hospitalisation At 3 months post-infection T Cell Receptor (TCR) sequencing and RNA Sequencing were preformed to investigate immunopathological signatures associated with clinical outcome and recovery. This dataset contains both TCR-seq and RNA-seq data for all participants that took part in this study.

  Dac EGAC50000000594

• Transcriptome analysis of kidney organoids lacking NPHP1gene

  To explore the molecular mechanisms of cyst formation in kidney organoids lacking NPHP1, we performed RNA-seq transcriptome experiments. Because the potential for cyst formation by suspension culture should already be derived from kidney organoids at the adherent culture, we compared the global gene expression pattern of kidney organoids on day 18 between healthy group and NPHP1-deficient group

  Study JGAS000683

• Microarray genotyping of idiopathic hypersomnia patients (11 orexin mutation-positive patients, 85 orexin mutation-negative patients)

  We performed a principal component analysis (PCA) to determine whether population stratification or differences in the genetic background are present between the orexin mutation-positive and -negative idiopathic hypersomnia groups. Genome-wide single nucleotide polymorphism (SNP) data in patients with idiopathic hypersomnia (orexin mutation-positive patients and orexin mutation-negative patients) were utilized for the PCA.

  Study JGAS000508

• Systematic identification of long non-coding RNAs potentially involved in gastrointestinal carncer

  Recent work has suggested various important functions and molecular mechanisms for long non-coding RNAs (lncRNAs) and they are also thought to play critical roles in cancer. However the importance of lncRNAs in cancer biology is still unclear. In this study, we aim to comprehensively identify novel lncRNAs that are critically involved in tumorigenesis and progression in gastrointestinal cancer.

  Study JGAS000011

• Mutation screening in a large series of Japanese hearing loss patients using massively parallel DNA sequencing analysis.

  In the present study, mutation screening in a large series of Japanese hearing loss (HL) patients to clarify the prevalence and clinical characteristics of each deafness causative genes. Massively parallel DNA sequencing of 63 or 68 target genes were performed in 2969 unrelated Japanese HL patients to identify genomic variations responsible for HL.

  Study JGAS000490

• Analysis of chromosomal background of cancerous mutations using a long-read sequencer

  In our previous study detecting cancerous complex SVs, we performed whole-genome sequencing of lung cancer clinical samples using PromethION. In this study, its depth and quality was substantially enriched and we conducted the phasing analysis in human lung cancer genomes. In addition, long read and short read RNA-seq was performed for transcriptome analysis.

  Study JGAS000349

• RNA-seq data of proliferative vitreoretinal diseases and healthy human retinal pigment epithelium

  This Data Access Committee (DAC) evaluates access requests for RNA-seq data generated from: - Membranes from proliferative vitreoretinal diseases, including proliferative vitreoretinopathy and epiretinal membranes. - Retinal pigment epithelial cells isolated from healthy ocular globes obtained from deceased donors. Collection and analysis of these residual human materials were conducted with the approval of the ULB-Erasme Ethical Committee (P2019/066 A2022/136) and of the Eye Bank (CHU Liège), with no need for informed consent in compliance with Belgian law. All data are pseudonymised, and access is restricted to qualified researchers whose proposed use of the data is consistent with the applicable ethical approval and legal requirements, including the General Data Protection Regulation (GDPR).

  Dac EGAC50000000721

• ICARUS-LUNG01-GEOMx

  A GeoMx spatial transcriptomic study using 7 patients from the ICARUS LUNG01 trial focusing on tumour and immune cell compartments. We selected 7 paired baseline and on-treatment patient samples for analysis. We selected up to 4 regions of interest (ROI) per sample tissue. We identified tumour and immune cell areas of illumination (AOI) using CK and CD45 antibodies respectively

  Study EGAS50000001679

• Variant analysis on FFPE specimen from NSCLC patients (OCAPlus)

  This study assessed the presence of somatic variants via the Oncomine Comprehensive Panel Plus panel (ThermoFisher) for commonly mutated cancer genes and measure tumor mutational burden using next-generation sequencing. It was performed on genomic DNA from FFPE tissue of tumor resections. Mutations were used to draw OncoPrints and to assess TMB in relation with response metrics.

  Study EGAS50000001136

• Mutagenic impact of radiotherapy in B-cell lymphoma and multiple myeloma

  For refinement of the single base substitution and indel profiles induced by genotoxic platinum and ionizing radiation, DHL4 cells were treated with cisplatin or radiotherapy. Single cells from doses corresponding to lethal and half-lethal (medium), were expanded into single-cell derived colonies and then subjected to 60x whole genome sequencing. 16 bam files were generated.

  Study EGAS50000000997

• Pre-neoplastic somatic mutations including MYD88L265P in lymphoplasmacytic lymphoma

  Normal-cell counterparts of solid and myeloid tumors accumulate mutations years before disease onset; whether this occurs in B-lymphocytes prior to lymphoma remains uncertain. In this study, we sequenced multiple stages of the B-lineage in elderly individuals and patients with lymphoplasmacytic lymphoma, a singular disease for studying lymphomagenesis because of high-prevalence of mutated MYD88.

  Study EGAS00001005656

• Sputum bacterial microbiota in an overall healthy population in Guangdong province, China

  This repository contains raw sequencing data for sputum fungal microbiota in an overall healthy population in Guangdong province, China. The aim of the study is to provide a comprehensive insight on the multi-kingdom airway microbiome, how it may underlie the interplay between exposure and healthy outcomes, and whether it can be employed to inform airway health and diseases.

  Study EGAS00001006721

• Genetic and Microenvironmental Analysis of Peripheral T-cell Lymphoma

  This study enrolled 129 patients diagnosed with PTCL, comprising 94 cases of nTFHL and 35 cases of PTCL-NOS. Whole exome sequencing (WES) and RNA sequencing (RNA-seq) were performed using DNA and RNA of sufficient quality extracted from their tumor specimens. WES was conducted for all 129 cases, while RNA-seq was performed on 57 tumor samples.

  Study EGAS50000001258

• Determining off-target effects of splice-switching antisense oligonucleotides using short read RNAseq in neuronally differentiated human induced pluripotent stem cells

  Splice-switching antisense oligonucleotides (AONs) are designed to modulate pre-mRNA splicing, thereby for instance restoring protein expression or modifying the eventual protein to restore its function or reduce its toxicity. To determine off-target effects, RNA from neuronally differentiated human induced pluripotent stem cells transfected with splice-switching AONs was sequenced.

  Study EGAS50000001222

• μSeq: Universal mutation rate quantification via deep sequencing of a single clonal expansion

  We use patient-derived colorectal cancer organoids to introduce µSeq, a universal framework for inferring mutation rates in diverse biological systems. Our approach extracts mutation rates from deep sequencing of single clonal expansions, with a time gain of tenfold or more compared to a mutation-accumulation line, at the cost of three billion read whole-genome sequencing.

  Study EGAS50000001761

• cfDNA in health

  This study investigates baseline methylome and fragmentomic profiles in circulating cell-free DNA (cfDNA) from healthy individuals. Two cohorts were assembled: a diurnal cohort to evaluate temporal variation in cfDNA features, and a cross-sectional cohort to assess inter-individual variability. The project’s goal was to generate a reference dataset for plasma cfDNA to support future studies in biomarker discovery and disease detection.

  Study EGAS50000001209

• Sputum fungal microbiota in an overall healthy population in Guangdong province, China

  This repository contains raw sequencing data for sputum fungal microbiota in an overall healthy population in Guangdong province, China. The aim of the study is to provide a comprehensive insight on the multi-kingdom airway microbiome, how it may underlie the interplay between exposure and healthy outcomes, and whether it can be employed to inform airway health and diseases.

  Study EGAS00001006720

• Molecular profiling of MBD4-deficient acute myeloid leukaemia

  We describe two cases of MBD4-deficient acute myeloid leukaemia (AML). Clinical samples were used for molecular analysis, including genomic profiling (genome and exomes), methylation analysis (RRBS) and transcriptional profiling (RNA-sequencing). An analysis and methodological description has been published: “MBD4 guards against methylation damage and germline deficiency predisposes to clonal hematopoiesis and early-onset AML” [PMID: 30049810]

  Study EGAS00001002581

• Whole genome sequencing data of paediatric ETV6::RUNX1 acute lymphoblastic leukemia

  ETV6::RUNX1 (E::R) subgroup is the second most frequent form of B cell acute lymphoblastic leukemia (B-ALL) in childhood. This subgroup of ALL generally presents with low-risk features and responds well to chemotherapy with ensuing favorable prognosis. Some patients, however, have a slow response to induction treatment and carry increased risk for relapse.

  Study EGAS50000001599

• RNA-sequençing of 21 inflammatory hepatocellular adenomas

  The French ICGC project on liver tumors is coordinated by Pr Jessica Zucman-Rossi and funded by Inca (French Institute for Cancer). The aim of the present project is to identify the catalog of somatic and germline mutations in liver tumors.The present series corresponds to 21 RNA-seq of IHCA samples. Aligned bam files correspond to hg38 human reference.

  Study EGAS00001003685

• ICGC_Benchmarking_Exercise

  The main objective of this benchmark is the comparison of the full sequencing pipeline of different ICGC partners, including procedures, methods and performance of library preparation and whole-genome deep-sequencing. A secondary objective will be a follow-up comparison of data analysis pipelines for identification of germline and somatic variants subsequent to the results of the ICGC Somatic Variant Calling Pipeline Benchmark.

  Study EGAS00001000433

• Reproducible gut microbial signatures in bipolar and schizophrenia spectrum disorders: A metagenome-wide study

  This is a case-control study in which differences in the gut microbiome of patients with bipolar disorder and schizophrenia spectrum disorders were assessed. The study contains the samples in this dataset, except for G002, G025, G041, G093, G106, G107, G120 and G123. These samples were not yet available at the time the study was performed.

  Study EGAS50000000969

• Investigating transcriptional changes in rapidly differentiated iPSC-derived neurons (i3Ns) harbouring the SNCA A53T mutation +/- RSL3

  In this study we performed bulk RNA sequencing of a iPSC-derived rapid neuronal model harbouring the Parkinson's disease associated A53T mutation in SNCA. These neurons were subsequently treated with a low dose of RSL3 (300nM) for 6 hours to establish the transcriptional impact of ferroptosis induction in the presence or absence of SNCA A53T mutation.

  Study EGAS50000001536

• Low_depth_whole_genome_sequencing_across_multiple_isolated_populations

  Isolated populations have unique population genetics characteristics that can help boost power in genetic association studies for complex traits. Leveraging these advantageous characteristics requires an in-depth understanding of parameters that have shaped sequence variation in isolates. This study performs a comprehensive investigation of these parameters using low-depth whole genome sequencing (WGS) across multiple isolates.

  Study EGAS00001001597

• Investigating_the_impact_of_MBD4_on_the_mutability_of_the_germline

  We will be testing the hypothesis that MBD4 PTV germline carriers also show an increased number of C toT germline mutations in their offspring. 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/

  Study EGAS00001002861

• Whole_exome_sequencing_for_HELIC

  The HELIC study has been whole genome sequencing individuals from 2 Greek isolatedpopulations at 1x depth. The genotype calling process crucially involves a VQSR stepfollowed by imputation-based refinement. We have been investigating optimal ways toincrease calling accuracy. To aid us in setting appropriate parameters for VQSR and otherQC steps, we have carried out whole exome sequencing of a small number ofHELIC samples.

  Study EGAS00001000602

• SARS-CoV-2 induced alterations of the upper airway DNA methylome exert long-term impacts on ciliary genes involved in ciliary function

  Enzymatic DNA methylome (n=33) and single-cell RNA (n=24) sequencing were performed in nasal cells of COVID-19 patients and controls. In addition, we re-sampled a subset of patients for transcriptome analyses at 3 and 12 months post-infection and followed the expression of differentially regulated genes over time.

  Study EGAS50000000273

• Prostate_Cancer_Whole_Genome_Validations

  We propose to definitively characterise the somatic genetics of Prostate cancer through generation of comprehensive catalogues of somatic mutations by high coverage genome sequencing. This study will aim to validate the findings of the whole genome study by re-sequencing regions of interest using a bespoke pulldown bait. See ICGC website for more information: http://icgc.org/icgc/cgp/70/508/71331

  Study EGAS00001000427

• Longread sequencing of selected 12q-amplified osteosarcomas

  Longread sequencing of selected 12q-amplified osteosarcomas for verification of SV data. This was carried out in order to verify findings from mate-pair sequencing regarding the structure of the chromosome 12q-amplicons and whether material from other chromosomes is also intertwined and amplified in a bid to further characterise these tumours beyond CDK4 and MDM2 amplification.

  Study EGAS50000000495