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• Multiplexed biomarkers dynamically detect heterogeneous residual neuroblastoma cell clone activity in the bone marrow niche

  Our objective was to develop a patient-specific, genomics-informed minimal residual disease (MRD) monitoring strategy for pediatric high-risk neuroblastoma using individualized multiplexed mediator-probe PCR (MP-PCR) assays. Tumor-specific somatic mutations or structural variants were identified through hybrid-capture panel sequencing. We examined tumor material from 8 patients, including 11 primary tumor samples, 3 of which represent spatially distinct primary tumor samples and 2 samples obtained at relapse. Provided are FASTQ data files, bam and bambai files, as well as breakpoint spanning and encompassing read (enspan) bam and bambai files. Sequencing bam data files are aligned to GRCh37.p13 reference genome (processed). Sequencing data were aligned to the GRCh37.p13 reference genome and processed using validated pipelines.

  Study EGAS50000001581

• Team

  The Team Mallory Freeberg Roderic Guigó Arcadi Navarro Helen Parkinson Jordi Rambla Ana T. Alonso Silvia Bahena Àlex Bedmar Kenneth Buckley Aldar Cabrelles Ángel Carreño Marcos Casado Giulia Cellerino Amy Curwin Teresa D'Altri Abeer Fadda Teresa Garcia Sara Gregorio Max Fischer Bela Juhasz Oriol Lopez-Doriga Mireia Marin Óscar Martínez Andrea Mero Akiris Moctezuma Aurora Moreno Liina Nagirnaja Francesc de Puig Santiago Rensonnet Gabriele Rinck Aravind Sankar Andres Silva Coline Thomas Sabela de la Torre Gemma Vicente The EGA Team at the CRG co-manages the European Genome and phenome Archive together with the EGA Team at the European Bioinformatics Institute. In addition to maintaining and distributing data, we enrich the contents of the EGA contributing with our knowledge about genomics and the relationship between genomes and phenomes. Previous Team Members Alexander Vikhorev Jeff Almeida-King Mario Alberich Sergi Aguilo Pablo Arce Minjie Ding Alfred Gil Leslie Glass Jag Kandasamy Vasudev Kumanduri llkka Lapalainen Audald Lloret i Villas Sira Martinez Anand Mohan Dietmar Orth Justin Paschall Saif Ur Rehman Gary Saunders Thomas Smith Ashutosh Shimpi Marc Sitges Dhvani Solanki Giselle Kerry Nino Spataro Dylan Spalding Matthieu Vizuete-Forster Cristina Yenyxe Gonzalez Garcia Paul Flicek Anna Foix Emilio Garcia Rios Jorge Izquierdo Roberto Ariosa Marta Ferri Peradalta Daniel Barrowdale Babita Singh Umuthan Uyan Aleix Canalda Dona Shaju Mauricio Moldes Carles Garcia Frédéric Haziza Alegria Aclan Lauren Fromont Alvis Brazma Marta Huertas Arnau Soler Gemma Milla Claudia Vasallo Aina Jené Csaba Halmagyi Raül Garcia Thomas Keane Mei Gascón

  Documentation about/team

• Targeted next-generation sequencing detects novel gene-phenotype associations and expands the mutational spectrum in cardiomyopathie

  Cardiomyopathies are a heterogeneous group of primary diseases of the myocardium,including hypertrophic cardiomyopathy (HCM), dilated cardiomyopathy (DCM), andarrhythmogenic right ventricular cardiomyopathy (ARVC), with higher morbidity andmortality. These diseases are genetically diverse and associated with rare mutations ina large number of genes, many of which overlap among the phenotypes. To betterinvestigate the genetic overlap between these three phenotypes and to identify newgenotype-phenotype correlations, we designed a custom gene panel consisting of 115genes known to be associated with cardiomyopathic phenotypes and channelopathies.A cohort of 38 unrelated patients, 16 affected by DCM, 14 by HCM and 8 by ARVC,was recruited for the study on the basis of more severe phenotypes and family historyof cardiomyopathy and/or sudden death.

  Study EGAS00001002506

• Molecular profiling of tissue autopsies and ctDNA

  The dataset contains high-throughput sequencing data derived from a cancer autopsy series of 10 patients. As part of this study, whole-exome sequencing and RNA-seq were performed for spatially distinct tissue biopsies from the patients. In addition, plasma samples from the patients were sequenced using a custom panelt to profile ctDNA. There are 106 files containing whole-exome sequencing data, 107 files containing RNA-seq data, and 9 files containing plasma sequencing data.

  Dataset EGAD00001007040

• Dataset for hepatopancreaticobiliary_malignancy-RNA

  Rare cancer sequencing data of 119 runs in tumor/control pairs, which were uploaded to umbrella studies. The sequencing was always paired

  Dataset EGAD00001008863

• CCOC WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

  For CCOC cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All CCOC tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

  Dataset EGAD00001003265

• GCT WGS for the study Genomic consequences of aberrant DNA repair mechanisms stratify ovarian cancer histotypes

  For GCT cohorts, OvCaRe cases were reviewed, including frozen material, by at least two expert gynecopathologists prior to inclusion in the sequencing cohort who provided the confirmation on final selected cohort. Frozen H&E from Tokyo were also used for evaluation along with representative H&E photos and review done at the Jikei School of Medicine. All GCT tumours are primary tumour samples. Library construction and sequencing Frozen specimens with >50% tumour cellularity (based on initial slide review) were used for cryosectioning and subsequent nucleic acid extraction. Patient tumour and normal blood samples derived from primary, untreated fresh frozen tumour specimens harvested at diagnosis during standard of care debulking surgery. Germline DNA was provided from peripheral blood buffy coat on all specimens except 13 from Tokyo, where non-cancer frozen tissue was used as a germline source. DNA extraction from both matched normal (blood) and tumour samples (frozen tissue) were performed using the QIAamp Blood and Tissue DNA kit (Qiagen) and quantified using a Qbit fluorometer and reagents (high-sensitivity assay). Three lanes of Illumina HiSeq 2500 v4 chemistry for normal samples and five lanes for tumour samples were obtained. The PCR-free protocol was adopted to eliminate the PCR-induced bias and improve coverage across the genome.

  Dataset EGAD00001003267

• COVID-19: Post-Hospital Thromboprophylaxis A Multicenter, Adaptive, Prospective, Randomized Trial Evaluating the Efficacy and Safety of Antithrombotic Strategies in Patients with COVID-19 Following Hospital Discharge (ACTIV-4C)

  This study is an adaptive, prospective, randomized trial designed to compare the effectiveness and safety of antithrombotic therapy with no antithrombotic therapy after hospitalization for 48 hours or longer for COVID-19. For Stage 1 of this study, participants will be randomized to either prophylactic anticoagulation or no anticoagulant therapy for 30 days, and then followed for an additional 60 days after the completion of treatment (total duration of follow-up, approximately 90 days). Biobanking of samples for future biomarker and mechanistic studies will be available for centers able to participate and collect samples from eligible participants. Samples will be collected at the time of enrollment and after the completion of 30 days of therapy.

  Study phs003063

• RNA-seq data from 224 advanced prostate tumors generated by the West Coast Dream Team

  224 pairs of FASTQ files from metastatic Castration-Resistant Prostate Cancer (mCRPC) sequenced on HiSeq 4000 instruments. Patients were enrolled in the West Coast Dream Team study. Biopsies include various tissue sites including bone, soft tissue, and lymph node.

  Dataset EGAD00001008487

• WGS of HSPC clones of healthy individual sequenced with Illumina NovaSeq 6000

  Dataset contains WGS sequecing data from clonally expanded hematopoietic stem cells from 7 individual pediatric cancer patients. Samples were taken before (DX - diagnosis) or Follow-up (DX2/REM/FU - Diagnosis 2, remission or follow-up, respectively). In addtion, cord blood clones (Designated CB) treated with X-ray radiation, Cisplatin, Maphosphamide, Vincristine and Doxorubicin and untreated cord blood hematopoietic stem/progenitor cells were have been whole-genome sequenced. (Abbreviations RAD, CISPL, MAPH, VINC, DOX and CTRL, respectively)

  Dataset EGAD00001007078