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• An epigenomics time course analysis of covid19 patients from Quebec, Canada

  Investigating the cellular and epigenetic changes at play in severely ill hospitalized COVID-19 patients at admission and how it evolves with prognosis. Single-cell RNA-seq analysis done on longitudinal samples highlighted changes in the monocytic compartment, which we explored using whole-genome epigenomics methods (ATACseq abd WGBS).

  Study EGAS00001005468

• A first step towards clinical routine long-read sequencing in Sweden, a national pilot study on chromosomal rearrangements

  Here, the Genomic Medicine Sweden Rare Diseases (GMS-RD) consortium validated HiFi Revio long-read whole genome sequencing (lrGS) for clinical digital karyotyping of SVs nationwide. The first 16 samples included in this study were collected from all health care regions in Sweden. We established a national pipeline and a shared variant database for variant calling and filtering. The included validation samples cover a spectrum of simple and complex SVs including inversions, translocations and copy number variants.

  Study EGAS50000000468

• UCSF Pediatric Bithalamic Glioma Genome Project

  Brain tumors are the most common solid tumors of childhood, and the genetic drivers and optimal therapeutic strategies for many of the different subtypes remain unknown. We performed targeted next-generation sequencing of approximately 500 cancer-associated genes on a cohort of 13 pediatric bithalamic diffuse gliomas, a lethal brain tumor of childhood for which the genetic basis is largely unknown. We identified that bithalamic diffuse gliomas harbor frequent mutations in the EGFR oncogene in the absence of accompanying gene amplification and only rare histone H3 mutation. These EGFR mutations were either small in-frame insertions within exon 20 (intracellular tyrosine kinase domain) or missense mutations within exon 7 (extracellular ligand-binding domain). Accompanying alterations included frequent TP53 mutation, CDK6 amplification or CDKN2C mutation, and BCOR and BCORL1 mutation or deletion.

  Study EGAS00001004033

• Chromosomally integrated HHV6 data of parent-infant pairs

  Raw data used in the analysis of chromosomally integrated HHV6 genomes in parent-infant pairs, generated by means of full viral genome sequencing by SureSelect target enrichment, in the context of a larger study investigating the relationship between HHV6 and adverse pregnancy outcome.

  Dataset EGAD00001004592

• PRADO trial - Personalized response-directed surgery and adjuvant therapy after neoadjuvant ipilimumab plus nivolumab in stage III melanoma

  The dataset includes WES sequencing data on PRE- treatment biopsies of lymph node metastasis (n=79) The technology used for sequencing is llumina HiSeq. The PRADO trial tested a personalized response-directed treatment approach based on the pathologic response after neoadjuvant ipilimumab plus nivolumab in stage III melanoma patients. In patients achieving a major pathologic response, in their index lymph node (the largest lymph node metastasis at baseline), therapeutic lymph node dissection (TLND) and adjuvant therapy were omitted. Patients with partial response underwent TLND only, whereas patients with pathologic non-response underwent TLND and adjuvant systemic therapy ± synchronous radiotherapy.

  Dataset EGAD50000000393

• Identification of fungal species in brain tissue from Alzheimer's disease

  Identification of fungal species present in the central nervous system tissue from Alzheimer's disease patients by next-generation sequencing.

  Study EGAS00001002228

• Genome-wide array data Tunisia and Morocco

  This dataset contains genome-wide array data from Tunisian and Moroccan individuals. Tunisian individuals were sampled in the city of Tunis (n = 64), and Moroccan individuals in different urban areas in the country (n = 45).

  Dataset EGAD00001009071

• Targeted sequencing of in vitro colonies - bulks (2020-05-05)

  In this study we will perform targeted sequencing on the bulk samples of in vitro colonies. This dataset contains all the data available for this study on 2020-05-05.

  Dataset EGAD00001006118

• Sequencing of longitudinal glioma pairs

  Clonal evolution drives cancer progression and therapeutic resistance. Recent studies revealed divergent longitudinal trajectories in gliomas, but early molecular traits steering post-treatment cancer evolution remain unclear. We analyzed sequencing data of 544 initial-recurrent adult diffuse glioma pairs to identify genomic and transcriptomic early predictors of tumor evolution in each molecular subtype.

  Dataset EGAD00001009845

• Reliable detection of somatic mutations in single DNA molecules

  This dataset contains 160 single-cell derived blood colonies from two neonates and 6 adults. It also contains 18 samples that were used as matched normals to call mutations in NanoSeq data (dataset EGAD00001006459).

  Dataset EGAD00001006595