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• DAC for Genome-Wide Scans of Signals of Selection

  Dac EGAC00001001351

• Tytgat Institute for Liver and Intestinal Research Data Access Committee

  Dac EGAC00001001483

• Tytgat Institute for Liver and Intestinal Research Data Access Committee

  Dac EGAC00001001485

• Tytgat Institute for Liver and Intestinal Research Data Access Committee

  Dac EGAC00001001615

• Epichaperome - Englander Institute for Precision Medicine - Weill Cornell Medicine DAC

  Dac EGAC00001001890

• Tytgat Institute for Liver and Intestinal Research Data Access Committee

  Dac EGAC00001002437

• DAC for COPD human sputum 16s rRNA gene sequencing data

  Dac EGAC00001002779

• Data access committee for sequencing data at Kyoto University

  Dac EGAC50000000045

• Data access committee for neural retina and retinal organoid data

  Dac EGAC50000000019

• Centre for Drug Repurposing and Medicines Research Data Access Committee

  Dac EGAC00001002764

• XClone for analyzing somatic copy number alterations Data Access Committee

  Dac EGAC00001003492

• Single cell multi-omics committee for CK-AML

  Dac EGAC00001003353

• Developmental and Stem Cell Biology department - Hospital for Sick Children

  Dac EGAC00001002951

• Data access committee for sequencing data generated by Wyatt Lab

  Dac EGAC50000000538

• University of Melbourne Centre for Cancer Research (UMCCR) Data Access Committee

  Dac EGAC00001003567

• AGLCD sequencing data

  sequencing datasets for AGLCD patient

  Dac EGAC50000000852

• MK Clinical Trial DAC

  DAC for MK Clinical Trial Data

  Dac EGAC50000000677

• DAC_TWINS

  DAC related to monozygotic twins discordant for ALS

  Dac EGAC50000000517

• WGBS and oxBS-seq for APL

  Study EGAS00001005610

• EGAD00010000819

  Summary statistics from meta-analysis for BP phenotypes

  Dataset EGAD00010000819

• Anne Eugster, Center for Regenerative Therapies Dresden, TU Dresden

  Dac EGAC50000000315

• Aberrant RNA-splicing (neojunctions) offers a new source for targets, and our neoantigen discovery platform (SNIPP) characterizes a novel class of clonally-expressed splicing-derived neoantigens that elicit a CD8+ T-cell-mediated tumor killing response.

  RESULTS: Our pipeline identified 789 public neojunctions, with 32 neojunctions concurrently identified in transcriptomic and proteomic glioma data and predicted to be presented by HLA-A*02:01 with high confidence. IVS and subsequent 10x VDJ scRNA-seq identified TCR clonotypes reactive against neojunctions in RPL22 (n=7) and GNAS (n=1), the latter being highly intratumorally-conserved (detected in > 90% of spatially-mapped biopsies across 17/56 patients (26.78%)). TCR-transduced T-cells demonstrated recognition and immunogenic activation against endogenously processed and presented neoantigens in multiple GBM PDX cell lines. Furthermore, IDH1-mutant oligodendroglioma samples demonstrated significantly elevated expression of neojunctions over IDH1-mutant astrocytoma and IDH1wt subtypes. Differential gene expression (DESeq2) identified decreased expression of splicing factors due to oligodendroglioma-specific co-deletion of Chromosomes 1p/19q. siRNA knockdown of these splicing factors (e.g. SF3A3, SNRPD2) in IDH1wt glioma cells resulted in significantly increased expression of corresponding neojunctions.

  Study EGAS00001007986

• Whole Exome Sequencing of Parathyroid Cancer Identifies Candidate Driver Mutations and Core Pathways

  Here we performed genomic characterization of twenty-nine sporadic parathyroid cancers using next generation whole exome sequencing. Thirty-three novel candidate driver genes for sporadic parathyroid cancer were proposed, in addition to previously known driver genes CDC73 and MEN1.

  Study phs001765

• Whole exome sequencing of virus-associated HCC

  To understand comprehensive combinations of molecular alterations and seek for potential therapeutic targets/pathways in virus-associated HCC, we have conducted a whole exome sequencing (in-solution capturing all human coding exons) of 150 pairs of HCC cases.

  Study EGAS00001000389

• Liquid biopsy to identify taxane resistance in castration-resistant prostate cancer patients

  Taxanes are life-prolonging treatments for patients with advanced prostate cancer. However, treatment resistance and lethal disease invariably develops. We here used liquid biopsies to identify and characterize resistance to cabazitaxel using a targeted sequencing panel (PCF-SELECT).

  Study EGAS50000001292