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• Spatiotemporal single cell transcriptomic analysis of human gut macrophages team commitee

  Dac EGAC00001002166

• DAC - U1085 Team Physiology and Physiopathology of the urogenital tract (INSERM / IRSET)

  Dac EGAC00001002830

• Tracking Therapy-Resistant Alterations in Childhood Acute Lymphoblastic Leukemia

  Relapse is currently the major cause of death in children with B-ALL. The goal of this study is to uncover the genetic underpinnings of relapsed B-ALL in the AALL1331 cohort (PMID: 33651090) via whole genome and transcriptome sequencing of matched diagnosis, relapse, and remission specimens. We aim to discover genetic alterations that drive treatment resistance in relapsed tumors. We also aim to investigate the feasibility of detecting residual tumors from remission samples with the ultimate goal to improve risk stratification using NGS-based minimal residual disease (MRD) detection. Here we only report data from patients in remission with the aim of determining MRD. We will submit corresponding data for the diagnosis and relapse components of our cohort in a future version of our study.

  Study phs003409

• WGS of Multiple Myeloma/MGUS/SMM cases (germline) - VCF files (SNPs)

  WGS - PCR-free library preparation (whole blood gDNA), paired-end (2x100bp) sequencing on DNBseq sequencing platform (BGI) Number of samples: 26

  Dataset EGAD50000001800

• DAC for Hungarian human exome team (Department of Medical Biology, University of Szeged, Hungary)

  Dac EGAC00001000838

• scRNA-seq analysis of HGSC tumors, including immune TME, before and after NACT

  Gene expression profiles of single cells from 26 tumor and ascites samples samples from 17 patients

  Dataset EGAD50000000862

• Location and Function of NSun2-Mediated Cytosine-5 Methylation in RNA and its Effect on Translation

  Mutations in the cytosine-5 RNA methyltransferase NSun2 can cause neurodevelopmental disorders and symptoms commonly found in patients with Dubowitz-like syndrome. Some tRNAs are known to be methylated NSun2, however the occurrence of cytosine-5 methylation (m5C) in other RNA biotypes is still under debate. Location in RNA and function of m5C has not been studied yet. This study is aimed at identifying new m5C methylated RNA biotypes, as well as the location at specific structures or sequences and the ultimate biological function. The impact of the loss of NSun2-mediated methylation is also determined by comparing gene expression data with the global cytosine-5 RNA methylome in Dubowitz-like syndrome patients. We also use ribosomal profiling to assess the impact of the loss and rescue of Nsun2-mediated cytosine-5 RNA methylation on translation rates and ribosome occupancy.

  Study phs000645

• Whole Transcriptome Sequencing of Resectable Stage III/IV Melanoma Evaluated After Starting Hu14.18-IL2 Predicts Outcome

  Background: We analyzed whole transcriptome sequencing in tumors from 23 patients with stage III or IV melanoma from a pilot trial of the anti-GD2 immunocytokine, hu14.18-IL2, to identify predictive immune and/or tumor biomarkers in melanoma patients at high risk for recurrence. Methods: Patients were randomized to receive the first of 3 monthly-courses of hu14.18-IL2 immunotherapy either before (Group A) or after (Group B) complete surgical resection of all known disease. Tumors were evaluated by histology and whole transcriptome sequencing. Results: We report here that tumor infiltrating lymphocyte (TIL) levels directly associate with relapse-free survival (RFS) and overall survival (OS) in resected tumors from Group A, where early responses to the immunotherapy agent could be assessed. TIL levels directly associated with a previously reported immune signature which associated with RFS and OS, particularly in Group A tumors. In Group A tumors there were decreased cell cycling gene RNA transcripts, but increased RNA transcripts for repair and growth genes. We found that outcome (RFS and OS) was directly associated with several immune signatures and immune-related RNA transcripts and inversely associated with several tumor growth-associated transcripts, particularly in Group A tumors. Most of these associations were not seen in Group B tumors. Conclusion: We interpret these data to signify that both immunologic and tumoral cell processes, as measured by RNAseq analyses detected shortly after initiation of hu14.18-IL2 therapy are associated with long term survival and could potentially be used as prognostic biomarkers in tumor resection specimens obtained after initiating neoadjuvant immunotherapy. Note: RNA sequences and expression data can be found at NCBI GEO GSE133713

  Study phs001947

• H3Africa H3AChipDesign TrypanoGEN1

  26 samples from Cameroon generated for the H3Africa Chip Design Study. The dataset includes BAM, FASTQ and decompressed gVCF files.

  Dataset EGAD00001004393

• Phenotype information

  This study explores the cell-free transcriptome in a humanized DLBCL patient-derived tumor xenograft (PDTX) model. Blood plasma samples (n=171) derived from a DLBCL PDTX model in-cluding 27 humanized (HIS) PDTX, 8 HIS non-PDTX and 21 non-HIS PDTX non-obese diabetic (NOD)-scid IL2Rgnull (NSG) mice were collected during humanization, xenografting, treatment, and sacrifice. The mice were treated with either rituximab, cyclophosphamide, doxorubicin, vincris-tine, and prednisone (R-CHOP), CD20-targeted human IFNα2-based AcTaferon combined with CHOP (huCD20-Fc-AFN-CHOP), or phosphate-buffered saline (PBS). RNA was extracted using the miRNeasy serum/plasma kit and sequenced on the NovaSeq 6000 platform using the using the SMARTer Stranded Total RNA-Seq Kit v3.

  Dataset EGAD50000000806