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Datasets Discovered: DLBCL Cohort

Sep 15, 2021 11:00:00 AM / by Champions Oncology

Lumin Bioinformatics DLBCL Datasets Discovered

Importance of the Dataset

Diffuse Large B-Cell Lymphoma (DLBCL) is a cancer of the B cells and is the most common form of non-Hodgkin’s Lymphoma (NHL) among adults. Champions’ DLBCL models encompass various subtypes of the disease, including ABC (Activated B cell), GCB (Germinal Center B cell), and Richter. These models are well-characterized and include patient clinical attributes, disease status, treatment history and in vivo drug responses to a range of therapies, including CHOP or a Rituximab-CHOP (R-CHOP) combination treatment. Champions DLBCL model cohort includes diverse molecular features such as double and triple hit mutations, as well as mutations in several key pathways such as proliferation, oncogenic signaling, and B cell differentiation. This unique dataset includes next generation sequencing (NGS), proteomics and phospho-proteomics from Champions’ DLBCL cohort.

Experimental Design

Each model included in this cohort was characterized by NGS sequencing (WES and RNA-Seq), proteomics and phospho-proteomics analyses. Our NGS workflow is a multi-step procedure; specifically, a primary sample undergoes preparation by thawing and subsequent extraction of gDNA and RNA. A library is then prepared and NGS sequencing (WES and RNA-Seq) is performed using Illumina Nextseq2000. Subsequently, raw data is collected, processed, and analyzed. The data must meet Champions’ Quality Control requirements, including sample QC, library QC and sequencing data QC. Finally, data is uploaded and stored in the user’s unique Lumin instance, where it can be visualized and further analyzed in various modules.

Champions has partnered with BGI Genomics to obtain proteomics and phospho-proteomics data; specifically, proteins are extracted from cells and/or tissues to obtain a protein mixture, which are broken down by digestion enzymes to yield a peptide mixture. This peptide mixture undergoes phospho-peptide enrichment to give a phospho-peptide mixture, which is then analyzed by LC/MS, using either data-dependent acquisition (DDA) or label-free data-independent acquisition (DIA) for data quantification.BlogLuminDLBCLApplications of the Dataset

The DLBCL model cohort dataset has been integrated into our revolutionary visualization and data analytics software, Lumin Bioinformatics. With a Lumin base subscription, you can access NGS data from our DLBCL model cohort. The following modules can be used in Lumin Bioinformatics to access proteomics and phospho-proteomics data and are available as an upgrade to the base license:

  • Network Viewer: Within the network viewer, users can color protein nodes based on gene expression, mutational status, quantitative protein expression or include molecular signatures. This tool overlays proteomics data from Champions’ PDX models or the public CPTAC database. Users can then evaluate quantitative protein expression and specific phosphorylation status across cancer types or within a defined tumor model.

  • Mutation Mapper: Researchers can visualize protein amino acid domains and identify mutations within Champions' PDX models. Through Champions’ phospho-proteomic sequencing, phosphorylation sites identified within our tumor bank were detected, and are aligned within the context of protein amino acid domains. Users can also visualize phosphorylation sites detected within the public CPTAC database as well as those predicted by PhosphositePlus.

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Tags: Lumin Bioinformatics