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Datasets Discovered: Addition of New NGS Model Datasets

Nov 24, 2021 11:48:39 AM / by Champions Oncology

Lumin Bioinformatics DLBCL Datasets Discovered

Importance of the Dataset

Champions’ PDX and Hematological models are well-characterized and include patient clinical attributes, disease status, treatment history and in vivo drug responses to a range of Standard of Care therapies. New NGS datasets spanning across various indications, have been recently added to our software platform, Lumin Bioinformatics, specifically 114 model datasets of RNA-Seq and 148 model datasets of WES. Below, we illustrate the model disease types that have been added to Lumin Bioinformatics that have both RNA-Seq and WES datasets. In particular, additional Acute Lymphoblastic Leukemia (ALL) models are currently available for research on our Hematological Screen. Additionally, a large cohort of Sarcoma, Colorectal, and Head & Neck Cancer model datasets have been incorporated into Lumin Bioinformatics. Champions also adds to its Glioblastoma model datasets with the 11 datasets included in this update to our platform.

 

NGS Circle Graph

Experimental Design

Each model included in this update was characterized by NGS sequencing (WES and RNA-Seq). Our NGS workflow is a multi-step procedure; specifically, a primary sample undergoes preparation by thawing and 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 and processed into a FASTQ file, which is sent to a bioinformatician for data analysis. Throughout the NGS workflow, stringent quality standards are applied, ensuring the generation of high-quality sequencing data. Finally, data is uploaded and stored in the user’s unique Lumin instance, where it can be visualized and further analyzed in various modules.

 

Applications of the Dataset

Data from these models has been integrated into our revolutionary visualization and data analytics software, Lumin Bioinformatics. With a Lumin base subscription, you can access NGS data for these models by using the following modules:

  • Mutation Mapper: Within the mutation mapper, users can visualize protein amino acid domains and identify mutations within Champions' PDX models.
  • Oncoprint: This tool allows for visualization of genetic alterations in user defined genes across Champions PDX and Hematological models.
  • t-SNE Clustering & Clustergrammer: Researchers can leverage Champions' proprietary clustering tools to interrogate Champions’ PDX models and TCGA public data sets using t-SNE and UMAP distributions. Users can also overlay gene expression or agent response data.
  • Binarize Datasets: In this module, users can compare gene expression across model cohorts by interrogating existing as well as customized gene signatures of any two variables to perform correlative and causative analyses. Users can input their pharmacological drug study data (%TGI or IC50 values) and run differential analyses to identify genes or mutations that are significantly up- or down-regulated in the context of model sensitivity or resistance.


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Tags: Lumin Bioinformatics