Advancing Cancer Research with New BaseSpace® Sequence Hub Apps
Analyzing the genetic basis of a given tumor is important for understanding the progression of cancer and developing new methods of treatment. Cancer researchers use a variety of methods but none of them efficiently cover all of the variations present in our genes. To help researchers address this challenge, Illumina offers TruSight® Tumor 170, a next-generation sequencing (NGS) assay designed to cover 170 genes associated with cancer.
To help TruSight Tumor customers analyze data from this assay, we are excited to announce two new apps in BaseSpace Sequence Hub:
Additionally, we have made a significant update to the Tumor Normal app. All 3 apps expand our portfolio of cancer research applications by delivering advanced, new methods NGS data generation and analysis.
TruSight Tumor 170 App
The TruSight Tumor 170 app enables streamlined analysis of samples prepared using the TruSight® Tumor 170 library prep kit. This comprehensive somatic panel targets 170 genes and is based on hybrid capture technology optimized for Formalin-Fixed, Paraffin-Embedded (FFPE) samples. By using both DNA and RNA input sample pairs, TruSight Tumor 170 can detect small variants (Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels), amplifications, structural variants (gene fusions), and splice variants. The TruSight Tumor 170 app performs alignment and variant calling for all variant types in a single analysis workflow, and can analyze up to 16 samples (both DNA and RNA) in a single run.
TruSight Tumor 170 + Watson for Genomics Converter App
To efficiently extract information from a TruSight Tumor 170 sample, Illumina has partnered with IBM Watson for Genomics to expedite variant analysis. By leveraging natural language processing (a form of artificial intelligence), Watson for Genomics delivers an annotated, prioritized variant summary containing curated information on the significance of variants detected by sequencing. This curated information includes drug guidelines, clinical trials, and literature matches. TruSight Tumor 170 customers have the option to purchase add-on access to Watson for Genomics when buying the library prep kit. The TruSight Tumor 170 + Watson for Genomics app converts the output from the standard TruSight Tumor 170 app into variant calling files with a format suitable for upload into the Watson for Genomics portal. This app does not have a compute cost, but upload into Watson for Genomics requires purchase of the add-on license.
Tumor Normal App
Lastly, we have updated the Tumor Normal app to version 4.0. This app has improved performance, while providing updated variant callers for more accurate detection of somatic variants. As with version 3.0, the Tumor Normal app can detect small variants (SNPs and InDels), structural variants (gene fusions), and copy number variants (amplifications and deletions).
For more information, contact us.