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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.

For Research Use Only. Not for use in diagnostic procedures. 

VCAT v3.0 and FASTQ Toolkit v2.2 – Usability Improvements and Gold Reference Updates

The Variant Calling Assessment Tool (VCAT) v3.0 BaseSpace® App has improved usability, several new gold references, adds BED file stratification, and delivers an enhanced in-browser report.

Improved VCF file selection

  • File chooser now allows multi-selection of VCFs
  • Easier usage of alternative labels for VCF files
  • File chooser now defaults to the current Project
  • Improved VCF file tooltips now show analysis name

Gold Reference Additions and Updates

  • Added Platinum Genomes reference data for NA12877 (male spouse of NA12878)
  • Added NIST GiaB gold reference data for NA24385 (Ashkenazi male)
  • Added gold reference data and novelty rate calculations for hg38
  • Updated NIST Genome in a Bottle reference data to version 3.2.2
  • Updated Platinum Genomes reference data to version 2016-01

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Introducing Enrichment v3.0 with Enhanced Variant Calling

Enrichment

Enrichment v3.0

The new Enrichment v3.0 BaseSpace® App (formerly called Isaac Enrichment) introduces major improvements and new features including:

  • Improved small variant calling
  • Copy number variant (CNV) calling
  • Structural variant calling
  • Somatic/low-frequency variant calling
  • Ability to start from FASTQ or BAM
  • GRCh38 reference added
  • Variant table CSV file including variant frequencies
  • Improved variant annotation engine
  • Improved metrics engine

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New RNA-Seq Alignment App with support for TruSight RNA Pan-Cancer and more

With the launch of the TruSight RNA Pan-Cancer panel, a targeted enrichment panel for the detection of variants, fusions, and gene expression profiles in 1385 cancer-associated genes, Illumina is pleased to provide an intuitive BaseSpace App, RNA-Seq Alignment v 1.0, that supports simple push button analysis of the data.

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RNA-Seq Alignment

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Human mtDNA Analysis in BaseSpace

Mitochondrial DNA (mtDNA) analysis enables forensic laboratories to extract genetic data from small biological samples, found in less than ideal condition. Mitochondria in humans cell contain about 1,000 copies of mtDNA. The ease-of-use of next-generation sequencing (NGS) and Nextera XT enables labs to speed up their workflow, reducing time and labor spent on prep, and generate deeper coverage data compared to Sanger sequencing at 1X coverage/rx.

The updated Illumina mtDNA demonstrated protocols provide a complete mitochondrial DNA solution – from targeted library prep and sequencing to bioinformatics analysis and report generation in BaseSpace – to help investigators draw conclusions in a straightforward and intuitive workflow.

The two new mtDNA apps in BaseSpace allow for variant analysis and easy visualization of mitochondrial sequence data. This workflow can analyze any part of the full circular genome, without any origin dead zone, using quality and coverage thresholds customized by the user (Figure 1).

Figure 1: mtDNA Analysis Workflow. Sequence data is streamed into BaseSpace. Initial processing is performed using the mtDNA Variant Processor app and the results are stored in your BaseSpace project. Use mtDNA Variant Analyzer to visualize the data and generate a downloadable Excel report.

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