Fusion Genes kits for detection and lists of targeted genes

Fusion genes arise through mutations such as translocations, insertions, and deletions, and have been implicated in a variety of human diseases.

Whole Transcriptome kits

Fusion genes can be detected with whole transcriptome sequencing, using one of the following kits:

• Illumina Stranded mRNA and TruSeq Stranded mRNA In the stranded mRNA workflows, polyadenylated transcripts are converted into sequencing libraries.

• Illumina Stranded Total RNA and TruSeq Stranded Total RNA In the stranded Total RNA workflows, mRNA and multiple forms of noncoding RNA are converted into sequencing libraries.

• Illumina RNA Prep with Enrichment and TruSeq RNA Exome with the Illumina Coding Exome Enrichment Panel (Catalog Number 20020183) With the Exome panel, the RNA coding regions of the human genome are selectively enriched in the final sequencing libraries.

While these kits differ in the library preparation strategies used, the resulting libraries all yield transcriptome information that can be analyzed for fusion gene detection.

Targeted sequencing kits (fixed panels)

Illumina also provides solutions for a targeted approach for analyzing specific gene fusions. The following kits are recommended to detect specific fusion genes:

• TruSight RNA Pan-Cancer TruSight RNA Pan-Cancer is an enrichment workflow that targets 1,385 genes and 21,043 exonic regions for detection of variants and gene expression changes in cancer samples. The list of targeted genes in this panel is found here (under Product Literature).

• TruSight RNA Fusion TruSight RNA Fusion is an enrichment workflow that covers a targeted subset of the TruSight RNA Pan-Cancer panel, focusing on 507 fusion-associated genes. The list of targeted genes in this kit is found here (under Product Literature).

• TruSight Oncology 500, TruSight Oncology 500 High-Throughput, and TruSight Oncology 500 ctDNA TruSight Oncology 500, TruSight Oncology 500 High-Throughput, and TruSight Oncology 500 ctDNA (for circulating tumor DNA or cell-free DNA) are enrichment-based assays that analyze 523 cancer-relevant genes from DNA and RNA. The DNA and RNA panels provide comprehensive coverage of biomarkers commonly mutated in numerous cancer types, including 55 genes for known and novel fusions and splice variants (See Table 3 for DNA content and Table 4 for RNA content in this data sheet). For TruSight Oncology 500 ctDNA, the gene list that includes 23 DNA fusions can be found here (under Product Literature).

• TruSight Tumor 170 TruSight Tumor 170 is an enrichment-based targeted panel for DNA and RNA, designed to cover 170 genes associated with common solid tumors. The content includes 55 genes for fusions and splice variants (see Table 1 in this data sheet).

• AmpliSeq for Illumina Panels - fixed panels AmpliSeq for Illumina is a highly multiplexed PCR-based library preparation assay that uses oligonucleotides to amplify regions of interest to investigate SNVs, indels, CNVs, and gene fusions.

AmpliSeq for Illumina Ready-to-Use Panels that detect fusion genes are listed below.

• AmpliSeq for Illumina Childhood Cancer Panel enables comprehensive evaluation of somatic variants associated with childhood and young adult cancers.

• AmpliSeq for Illumina Comprehensive Panel v3 targets 161 cancer-associated genes, including kinase domains and genes involved in DNA repair.

• AmpliSeq for Illumina Focus Panel assesses 52 genes with known relevance to solid tumors for DNA and RNA samples.

• AmpliSeq for Illumina Myeloid Panel studies biomarkers associated with hematological malignancies across 69 genes.

• AmpliSeq for Illumina Transcriptome Human Gene Expression Panel delivers comprehensive coverage of RNA coding sequences targeting > 20,000 genes or > 95% of the human RefSeq gene database.

Targeted sequencing kits (custom panels)

Custom panels for fusion detection can be generated for AmpliSeq for Illumina Custom RNA Fusion Panel and TruSeq Targeted RNA Expression.

• The AmpliSeq for Illumina Custom RNA Fusion Panel enables detection of fusion genes and gene expression profiling for 12 to 1,200 gene targets in a single assay (human samples only). Targeted panels can be designed from over 1,000 well-annotated fusion genes and > 20,000 human RefSeq genes using the web-based assay design software tool, DesignStudio. Targets can be added via multiple options in DesignStudio, including “add fusion”:

• Another option, compatible with mouse, rat, and human samples, is the TruSeq Targeted RNA Expression kit, which is an extension-ligation-based workflow for gene expression profiling, variant screening, and analysis of isoforms/splice junctions. The assay targets are added by selecting predeveloped probes in the DesignStudio software. Under the Add targets section, select Gene Fusion, and add the target as gene1:gene2 (see below for an example). A gene fusion assay list can be downloaded here.

For any feedback or questions regarding this article (Illumina Knowledge Article #3067), contact Illumina Technical Support [e-mail].