TruSeq Amplicon – Cancer Panel Dataset

As was demonstrated with the first public release of HiSeq 2500 data on this platform, BaseSpace has become the primary repository for new data released by Illumina in support of our assays and instruments. We like this because it makes accessing our reference datasets fast and easy, and will showcase BaseSpace functionality across a wide range of applications.

In that vein, I have some exciting targeted resequencing news. We recently announced the TruSeq Amplicon – Cancer Panel (TSACP), a highly multiplexed targeted resequencing assay for detecting somatic mutations across hundreds of mutational hotspots in cancer genomes.  The panel covers over 35 kb of target genomic sequence from 48 genes associated with a variety of cancers.  A key characteristic of running this RUO panel on a MiSeq is the ability to resolve mutations below 5% minor allele frequency.

The TruSeq Amplicon – Cancer Panel will begin shipping in mid-April but today in BaseSpace we are making available a dataset to demonstrate what is to be expected from TSACP data. For this dataset, we prepared genomic DNA from a formalin-fixed, paraffin embedded (FFPE) lung carcinoma sample. The sample was prepped with the TruSeq Amplicon – Cancer Panel and sequenced on a MiSeq, yielding almost 2 Gbases of sequence and a mean depth >33,000X.  The assay generated amplicons with 94% specificity and 90% uniformity. There were no amplicon dropouts. UPDATE: In several instances, in silico probe design predicted a potential off target amplicon match; rather than filtering these out we include them in this dataset and display the chromosome to where each amplicon could have mapped. In the unlikely scenario there were off target reads they would have segregated accordingly, however in this dataset no reads mapped off target and these regions will appear empty.

While you’re reviewing this data be aware that BaseSpace will soon be launching with a new somatic workflow for even better variant detection, so check back in a few weeks to see how even lower minor allele frequency mutations are detected in this dataset.

UPDATE: Access TSACP data using the somatic caller here:




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