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Illumina MiSeq: TruSeq Amplicon - Cancer Panel

In a previous post we explored some of the fixed AmpliSeq panels available for use on the Ion Torrent PGM.  The TruSeq Amplicon Cancer Panel is a similar panel available for the MiSeq.  In this post we’ll explore the similarities and differences between the TruSeq Amplicon Cancer Panel and the Ion Torrent AmpliSeq panels and describe our efforts to call the highest confidence SNPs possible with the TruSeq panel.  Since the throughput of the MiSeq is quite high, we tested the TruSeq Amplicon Cancer Panel on three well characterized cancer cell lines and barcoded two replicates of each over one MiSeq 2x150 run.  We tested the MiSeq default alignment (bwa) and variant calling (Illumina Somatic Variant Caller) pipeline as well as novoalign and several variant calling tools that we leverage in our exome sequencing pipeline and compared the results.  If you are interested in sequencing any of the panels mentioned in this post, please contact us.

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