Dr. Marilyn Li, director of the Cancer Genetics Laboratory (CGL) of Baylor College of Medicine, presented at 2012 AGBT some data relative to whole exome sequencing using the Ion Torrent PGM. The study was performed on one HapMap sample (NA12763) and on the DNA of a patient with Charcot Marie Tooth Neuropathy.10 runs using Ion Torrent 318 Chips were merged (about 7 Gb) to achieve a high average coverage (43 to 57 fold, see the slide above). The experiment was not particularly cheap but apparently the results are encouraging: variant calls were compared to SNP array data of the HapMap DNA sample resulting in the 99.1% concordance. Variants for the CMT sample were compared to the Illumina exome data, resulting in 92% SNP concordance and the identification of the 2 causative mutations in the SH3TC2 gene.
The AGBT presentation can be seen on this YouTube video (the exome part starts around min. 15:00)
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