High-throughput sequencing using the Ion Torrent personal genome machine for clinical evaluation of somatic hypermutation status in chronic lymphocytic leukemia.

For patients with chronic lymphocytic leukemia, an important prognostic indicator is the somatic hypermutation status of immunoglobulin heavy chain variable region nucleic acid within the clonal cell population. Current clinical assays for this evaluation rely on Sanger sequencing and are complex, such that availability of testing for patients is limited and costly. However, advances in high-throughput sequencing provide an opportunity to improve complex clinical sequencing applications. Our goal was to determine whether high-throughput sequencing technology could reliably perform the sequencing required for somatic hypermutation analysis and improve clinical testing for chronic lymphocytic leukemia patients. Blood or liquid bone marrow aspirate samples from 50 different patients were evaluated in parallel using a validated clinical assay based on Sanger sequencing and a modified protocol in which the sequencing was performed using an Ion Torrent personal genome machine. In each case, both methods gave identical results with respect to interpreted somatic hypermutation status and dominant immunoglobulin heavy chain variable region gene reported. The personal genome machine-based method had significant advantages over the Sanger-based method for use in clinical laboratories that perform long-read, high-throughput sequencing.