Molecular Pathology Abstracts, 7/17

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Cell-free DNA sequence analysis as a source of genomic information in multiple myeloma

A bone marrow aspirate is the specimen of choice for the diagnosis and therapeutic monitoring of multiple myeloma. Because patient monitoring, in particular, may require repeated sampling, significant limitations of this approach include patient discomfort and technical challenges with collecting adequate sample. Similar sampling challenges complicate the study of solid tumors. In the latter setting, cell-free tumor DNA (cfDNA) from blood has shown promise as an alternative source of tumor-specific genomic information. The authors of this study suggest that cfDNA may also serve as a reliable source of genomic information for multiple myeloma patients. They used a hybrid capture-based next-generation sequencing assay to sequence the coding regions of KRAS, NRAS, BRAF, EGFR, and PIK3CA in 64 cfDNA specimens obtained from the plasma of 53 multiple myeloma patients (11 newly diagnosed and 42 relapsed, of which 13 were enrolled in a clinical trial of the MEK inhibitor trametinib). The authors found that the yield of cfDNA from these patients was higher than they had observed in specimens from solid tumor patients. To improve the ability of their bioinformatics process to distinguish somatic mutations from germline variants, they first used training and validation groups of cfDNA specimens for which sequence information from matched bone marrow aspirate samples was available. These studies demonstrated a 96 percent concordance between mutations detected in cfDNA and matched bone marrow (26 of 27 bone marrow mutations detected in cfDNA). A KRAS mutation present at an allele fraction of 1.3 percent in a bone marrow specimen (found only by ultra-deep sequencing of the marrow) was not detectable in the corresponding cfDNA sample. The absence of this mutation in the cfDNA sample was confirmed by digital droplet PCR. Because this mutation was present at a level below the reportable range of the laboratory’s clinical assay—that is, 10 percent allele fraction—the overall concordance between the cfDNA assay and the clinical assay used for bone marrow analysis was 100 percent. Overall, mutant allele fractions were found to be highly concordant between cfDNA and bone marrow. The potential utility of this sampling approach was demonstrated by the ability to obtain sequence information from cfDNA samples for which corresponding bone marrow aspirate samples failed to yield adequate material for analysis (n=7). Furthermore, all 13 patients enrolled in the clinical trial of trametinib were correctly identified as biomarker positive or negative using the cfDNA assay. Although this study used an assay that is limited with regard to the scope of genes interrogated, it presents intriguing evidence supporting the value of a liquid biopsy approach to the diagnosis and monitoring of multiple myeloma patients.

Kis O, Kaedbey R, Chow S, et al. Circulating tumour DNA sequence analysis as an alternative to multiple myeloma bone marrow aspirates. Nat Comm. 2017;8:15086. doi:10.1038/ncomms15086.

Correspondence: Dr. Suzanne Trudel at suzanne.trudel@uhn.ca