Utility of plasma cell-free DNA for de novo detection and quantification of clonal hematopoiesis

Abstract

Although cell-free DNA (cfDNA) tests have emerged as a potential non-invasive alterative for bone marrow biopsies in monitoring of clonal hematopoiesis (CH) in hematologic diseases, whether commercial cfDNA assays can be implemented for de novo CH detection and quantification in place of blood cells is uncertain. In this study, peripheral plasma cfDNA samples available from patients with aplastic anemia (AA; n=25), myelodysplastic syndrome (MDS; n=27) and a healthy cohort (n=107) were screened for somatic variants in genes related to hematologic malignancies using a Clinical Laboratory Improvement Amendments-certified panel. Results were further compared to DNA sequencing of matched blood cells. In reported results, 85% of healthy subjects, 36% of AA patients and 74% of MDS patients were found to have somatic cfDNA variants, most frequently in DNMT3A, TET2, ASXL1 and SF3B1. However, concordance between cfDNA and blood cells was poor for CH detection when variants were at variant allele frequency <10%, which was mostly observed in the healthy and AA cohort but not in MDS. After filtering data for potential artifacts due to low variant allele frequency and sequencing depth, CH frequency in cfDNA from healthy and AA individuals decreased to 52% and 20%, respectively. cfDNA and matched blood cells were not interchangeable for tracking changes in allele burdens as their agreement by Bland-Altman analysis was poor. A commercial cfDNA assay had good performance for de novo detection of CH in MDS, but showed no advantage over blood cells in diseases with low allele burdens and healthy individuals.