Identification of Clonal Hematopoiesis Mutations in Solid Tumor Patients Undergoing Unpaired Next-Generation Sequencing Assays

Abstract

Purpose: In this era of precision-based medicine, for optimal patient care, results reported from commercial next-generation sequencing (NGS) assays should adequately reflect the burden of somatic mutations in the tumor being sequenced. Here, we sought to determine the prevalence of clonal hematopoiesis leading to possible misattribution of tumor mutation calls on unpaired Foundation Medicine NGS assays.

Experimental design: This was a retrospective cohort study of individuals undergoing NGS of solid tumors from two large cancer centers. We identified and quantified mutations in genes known to be frequently altered in clonal hematopoiesis (DNMT3A, TET2, ASXL1, TP53, ATM, CHEK2, SF3B1, CBL, JAK2) that were returned to physicians on clinical Foundation Medicine reports. For a subset of patients, we explored the frequency of true clonal hematopoiesis by comparing mutations on Foundation Medicine reports with matched blood sequencing.

Results: Mutations in genes that are frequently altered in clonal hematopoiesis were identified in 65% (1,139/1,757) of patients undergoing NGS. When excluding TP53, which is often mutated in solid tumors, these events were still seen in 35% (619/1,757) of patients. Utilizing paired blood specimens, we were able to confirm that 8% (18/226) of mutations reported in these genes were true clonal hematopoiesis events. The majority of DNMT3A mutations (64%, 7/11) and minority of TP53 mutations (4%, 2/50) were clonal hematopoiesis.

Conclusions: Clonal hematopoiesis mutations are commonly reported on unpaired NGS testing. It is important to recognize clonal hematopoiesis as a possible cause of misattribution of mutation origin when applying NGS findings to a patient's care.See related commentary by Pollyea, p. 5790.

Figure 1.

Violin plots displaying VAFs from FM NGS testing in nine genes recurrently mutated in clonal hematopoiesis. Variants of known significance (VKS) are depicted by red circles, and variants of unknown significance (VUS) are depicted by blue triangles. Boxes represent the 25th and 75th percentiles, with the horizontal line in the middle indicating the median, and the vertical lines representing the 95th percentile.

Figure 2.

Sequencing results for a patient with carcinoma not otherwise specified who had a DNMT3A mutation (left) in the blood sample and a TET2 mutation (right) in tumor tissue, both of which were reported on FM NGS testing of the carcinoma biopsy. The DNMT3A mutation is seen at a lower level in the tumor sample when compared with blood, indicating clonal hematopoiesis. The TET2 mutation is only observed in the tumor, confirming tumor somatic origin. VAFs for both tumor and blood specimens were obtained from UNCseq testing. Integrative Genomics Viewer images of these mutations are provided in Supplementary Fig. S1.

Figure 3.

Sequencing results for a patient with ovarian carcinoma who had DNMT3A, BRCA2, and TP53 mutations reported on FM NGS testing of the carcinoma biopsy. The DNMT3A mutation (left) is seen at a lower level in the tumor sample when compared with blood, indicating clonal hematopoiesis. The TP53 mutation (middle) was seen in the tumor tissue but absent in blood sample, consistent with a tumor somatic mutation. The BRCA2 mutation (right) was seen at a variant frequency of 50% in the blood sample (and 78% in the tumor tissue), representing a germline variant. VAFs for both tumor and blood specimens were obtained from UNCseq testing. Integrative Genomics Viewer images of these mutations are provided in Supplementary Fig. S2.