Mutational landscape and clinical characterization of over 17,000 patients with myeloid malignancies using real-world data.
Authors: Jensen Taylor J. , Hogg Grant , Cai Li , Hoffmann Heidi M. , Holden Kimberly A. , Fitzgerald Kerry D. , Kenyon Angela , Mooney Michael , Gardner Sabrina , Chen Wenjie , Nagan Narasimhan , Boles Deborah , Parker Scott , Richman Tamara J. , Letovsky Stanley , Dong Henry , Anderson Steven M. , Eisenberg Marcia , Chenn Anjen 
Published: June 2022

7022

Background: Myeloid neoplasms represent a broad spectrum of hematological disorders for which somatic mutation status in key driver genes is important for diagnosis, prognosis and treatment. Here we summarize the findings from 17,181 clinical samples analyzed by a targeted next generation sequencing (NGS) laboratory developed test. Samples were analyzed comprehensively and as part of individual cohorts specific to acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), and myeloproliferative neoplasms (MPN). Methods: Whole blood or bone marrow samples from patients with cause-for-testing for hematological symptoms were submitted for analysis by a referring clinician. DNA was extracted and assayed by a targeted, NGS panel to detect and report single nucleotide variants and small indels within 50 genes associated with myeloid malignancies and sequenced on Illumina DNA sequencers (Illumina, San Diego, CA). Results were reviewed, orthogonally confirmed unless previously validated, and reported by clinical laboratory directors. Disease status or symptoms were taken from test requisitions for each patient. Results: Overall, 34,581 Tier I, II, or III somatic variants were detected. The mean number of variants reported per patient was 1.98. This number increased with age (p < 0.001) and was highest in patients with AML. Mutations in genes associated with FDA-approved therapies ( FLT3, IDH1, IDH2, KIT, and JAK2) were observed in 22.3% (3836) patients while 28.0% of samples had mutations considered diagnostically relevant by the WHO. Clinical trials are in progress for therapies targeting TP53, NPM1, and CEBPA mutations and were observed in 12.5% (2144) of samples. FLT3, NPM1 and RUNX1 mutation which are diagnostic for AML were found in 29.0% (646 of 2225) of AML samples. Pair-wise mutation analyses found 21 mutually exclusive pairs including between genes associated with RNA splicing ( SF3B1, SRSF2 and U2AF1; OR < 0.29, p < 0.001) suggesting possible candidates for targeted therapy. The clinically favorable co-mutation of NPM1 with FLT3 internal tandem duplicate was significantly enriched (OR = 7.4, p < 0.001) in the AML population. Co-occurrence of ASXL1 with RUNX1 mutations which independently confer adverse risk was also enriched in AML (OR = 3.9, p < 0.001). Some patients (1021; 6.3%) were tested at multiple time-points with 48.8% showing loss or gain of a mutation between sample dates, potentially the result of tumor evolution and/or therapeutic intervention. Conclusions: This study shows that parallel testing of multiple genes in addition to the canonical driver mutations encompasses the mutations contributing to the etiology of these diseases. Despite the breadth of different mutations observed for myeloid neoplasms, consistent patterns are routinely observed that can help the clinician tailor the treatment and chart the progression of these diseases for each patient.