Inherited predisposition to myeloid malignancies is more common than previously appreciated. We analyzed the whole-exome sequencing data of paired leukemia and skin biopsy samples from 391 adult patients from the Beat AML 1.0 consortium. Using the 2015 ACMG guidelines for variant interpretation, we curated 1,547 unique variants from 228 genes. The pathogenic/likely pathogenic (P/LP) germline variants were identified in 53 AML patients (13.6%) in 34 genes. 41% of variants were in DNA damage response genes, and the most frequently mutated genes were CHEK2 (8 patients) and DDX41 (7 patients). 44% of the pathogenic germline variants were in genes considered clinically actionable (tier 1). Pathogenic germline variants were also found in new candidate genes (DNAH5, DNAH9, DNMT3A, SUZ12). No strong correlation was found between the germline mutational rate and age of AML onset. Among 49 patients who have a reported history of at least one family member affected with hematological malignancies, six patients harbored known P/LP germline variants and the remaining patients had at least one variant of uncertain significance, suggesting a need for further functional validation studies. Using CHEK2 as an example, we show that three-dimensional protein modeling can be one of the effective methodologies to prioritize variants of unknown significance for functional studies. Further, we evaluated an in-silico approach that applies ACMG/AMP curation in an automated manner using the tool for assessment and prioritization in exome studies (TAPES), which can minimize manual curation time for variants. Overall, our findings suggest a need to comprehensively understand the predisposition potential of many germline variants in order to enable closer monitoring for disease management and treatment interventions for affected patients and families.

Treated AML patients often have measurable residual disease (MRD) due to persisting low-level clones. This study assessed whether residual post-treatment somatic mutations, detected by NGS, were significantly prognostic for subsequent clinical outcomes. AML patients (n = 128) underwent both pre-and post-treatment testing with the same 42-gene MRD-validated NGS assay. After induction, 59 (46%) patients were mutation-negative (0.0024 VAF detection limit) and 69 (54%) had ≥1 persisting NGS-detectable mutation. Compared with NGS-negative patients, NGS-positive patients had shorter overall survival (17 months versus median not reached; P = 0.004; hazard ratio = 2.2 [95% CI: 1.3–3.7]) and a shorter time to relapse (14 months versus median not reached; P = 0.014; HR = 1.9 [95% CI: 1.1–3.1]). Among 95 patients with a complete morphologic remission (CR), 43 (45%) were MRD-positive by NGS and 52 (55%) were MRD-negative. These MRD-positive CR patients had a shorter overall survival (16.8 months versus median not reached; P = 0.013; HR = 2.1 [95% CI: 1.2–3.9]) than did the MRD-negative CR patients. Post-treatment persisting MRD positivity, defined by the same NGS-based test used at diagnosis, is thus a more sensitive biomarker for low-level leukemic clones compared to traditional non-molecular methods and is prognostic of subsequent relapse and death.

Treated AML patients often have measurable residual disease (MRD) due to persisting low-level clones. This study assessed whether residual post-treatment somatic mutations, detected by NGS, were significantly prognostic for subsequent clinical outcomes. AML patients (n = 128) underwent both pre-and post-treatment testing with the same 42-gene MRD-validated NGS assay. After induction, 59 (46%) patients were mutation-negative (0.0024 VAF detection limit) and 69 (54%) had ≥ 1 persisting NGS-detectable mutation. Compared with NGS-negative patients, NGS-positive patients had shorter overall survival (17 months versus median not reached; P = 0.004; hazard ratio = 2.2 [95% CI: 1.3–3.7]) and a shorter time to relapse (14 months versus median not reached; P = 0.014; HR = 1.9 [95% CI: 1.1–3.1]). Among 95 patients with a complete morphologic remission (CR), 43 (45%) were MRD-positive by NGS and 52 (55%) were MRD-negative. These MRD-positive CR patients had a shorter overall survival (16.8 months versus median not reached; P = 0.013; HR = 2.1 [95% CI: 1.2–3.9]) than did the MRD-negative CR patients. Post-treatment persisting MRD positivity, defined by the same NGS-based test used at diagnosis, is thus a more sensitive biomarker for low-level leukemic clones compared to traditional non-molecular methods and is prognostic of subsequent relapse and death.

Background: Next-generation sequencing (NGS) multigene panels allow the identification of genetic variants in patients with acute myeloid leukemia (AML). This study assessed the effect of the NGS panel size on positivity rate and clinic utility in helping predict survival outcomes. Design: This is a retrospective study of AML patients (n=76) who underwent both diagnostic and post-treatment testing with a large 220-gene NGS assay. Mutation profiles and measurable residual disease (MRD) status were assessed with the large panel or a subset of the genes on the panel (i.e., a medium-sized panel with 42 genes); MRD assessment excluded DTA mutations (i.e., mutations in preleukemic genes DNMT3A, TET2 and ASXL1). Kaplan-Meier method was used to compare overall survival between MRD positive and negative patients. Results: The 76 patients evaluated were diagnosed with de novo AML (n=69) or secondary AML (n=7). The median age at diagnosis was 57 (interquartile range [IQR], 49-66) years; 37 (49%) were women; and the median follow-up was 273 (IQR, 174-473) days. At diagnosis, the medium-sized panel detected 276 somatic variants in 35 genes (average 3.6 variants per patient) whereas the large panel detected 351 somatic variants in 74 genes (average 4.6 variants per patient). These variants were frequently detected in methylation and epigenetic genes (25%), signaling genes (20%) and transcription factors (12%). After treatment, MRD-negativity was indicated in 27 patients by the medium-sized panel versus 23 patients by the large panel; MRD-positivity was indicated in 49 patients by the medium-sized panel versus 53 patients by the large panel. Shorter overall survival was associated with MRD-positivity as determined by both panels: medium-sized panel (hazard ratio [HR], 3.00; 95% CI, 1.01-8.93; P<.05), large panel (HR, 3.41; 95% CI, 1.00-11.57; P<.05). Conclusion: A medium-sized NGS panel detected fewer somatic mutations than large NGS panel but both panels, when used as MRD markers, are similarly predictive of overall survival in AML patients. Citation Format: Yonghong Li, Jose Solis-Ruiz, Frederick K. Racke, Richard D. Press. Predicting survival outcomes in patients with acute myeloid leukemia: medium-sized versus large next-generation sequencing panels [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2204.