Prediction of risk for myeloid malignancy in clonal hematopoiesis

Abstract

Background: Clonal hematopoiesis of indeterminate potential (CHIP) and clonal cytopenia of undetermined significance (CCUS) are defined by somatic mutations in genes associated with myeloid neoplasms (MN) at a variant allele fraction (VAF) ≥ 0.02, in the absence and presence of cytopenia, respectively. CHIP/CCUS is highly prevalent in adults and defining predictors of MN risk would aid clinical management and research.

Methods: We analyzed sequenced exomes of healthy UK Biobank (UKB) participants (n = 438,890) in separate derivation and validation cohorts. Genetic mutations, laboratory values, and MN outcomes were used in conditional probability-based recursive partitioning and Cox regression to determine predictors of incident MN. Combined statistical weights defined a clonal hematopoiesis risk score (CHRS). Independent CHIP/CCUS patient cohorts were used to test prognostic capability of the CHRS in the clinical setting.

Results: Recursive partitioning distinguished CHIP/CCUS cases with 10-year probabilities of MN ranging from 0.0078 - 0.85. Multivariable analysis validated partitioning variables as predictors of MN. Key features, including single DNMT3A mutations, high risk mutations, ≥ 2 mutations, VAF ≥ 0.2, age ≥ 65 years, CCUS vs CHIP and red blood cell indices, influenced MN risk in variable direction. The CHRS defined low risk (n = 10018, 88.4%), intermediate risk (n = 1196, 10.5%), and high risk (n = 123, 1.1%) groups. In clinical cohorts, most MN events occurred in high risk CHIP/CCUS patients.

Conclusions: The CHRS provides simple prognostic framework for CHIP/CCUS, distinguishing a high risk minority from the majority of CHIP/CCUS which has minimal risk for progression to MN.

Figure 1 –. Features influencing risk of myeloid neoplasia (MN) in UKB participants with CHIP/CCUS.

(a) Cumulative incidence of myeloid neoplasia (MN) in individuals with CHIP/CCUS compared to those without CHIP/CCUS. (b) Subtypes of MN among CHIP/CCUS patients who develop MN. (c) Univariate cox proportional hazard regression analysis for the 14 most commonly mutated genes in CH and (d) for groups of mutations including splicing factor mutations (SRSF2, SF3B1, ZRSR2) and AML-like mutations (IDH1, IDH2, FLT3, and RUNX1).) (e) Univariate analysis of single-DNMT3A, TET2 and ASXL1. (f) Cumulative incidence of MN for CHIP/CCUS possessing a single-DNMT3A mutation (green) compared to the cumulative incidence for all other CHIP/CCUS genotypes (red) and individuals without CHIP/CCUS (black). (g) For UK Biobank participants with at least 10-years of follow-up (n=10,559), recursive partitioning (RP) analysis was performed based on conditional probability of incident MN within 10-years. Of these, 207 incident MN events were recorded. Each node is annotated with number of individuals (n =) and probability of incident MN. Nodes are color coded as follows: probability ≤ 0.02 is green, 0.02-0.4 is yellow and >0.4 is red. Partitioning variable are all binary (presence vs absence of feature) and include high risk mutation (mutations in SRSF2, SF3B1, ZRSR2, IDH1, IDH2, FLT3, RUNX1 and JAK2), single DNMT3A, having ≥2 mutations, variant allele fraction (VAF) ≥0.2, having CCUS instead of CHIP, red cell distribution width (RDW) ≥15%, mean corpuscular volume (MCV) ≥100fl, and age ≥ 65 years. (h) Multivariable cox regression adjusted for assigned sex at birth, prior history of cancer and any history of smoking as confounders was performed on the entire cohort (n = 11,337) using features selected in RP analysis. For all Cox regression models hazard ratios (HR) are shown with error bars representing 95% confidence interval and numerical values for HR [95% confidence interval] and p-value for each feature analyzed.

Figure 2 –. Clonal hematopoiesis risk score (CHRS) distribution and risk stratification in UKB Derivation Cohort.

(a) Number of individuals with each possible CHRS value (number of individuals with each score is indicated above the bar). (b) Risk-Categories were defined by CHRS value with cutoffs chosen to minimize risk in low-risk strata. For each category, the number individuals in the risk group, number of myeloid neoplasia (MN) events and crude event rate (N, %), as well as the 5- and 10-year cumulative incidences (± standard deviation) is shown. Cumulative incidence of MN for individuals without CHIP or CCUS (No CHIP/CCUS) in the derivation cohort is included for reference. (c) Cumulative incidence curves of MN by CHRS risk category. Curves correspond to cumulative incidence analysis used to derive figures in panel (b). Hazard ratios for incident MN were determined for CHRS risk strata using Cox proportional hazards models adjusted for sex, smoking history and history of prior cancer. Hazard ratios were calculated in models with low risk strata as the reference population (d) and using the population of 182406 UKB participants in the No CHIP/CCUS group as the reference population (e). (f) Survival by CHRS risk category is shown, with 10-year survival is annotated to the right of the graph for each category. For both cumulative incidence and survival curves, Black = No CHIP/CCUS, Green = Low Risk, Orange = Intermediate Risk, and Red = High Risk. The ribbon about each curve indicates the 95% confidence interval. Tables show number at risk. (g) results of Cox regression analyses for non-malignant outcomes by CHRS risk group. For all outcomes, NO CHIP/CCUS is the reference population. Outcomes shown include ischemic cardiovascular disease (CVD) which is a composite of atherosclerosis, ischemic heart failure, myocardial infarction and stroke; arterial thromboembolic events (ATE); venous thromboembolic events (VTE); chronic kidney disease (CKD); and chronic obstructive pulmonary disease (COPD). For panels (d), (e) and (g), forest plots indicate HR (95% confidence interval) and p-values for main effects.

Figure 3 –. External validation of CHRS in Hematology Patient Cohorts.

Distribution of mutations (a & c) and CHRS values in (b & d) in the DFCI/BWH CH cohort and Pavia CCUS cohorts. (e) CHRS risk categories and outcomes (incident MN) in DFCI/BWH cohort (left) and Pavia cohort (right). Number of patients with in each category is shown with percentage (N %). The number of incident myeloid neoplasia (MN) cases (MN events) and the event rate (MN events relative to number of individuals in that category, expressed as percentage). Cox proportional hazard models were used to obtain hazard ratios (95% CI) for each CHRS risk strata and performance of the CHRS model is estimated by the concordance statistic (c-index ± standard error) when applied to each cohort.