Clonal hematopoiesis, with and without candidate driver mutations, is common in the elderly

Abstract

Clonal hematopoiesis (CH) arises when a substantial proportion of mature blood cells is derived from a single dominant hematopoietic stem cell lineage. Somatic mutations in candidate driver (CD) genes are thought to be responsible for at least some cases of CH. Using whole-genome sequencing of 11 262 Icelanders, we found 1403 cases of CH by using barcodes of mosaic somatic mutations in peripheral blood, whether or not they have a mutation in a CD gene. We find that CH is very common in the elderly, trending toward inevitability. We show that somatic mutations in TET2, DNMT3A, ASXL1, and PPM1D are associated with CH at high significance. However, known CD mutations were evident in only a fraction of CH cases. Nevertheless, the highly prevalent CH we detect associates with increased mortality rates, risk for hematological malignancy, smoking behavior, telomere length, Y-chromosome loss, and other phenotypic characteristics. Modeling suggests some CH cases could arise in the absence of CD mutations as a result of neutral drift acting on a small population of active hematopoietic stem cells. Finally, we find a germline deletion in intron 3 of the telomerase reverse transcriptase (TERT) gene that predisposes to CH (rs34002450; P = 7.4 × 10^-12; odds ratio, 1.37).

Figure 1.

Age distribution of clonal hematopoiesis detected by WGS-outlier status. (A) Histograms showing the number of mosaic somatic mutations per person stratified by their age at blood sampling (adjusted as described in the supplemental Data). The vertical line shows the cutoff at 20 mosaic somatic mutations (corresponding to the 99.5% quantile of the distribution for ages younger than 35 years) that was used to classify individuals as WGS-outliers. (B) Prevalence of clonal hematopoiesis and CD mutations stratified by age class. Lavender bar, the fraction of samples classified as WGS-outliers; red bar, the fraction of samples with detected CD mutations from the 18-gene candidate list; green bar, the fraction of samples detected as outliers, using exon-restricted analysis; blue bar, combined fraction of samples detected with CD mutation or exon-restricted analysis. Error bars indicate 95% confidence intervals.

Figure 2.

Presence of candidate driver (CD) mutations by age. (A) VAF vs age at blood draw for the 16 CD genes where mutations were detected. The 177 subjects who were classified as WGS-outliers are plotted as blue points, and the 69 subjects who were not outliers are plotted as red points. (B) Conditional probability of being identified as a WGS-outlier given that a CD mutation was detected, stratified by age bins. P = 1.9 × 10⁻¹²; β = 0.10, assessed by logistic regression. Error bars indicate 95% confidence intervals. (C) Co-mutation plot for WGS-outliers and nonoutliers in whom CD mutations were detected. Each column represents a subject, each row a candidate pre-leukemic driver gene. Cells are shaded if a mutation was detected, and the color of the shading indicates the number of mutations detected for the particular gene. The vertical black line separates non–WGS-outlier from WGS-outlier subjects.

Figure 3.

Survival analysis using Cox proportional hazard model. Baseline was defined as subjects who were neither WGS-outliers nor carriers of a mosaic somatic CD mutation. Plots show HRs with 95% confidence intervals. (A) HRs for all-cause mortality adjusted for age at blood draw, year of birth, sex, previous diagnoses of cancer, and smoking. (B) HRs for subsequent hematological malignancy adjusted for age at blood draw and year of birth. Details of the subjects who developed hematological malignancies are shown in supplemental Table 6.

Figure 4.

Computer simulation of clonal hematopoiesis arising under neutral drift. The graph shows the proportion of simulations producing more than 20 observable mosaic somatic mutations with a VAF less than 0.2 as a function of subject age, for different choices of N, the size of the active HSC compartment. The value of p, the probability that an HSC division will produce 2 daughter stem cells, was set at 0.25. Other parameters were fixed at λ = 1 division per 40 weeks, mutation rate µ = 6.4 × 10⁻¹⁰ per base pair per division.

Figure 5.

Genome-wide association for germline variants associated with clonal hematopoiesis detected by WGS-outlier status. (A) Manhattan plot of association [expressed as –log₁₀(P)] with WGS-outlier status, determined using logistic regression. (B) Locus zoom of the signal in the TERT gene on chromosome 5. The location of the 8-bp indel rs34002450 (chr5:1280825) giving the strongest signal is indicated by a purple diamond. Other variants are plotted in colors corresponding to their r² values relative to rs34002450, as indicated in the legend. Recombination rates, in cM/Mb and based on Icelandic data, are plotted as a red line. The lower panel shows the locations of RefSeq genes and the chromosomal position (GRCh38/hg38).