Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life

Abstract

Clonal hematopoiesis results from somatic mutations in hematopoietic stem cells, which give an advantage to mutant cells, driving their clonal expansion and potentially leading to leukemia. The acquisition of clonal hematopoiesis-driver mutations (CHDMs) occurs with normal aging and these mutations have been detected in more than 10% of individuals ≥65 years. We aimed to examine the prevalence and characteristics of CHDMs throughout adult life. We developed a targeted re-sequencing assay combining high-throughput with ultra-high sensitivity based on single-molecule molecular inversion probes (smMIPs). Using smMIPs, we screened more than 100 loci for CHDMs in more than 2,000 blood DNA samples from population controls between 20 and 69 years of age. Loci screened included 40 regions known to drive clonal hematopoiesis when mutated and 64 novel candidate loci. We identified 224 somatic mutations throughout our cohort, of which 216 were coding mutations in known driver genes (DNMT3A, JAK2, GNAS, TET2, and ASXL1), including 196 point mutations and 20 indels. Our assay's improved sensitivity allowed us to detect mutations with variant allele frequencies as low as 0.001. CHDMs were identified in more than 20% of individuals 60 to 69 years of age and in 3% of individuals 20 to 29 years of age, approximately double the previously reported prevalence despite screening a limited set of loci. Our findings support the occurrence of clonal hematopoiesis-associated mutations as a widespread mechanism linked with aging, suggesting that mosaicism as a result of clonal evolution of cells harboring somatic mutations is a universal mechanism occurring at all ages in healthy humans.

The rate and spectrum of mosaic mutations during embryogenesis revealed by RNA sequencing of 49 tissues

“…We therefore screened for late embryonic mosaic mutations (LEMMs, Figure 1b), which we defined as tissue-specific mutations at high cell fraction (VAF >= 0.2). Here, we excluded tissues previously shown to be affected by clonal expansion of mutated cells such as esophagus-mucosa, sun-exposed skin (Martincorena et al, 2015(Martincorena et al, , 2018Chalmers et al, 2017;Yizhak et al, 2019;Yokoyama et al, 2019) and whole blood (Acuna-Hidalgo et al, 2017), which also showed the highest somatic mutation rates in our analysis (Supp. Figure 3).…”

“…The timing of mutations during embryogenesis (e.g. cleavage, blastulation, implantation, gastrulation, neurulation and organogenesis) influences the fraction of affected cells and organs in the organism Acuna-Hidalgo et al, 2017). Moreover, when occurring during gametogenesis mosaic mutations can be passed on constitutionally to multiple offspring (Acuna-Hidalgo et al, 2016).…”

Clonal hematopoiesis and preleukemia—Genetics, biology, and clinical implications

“…The frequency of CH is even considerably higher when more sensitive methods are used to reveal gene mutations at very low variant allele frequencies (VAFs), allowing the detection of small clones of blood cells. 21,22 For instance, Young et al detected CH in 19/20 individuals aged between 50 and 60 years using an error-corrected sequencing approach that allowed detection of mutations with VAFs as low as 0.03%. 23 Likewise, analyses of mosaic somatic mutations by whole genome sequencing suggests that CH becomes very common in old adults, affecting >50% of persons older than 85 years.…”

A characterization of postzygotic mutations identified in monozygotic twins

“…Additionally, we tested for enrichment of putative mosaic mutations in two genes, DNMTA3 (HGNC:2978) and TET2 (HGNC:25941), both linked to clonal expansion of hematopoietic stem cells. Somatic mosaicism in these genes was reported to be common in the elderly (Acuna‐Hidalgo et al., ; van den Akker et al., ; Zink et al., ). We found a slight enrichment for low‐mutational ratio mosaicism in these genes in both twin pairs (minimal difference in allelic ratio threshold > 0.05, 40‐year‐old twin pair p = 0.0023, 100‐year‐old twin pair p = 0.0031; ).…”