Somatic point mutations occurring early in development: a monozygotic twin study

Abstract

The identification of somatic driver mutations in cancer has enabled therapeutic advances by identifying drug targets critical to disease causation. However, such genomic discoveries in oncology have not translated into advances for non-cancerous disease since point mutations in a single cell would be unlikely to cause non-malignant disease. An exception to this would occur if the mutation happened early enough in development to be present in a large percentage of a tissue's cellular population. We sought to identify the existence of somatic mutations occurring early in human development by ascertaining base-pair mutations present in one of a pair of monozygotic twins, but absent from the other and assessing evidence for mosaicism. To do so, we genome-wide genotyped 66 apparently healthy monozygotic adult twins at 506 786 high-quality single nucleotide polymorphisms (SNPs) in white blood cells. Discrepant SNPs were verified by Sanger sequencing and a selected subset was tested for mosaicism by targeted high-depth next-generation sequencing (20 000-fold coverage) as a surrogate marker of timing of the mutation. Two de novo somatic mutations were unequivocally confirmed to be present in white blood cells, resulting in a frequency of 1.2×10(-7) mutations per nucleotide. There was little evidence of mosaicism on high-depth next-generation sequencing, suggesting that these mutations occurred early in embryonic development. These findings provide direct evidence that early somatic point mutations do occur and can lead to differences in genomes between otherwise identical twins, suggesting a considerable burden of somatic mutations among the trillions of mitoses that occur over the human lifespan.

Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair

“…The average somatic mutation rate has been reported to be 7.7×10 −10 20. A more recent study that surveyed the whole genome estimated the somatic mutation rate for common SNPs in healthy monozygotic twins to be 1.2×10 −7 per base pair 12. Conrad and his colleagues distinguished the germline and non-germline (somatic and cell line derived) mutations through whole-genome sequencing of a CEU trio and provided a rate of 2.52×10 −7 per nucleotide for non-germline mutations.…”

“…RAF is the total number of reads supporting the reference allele as a fraction of total number of reads supporting both reference and alternative allele 12. For the putative de novo SNVs that are present in a heterozygous state, RAF threshold was determined as 0.5–0.7 for the twins and 0.95–1.0 for the parents.…”

Why Accurate Knowledge of Zygosity is Important to Twins

“…A further false assumption, not highlighted in our study, is that fused placentas in DZ twins could be misclassified as monochorionicity. In addition, in rare circumstances, MZ (Edwards et al, 1966) or monochorionic (Umstad et al, 2012) twins may be of opposite sex (Edwards et al, 1966;Umstad et al, 2012) and mosaicism (Li et al, 2014;Petersen et al, 2014) or chimerism (Fumoto et al, 2014;Lee et al, 2014;Waszak et al, 2013) could potentially confound zygosity tests.…”

Recent advances in the study of somatic mosaicism and diseases other than cancer

“…Germ line selection for dominant mutations in the male spermatogonia, resulting in high frequencies of single base pair changes for several disorders of fibroblast growth factor-RAS pathways, especially achondroplasia, is well described (reviewed in [15]). A study of 33 identical twin pairs found somatic differences for only two genes [16] and these were not mosaic suggesting very early events. The full answer to the question of possible selection for somatic clones would probably require post-mortem examination of many samples of many tissues.…”