Somatic genetic variation in healthy tissue and non-cancer diseases.

The study of the genetic aetiology of complex disorders was traditionally focused on the role of common genetic variants identified by linkage and association studies. Later, NGS allowed exploring the role of rare genetic variation thanks to the development of new statistical approaches mostly optimized to identify the enrichment of this type of variants in patients compared to controls, or even to explore the role of de novo genetic variants in particular individuals that would therefore better fit to a Mendelian inheritance. The de novo scenario has been particularly explored for neurodevelopmental disorders, where these mutations would be unlikely to be observed as germinal because of the low reproductive rates of affected individuals [ 61 ]. Similarly, new genetic variants arising during development or even in adult neurons could also contribute to the development of these disorders. Several works propose a possible relation of somatic variants to neurological disorders such as Alzheimer’s disease [ 62 ] or Parkinson’s disease [ 63 ]. Also, individuals with a neurodegenerative condition showed an increase in the number of somatic SNVs in comparison with matched healthy individuals of similar age. A somatic copy number alterations was found to be responsible for the neuropsychiatric disease [ 64 ] at VAFs below 20 %. Also, in autism spectrum disorder, structural variants affecting 3–70 % of the cells were detected by microarrays [ 65 ]. Interestingly, in this case, the event size positively correlated with the severity of the patients’ symptoms [ 65 ]. Recently, following the idea that LINE1 does play a role in the diversity of the neuron’s genome, Zhu et al. corroborated the possible pathogenic effect of retrotransposon insertion on neurologic disease [ 66 ]. As mentioned before, CH is related to a group of complex diseases, also beyond cancer. For instance, there is a relationship between chronic ischaemic heart failure and the mutations causing the CH [ 67 ]. The somatic variant landscape has been also studied in endometriosis [ 68 ], in which the authors performed WES on 13 endometriotic and 11 normal endometrial epithelium samples. They also performed targeted sequencing on a larger validation dataset of 94 endometriotic epitheliums from 45 individuals and 71 normal epitheliums from 29 individuals. They discovered two oncogenes, KRAS and PIK3CA , to be the most frequently mutated in both scenarios, but with VAFs significantly higher in endometriosis. Thus, the authors suggested a potential role in the development of endometriosis of the generated clonal expansion due to the presence of these cancer-associated mutations. Following a previous publication on colonic crypts [ 12 ], and using the generated samples in that study as healthy controls, inflammatory bowel disease (IBD) has been explored. In this new study, WGS was performed on 446 crypts from 46 IBD patients with a median coverage of 18.2× [ 69 ]. They sequenced 28 ulcerative colitis patients and 18 Crohn’s disease patients and described an average of ~2.4-fold increase in the mutation rates of IBD patients compared to controls, and reported no significant differences between the patients of both diseases. They observed that around 80 % of the increase in mutation burden is explained by mutational signatures also present in the healthy colon, pointing to an acceleration of the normal age-related mutational processes. Besides this, the clonal expansion found in patients with IBD is much larger than in healthy individuals, with an important number of clones bigger than 2 mm. They also found signatures of positive selection in genes ARID1A , FBXW7 , PIGR and ZC3H12A , as well as in some of the IL-17 and Toll-like receptor pathways, suggesting differences in selection mechanisms in IBD colons. Finally, the authors suggest a potential causal role of somatic mutations in IBD. The case of ulcerative colitis has also been studied in another work, in which WES was performed on 76 clonal human colon organoids [ 70 ]. Similarly, the authors observed an accumulation of somatic mutations in genes of the IL-17 signalling pathway such as NFKBIZ , ZC3H12A and PIGR . These genes are not particularly related to colorectal cancer.

The number of evidences of the role of postzygotic mutations in non-cancer diseases is growing in parallel with the development of experimental and analytical methodologies to detect and characterize somatic genetic variants. Sampling methods are being refined allowing the characterization of genetic variants at the single-cell level in an increasing number of cell types. Simultaneously, bioinformatics pipelines are being adapted to different experimental designs to identify real somatic variants while discarding false positives generated by sequencing, mapping and mostly calling artefacts because of the relaxation of allelic imbalance thresholds. Of importance, a proper biological interpretation of the results can only be done based on the understanding of the presence and distribution of somatic genetic variants in healthy tissue, which provides a baseline for the analysis of somatic variation in disease. While there exist some commonalities across tissues as the accumulation of somatic variants with age and exposure to external agents such as tobacco, alcohol or sun radiation, we should ideally consider the specificities and different mutagenic patterns shown by each cell type.

Mutation is the biological process that originates a genetic variant. Thus, somatic variants are caused by postzygotic mutations, those arising after the encounter of the spermatozoid and the ovule. They can occur from the beginning of the development of the organisms to any point during their life. Postzygotic mutations give rise to mosaicism, in which different cells of the same individual present dissimilarities in their genomes, in contrast to germline variants, inherited by the individuals from their parents and present in every cell of the body. To our knowledge, the first mention of the concept of the accumulation of somatic mutations, which were referred to as “ageing hits” on somatic cells, appeared in 1959 by Leo Szilard [ 1 ]. It represented the first remarkable effort that linked genetic damage and senescence. He developed his theory from a mathematical point of view and mentioned mutational agents such as ionizing radiation. Also, the concept of the somatic hypermutability in antibodies has been known since the 1980s. However, in the last 15 years, there has been an acceleration in the study of somatic variation, both in health and disease status, mostly because of the advances in next-generation sequencing (NGS) technologies. Somatic mutations accumulate with time, with aged individuals presenting significantly more variants than younger ones. It is also well known that both extrinsic (tobacco smoke, alcohol, radiation) and intrinsic (cytosine deamination, oxidative damage, DNA replication errors) mutational agents contribute to the emergence of somatic mutations. Also, certain somatic variants are the causative agent of different diseases: many driver mutations have been described in cancer, and some of them cause monogenic diseases. For complex diseases, the link is harder to establish, although some studies have suggested that somatic variants may play an important role in neurological and other disorders. Recent technological advances allow a better characterization of somatic variation in human tissues. However, there are still many questions to be answered on its role and relative contribution to human disorders, for which it is first crucial to understand the mechanisms that govern somatic variation origin, distribution and transmission. In this review, while being virtually impossible covering the whole extensive and diverse literature on these topics, we aim to provide a description for understanding the current state of this research field, including the evolution of the different methodological strategies for the detection and analysis of somatic genetic variants, the knowledge of the presence and dynamics of somatic genetic variants in healthy tissue, and their effect on non-cancer disorders.