Identification of Somatic Mutations From Bulk and Single-Cell Sequencing Data

Abstract

Somatic mutations are DNA variants that occur after the fertilization of zygotes and accumulate during the developmental and aging processes in the human lifespan. Somatic mutations have long been known to cause cancer, and more recently have been implicated in a variety of non-cancer diseases. The patterns of somatic mutations, or mutational signatures, also shed light on the underlying mechanisms of the mutational process. Advances in next-generation sequencing over the decades have enabled genome-wide profiling of DNA variants in a high-throughput manner; however, unlike germline mutations, somatic mutations are carried only by a subset of the cell population. Thus, sensitive bioinformatic methods are required to distinguish mutant alleles from sequencing and base calling errors in bulk tissue samples. An alternative way to study somatic mutations, especially those present in an extremely small number of cells or even in a single cell, is to sequence single-cell genomes after whole-genome amplification (WGA); however, it is critical and technically challenging to exclude numerous technical artifacts arising during error-prone and uneven genome amplification in current WGA methods. To address these challenges, multiple bioinformatic tools have been developed. In this review, we summarize the latest progress in methods for identification of somatic mutations and the challenges that remain to be addressed in the future.

Keywords: bioinformatic tool; bulk sequencing; single-cell sequencing; single-nucleotide variant; somatic mutation.

FIGURE 1

Occurrence of somatic mutations and their identification in next-generation sequencing data. (A) Somatic mutations that occur postzygotically after fertilization. Mutations arising during embryogenesis or under clonal expansion (green and blue) are shared in a fraction of the cell population, whereas mutations accumulating during the aging process (purple) may only be present in a single cell. (B) Identification of somatic mutations using bulk or single-cell sequencing. Bulk sequencing is suitable for detecting somatic mutations shared across multiple cells, though mutations with low allele fractions are difficult to distinguish from sequencing errors. Private somatic mutations can be detected with single-cell sequencing, but the whole-genome amplification before sequencing may introduce additional artifacts resulting from amplification errors.