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Journal Article
Role of non-coding sequence variants in cancer
2016
Overview
Key Points
Germline and somatic sequence variants in non-coding regions can play an important role in cancer.
Many different modes of action of non-coding variants are known. For example, point mutations and complex genomic rearrangements can disrupt or create transcription factor-binding sites or affect non-coding RNA loci.
Oncogenesis involves an interplay between germline and somatic variants.
Drivers in non-coding regions can be identified using computational methods that analyse functional effects of variants and recurrence across multiple samples.
Functional effects of non-coding variants can be studied by various experimental approaches.
The overall role of non-coding variants in tumorigenesis is currently likely underestimated as only a handful of genome-wide studies of tumours have analysed them. However, current and future efforts involving large-scale whole-genome sequencing of tumours are likely to shed more light on the importance of non-coding variants in cancer.
Genomic analyses of cancer genomes have largely focused on mutations in protein-coding regions, but the functional importance of alterations to non-coding regions is becoming increasingly appreciated through whole-genome sequencing. This Review discusses our current understanding of non-coding sequence variants in cancer — both somatic mutations and germline variants, and their interplay — including their identification, computational and experimental evidence for functional impact, and their diverse mechanisms of action for dysregulating coding genes and non-coding RNAs.
Patients with cancer carry somatic sequence variants in their tumour in addition to the germline variants in their inherited genome. Although variants in protein-coding regions have received the most attention, numerous studies have noted the importance of non-coding variants in cancer. Moreover, the overwhelming majority of variants, both somatic and germline, occur in non-coding portions of the genome. We review the current understanding of non-coding variants in cancer, including the great diversity of the mutation types — from single nucleotide variants to large genomic rearrangements — and the wide range of mechanisms by which they affect gene expression to promote tumorigenesis, such as disrupting transcription factor-binding sites or functions of non-coding RNAs. We highlight specific case studies of somatic and germline variants, and discuss how non-coding variants can be interpreted on a large-scale through computational and experimental methods.
Publisher
Nature Publishing Group UK,Nature Publishing Group
