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Whole genome sequencing analysis for cancer genomics and precision medicine

Explosive advances in next‐generation sequencer (NGS) and computational analyses have enabled exploration of somatic protein‐altered mutations in most cancer types, with coding mutation data intensively accumulated. However, there is limited information on somatic mutations in non‐coding regions, in...

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Autores principales: Nakagawa, Hidewaki, Fujita, Masashi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5834793/
https://www.ncbi.nlm.nih.gov/pubmed/29345757
http://dx.doi.org/10.1111/cas.13505
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author Nakagawa, Hidewaki
Fujita, Masashi
author_facet Nakagawa, Hidewaki
Fujita, Masashi
author_sort Nakagawa, Hidewaki
collection PubMed
description Explosive advances in next‐generation sequencer (NGS) and computational analyses have enabled exploration of somatic protein‐altered mutations in most cancer types, with coding mutation data intensively accumulated. However, there is limited information on somatic mutations in non‐coding regions, including introns, regulatory elements and non‐coding RNA. Structural variants and pathogen in cancer genomes remain widely unexplored. Whole genome sequencing (WGS) approaches can be used to comprehensively explore all types of genomic alterations in cancer and help us to better understand the whole landscape of driver mutations and mutational signatures in cancer genomes and elucidate the functional or clinical implications of these unexplored genomic regions and mutational signatures. This review describes recently developed technical approaches for cancer WGS and the future direction of cancer WGS, and discusses its utility and limitations as an analysis platform and for mutation interpretation for cancer genomics and cancer precision medicine. Taking into account the diversity of cancer genomes and phenotypes, interpretation of abundant mutation information from WGS, especially non‐coding and structure variants, requires the analysis of large‐scale WGS data integrated with RNA‐Seq, epigenomics, immuno‐genomic and clinic‐pathological information.
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spelling pubmed-58347932018-03-06 Whole genome sequencing analysis for cancer genomics and precision medicine Nakagawa, Hidewaki Fujita, Masashi Cancer Sci Thematic Section: Cancer Genomics Explosive advances in next‐generation sequencer (NGS) and computational analyses have enabled exploration of somatic protein‐altered mutations in most cancer types, with coding mutation data intensively accumulated. However, there is limited information on somatic mutations in non‐coding regions, including introns, regulatory elements and non‐coding RNA. Structural variants and pathogen in cancer genomes remain widely unexplored. Whole genome sequencing (WGS) approaches can be used to comprehensively explore all types of genomic alterations in cancer and help us to better understand the whole landscape of driver mutations and mutational signatures in cancer genomes and elucidate the functional or clinical implications of these unexplored genomic regions and mutational signatures. This review describes recently developed technical approaches for cancer WGS and the future direction of cancer WGS, and discusses its utility and limitations as an analysis platform and for mutation interpretation for cancer genomics and cancer precision medicine. Taking into account the diversity of cancer genomes and phenotypes, interpretation of abundant mutation information from WGS, especially non‐coding and structure variants, requires the analysis of large‐scale WGS data integrated with RNA‐Seq, epigenomics, immuno‐genomic and clinic‐pathological information. John Wiley and Sons Inc. 2018-02-26 2018-03 /pmc/articles/PMC5834793/ /pubmed/29345757 http://dx.doi.org/10.1111/cas.13505 Text en © 2018 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association. This is an open access article under the terms of the Creative Commons Attribution‐NonCommercial (http://creativecommons.org/licenses/by-nc/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
spellingShingle Thematic Section: Cancer Genomics
Nakagawa, Hidewaki
Fujita, Masashi
Whole genome sequencing analysis for cancer genomics and precision medicine
title Whole genome sequencing analysis for cancer genomics and precision medicine
title_full Whole genome sequencing analysis for cancer genomics and precision medicine
title_fullStr Whole genome sequencing analysis for cancer genomics and precision medicine
title_full_unstemmed Whole genome sequencing analysis for cancer genomics and precision medicine
title_short Whole genome sequencing analysis for cancer genomics and precision medicine
title_sort whole genome sequencing analysis for cancer genomics and precision medicine
topic Thematic Section: Cancer Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5834793/
https://www.ncbi.nlm.nih.gov/pubmed/29345757
http://dx.doi.org/10.1111/cas.13505
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