Abstract
Cancer is a disease largely caused by genomic aberrations. Utilizing many rapidly emerging sequencing technologies, researchers have studied cancer genomes to understand the molecular statuses of cancer cells and to reveal their vulnerabilities, such as driver mutations or gene expression. Long-read technologies enable us to identify and characterize novel types of cancerous mutations, including complicated structural variants in haplotype resolution. In this review, we introduce three representative platforms for long-read sequencing and research trends of cancer genomics with long-read data. Further, we describe that aberrant transcriptome and epigenome statuses, namely, fusion transcripts, as well as aberrant transcript isoforms and the phase information of DNA methylation, are able to be elucidated by long-read sequencers. Long-read sequencing may shed light on novel types of aberrations in cancer genomics that are being missed by conventional short-read sequencing analyses.
Highlights
Cancer cells harbor mutations in their genomes, parts of which affect the function of driver and tumor suppressor genes, resulting in the abnormal proliferation and initiation or progression of carcinogenesis
EGFR tyrosine kinase inhibitors are effective for lung adenocarcinomas with EGFR mutations [1]
Modern sequencing technologies are rapidly being developed to enable us to identify and characterize mutations in each cancer case more. Many consortiums, such as ICGC [2] and TCGA [3], have sequenced, analyzed, and reported on the genomic statuses specific to each cancer subtype. They have mainly focused on point mutations, such as single-nucleotide variants (SNVs) and short indels, because short-read sequencing techniques are generally being used for genotyping
Summary
Cancer cells harbor mutations in their genomes, parts of which affect the function of driver and tumor suppressor genes, resulting in the abnormal proliferation and initiation or progression of carcinogenesis. Modern sequencing technologies are rapidly being developed to enable us to identify and characterize mutations in each cancer case more . Many consortiums, such as ICGC [2] and TCGA [3], have sequenced, analyzed, and reported on the genomic statuses specific to each cancer subtype. Singlemolecule real-time sequencing (SMRT) [8] is one of the long-read methods developed by Pacific Biosciences (PacBio). This method is based on a single-DNA polymerase attached in a zero-mode waveguide (ZMW), which is a nanostructure for fluorescence detection. Protein nanopores are arrayed on a membrane to detect changes in an electrical current when a DNA or an RNA molecule passes through
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