A new era of long-read sequencing for cancer genomics.

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.

Single-Cell DNA-Seq and RNA-Seq in Cancer Using the C1 System.

Heterogeneous phenotypes of cancer cells enable them to adapt to various environments. The heterogeneity results from diversity of genome, transcriptome, and epigenome at a single-cell level. The C1 system can automatically perform single-cell capture and whole genome amplification (WGA) or whole transcription amplification (WTA) by MDA or Smart-Seq, respectively.

Evaluation and application of RNA-Seq by MinION.

The current RNA-Seq method analyses fragments of mRNAs, from which it is occasionally difficult to reconstruct the entire transcript structure. Here, we performed and evaluated the recent procedure for full-length cDNA sequencing using the Nanopore sequencer MinION. We applied MinION RNA-Seq for various applications, which would not always be easy using the usual RNA-Seq by Illumina.

Identification of potential regulatory mutations using multi-omics analysis and haplotyping of lung adenocarcinoma cell lines.

The functional relevancy of mutations occurring in the regulatory regions in cancers remains mostly elusive. Here, we identified and analyzed regulatory mutations having transcriptional consequences in lung adenocarcinoma-derived cell lines. We phased the mutations in the regulatory regions to the downstream heterozygous SNPs in the coding regions and examined whether the ChIP-Seq variant tags of the regulatory SNVs and the RNA-Seq variant tags of their target transcripts showed biased frequency between the mutant and reference alleles.