Long-Read Whole-Genome Sequencing Using a Nanopore Sequencer and Detection of Structural Variants in Cancer Genomes.

Long-read sequencing technologies enable us to precisely identify structural variants (SVs), which would be occasionally associated with various types of diseases, including cancers. In this section, we introduce experimental and computational procedures for conducting long-read whole-genome sequencing (WGS) of cancer genomes from fresh frozen tissues/cells. We also demonstrate the analysis of SVs in cancer genomes using long-read WGS data from lung cancer cell lines by several representative computational tools, such as cuteSV and Sniffles2, as examples.

De Novo Genome Assembly of Japanese Black Cattle as Model of an Economically Relevant Animal.

A genetic analysis of Japanese Black cattle using short reads and guided by the reference genome from Western breeds would miss the structural variation and/or other unique characteristics of Japanese Black cattle. To overcome this difficulty, a de novo genome assembly independent from the reference genome is required. This chapter describes the technical developments, with respect to both experimental and bioinformatics procedures, including the use of short and long reads, required for de novo genome assembly of Japanese Black cattle.

Single-cell analytical technologies: uncovering the mechanisms behind variations in immune responses.

The immune landscape varies among individuals. It determines the immune response and results in surprisingly diverse symptoms, even in response to similar external stimuli. However, the detailed mechanisms underlying such diverse immune responses have remained mostly elusive.