The 66th In Silico Megabank Research Seminar(December 8, 2015)

The 66th In Silico Megabank Research Seminar will be held on Tuesday, December 8. This Time, we will be welcoming Dr. Wojciech Makalowski, University of Muenster as our lecturer, and he will be speaking on “Nanopore Sequencing for Genotyping Pathogens of Tropical Diseases”.

・Date/Time: December 8(Tuesday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Nanopore Sequencing for Genotyping Pathogens of Tropical Diseases – Bioinformatics Challenges
・Lecturer: Wojciech Makalowski(Institute of Bioinformatics, University of Muenster)

*This lecture is transferable as a class in the medical research-related lecture course.

・Abstract: Sequencing technology continues to revolutionize life sciences. However, all the main stream technologies share several weaknesses, such as short reads and bulky instruments with high price tag. The latter prohibits usage of the sequencing directly in the field or in rural hospitals. Therefore there’s a pressing need for a simple and low-cost instrument that could be used for rapid disease diagnosis or biological sample identification. Recently introduced MinIONTM by Oxford Nanopore Technologies meets these expectations as it’s very portable with just four inches in length and operability via the USB port of a laptop computer. As a part of the Oxford Nanopore MinIONTM Access Program (MAP) we have tested applicability of the nanopore technology for genotyping of tropical diseases. In particular, it was applied to two different tasks: serotype determination of the dengue virus and genotyping of the malaria parasites. Despite very low accuracy of a single molecule read we were able successfully discriminate between different dengue virus serotypes using multiple-sequence alignment and majority rule for the base call. We demonstrate that sequence depth generated by a single run of the MinIONTM is sufficient for precise serotyping of the virus. Similarly, our preliminary results suggest that the nanopore sequencing should be useful in genotyping of the malaria parasite. Since Oxford Nanopore Technologies don’t provide any specialized software for the sequence analysis, we built a simple web-based pipeline for sero- and genotyping. The pipeline is freely available at

・Organizer: Yumi Yamaguchi, Masao Nagasaki