Annual Report 2020
Section of Genome Analysis Platform
Yuichi Shiraishi, Ai Okada, Kenichi Chiba, Naoko Iida
Introduction
The Section of Genome Analysis Platform in the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) focuses on developing and evaluating (1) methodologies for detecting various types of somatic variants (SNV, indel, structural variations, etc.) in cancer genomes, (2) normalization of cancer genome data formats, (3) workflows for cancer genome analysis, and (4) platform for analyzing and sharing cancer genome data using cloud computing. These products created by our efforts will be best utilized in the project for collecting and managing cancer genome data. We are also preparing for a platform for whole genome sequencing analysis in clinical settings.
Research activities
1. Construction of the utilization system
In C-CAT, the results of gene panel tests and corresponding medical information from each patient are collected and stored with individual consent. We are developing a search portal (a portal site for browsing and searching case information) and a utilization cloud (a virtual desktop for performing analysis) employing a cloud system. Since the registered case data includes sequence and mutation data, we are designing and developing a secure usage environment.
2. Development of the genome analysis pipelines and frameworks using a cloud system
To produce sequence data and mutation data to be used in the C-CAT utilization system, we constructed a genome analysis framework that includes alignment software (bwa, GATK), mutation call software for somatic analysis (GenomonMutationCall, GenomonSV, mutectcaller, GIDSS, manta), and mutation call software for germline analysis (haplotypecaller, GIDSS, manta). For GenomonMutationCall and GenomonSV, which we developed, we improved the realignment process.
Education
We have supported many researchers using our analysis pipeline by answering their bioinformatics questions. We have hired postdocs and supported their research.
Future Prospects
Using current new sequencing technologies, we will develop new bioinformatics methods and computer systems for cancer genomics and clinical sequencing.