Title: Data management and bioinformatics of thousands Japanese whole-genome project
Symposium Name: Karolinska-Tohoku Joint Symposium on Medical Sciences
Date: 2014/Nov/8 (Sat) 15:05-15:30
Location: Tohoku Mediacl Megabank Building Meeting Room Tohoku University
Presenter: Prof. Masao Nagasaki
URL: http://www.megabank.tohoku.ac.jp/english/news/detail.php?id=829&c1=3

The 50th In Silico Megabank Research Seminar will be held on Friday, September 26.
This Time, we will be welcoming Dr. Kitano, Ibaraki University as our lecturer, and he will be speaking on “Evolution of Blood Group Genes”.

・Date/Time: September 26(Fri.) 17:00‐18:30
・Venue : Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Evolution of Blood Group Genes
・Lecturer: Takashi Kitano (Department of Biomolecular Functional Engineering,
College of Engineering, Ibaraki University)

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

・Abstract :. Small variance in the structure of erythrocyte cell surface is categorized into groups based on the antigen-antibody reaction, and this is what we call blood groups. The antigens of ABO type blood groups are sugar chains. The base is the sugar chain of type O. The sugar chain comprised of the base with a terminal N-Acetylgalactosamine is type A and with a terminal galactose is type B. ABO type blood group genes are ones that code glycosyltransferase to link those terminal sugars. The difference in 2 amino acids above exon 7 creates the difference in the sugar attached, which in turn forms the sugar chain of type A or type B. Also, the frame shift due to single base deletion above exon 6 causes inhibition of the production of functional glycosyltransfrase, and as a consequence neither terminal sugar is attached. This is the sugar chain of type O. On the other hand, RH blood group genes are the ones that code proteins for transporters with 12 transmembrane domains, and the different types of the amino acids placed outer-membrane of these proteins are categorized in this group.
In this lecture, molecular basis and evolution of ABO and RH blood group genes are introduced.

・Organizer : Yosuke Kawai, Masao Nagasaki

On August 8th 2014, we, Tohoku University’s Medical Megabank, published an allele frequency of more than 5% on known variants in order to advance the validation of our Genome Reference Panel Draft. Though variant information of more than 1% will be sold in the future, we aim to improve the verification and accuracy of our draft version. Therefore, we are proud to announce that we are accepting research proposals aimed at achieving an allele frequency of less than 1% within variants.

1.)     Joint Research related to single nucleotide polymorphism with in the
ToMMo Genome Reference Panel Draft.
2.)     Joint Research related to deleting, inserting, and copying within the
ToMMo Genome Reference Panel Draft.
3.)     Joint Research contrasting the ToMMo Genome Reference Panel Draft to
healthy people.
4.)     Joint Research involving a case-compare study on an SNP array used on
Japanese people.

For more information click on the link below:
http://www.megabank.tohoku.ac.jp/news/5710

Symposium Name: in Japanese: Sin-Seimei-Kagaku Bunya Kaitaku to Super Computer “Kei”
Title:Supercomputer system and large scale cohort in Tohoku Medical Megabank Organization (in Japanese: Tohoku Medical Megabank Kikou no daikibo genome cohort to keisan inhura)
Date: 16/Sep/2014 (Tue), 14:25 to 15:10
Location: Kyushu University’s Medical facility’s Hundred Year Auditorium
Presenter: Prof. Nagasaki
Presentation Language: Japanese
URL: Official website (only in Japanese)

The 49th In Silico Megabank Research Seminar will be held on Friday, September 12.

This Time, we will be welcoming Dr. Kohda, Saitama Medical University　as our lecturer, and he will be speaking on “Comprehensive Genomic Analysis on Mitochondrial Respiratory Chain Disorder”.
・Date/Time : September 12(Friday) 17:00‐18:30
・Venue : Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title : Comprehensive Genomic Analysis on Mitochondrial Respiratory Chain Disorder
・Lecturer : Masakazu Kohda（Research Center for Genomic Medicine, Saitama Medical University）

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

・Abstract : Mitochondrial respiratory chain disorder (MRCD) is one of the intractable diseases and is an inborn error of metabolism with frequent incidence of 6.2 in 100,000 infants. Abnormality of various protein involved in respiratory chain complex has been revealed as a cause of MRCD; until now approximately 150 causative genes have been found. However, some part of causative genes and the mechanism of the development still remain unknown. In the research, 6 mitochondria-related genes were successfully found as new causative genes through comprehensive genomic analysis on MRCE. Furthermore, multiple genes with unknown direct relationship with MRCD were identified as causative genes for the occurrence of phenotype in patients. Data obtained in this research can contribute to the development of the foundation of genomic analysis for MRCD; thus, high usability of the findings from the data on the understanding of genes, which have been yet remained unknown, is expected.

・Organizer : Masao Nagasaki

An article of quality control software for ultra-high-throughput DNA data was published and marked as “highly accessed” article of the journal.

Title: SUGAR: graphical user interface-based data refiner for high-throughput DNA sequencing
BMC Genomics. 2014, 15: 664 (doi: 10.1186/1471-2164-15-664)
PMID:25103311

This is to announce that the 49th In Silico Megabank Research Seminar planned to be held on July 25th will be postponed due to various circumstances. We are sorry for the last minute notice. We will communicate on the future schedule as soon as it is decided.

The 49th In Silico Megabank Research Seminar will be held on Friday, July 25.

This Time, we will be welcoming Dr. Osamu Ogasawara, National Institute of Genetics  as our lecturer, and he will be speaking on “The Evolution Model of Gene Expression”.

・Date/Time : July 25(Friday) 17:00‐18:30
・Venue : Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title : The Evolution Model of Gene Expression
・Lecturer : Osamu Ogasawara（National Institute of Genetics）)

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

・Abstract : There has been a hypothesis that the evolution of gene expression is the possible key to link morphological evolution and molecular evolution since 1970’s. This hypothesis has left unverified for a long time since it was difficult to obtain data; however, the emergence and prevalence of the measurement methodology of genome-wide gene expression level started enabling the study on the evolutionary changes. Until now several observations have been reported using microarrays or EST, RNASeq, but the interpretation of the results is not consistent. The possible reason for this is that no clear model on the evolution of gene expression yet exists and interpretation is made based on the analogy of molecular evolutionary model of gene sequence. In this seminar, we will give the outline of gene expression evolutionary model until today and introduce the establishment of gene expression evolutionary model that explains the past observation integrally.

・Organizer : Masao Nagasaki

The 48th In Silico Megabank Research Seminar will be held on Friday, July 11.
This Time, we will be welcoming Dr. Takashi Makino, Graduate School of Life Sciences, Tohoku University as our lecturer, and he will be speaking on “Evolutionary Study of Duplicate Genes and Application to Ecology and Medicine”.

・Date/Time: July 11(Friday) 17:00‐18:30
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Evolutionary Study of Duplicate Genes and Application to Ecology and Medicine ・Lecturer: Takashi Makino (Graduate School of Life Sciences, Tohoku University )

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

・Abstract: Gene duplication is a mutation where genes are duplicated and has drawn attention mainly as the emergent mechanism of genes with new functions. It can be assumed that increase in genes with functional differentiation through gene duplication also increases robustness toward various disruption from environment. In this study, species that we already have genome information in mammals and Drosophila were focused, and it was found that the higher the percentage of duplicate genes are in genome, more variable their habitat environment was. If examining duplicate genes in genome enables vulnerability to environmental change and invasiveness in certain species, new initiative for alien species issues and organism conservation with a totally new approach will become promising. In addition, in rare cases whole genome duplication where all genes are doubled in the process of evolution occurs instead of duplication of individual genes. Whole genome duplication enhances the robustness of biological system dramatically and has contributed to the macroevolution such as prevention of extinction and establishment of spermatophyte and vertebrates. On the other hand, duplicate genes that are kept without disappearing after whole genome duplication (ohnolog) do not contribute to the robustness; thus, it is necessary to differentiate from other duplicate genes. In fact, ohnolog has strong tendency to be involved in disorders.
In this lecture, overview of gene dosage equality, unique characteristics of ohnolog, is discussed and concrete examples of ohnolog as disease-related genes are introduced.

・Organizer: Yukuto Sato, Masao Nagasaki

Prof. Nagasaki will give a lecture at the 74th Symposium of Japan Society for Analytical Chemistry.

・Date : Sunday, May 25, 2014  9:00- 9:30 am
・Venue : D2001, Building #70, College of Engineering, Nihon University http://www.ce.nihon-u.ac.jp/english/access.html#top
・Title : Human Whole Genome Analysis and Big Data