First year Phd student Yuji Yoshida received Tohoku University’s Research Encouragement Award for his study about the development and evaluation of mitochondrial mutation detection at the 8thAnnual Retreat Student Conference on 17th January.
He greatly anticipates the progress of his doctoral research based on his results since last April and its future direction.

First year Phd student Yuji Yoshida

The 53rd In Silico Megabank Research Seminar will be held on Friday, January 9.

This Time, we will be welcoming Dr. Tomoko Shibata, The National Institute for Basic Biology as our lecturer, and she will be speaking on “Development of a New Genomic Analysis Method Using Single Module Sequencing from Small Quantities of DNA”.

・Date/Time: January 9 (Friday) 9:00‐10:15
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Development of a New Genomic Analysis Method Using Single Module Sequencing from Small Quantities of DNA
・Lecturer: Tomoko Shibata (The National Institute for Basic Biology )

・Abstract: Single Module Sequencer, PacBio RSII, has a long average length of readable sequence of 7−8 kb with maximum of 30 kb, and it is possible to determine the base sequence without the amplification through PCR during the process of sequencing. Thus, domains with difficulty in amplification and long repetitive sequences became readable, which enabled more exhaustive genomic analysis. However, on the contrary to the unnecessity of amplification, large quantities of DNA are required for analyses. Moreover, in many cases sufficient amount of DNA cannot be secured depending on living organisms. Hence, we aimed to develop a method which enables genomic analyses with small quantities of DNA by using PacBio sequencer on DNA amplified with Phi29 DNA polymerase which is known to amplify DNA without causing a bias. In this seminar, we will introduce the results of the data analysis of bacterial genome and eukaryotic genome and discuss the future prospects.

・Organizer: Masao Nagasaki

The 52nd In Silico Megabank Research Seminar will be held on Wednesday, January 7.

This Time, we will be welcoming Dr. Andre Fujita, University of Sao Paulo as our lecturer, and he will be speaking on “Computational Statistics in Biological Big Data: Methods and Applications”.

・Date/Time: January 7(Wednesday) 17:00‐18:30
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building 
・Title: Computational Statistics in Biological Big Data: Methods and Applications
・Lecturer: Andre Fujita （University of Sao Paulo）

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

・Abstract: The understanding of the biological mechanisms underlying human diseases is one of the main challenges in biological sciences. Although several efforts, the large number of heterogeneous factors that influence the genesis of a disease makes it a very hard task. One of the challenges consists in understanding diseases by developing methods to statistically analyze and computationally manipulate big data. This difficulty is generated by ultra large data size, heterogeneity, multidimensionality, and presence of intrinsic noise. In this context, computationally intensive statistical methods developed by our group are presented with applications in neuroscience and molecular biology. In neuroscience, the focus is on the analysis of resting-state fMRI data of ~600 individuals diagnosed with ADHD and ~900 subjects with ASD. In the context of molecular biology, partial results obtained from the study of miRNA expression of a cohort of ~2,000 breast cancer subjects are presented.

・Organizer : Kaname Kojima, Masao Nagasaki

The 51st In Silico Megabank Research Seminar will be held on Friday, December 12 . This Time, we will be welcoming Dr. Ryosuke Kimura, University of the Ryukyus as our lecturer, and he will be speaking on “Encouragement of Learning Genome Anthropology”.

・Date/Time: December 12 (Friday) 17:00‐18:30
・Venue : Small Conference Room 2(3rd Floor), Tohoku Medical Megabank
・Title: Encouragement of Learning Genome Anthropology
・Lecturer : Ryosuke Kimura (Faculty of Medicine, University of the Ryukyus)

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

・Abstract : Each human being has different combinations of genomes, which creates genomic variations. Thus, there are variations in phenotypes such as people’s appearances and constitutions. In order to understand how human biological variability was shaped and maintained, it is important to know 1) how humans spread all over the world and how they have adapted to their environment, 2) how large the variability generated as a result of chance. At present, in our laboratory, we put special focus on the people in the Ryukyu Chain to deepen our research on the features of genome and phenotypes in Asians and the background on how such features were formed. Furthermore, we are tackling to identify the genomic factors on visible traits such as complexion. The advancement of the recent genome analysis technology and dense catalog of genomic variations have dramatically transformed the strategy of biomedical studies, and it was required for researchers to face a large volume of data. In this seminar, we would like to introduce our study as well as to show the overview of the fast-evolving research methods of population genomics.

・Organizer : Yosuke Kawai, Masao Nagasaki

Tohoku University announced the Japonica array®, which was developed at our laboratory.

Tohoku Medical Megabank Organization 2014.11.18 News (in Japanese)

TOHOKU UNIVERSITY 2014 Press release (in Japanese)

Symposium Name: Biohackathon 2014
Title: Introduction to the Tohoku Medical Megabank Organization and What is Happening in the Human Reference Genome?
Date: Nov/8/2014 10:20-10:40
Location: Tohoku Mediacl Megabank Building Meeting Room Tohoku University
Presenter: Prof. Masao Nagasaki
Reference: BioHackathon 2014 Official Website

Tohoku University Graduate School of Medicine briefing session will be held on December 6th.

For the information for the entrance exams, please click here

・Date/Time: December 6(Sat) 10:30‐12:00 (The room will be available from 10:00)
・Venue: Lecture Room 1, Building #1, Tohoku University School of Medicine

Briefing session is for those who are planning to major in Medical Science, Disability Science, Health Science, and Public Health or applying for graduate programs for next year onward.
Contents：Messages from Dean, Graduate School of Medicine, introductions of each major, presentations by graduate students (Medical Science, Disability Science, Health Science, and Public Health), financial aid, and points of attention concerning application, and Q&As.

・The time for visiting a laboratory is allocated after the end of the session.
・Please be advised that you should make a direct contact with the field you hope to visit in advance.
・Neither prior application nor participation fee is necessary.
・Since parking lot is not available, visitors are encouraged to use public transportation.

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