The 77th In Silico Megabank Research Seminar(November 10, 2016)

The 77th In Silico Megabank Research Seminar will be held on Thursday, November 10. This Time, we will be welcoming Dr. Koji Yahara, National Institute of Infectious Diseases as our lecturer, and he will be speaking on “Method to infer the tracemarks of recombination and population structure and its application based on genome data”.

・Date/Time: November 10 (Thursday) 5:00 pm‐6:30 pm
・Venue: Conference Room 2 (1st Floor), Building #6, Tohoku University School of Medicine
・Title: Method to infer the tracemarks of recombination and population structure and its application based on genome data
・Lecturer: Koji Yahara (National Institute of Infectious Diseases)

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

・Abstract: Mutation and recombination are the source of adaptive revolution of creatures which cause genomic diversity. Mutation rate is known to be high in certain regions within genome, and its relation with diseases is drawing attention. On the contrary, recombination is more difficult to detect than mutation. Especially, it is difficult to estimate the number of its occurrence. In the first half of this seminar, we will calculate the index of recombination rate at single nucleotide level along genome using genome data in bacterial genome and introduce new approach to infer recombination “hot regions” and its application to 11 types of pathogenic bacteria. In the latter half, the estimate of population structure which should be done at the very first of the process of population-level genome data analysis is to be discussed. Also, it is introduced that the as the first step method to detect the tracemarks of genome-wide recombination reveals the detailed population structure and also the method is useful to quantitatively understand the flow of genome information between populations.

・Organizer: Yosuke Kawai, Masao Nagasaki

 

Professor Nagasaki will give a lecture at the 23rd Annual Meeting of the Japanese Society Gene Diagnosis and Therapy on October 7

Professor Nagasaki will give a lecture at the 23rd Annual Meeting of the Japanese Society Gene Diagnosis and Therapy on October 7

・Date: October 7 (Friday)
・Venue: Iino Hall & Conference Center
・Session&Thema: Symposium3 “Basics of Genome Statistics and its Clinical Application”
・Title: 日本人2049人の全ゲノムリファレンスパネルの構築と今後

The 75th In Silico Megabank Research Seminar(September 2, 2016)

The 75th In Silico Megabank Research Seminar will be held on Friday, September 2.

This Time, we will be welcoming Dr. Makoto Shimada, Fujita Health University as our lecturer, and he will be speaking on “Explore the relationship between triplet repeat disease and human revolution through selective pressure for human STR sequence ”.

・Date/Time: September 2 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building 
・Title: Explore the relationship between triplet repeat disease and human revolution through selective pressure for human STR sequence
・Lecturer: Makoto Shimada (Institute for Comprehensive Medical Science, Fujita Health University)

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

・Abstract: In STR (Short Tandem Repeat), repeating sequences of very short base segments, the number of tandem repeats changes very frequently. Thus, there has been a hypothesis that adaptive trait and evolutionary stable state were quickly established using the high variability of the number of tandem repeat. On the contrary, human STR sequence is known to have multiple repetitive sequences which are the cause of neurodegenerative diseases. However, why such dangerous repetitive sequences are maintained among human population is not yet known well. We have identified the number of the STR repetition and repeat polymorphism within human genome by integrating information of polymorphism into H-invDB, the genetic database that we developed and released to the public. Furthermore, we evaluated the selective pressure for each STR through intercomparison. The result showed that repetitive amino-acid sequences were formed in STR in amino acid coding regions due to 2 mechanisms each of which are represented by proline repeats and glutamine repeats while keeping the repeats short at the DNA sequencing level.. Moreover, it was revealed that glutamine repeats have a tendency to have longer repeats at amino-acid level and that especially the repeat polymorphism exists in the genes related to the regulation of the generation of nervous system and brain. These results suggest the possibility that polymorphism of these repeats facilitated the diversification of the functions related to the regulation of the generation of nervous system and brain. In our article, we have further argued the relationship between the evolution of sociality throughout human evolution and the switch function for the regulation of STR neural development.

・Organizer: Yosuke Kawai, Kazuharu Misawa, Masao Nagasaki

The 73rd In Silico Megabank Research Seminar(February 12, 2016)

The73nd In Silico Megabank Research Seminar will be held on Friday, February 12, 2016. This Time, we will be welcoming Dr. Yuki Hitomi, Graduate School of Medicine, The University of Tokyo as our lecturer, and he will be speaking on “Search for Genetic Factors of Immune-related Diseases”.

・Date/Time: February 12 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Search for Genetic Factors of Immune-related Diseases
・Lecturer: Yuki Hitomi (Department of Human Genetics, Graduate School of Medicine, The University of Tokyo)

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

・Abstract: Genome-wide Association Study (GWAS) has been conducted in large scale globally especially as a statistical genetic approach that exhaustively search disease sensitive genes for multifactorial diseases. On the other hand, it is known that there is genetic risk, Missing Heritability, which is unaccountable with GAWS. Therefore, further advancement of research is currently highly anticipated for understanding of whole genetic factors for disease onset.  In this seminar, diseases that are considered to be attributable to immune system being the target, we will give an outline of genetic factors which have been revealed until today (especially HLA) as well as the pathologies. Additionally, we will introduce joint-research having been conducted with ToMMo for the purpose of exhaustive search for genetic factors in association with the development of Primary biliary cirrhosis (PBC) and Stevens-Johnson Syndrome (SJS)

・Organizer: Kaname Kojima, Masao Nagasaki

The 72nd In Silico Megabank Research Seminar(January 26, 2016)

The 72nd In Silico Megabank Research Seminar will be held on Tuesday, January 26, 2016. This Time, we will be welcoming Dr. Ryu Takeda, The Institute of Scientific and Industrial Research, Osaka University as our lecturer, and he will be speaking on “Recent Machine Learning and Component Technology for Speech Dialog System”.
・Date/Time: January 26 (Tuesday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Recent Machine Learning and Component Technology for Speech Dialog System
・Lecturer: Ryu Takeda(The Institute of Scientific and Industrial Research, Osaka University)

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

・Abstract: A speech dialog system is a system that understands and corresponds to human voice questioning to it. Such system is applied to the interface of mobile terminals (Siri), robots (Pepper), and so on. At our laboratory, we conduct studies focusing not only on the linguistic understanding of user speech but on hierarchical understanding of speech behavior and mutual adaptation between system and user. For these types of studies machine learning is an inevitable technology, and it is widely used from signal processing, and voice recognition to the core dialog strategy and user model learning.  In this seminar, challenges and necessary technologies for speech dialog system and application of machine learning technology including our study cases will be introduced. In addition, examples of the application of recent Deep Learning in component technology and my approaches and efforts are also introduced.

・Organizer: Kaname Kojima, Masao Nagasaki

The 71st In Silico Megabank Research Seminar(January 22, 2016)

The 71st In Silico Megabank Research Seminar will be held on Friday, January 22, 2016. This Time, we will be welcoming Dr. Masahiro Kasahara, Graduate School of Frontier Sciences, The University of Tokyo as our lecturer, and he will be speaking on “Information Processing Technology for Genomic Sequencing”.

・Date/Time: January 22 (Friday) 5:00 pm‐6:30 pm
・Venue: Small Conference Room 2(3rd Floor), Tohoku Medical Megabank Building
・Title: Information Processing Technology for Genomic Sequencing
・Lecturer: Masahiro Kasahara(Graduate School of Frontier Sciences, The University of Tokyo)

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

・Abstract: Whole Genome Shotgun Method using PacBio RS, which is the world’s fist real-time single-molecule DNA sequencer for commercial use, is on the verge of becoming the de facto standard as the method to determine genomic sequencing in highly efficient and highly accurate manner. However, in comparison to the previous DNA sequencers, the read length is larger by one digit and the read error rate for base is higher by one digit or more. Thus, it has been difficult to perform genome assembly for large genomes by fully utilizing output information. In this lecture, the advancement of information processing technology to perform genome assembly, especially the error-correction techniques for base and the invention of data structure to correspond to large genomes will be introduced. In addition, the movement of germinating genomic sequencing technology using new observation technologies other than PacBio is to be introduced.

・Organizer: Tomoko Shibata, Masao Nagasaki

The 69th In Silico Megabank Research Seminar(January 12, 2016)

The 69th In Silico Megabank Research Seminar will be held on Tuesday, January 12, 2016. This Time, we will be welcoming Dr. Gen Sobue, Nagoya University Graduate School of Medicine as our lecturer, and he will be speaking on “Search for amyotrophic lateral sclerosis pathologically related genes using Japanese genome”.

・Date/Time: January 12 (Tuesday) 3:30 pm‐5:00 pm
・Venue: Conference Room(3rd Floor), Tohoku Medical Megabank Building
・Title: Search for amyotrophic lateral sclerosis pathologically related genes using Japanese genome
・Lecturer: Gen Sobue(Nagoya University Graduate School of Medicine)

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

・Abstract: Amyotrophic lateral sclerosis (ALS) is an intractable neurological disease that requires permanent wearing of a respirator or results in death after a few years from its onset due to worsening muscular atrophy and worsening muscle weakness caused by the altered decidual of motor neurons. About 10% of ALS patients are thought to have a monogenic disease and multiple causative genes are identified; however, the pathologically related genes or molecules for the vast majority of sporadic ALSs are not yet fully revealed. It is necessary to identify sporadic ALS pathologically related genes and molecules in order for the pathophysiological analysis and the development of treatment methods.    We have developed a JaCALS which is the multi-institutional joint registry system of ALS patients and accumulated prospective clinical information, genomic DNA, and immortalized lymphocytes of 1140 ALS patients. Also, utilizing this resource, we have produces some results such as the identification of ZNF512B as a sporadic ALS pathologically related gene and the indication that low expression of Titin is related to rapidly progressive sporadic ALS by conducting genome-wide association studies (GWAS) based on Single Nucleotide Polymorphisms (SNPs).
In recent years multiple rare variants hypothesis, where numbers of variants with low allele frequency and uncommon SNPs are contributing to the pathophysiology of sporadic diseases, has been proposed. The purpose of this study is to identify sporadic ALS related variants through association studies using sporadic ALS genome of JaCALS and control at Tohoku Medical Megabank Organization. It is expected that the analysis of exome sequencing of 750 sporadic ALS patients will be complete by the end of this year, which means that we are well established enough to start association study smoothly. If any sporadic ALS related gene is found as a result of the study, we plan to proceed with the preparation of disease model, pathophysiological analysis, and treatment agent screening by iPS cell generation from patient with specific genotype.

・Organizer: Masao Nagasaki