Design of 'Japonica Array'
A SNP array optimized for the Japanese population
2015-09-02
(Press-News.org) A research group, led by Professor Masao Nagasaki and Senior Assistant Professor Yosuke Kawai at Tohoku University Tohoku Medical Megabank Organization, has successfully designed the first ever SNP*1 array that has been optimized for the Japanese population.
SNP, which stands for Single Nucleotide Polymorphism, is a DNA sequence variation that occurs commonly within a population.
This new array, called the "Japonica Array," covers the whole-genome region from which the SNPs possessed by Japanese people can be obtained with a high degree of accuracy.
The design of the Japonica Array was accomplished by developing and implementing a unique SNP selection algorithm and analyzing, on a supercomputer, all of the genome information from the 1,070 individuals who participated in the cohort studies*2 of the Tohoku Medical Megabank Project.
By using genotype imputation*3 technology, information on a maximum of 20 million SNPs are presumed from only 659,253 SNPs on the Japonica Array.
The Japonica Array has an imputation accuracy that is at least 10% better than other existing SNP arrays that contain an equivalent number of SNPs, and offers a level of performance that is equivalent to or higher than existing SNP arrays that contain three or more times the number of SNPs.
This research has produced a basic analysis tool for the large-scale identification and study of the genes related to the physical constitution and diseases that are peculiar to the Japanese. It has so far yielded important results that can accelerate the research of personalized healthcare and medicine.
The results of this research were released in the online version of the Journal of Human Genetics on June 25, 2015.
INFORMATION:
[Background]
Tohoku University Tohoku Medical Megabank Organization (known as ToMMo) has been working in cooperation with Iwate Medical University on the Tohoku Medical Megabank Project. It is part of the universities' contribution towards reconstruction, following the Great East Japan Earthquake in 2011.
Since 2013, the two universities have been conducting cohort studies, which include some150,000 community residents in Miyagi and Iwate prefectures.
[Description of terms]
*1 Single nucleotide polymorphism (SNP): A variation of a single base of the genome sequence among individuals. Usually, a variation that exists at a constant frequency or higher is called a SNP.
*2 Cohort study: A study in which a specific group of people is tracked for a given period of time to reveal the relationship between diseases and environmental factors such as lifestyle habits, genetics and other factors.
*3 (Genotype) imputation: An information science technique for estimating the genotype of several millions of unmeasured SNPs with a SNP array by combining it with a reference panel.
[Publication details]
Publication: Journal of Human Genetics
Title: Japonica Array: Improved Genotype Imputation by Designing a Population-Specific SNP Array with 1,070 Japanese Individuals
doi: 10.1038/jhg.2015.68
Date: June 25, 2015
Authors: Yosuke Kawai, Takahiro Mimori, Kaname Kojima, Naoki Nariai, Inaho Danjoh, Rumiko Saito, Jun Yasuda, Masayuki Yamamoto, Masao Nagasaki
[Attachments] See images for this press release:
ELSE PRESS RELEASES FROM THIS DATE:
2015-09-02
Young women who are attracted to both sexes or who are unsure about who they are attracted to are more likely to develop an eating disorder than those attracted to only one sex, according to a new study from Drexel University.
However, the results of the study suggest that females attracted to the same-sex are no more likely to experience disordered eating symptoms than their peers with opposite-sex attractions. This finding is contrary to previous assumptions that same-sex attraction plays a protective role against eating pathology in females.
"The results of this ...
2015-09-02
London, 2 September 2015: With 32,773 registrations this year (1), ESC Congress 2015 broke yet another record in attendance. "We are proud to have brought together so many delegates and the latest research from all over the world," said ESC President, Professor Fausto Pinto, from Portugal.
"By 2030, 40% of Europeans will suffer from some form of CVD," said Prof Fausto Pinto, ESC President, "so what is going on in our congress is relevant to everyone, not only health professionals." (2)
Despite improvements in mortality and morbidity, CVD remains the main killer ...
2015-09-02
The word "apple", as we pronounce it, is a sequence of sounds (phonemes) that we use whenever we want to refer to the object it indicates. If we did not know that a referential relationship exists between the sound and the object it would be impossible for us to use, and learn, a language. Where does this implicit knowledge come from, and how early in human development does it manifest? This is the question Hanna Marno and her SISSA colleagues Marina Nespor and Jacques Mehler in a collaboration with Teresa Farroni, from the University of Padova, attempted to answer in a ...
2015-09-02
Meningiomas are a type of brain tumor that form on membranes covering the brain and spinal cord just inside the skull. They occur at an annual incidence of up to 13 per 100 000, and approximately 20% of these exhibit aggressive behavior and burden patients with tumor recurrences as well as infiltration of the surrounding bone, brain, or soft tissue.
Dr. Matthias Preusser of the Medical University Vienna - General Hospital AKH and Coordinator of this study says, "High-grade meningiomas are characterized by prominent infiltration with tumor-associated macrophages and angiogenesis. ...
2015-09-02
This news release is available in German. What did the universe look like shortly after it came into being? The ALICE experiment (A Large Ion Collider Experiment) at CERN in Switzerland concerns itself with this question. At the largest particle accelerator in the world, the Large Hadron Collider (LHC), researchers let lead nuclei and protons collide at the highest beam energies to date. The temperatures thereby created are 100,000 times higher than those in the center of the Sun. "A state is created that is very similar to the one after the Big Bang," explains Laura ...
2015-09-02
(Boston)--There is strong evidence that the protein complex APC/C may function as a tumor suppressor in multiple cancers including lymphoma, colorectal and breast cancer, and now melanoma. A new study has revealed that a genetic mutation leading to repression of a specific protein, Cdh1, which interacts with APC/C, is present in melanoma cancer cells.
The study, led by researchers at Boston University School of Medicine (BUSM), reports sporadic mutations in the APC/C protein complex, specifically in the essential protein component Cdh1, which may predispose humans to ...
2015-09-02
The study, published in the journal Financial Stability, introduces a new method that allows researchers to estimate the systemic risk that emerge from multiple layers of connectivity.
"Systemic risk is the risk that a significant part of the financial system stops working--that it cannot perform its function," says IIASA Advanced Systems Analysis program researcher Sebastian Poledna, who led the study. For example if a major bank fails, it could trigger the failure of other financial institutions that are linked to it through loans, derivatives, securities, and foreign ...
2015-09-02
Scientists have developed a simple process to treat waste coffee grounds to allow them to store methane. The simple soak and heating process develops a carbon capture material with the additional environmental benefits of recycling a waste product.
The results are published today, 03 September 2015, in the journal Nanotechnology.
Methane capture and storage provides a double environmental return - it removes a harmful greenhouse gas from the atmosphere that can then be used as a fuel that is cleaner than other fossil fuels.
The process developed by the researchers, ...
2015-09-02
Although most of the world's biodiversity is below ground, surprisingly little is known about how it affects ecosystems or how it will be affected by climate change. A new study demonstrates that soil bacteria and the richness of animal species belowground play a key role in regulating a whole suite of ecosystem functions on Earth. The authors call for far more attention to this overlooked world of worms, bugs and bacteria in the soil.
Ecosystem functions such as carbon storage and the availability of nutrients are linked to the bugs, bacteria and other microscopic ...
2015-09-02
CAMBRIDGE, Mass. (September 2, 2015) - Altering the protein recycling complexes in human cells, including cancer cells, allows the cells to resist treatment with a class of drugs known as proteasome inhibitors, according to Whitehead Institute scientists.
"This is why some cancers can be so difficult to treat with chemotherapy, because the cells can be in different states--some sensitive to treatment and some resistant to treatment, all in the same tumor," says Sandro Santagata, a former visiting scientist in the lab of Whitehead Member Susan Lindquist. Santagata is now ...
LAST 30 PRESS RELEASES:
[Press-News.org] Design of 'Japonica Array'
A SNP array optimized for the Japanese population
