A*STAR for Hitachi

Hitachi and Singapore’s A*STAR design novel method to reduce genome data storage

Lloyd Dunlap
SINGAPORE—Hitachi Asia Ltd. and the Data Storage Institute(DSI), a research institute of the Agency for Science, Technology and Research(A*STAR), are devising a data compression technique to tackle the increasingvolume of genome sequencing data generated by the healthcare and biomedicalindustry.
 
 
DSI's executive director, Dr. Pantelis Alexopoulos, claimsthat DSI's proposed data compression technique can achieve very highcompression ratios compared to conventional methods, but he declined to be morespecific for competitive reasons.
Citing the fact that the volume of genome sequencing datahas been forecasted to double annually, the collaborators aim to develop a moreefficient data-storage technology that will compress genome sequencing datamore effectively than existing methods. This is an extension of an earlierpartnership where Hitachi and DSI researchers reported that they discovered thepattern of typical massive genome data transactions that would enable currentstorage systems to function optimally.
 
 
Genome data analysis goes through three stages (primary,secondary and tertiary), Alexopoulos notes, and uses separate storage systemsfor each stage, resulting in the same data being copied multiple times andwasting storage space. In a bid to address the current computational andscalability limitations, DSI researchers were commissioned by researchers fromthe Genome Institute of Singapore (GIS), another A*STAR research institute, tostudy how genome sequencing data can be optimized. 
 
Hitachi and DSI will develop a prototype storage platformthat will be used as a test bed for sequencing research facilities such as GISand other biomedical research institutes. Research into the characteristics ofgenome data revealed that existing data compression methods are unlikely tomanage current workloads due to inefficiencies and heavy demands for largermemory storage. Building on the collective insights from this earlier projectcollaboration, Hitachi and DSI are now working toward eliminating theshortfalls identified in current data storage models to design an innovativegenome data-compression method, reduce data storage capacity needs, quickendecompression speeds and lower storage costs.
 
Ultimately, DSI will benefit from commercializing theintellectual property generated as a result of the compression algorithms andsoftware developed. Hitachi will be able to utilize the outcome of thecollaboration to differentiate its IT platform in the area of bioinformaticsand other big data-related domains, says Mr. Nobutoshi Sagawa, chief technologyofficer and general manager of Hitachi Asia's research and development center.
 
"By raising compression capacity, we can envision smallergenome sequencing facilities to handle petabytes of data in a year compared tocurrent terabytes levels which are mostly restricted to large genome-sequencingcenters due to storage limitations. DSI will continue to play a pivotal role inenabling new storage technologies for the biomedical research and healthcareindustry to accelerate research findings and discoveries," says Alexopoulos.
 
 
"We are delighted to continue our long-standing partnershipwith DSI in the research field of networked storage. I am confident that theoutcome of this collaboration will lead to more innovative solutions that couldpotentially be one of Hitachi's future areas of business expansion," statesMakoto Nagashima, managing director of Hitachi Asia.
 
 
Hitachi Asia, a subsidiary of Hitachi Ltd., was establishedin Singapore in 1989 and operates across six Asian countries (Indonesia,Malaysia, Philippines, Singapore, Thailand and Vietnam). Its business includesinformation systems, power and industrial systems, digital media systems andinternational procurement.
 
 
A*STAR fosters scientific research and talent for aknowledge-based and innovation-driven Singapore. The agency oversees 14biomedical sciences, physical sciences and engineering research institutes, andseven consortia and centers, which are located in Biopolis and Fusionopolis, aswell as their immediate vicinity. A*STAR supports Singapore's key economicclusters by providing intellectual, human and industrial capital to itspartners in industry. It also supports extramural research in universities,hospitals and research centers, as well as with other local and internationalpartners.
 
 

 
A*STAR, partnersidentify cellular origin of cervical cancer
 
 
SINGAPORE—On June 12, a team of scientists from A*STAR'sInstitute of Medical Biology (IMB) and the Genome Institute of Singapore (GIS),together with clinicians from Boston's Brigham and Women's Hospital (BWH),announced that they have identified a unique set of cells in the cervix thatare the cause of human papillomaviruses (HPV) and related cervical cancers.
 
 
Significantly, the team also showed that these cells do notregenerate when excised. According to the partners, these findings have immenseclinical implications in the diagnosis, prevention and treatment of cervicalcancer. The study was published in the Proceedingsof the National Academy of Sciences (PNAS).
 
 
Cervical cancer is the 7th most common female cancer inSingapore, and about 200 cases are diagnosed every year. Infection with HPV isthe most common cause or risk factor for cervical cancer. HPV infection causespreinvasive cancer, termed CIN (Cervical Intraepithelial Neoplasia), which areprecancerous lesions that can progress and potentially become invasive cancerif left untreated.
 
 
"It has been a decades-old mystery why cervical cancerscaused by HPV arise only from a discrete region of the cervix, known as the'squamocolumnar junction,' despite the presence of the virus throughout thegenital tract," said Dr. Christopher P. Crum, director of Women's and PerinatalPathology in the Department of pathology at BWH. "The discovery of these cellsfinally resolves this mystery and will have wide-ranging impact from developingmore meaningful animal models of early cervical carcinogenesis to clinicalimplications."
 
The team discovered that this discrete set of cells, locatedat the squamocolumnar junction of the cervix, uniquely express biomarkers thatare seen in all forms of invasive cervical cancers linked to HPV. This meansthat the signature markers of this population of cells can provide a way ofdistinguishing potentially dangerous precancerous lesions from those with abenign prognosis.
 
 
"Our study also revealed that this exotic population ofcells does not reappear after ablation by cone biopsy," said Dr. Wa Xian,principal investigator at IMB. "This finding helps to explain the low rate ofnew HPV infections in the cervix after excisional therapy, and also raises the distinctpossibility that preemptive removal of these cells in young women could reducetheir risk of cervical cancer. This could be an alternative to current vaccineswhich only protect against HPV 16 and 18."
 
 
"This study is a fine example of how A*STAR researchinstitutes can integrate our research capabilities to better collaborate withan international partner like the Brigham and Women's Hospital to carry outexcellent research with strong clinical and translational applications," saidProf Ng Huck Hui, acting executive director of GIS. 
 
 

Lloyd Dunlap

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