加拿大Genizon Biosciences www.genizon.com
位于加拿大蒙特利尔省的Genizon BioSciences生物科学公司利用5万个被试建立了魁北克法裔加拿大人的群系,大大扩大其拥有的DNA的样品量,他们同时还对25种疾病的遗传基础进行研究。这家公司完成了10种疾病的全基因组扫描,其中包括克罗恩病、哮喘、阿尔茨海默氏病、和注意力缺失/过动症等。
Genizon生物科学公司的IT构架整合了一个FDA兼容的LabVantage Sapphire LIMS构架、一个包含电子数据捕捉和信号兼容的eResearch技术临床数据库管理系统、一个32-千兆的网络存储、和一个288-CPU的计算网格,进行他们需要的数据分析。Genizon生物科学公司的软件构架的领航者Borivoj (Bora) Stojkovic说,他们公司以积极的策略来应对无限膨胀的SNP密度和GWA样品的规模。他们模拟大规模数据,测试并开发新的方法预先突破未来可能出现的瓶颈。Stojkovic说,由于在数据压缩方面有经验,“我们把压缩后的数据加载到内存。这样的话,既可以使用全部的数据,又不必占满整个内存空间。同时,我们把内存空间进行分割,把小的数据集分配其中。”通过把数据集分配到更小的块中,利用多个CPU处理不同的块。
Stojkovic 说,Genizon生物科学公司的最新压缩策略能够把公司的文件存储覆盖区降低到原来的二十分之一。对于有不同计算强度需求的分析,他们能够做到在流程涉及到的网格和机群中分配数据库。公司的内部网格能够在机群的数千个CPU上自动分配数据。为了管理不同类型的数据,他们把内部数据格式标准化,通过转换过滤器把外部进来的数据进行过滤,实现标准化转换。
然而,Stojkovic强调说,虽然分布式或者网格计算的各种方法确实很有效,但是现在最重要的困难是如何把计算的思想过程和算法流程实现流水线化并进一步地优化,以提高整个系统的整合程度和关联度,并且使语言和流程更加紧凑、精练。
Genizon Biosciences Inc. discovers genes and biomarkers in common diseases using genome wide association studies (GWAS), leveraging its proven and proprietary technology platform and access to patients from the Quebec Founder Population.
Genizon has one of the largest GWAS programs worldwide, addressing many common diseases and traits. Several of these have been successfully completed, generating comprehensive maps of interacting genes, biomarkers and biological disease pathways (known as GeneMaps), providing strong validation of the power of the Company’s discovery platform.
Genizon has out-licensed some of the therapeutic and diagnostic rights to GeneMaps for Crohn’s disease (to Genentech) and attention deficit hyperactivity disorder, endometriosis and Alzheimer’s disease (disease-state diagnostic rights to Pfizer). GeneMaps have also been generated from GWAS in schizophrenia, psoriasis and longevity. GWAS are in progress for rheumatoid arthritis, Alzheimer’s disease, and coronary heart disease and its precursors, obesity, type II diabetes, dyslipidemia and hypertension (collectively metabolic syndrome).
Genizon’s technology platform and discoveries can complement current R&D programs by using human genetics to significantly enhance research and by adding value at multiple stages of the drug development process.
Genizon is continually developing and enhancing its gene and biomarker discovery platform. For example, the company is assessing the role of copy number variations (CNVs) in diseases- applying new methods to ongoing large-scale GWAS in rheumatoid arthritis and metabolic syndrome, and retrospectively to previous studies.
Genizon also leverages its platform and expertise by offering high throughput, high quality SNP genotyping, statistical genetics, gene expression and pharmacogenomics services to academic institutions, research organizations and the biopharmaceutical industry.