标记档案: GA4GH


一周的视频提示: Your DNA, Your Say. GA4GH wants to hear from you. 和你.

基因组学与健康全球联盟 (GA4GH) has come up a few times on our blog. The last time we highlighted them for a tip, it was about their Beacon tool. The idea of the Beacon is that it could interrogate a database but in a very subtle way, without needing access to the entire sequence information of a patient. It would ask a simple yes/no question about a given sequence variant–and if a “是的” came back, then a researcher could go through the process of getting proper access to protected patient data.

So it was a way to keep people from pawing through data that they don’t need. And yet it could still connect people who might benefit from research, with researchers who need information.

But certainly issues of patient or donor privacy are hot topics. More and more data will come in from large projects, or from diagnostic samples, and cancer vs normal tissue comparisons, and we are going to struggle with the access vs. privacy matters for a while. The general public is only now becoming aware of the impacts. But we certainly need people to understand and we’ll want them to contribute to expanding our knowledge about health and disease.

That’s why the folks associated with GA4GH, the Wellcome Trust, and the Wellcome Genome Campus are eager to engage the public on their feelings on use of genomic sequence data. 他们有 launched a project called “Your DNA Your Say”[PDF格式], in the form of a survey with videos to help understand where people are on this issue. Here’s the intro video to entice you to answer the survey:

I answered the survey because I do have concerns about access to information that will help us drive the science forward, as well as about the potential for misuse of the information. But I would like them to hear from as many people as possible, so that we can understand the barriers to research and donation that are looming. Have your say. 传播消息.

You can learn more about their ideas in a variety of publications–I’ll link to one below, but there are other publications and more details about the overall projects and individual tools at the GA4GH web site.


Survey site: YourDNAYourSay.org

GA4GH: http://genomicsandhealth.org/


Lawler, 米, Siu, 属, 雷姆, 阁下, Chanock, 学, Alterovitz, 克, Burn, j的, 卡尔沃, 楼, Lacombe, 四, 这些, 二, 北, 光, Sawyers, 三, & , . (2015). All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health Cancer Discovery, 5 (11), 1133-1136 分类号: 10.1158/2159-8290.CD-15-0821


一周的视频提示: PhenomeCentral

Silos. This is a big problem for us with human genome data from individuals. We’re getting sequences, but they are locked up in various ways. David Haussler’s talk at the recent Global Alliance for Genomics and Health meeting (GA4GH) emphasized this barrier, and also talked about ways they are looking to work around the legal, 社会, and institutional barriers that we’ve created. He talked about Beacon, which I highlighted recently as a Tip of the Week. But there are other strategies needed to connect physicians and patients with other folks who might help them get to answers. Heidi Rehm’s talk provided information about a possible tool for this: PhenomeCentral.

不幸的, the videos aren’t uploaded to YouTube, you have to go to the 六月 10 Meeting page and obtain them from there. The one that contained the information on PhenomeCentral is the one called “Matchmaker Exchange”.

PhenomeCentralLogoThe mission of PhenomeCentral, according to their site, 是:

PhenomeCentral is a repository for secure data sharing targeted to clinicians and scientists working in the rare disorder community. PhenomeCentral encourages global scientific collaboration while respecting the privacy of patients profiled in this centralized database.

Certainly people in bioinformatics are familiar with the really crucial information from OMIMOrphanet. But these are aggregators of information, not patient-specific. There may be lists of features of a condition, but how they appear in a given patient’s situation might vary.

What this new strategy will do is let doctors and researchers take the phenotype and genotype data (you can upload VCF files), and make predictions about the genes involved. They also have ways to “matchmake” possibly similar disease manifestations. This project is part of the larger “MatchMaker Exchange” 集 (注意:: MME is not a dating site…it’s also still under development). But the idea is that with patient details one could search for matches with other similar patients (depending on the privacy level of the records, 当然). It sounded to me like a kind of BLAST for medical conditions (they didn’t call it that). But it also has ways to semantically link phenotype concepts, because they might be entered differently by different evaluating physicians, yet be the same type of issue underneath. 这 Human Phenotype Ontology (HPO) 这 I’ve covered a couple of times lately enables this.

他们有 3 levels of privacy settings included: private, matchable (where you can find it in a search, but it’s not wide open to everyone), and public.

So although I used the GA4GH talk as a launching point to learn more about the features and conceptual parts of the PhenomeCentral software, I also came across this other webinar that was more specific about the software features (which is what I typically prefer for our tips, the specific software tools). 该 遗传联盟 is a patient-centric group interested in answers for genetic and genome-variant medical situations, actively working with advocacy groups and researchers to bridge the needs of both. In their webinar series last year they included PhenomeCentral.

What I didn’t realize from the GA4GH overview was that there are additional tools, including a pedigree tool in the PhenoTips 部分. We find a lot of people find our blog searching for pedigree tools, so I wanted to be sure to mention that specifically. You can try it out by entering fake data in the playground over there, and accessing the Pedigree Tool from that record. This was also handy for me because I didn’t create a login for the main PhenomeCentral site due to the privacy issues.

So have a look at PhenomeCentral. And from the GA4GH video I learned that there is a special journal issue coming up in the fall that will have papers related to these projects. So I’ll link to the PhenoTips publication below now, but when more references become available for this tool or project I’ll add them in. I expect there will be metrics about algorithms in use and other technical details that are important for fully evaluating the tool.


PhenomeCentral: 通过https://phenomecentral.org/

PhenoTips: 通过https://phenotips.org/ (has the playground + pedigree tool)

GA4GH videos: http://genomicsandhealth.org/news-events/events/june-10th-meeting-presentations

Girdea, 米, Dumitriu, 学, Fiume, 米, Bowdin, 学, Boycott, 光, Chénier, 学, Chitayat, 四, Faghfoury, 阁下, Meyn, 米, Ray, 体育, 因此,, j的, Stavropoulos, 四, & Brudno, M. (2013). PhenoTips: Patient Phenotyping Software for Clinical and Research Use 人类基因突变, 34 (8), 1057-1065 分类号: 10.1002/humu.22347



This week’s SNPpets include several new tools that I want to examine, including functional annotations in a couple of different ways. But other stuff includes designing DTC consumer products, NLM’s future directions, a new Genomics subreddit, and stunning phylogenetics representations among other interesting reads.

欢迎来到我们的链接集合星期五功能: SNPpets. 一周之内,我们遇到了很多链接和读取,我们认为很有趣, 但不要到一个博客帖子. 在这里,他们是您的享受…


一周的视频提示: 指路明灯, 找到潜在临床意义的基因组变异

本周本周视频提示如下的 关于DNA的互联网上周的唠叨. 正如我提到的话, 灯塔工具,我们谈到要得到更多的报道. 因此,本周的视频是由信标团队提供, 的较大部分 基因组学与健康全球联盟 项目 (GA4GH).

我已经谈到了一些 在过去GA4GH工作. 我听到更多关于一个非常有趣的一件从 大卫·豪斯勒在最近TRICON会议.

D. Haussler, slide from TRICON talk.

ð. 豪斯勒速度, 幻灯片从TRICON谈话.

讲座被称为 “稳定的参考结构的人类基因组分析” 而对我来说,看到这是非常重要的. 我一直在角力与一些文学 (下面链接) 描述方法来表示人类庞大的数字中的基因组变异. 这真的帮助我听到它描述和幻灯片不太喜欢方程式显示为动画片. 而这将如何发挥出来的图形和可视化软件工具是特别感兴趣的我.

所以GA4GH的数据工作组中的一个分支的任务是如何表示的变型的多条路径为图形, 而不是一个线性的参考基因组,我们认为今天的. 它必须适应多种类型的变化的–投资, 删除, 重复, 以及刚刚的SNP. 因此,, 随着孩子们今天说,, 情况很复杂. 但是,我们必须弄明白. 敬请关注, 我敢肯定,我们将更多地谈论这几年来.



这个项目的另一个分支的任务是试图找出如何对这些数据的所有国际生产商之间共享基因组数据. 如果我们不能共享数据, 我们不能看变化在人类中,并从他们身上学到, 没关系显示它们. 这有社会和法律的复杂性,我们才刚刚开始面对额外的层. 作为第一通在共享这些数据, 一 “指路明灯” 制度已经实施,以帮助研究人员找到感兴趣的变化给他们.

你应该阅读整 灯塔理念,看看它的当前实现 在他们的网站. 从我搜集, 它是一个最小的方式来分享基因组信息, 而不会产生,如果你是一个全基因组拉下可能被击中的隐私和同意的障碍. 您可以查询它实现了一个灯塔问任何网站: 你有一个变化,在这个位置上? 和信标可以响应 “是的” 或 “在”. 如果有有用的变化, 那么你可以从那里他们追求, 如果您需要访问更多的,你可以去通过渠道再. 但至少你可能会发现在某些草堆一些针,你可能不知道,否则大概.

灯塔团队已经做了一个简短的视频解释这个. 它没有音频, 与图形只是说明性文字. 马克里耶卡给了我允许它嵌入在这里.

该 “灯塔的灯塔” 汇总查询到它发送给所有已知的灯塔. 你可以用它今天来搜索这类数据. 视频还指出,您可以遮盖该机构的名称,以保护患者隐私.

我一直更敏锐地关注比我的一些同伙基因隐私问题在这个舞台上. 我完全同意,不会有隐私–我要的是保护信息滥用, 我觉得这缺乏在美国法律框架,现在. 这就是说, 我认为灯塔是一个很好的解决方法为. 如果我有一个值得关注的变种, 我可以ping通其它网站,看看别人了吧. 反之亦然. 但在其下该材料的供体所提供的数据中的框架将不会被刺穿. 这使得总的感觉给我, 我可以接受这样的策略.

分享从测序个人基因组数据将是棘手和复杂的. 但我希望看到的GA4GH组解决它. 我喜欢几个,我到目前为止看到的方向. 但现在–退房灯塔. 落实一个,如果你有这种数据, 让我们看看它的工作原理.


基因组学与健康全球联盟: http://genomicsandhealth.org/

指路明灯 (项目详细信息页面): http://ga4gh.org/#/beacon

灯塔的灯塔 (在那里你会做一个搜索): http://ga4gh.org/#/beacon/bob


Nguyen N., 格伦·希基, 丹尼尔 - [R. 垫, 布莱恩·雷尼, 登特伯爵, 乔尔·阿姆斯特朗, 在. 詹姆斯肯特, 大卫豪斯勒 & 本笃专利 (2015). 建立一个泛基因组参考的人口, 杂志计算生物学, 150107093755006. 分类号: http://dx.doi.org/10.1089/cmb.2014.0146

在大卫·豪斯勒的谈话, 他也引用这些报纸:

答案是什么? (互联网的DNA)

本周高亮讨论铲球 “互联网的DNA”, 一个故事,我上周回升 在我SNPpets后, 已经起泡了别处. 和映泰人看的更多的技术含义 “数以百万计的基因组的全球网络….”

Biostars 网站是一个要求, 生物信息学的问题和问题的回答和讨论. 我们的成员 Biostars_logo 社区和发现它非常有用. 常的问题和答案出现在Biostars是有密切关系的读者 (基因组学的最终用户资源). 逢星期四,我们将突出这些项目或讨论,在这个线程. 您可以询问一下该线程问题, 或者你可以随时参加在Biostars.

这一周的讨论之际,一个有趣的一周在个性化医疗前部. 一大堆的事情走到一起–美国得到一个 首席数据科学家谁谈论生物信息学, 该 NEJM谈论训练医生应对医学基因组 问题, 和 “互联网的DNA” 让外面​​的科普媒体领域. 所以,看看有什么生物信息学书呆子由本, 以及他们的想法是:

论坛: 数以百万计的基因组的全球网络可能是医学的下一个伟大的进步. | 指路明灯



可用性: 1-2 年

诺亚是六十岁患的疾病没有名字. 今年, 他的医师将开始发送自己在互联网上的遗传信息,看看是否有任何人, 随地, 在世界上像他.


你认为这会发生在 2 年?



灯塔项目 是一个项目来测试国际网站愿意分享最简单的所有技术背景的基因数据. 它被定义为任何机构可以作为服务实现一个简单的公共网络服务. 该服务被设计仅接受形式的查询 “你有任何基因组与'A’ 在位置 100,735 3号染色体″ (或类似的数据) 并与一个响应 “是的” 或 “别。” 一个网站提供这项服务被称为 “指路明灯”.


所以它只是在多个大型基因组学联合查询 (+ 表型) 数据集. 全基因组不集中, 或移动, 因此隐私是那么重要.


并请, 在那里贡献自己的想法. 我们需要具有此讨论. 还, 观看更多关于这个灯塔….

一周的视频提示: 谷歌基因组学, API和GAbrowse

本周的视频头达到我们从谷歌–它是关于他们在参与 “基因组学与健康全球联盟” 联盟. 全球联盟旨在开发基因组数据标准的互操作性, 他们一直在努力创建框架 (下面引用一些背景链接将提供进一步的细节). 它拥有超过 170 成员, 而这些成员之一是谷歌. 虽然谷歌谈到这 今年年初的时候,他们加入这个团体, 最近作品已经开始出现有关方向和具体工具. 谷歌的努力所作的主流新闻近日在其公布有关工作的一个项目,以 检查与孤独症相关的基因组数据.

虽然这个视频不谈论一个特定的工具像我们平时覆盖, 它提供了更详细的关于这个框架的构建工具,了解这一点很重要. 而在这部影片中我了解了这个项目下开发了一个新的浏览器,我也有一个快速浏览一下, 我会在下面添加.

他们的浏览器,他们引用被称为GAbrowse–我认为,这意味着全球联盟浏览–但有没有很多的细节. 他们 “关于” 对话框说,这:

GABrowse旨在演示的功能的示例应用程序 GA4GH API V0.1.

目前, 你可以从谷歌浏览数据, NCBI和EBI.

  • 使用左侧的按钮选择一个读集或Callset.
  • 一旦装, 选择一个染色体和放大或拖动主图探索 读取数据.
  • 个人 的基础 会出现,一旦你放大到足够程度.

此应用程序的代码是在 GitHub上 并且是一个进展中的工作. 欢迎提交补丁!

我踢轮胎有点, 但它显然不是完全充实在这一点上. 当我试图从核苷酸水平上放大了它去了一下, 但最终你打一个点,说 “此缩放级别即将推出!” 所以肯定还有更多的惊喜, 和很多更多的功能,这将是必要的. 但它的早期. 它只是一个演示. 我不知道,如果它打算成为一个独立的公共浏览器.

所以,如果你有兴趣发行人基因组数据的交叉兼容性 (而据我可以告诉这一切都是以人为中心, 我倒要看看这个更广泛的对话), 它可能是值得了解的是谷歌将提供在这里. 你也应该知道全球联盟正在做的工作. 下面我加了一些我见过他们的努力,出版物和媒体.

帽尖到CAN Holyavkin在Google 上的链接到视频. https://plus.google.com/u/0/114690993717100405711/posts/gwNy5E7E6Vb?cfem=1


基因组学与健康全球联盟: 銈://genomicsandhealth.org /

谷歌基因组学: https://developers.google.com/genomics/

GAbrowse: http://gabrowse.appspot.com

(2013). 全球联盟,以创建标准共享基因组数据, 医学遗传学A部分美国杂志, 161 (9) 有的,有的. 分类号: http://dx.doi.org/10.1002/ajmg.a.36168

卡拉威Ë. (2014). 全球基因组的数据共享工作揭开序幕, 自然, 分类号: http://dx.doi.org/10.1038/nature.2014.14826

白皮书 2013: http://www.broadinstitute.org/files/news/pdfs/GAWhitePaperJune3.pdf

基因组的负责共享和健康相关的数据框架 – 草稿 # 7 http://genomicsandhealth.org/our-work/work-products/framework-responsible-sharing-genomic-and-health-related-data-draft-7

特里S.F. (2014). 基因组学的全球联盟 , 基因检测和分子生物标志物, 18 (6) 375-376. 分类号: http://dx.doi.org/10.1089/gtmb.2014.1555 [这里可从GA: http://genomicsandhealth.org/files/public/gtmb%252E2014%252E1555%5B2%5D.pdf]