标记档案: 罕见的疾病


一周的视频提示: MyGene2, 与对方罕见的情况下连接家庭

Last week’s tip encouraged people to think about how their DNA may be used by various stakeholders. This could be researchers, physicians, pharmaceutical companies, 等. But one thing it didn’t really cover–now that I think of it–was connecting with other families who may share variations that impact the health of someone in their household. If there isn’t research, or treatment, this connection alone might be worth it for some families.

So when NPR recently had a story on a database for families with rare genetic conditions, 我去看看: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

该网站是 MyGene2, and it can help unrelated folks who have the same genome challenges connect with each other. It also can connect folks to researchers interested in the topic. But it does seem to be aimed more specifically at families seeking each other. It was recently awarded a chance to compete for the final prize in the Open Science Prize effort, and they got a funding boost to keep going.

有一 “欢迎” video that they’ve made, but it’s light on the software details. 仍, 虽然, I wanted to share the information so families may find it, and researchers may want to know about this resources as well. The video isn’t embeddable, 虽然, so you’ll have to click to view it:


You can learn more about the resources from their FAQ collection. I’ve found a couple of references (下面) that provide some further information about the project [注意:: 的 医学遗传学 one goes to a paywalled, 片–but you can access the pre-print version PDF at bioRxiv]. As more and more families who are seeking answers will have sequencing information available, they’ll need a place to go with that. I hope they find each other, and find answers.


MyGene2: http://www.mygene2.org

按照他们的Twitter: https://twitter.com/MyGene2

Find them on Facebook: https://www.facebook.com/MyGene2/

(该 医学遗传学 piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)


Panko, 乙. (2016). Six finalists to compete for Open Science Prize 科学 分类号: 10.1126/science.aaf9980

Chong, j的, 于, j的, Lorentzen, 体育, 公园, 光, Jamal, 学, Tabor, 阁下, Rauch, 答:, Saenz, 米, Boltshauser, 大肠杆菌, Patterson, 光, 尼克森, 四, & Bamshad, M. (2015). Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features 医学遗传学 分类号: 10.1038/gim.2015.161

Genomics England is responsible for the 100,000 Genomes Project

一周的视频提示: PanelApp, 从 100000 基因组计划

Genomics England is responsible for the 100,000 Genomes Project

Genomics England is responsible for the 100,000 基因组计划

Last week I talked about the 100,000 基因组计划 in the UK. That video tip was an introduction and overview of the project. 这一周, 虽然, we’ll highlight one software piece that is in place now. PanelApp is a collection of gene lists, with information about the evidence associated with variations in these genes. The goal is to inform clinical interpretation based on the best quality evidence.

It’s a straigtforward interface, with a traffic-light based system (绿色, 黄色, 红色) to assist with quick diagnostic assessments. The lists are based on a set of rare disease categories and phenotypes, and the idea is that qualified reviewers will create a definitive list of evidence for certain variations, and rate the genes accordingly. Ultimately they want to create a consensus gene panel collection. They describe the evidence thresholds this way:

  • Green = highest level of confidence; a gene from 3 或 4 来源.
  • Amber = intermediate; a gene from 2 来源.
  • Red = lowest level of confidence; 1 的 4 sources or from an expert list.

You can learn more about the strategy from their announcement: New rare disease gene tool launched – PanelApp. This first video will give you an idea of how this looks. A public interface is available for anyone to look around and download the information. You don’t need to log in, you can click on the “Browse Panels” tab for an idea of the organization and information content.

So crowd-sourcing this evidence is the idea here. And they are interested in having people contribute to these panels. A separate video describes the roles for people who are interested in contributing to the collection and curation of the information. Reviewers will evaluate the existing items and also add new genes. 他们有 detailed instructions and guidelines available to help. 不过, the first round of review ended already (十月 19 2015). The panels will remain available to explore and download. But there will be another review period opening in the future. So if you are considering a contribution to this work, not to worry–your chance will come and it won’t hurt to be prepared. 还, if you are considering using the panels, I think it’s a good idea to know how the curation and review is done.

The information in the panels now has been seeded by many key sources that you may be familiar with. They have used data from OMIM, OrphaNet, 遗传学首页参考, 的 Decipher DDD project, HGNC, ClinVar, UniProt, NCBI Nucleotide, 和 ENSEMBL among others to add phenotype and gene details of many types. So for any gene you can keep digging for addtional information.

There are a long more details over at the announcment post: New rare disease gene tool launched – PanelApp. But I think the structure and color cues are helpful. (等待, 颜色, 正确的? UK variation). Check it out yourself, 虽然, with the link below. You can hear more in this podcast as well.


PanelApp: 通过https://bioinfo.extge.co.uk/crowdsourcing/PanelApp/

100,000 基因组计划: http://www.genomicsengland.co.uk/


Siva, ñ. (2015). UK gears up to decode 100 000 genomes from NHS patients 柳叶刀, 385 (9963), 103-104 分类号: 10.1016/S0140 - 6736(14)62453-3

Caulfield M., Davies J., Dennys M., et al “The 100,000 Genomes Project Protocol” London: Genomics England (2014) Available at: genomicsengland.co.uk/?wpdmdl=5168 (访问: 十月 8 2015)


This week’s SNPpets includes updates to existing tools, 像 ReactomeIMG, the biggest JBrowse display I ever saw, various tidbits from #ASHG15 as word clouds, 基因编辑, slices through personalized medicine and rare diseases, 和 Virtual Machine catalog. Most unusual thing this week: recent evolutionary genomics work gets onto The Big Bang Theory. 而更多的….

SNPpets_2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…

If the survey is closed by the time you come across this, see the answers (and the twitter discussion thread is hilarious)


答案是什么? (genomics guidance for the general public)

This week’s highlighted discussion at Biostars was one that I opened. I’ve been thinking a lot about this, because I’m seeing it come up in a number of different ways. There are folks who are googling and finding genomics nerds in a variety of places. Some of the communities will be more welcoming than others. But I think it’s in our best interest to be helpful to families with data, and not come off too harsh because it’s not exactly how our forum works….

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). Thursdays we will be highlighting one of those items or discussions here in this thread. 您可以询问一下该线程问题, 或者你可以随时参加在Biostars.

论坛: For the general public seeking advice from this community


Yesterday I saw a thread posted by a member of the general public, looking for advice for their child’s medical issues. This thread has been deleted (我觉得), but I was able to read some of the commentary before it disappeared.

The community had some concerns about private medical information being revealed. And some concerns about seeking advice from strangers on the internet instead of qualified practitioners in real life. These are valid issues.

不过, my point is more general. This may become increasingly an issue here as more people have (or hear about) 序列信息, and want some advice for it. I think it is wise for this community to stay away from diagnosis. But I think we could offer these folks some guidance to appropriate resources.

Please have some compassion for the desperation that the parents of kids with undiagnosed conditions face. And keep in mind that their thresholds for privacy are not the same as everyone else, 可能. And understand that they are hearing stories about how familes connected with researchers who could help them from random internet forums. The most recent one I saw was this: 答案.

But other stories like this are widely read: How Genome Sequencing Creates Communities Around Rare Disorders.

Could we possibly have a place to point these families, like a thread that we can sticky or something? Where we can offer them connections to the Rare Disease sequencing projects, or genetic counseling resources, non-wonky information sources like 遗传学首页参考, 什么? The international group here probably could collect a good set of pointers for people around the world.

I guess I’m asking for a constructive place for some guidance for families, and a policy about how to deal with those kinds of threads.

Open for discussion.

Has any of the genomics nerd discussion communities developed a policy on this? Should we reach out to genetic counselors, 也许? We may also need legal advice. Anyone seen other places take this on? Please add your thoughts over at Biostars.



This week’s SNPpets offered a lot of good stuff, everybody must be out of their summer vacation mode and back to the lab. 有一个 BLASTX alternative, a helpful tip in workshop teaching, quack DTC tests, handy errors (真的), new variant database DIVAS, exome sequencing patients and outcomes, imputation, 24M novel rare variants, variant caller comparison, the long term evolution experiment hits a milestone, new citrus resources, eQTLsʲÔ, 多. The best item this week, 虽然, was a story of a family with a rare disease situation that found genomics researchers via Reddit, and that gave them answers and hope.

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…

提示的周: Orphanet罕见疾病信息

当我环顾四周在新OMIM从网站的链接相关的一些资源, 我注意到有到Orphanet链接. 我以前听说过Orphanet–根据他们的信息,因为他们一直在周围 1997, 但没有看着它密切. 因此,本周的周提示,我们将探讨Orphanet.

我开始探索在主着陆页, http://www.orpha.net/. 从登陆页面,您可以访问广泛的搜索类型和数据收集. 靠近顶端的标签导航区提供的切入点,从众多的角度: 罕见疾病, 孤儿药, 专家中心, 诊断测试, 研究和试验, 病人组织, 目录, 多. 这是一个很好地组织有关罕见疾病的信息门户.

在电影中提示,我不会有时间去到所有这些组件的, 我鼓励你自己看看周围. 我将重点放在寻找一种罕见的疾病, 并期待在该网页上提供的功能. 当时如果写这篇文章, 有近 6000 信息记录存储在网站的罕见疾病, (5954).

一个功能,我真的很喜欢最近添加–临床应用基因卡 (CUGCs). 有关DNA测试的野生西的事情,我们现在发现自己在一个测试工具,有时并不明显. 在这些疾病的情况下, 实用工具是重要的, 他们从这些网页上的测试提供了指导. 它描述了许多方面的效用–他们考虑如何有用的测试可能是一个很好的的通用模型, 我觉得, 评估测试将真正给人们提供. 作为一个例子, 检查出这一个 亨廷顿氏病 (PDF格式).

我想提供一个参考,为我们探索的资源, 但我无法找到一个关于Orphanet. 不过, 你可以探索 帮助部分 了解如何使用网站, 和自己的使命和资金来源. 他们在参考有一件事情是他们与 EuroGenTest, 一个网站,我提醒 GeneTests资源 在NCBI的. 执行一个测试实验室EuroGenTest搜索带您回到Orphanet反正, 使用诊断测试的搜索.


Orphanet: 銈://www.orpha.net

EuroGenTest: http://www.eurogentest.org/

GeneTests在NCBI: http://www.ncbi.nlm.nih.gov/sites/GeneTests