الوسم المحفوظات: مرض نادر


تلميح فيديو للأسبوع: MyGene2, ربط الأسر التي لديها حالات نادرة مع بعضها البعض

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, وهلم جرا. 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, ذهبت لالقاء نظرة: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

الموقع هو 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.

هناك “ترحيب” video that they’ve made, but it’s light on the software details. لا يزال, رغم أن, 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, رغم أن, 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 (أقل من) that provide some further information about the project [لاحظ: و علم الوراثة في الطب one goes to a paywalled, قطعة–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.

وصلات سريعة:

MyGene2: http://www.mygene2.org

متابعتها على تويتر: https://twitter.com/MyGene2

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

علم الوراثة في الطب piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)


Panko, B. (2016). Six finalists to compete for Open Science Prize العلم دوى: 10.1126/science.aaf9980

Chong, ج., يو, ج., Lorentzen, P., متنزه, ك., Jamal, س., Tabor, ه., Rauch, أ., Saenz, م., Boltshauser, E., Patterson, ك., نيكرسون, د., & Bamshad, M. (2015). Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features علم الوراثة في الطب دوى: 10.1038/gim.2015.161

Genomics England is responsible for the 100,000 Genomes Project

تلميح فيديو للأسبوع: PanelApp, من 100000 مشروع الجينوم

Genomics England is responsible for the 100,000 Genomes Project

Genomics England is responsible for the 100,000 مشروع الجينوم

Last week I talked about the 100,000 مشروع الجينوم in the UK. That video tip was an introduction and overview of the project. هذا الاسبوع, رغم أن, 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 (أخضر, أصفر, أحمر) 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 أو 4 مصادر.
  • Amber = intermediate; a gene from 2 مصادر.
  • Red = lowest level of confidence; 1 من 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. لديهم detailed instructions and guidelines available to help. ومع ذلك, the first round of review ended already (أكتوبر 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. أيضا, 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, علم الوراثة الرئيسية المرجعي, و Decipher DDD project, HGNC, ClinVar, UniProt, NCBI Nucleotide, و 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. (انتظر, اللون, حق? UK variation). Check it out yourself, رغم أن, with the link below. You can hear more in this podcast as well.

وصلات سريعة:

PanelApp: HTTPS://bioinfo.extge.co.uk/crowdsourcing/PanelApp/

100,000 مشروع الجينوم: http://www.genomicsengland.co.uk/


Siva, N. (2015). UK gears up to decode 100 000 genomes from NHS patients لانسيت, 385 (9963), 103-104 دوى: 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 (الوصول: أكتوبر 8 2015)

الجمعة SNPpets

This week’s SNPpets includes updates to existing tools, مثل ركتوم و IMG, the biggest JBrowse display I ever saw, various tidbits from #ASHG15 as word clouds, التحرير الجين, slices through personalized medicine and rare diseases, و Virtual Machine catalog. Most unusual thing this week: recent evolutionary genomics work gets onto The Big Bang Theory. وأكثر من ذلك….

SNPpets_2ترحيب لدينا ميزة جمع الجمعة الارتباط: SNPpets. خلال الأسبوع صادفنا الكثير من الروابط والقراءات التي نعتقد أنها مثيرة للاهتمام, ولكن لا تجعل من لبلوق وظيفة. ها هم لمتعتك…

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


ما هو الرد? (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 هو موقع لطرح, الإجابة ومناقشة المسائل والقضايا المعلوماتية الحيوية. نحن أعضاء Biostars_logo المجتمع وتجد أنه من المفيد جدا. غالبا ما تنشأ الأسئلة والأجوبة في Biostars التي ثيق لقرائنا (المستخدمين النهائيين للموارد الجينوميات). Thursdays we will be highlighting one of those items or discussions here in this thread. يمكنك طرح الأسئلة في هذا الموضوع, أو يمكنك الانضمام دائما في في Biostars.

المنتدى: For the general public seeking advice from this community

مرحبا الناس–

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 (أعتقد), 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.

ومع ذلك, my point is more general. This may become increasingly an issue here as more people have (or hear about) تسلسل المعلومات, 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, ربما. 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: إجابات.

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 علم الوراثة الرئيسية المرجعي, أو أي شيء? 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, ربما? We may also need legal advice. Anyone seen other places take this on? Please add your thoughts over at Biostars.


الجمعة SNPpets

This week’s SNPpets offered a lot of good stuff, everybody must be out of their summer vacation mode and back to the lab. هناك BLASTX alternative, a helpful tip in workshop teaching, quack DTC tests, handy errors (حقا), 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, eQTLs, وأكثر. The best item this week, رغم أن, was a story of a family with a rare disease situation that found genomics researchers via Reddit, and that gave them answers and hope.

ترحيب لدينا ميزة جمع الجمعة الارتباط: SNPpets. خلال الأسبوع صادفنا الكثير من الروابط والقراءات التي نعتقد أنها مثيرة للاهتمام, ولكن لا تجعل من لبلوق وظيفة. ها هم لمتعتك…

نصيحة الأسبوع: Orphanet للحصول على معلومات مرض نادر

وكنت أبحث في بعض أنحاء الارتباطات إلى الموارد ذات الصلة من موقع OMIM جديدة, لاحظت أن هناك صلات مع Orphanet. لقد سمعت من قبل Orphanet–وفقا لمعلوماتهم لقد كانت موجودة منذ 1997, ولكنه لم ينظر الى الامر عن كثب. حتى تلميح لهذا الاسبوع من أسبوع سوف نستكشف Orphanet.

لقد بدأت لاستكشاف في الصفحة المقصودة الرئيسية, http://www.orpha.net/. من الصفحة المقصودة ، يمكنك الوصول إلى مجموعة واسعة من أنواع البحث وجمع البيانات. وثمة مجال الملاحة كلفه بالقرب من أعلى نقطة دخول عروض عديدة من وجهات نظر: الأمراض النادرة, يتيم المخدرات, مراكز للخبراء, اختبارات تشخيصية, البحوث والتجارب, المريض المنظمات, دليل, وأكثر. بل هو المدخل المنظمة لطيف للحصول على معلومات حول الأمراض النادرة.

في الطرف الفيلم وأنا ليس لدي الوقت للذهاب الى كل من هذه المكونات, وأهيب بكم أن ننظر حولنا لنفسك. سأكون مع التركيز على البحث عن مرض نادر, وبالنظر إلى الميزات المتوفرة في هذه الصفحة. في وقت كتابة هذه السطور إذا, هناك ما يقرب من 6000 الأمراض النادرة المسجلة مع المعلومات التي يتم تخزينها في الموقع (5954).

وأضيف مؤخرا ميزة واحدة أحببت حقا–السريرية بطاقات المساعدة الجينات (CUGCs). واحدة من الأشياء عن الغرب المتوحش لاختبار الحمض النووي الذي نجد أنفسنا الآن هو أن في بعض الأحيان أداة للاختبار غير واضح. في حالة من هذه الأمراض, فائدة مهمة, وأنها توفر توجيهات بشأن الاختبار من هذه الصفحات. ويصف العديد من جوانب الأداة–فهي نموذج لطيفة العامة للنظر في مدى الفائدة التي قد تكون اختبارا, أعتقد, اختبار وتقييم ما سيوفر الناس فعلا. كمثال, تحقق من هذا واحد لل مرض هنتنغتون (قوات الدفاع الشعبي).

أود أن توفير مرجع للموارد نستكشف, ولكن كنت غير قادر على تحديد موقع واحد حول Orphanet. ومع ذلك, يمكنك استكشاف بهم مساعدة القسم لمعرفة المزيد عن كيفية استخدام الموقع, وحول مهمتهم ومصادر التمويل. شيء واحد أنها إشارة هناك علاقتهم EuroGenTest, أحد المواقع التي ذكرتني GeneTests الموارد في NCBI. إجراء بحث عن مختبر التجارب في EuroGenTest تعيدك إلى Orphanet على أي حال, البحث باستخدام اختبارات تشخيصية.

وصلات سريعة:

Orphanet: المتشعب://www.orpha.net

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

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