Tag Archives: maladie rare

Mygene2_vid

Astuce Vidéo de la semaine: MyGene2, connecting families with rare conditions with each other

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, et ainsi de suite. 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, Je suis allé jeter un oeil: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

Le site est 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.

Il ya un “accueil” video that they’ve made, but it’s light on the software details. Toujours, si, 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, si, so you’ll have to click to view it:

Mygene2_vid

You can learn more about the resources from their FAQ collection. I’ve found a couple of references (ci-dessous) that provide some further information about the project [Remarque: l' Génétique en médecine one goes to a paywalled, pièce–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.

Liens rapides:

MyGene2: http://www.mygene2.org

Suivez-les sur twitter: https://twitter.com/MyGene2

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

(L' Génétique en médecine piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)

Références:

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

Chong, J., Yu, J., Lorentzen, P., Parc, K., Jamal, S., Tabor, H., Rauch, A., Saenz, M., Boltshauser, E., Patterson, K., Nickerson, D., & Bamshad, M. (2015). Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features Génétique en médecine DOI: 10.1038/gim.2015.161

Genomics England is responsible for the 100,000 Genomes Project

Astuce Vidéo de la semaine: PanelApp, de l' 100000 Projet Génomes

Genomics England is responsible for the 100,000 Genomes Project

Genomics England is responsible for the 100,000 Projet Génomes

Last week I talked about the 100,000 Projet Génomes in the UK. That video tip was an introduction and overview of the project. Cette semaine, si, 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 (verts, jaunes, rouges) 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 ou 4 sources.
  • Amber = intermediate; a gene from 2 sources.
  • Red = lowest level of confidence; 1 de l' 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. Ils ont detailed instructions and guidelines available to help. Cependant, the first round of review ended already (Octobre 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. Aussi, 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, Genetics Home Reference, l' Decipher DDD project, HGNC, ClinVar, UniProt, NCBI Nucleotide, et 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. (Attendez, couleurs, droit? UK variation). Check it out yourself, si, with the link below. You can hear more in this podcast as well.

Liens rapides:

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

100,000 Projet Génomes: http://www.genomicsengland.co.uk/

Références:

Siva, N. (2015). UK gears up to decode 100 000 genomes from NHS patients The Lancet, 385 (9963), 103-104 DOI: 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 (Accédé: Octobre 8 2015)
SNPpets_2

SNPpets vendredi

Les SNPpets de cette semaine inclut les mises à jour des outils existants, comme Reactome et IMG, the biggest JBrowse display I ever saw, diverses bribes de # ASHG15 que les nuages ​​de mots, édition de gène, tranches à travers la médecine personnalisée et les maladies rares, et une Virtual Machine catalog. La chose la plus inhabituelle cette semaine: les travaux récents de la génomique évolutive se met sur The Big Bang Theory. Et plus….


SNPpets_2Bienvenue à notre collection vendredi lien fonction: SNPpets. Au cours de la semaine, nous avons rencontré beaucoup de liens et de lectures qui nous paraissent intéressants, mais ne pas se rendre à un billet de blog. Ici, ils sont pour votre plaisir…


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

Biostars

Quelle est la réponse? (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 est un site pour poser des, répondre et de discuter des questions et des problèmes bioinformatiques. Nous sommes membres de la Biostars_logo communauté et de trouver cela très utile. Souvent les questions et les réponses se posent à Biostars qui se rapportent à nos lecteurs (les utilisateurs finaux des ressources en génomique). Thursdays we will be highlighting one of those items or discussions here in this thread. Vous pouvez poser des questions sur ce sujet, ou vous pouvez toujours joindre à Biostars.


Forum: For the general public seeking advice from this community

Bonjour les gens–

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 (Je pense que), 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.

Cependant, my point is more general. This may become increasingly an issue here as more people have (or hear about) information sur la séquence, 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, éventuellement. 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: Réponses.

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 Genetics Home Reference, ou quelque chose? 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, peut-être? We may also need legal advice. Anyone seen other places take this on? Please add your thoughts over at Biostars.

dna_cutting_with_scissors_hr-150x150

SNPpets vendredi

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


Bienvenue à notre collection vendredi lien fonction: SNPpets. Au cours de la semaine, nous avons rencontré beaucoup de liens et de lectures qui nous paraissent intéressants, mais ne pas se rendre à un billet de blog. Ici, ils sont pour votre plaisir…


Astuce de la semaine: Orphanet pour les maladies rares informations

Comme je regardais autour de quelques-uns des liens vers des ressources connexes du nouveau site OMIM, J'ai remarqué qu'il y avait des liens vers Orphanet. J'ai entendu parler d'Orphanet, avant–selon leurs informations, ils ont été autour depuis 1997, mais qu'il n'avait pas regardé de près. Donc, pour cette semaine Astuce de la semaine nous allons explorer Orphanet.

J'ai commencé à explorer sur la page d'atterrissage principal, http://www.orpha.net/. Depuis la page d'atterrissage, vous pouvez accéder à un large éventail de types de recherche et de collectes de données. Une zone de navigation par onglets dans la partie supérieure offre des points d'entrée à partir de nombreuses perspectives: Les maladies rares, Les médicaments orphelins, Centre expert, Les tests diagnostiques, Recherche et essais, Les organisations de patients, un répertoire, et plus. C'est un portail bien organisé pour plus d'informations sur les maladies rares.

Dans la pointe de cinéma, je n'aurai pas le temps d'aller dans tous ces composants, Je vous encourage à regarder autour de vous. Je serai en se concentrant sur la recherche d'une maladie rare, et en regardant les fonctionnalités disponibles sur cette page. À l'heure si cette écriture, il ya près de 6000 maladies rares enregistrés avec des informations qui sont stockées sur le site (5954).

Une caractéristique que j'ai vraiment aimé a été récemment ajouté–Clinique Cartes Gene Utilitaire (CUGCs). Une des choses à propos de l'ouest sauvage des tests ADN que nous nous trouvons maintenant dans est que parfois l'utilité du test n'est pas évident. Dans le cas de ces maladies, l'utilité est important, et ils offrent des conseils sur les essais de ces pages. Et il décrit de nombreux aspects de l'utilité–ils sont un beau modèle général pour considérer l'utilité d'un test peut être, Je pense que, et d'évaluer ce test va vraiment offrir aux personnes. Comme un exemple, consulter celui-ci pour La maladie de Huntington (PDF).

Je tiens à fournir une référence pour les ressources, nous explorons, mais j'ai été incapable de trouver un sur Orphanet. Cependant, vous pouvez explorer leur Section Aide à apprendre sur la façon d'utiliser le site, et sur leur mission et les sources de financement. Une chose qu'ils référence, il est leur relation avec EuroGenTest, un site qui m'a rappelé le GeneTests ressources au NCBI. Effectuer une recherche pour un laboratoire d'essais au EuroGenTest vous ramène à Orphanet toute façon, en utilisant la recherche diagnostique des tests.

Liens rapides:

Orphanet: http://www.orpha.net

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

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