Tag Archives: seltene Krankheit

Mygene2_vid

Video Tipp der Woche: 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, und so weiter. 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, Ich ging, um einen Blick haben: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

Die Website ist 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.

Es gibt eine “willkommen” video that they’ve made, but it’s light on the software details. Still, obwohl, 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, obwohl, 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 (unten) that provide some further information about the project [Note: der Genetik in der Medizin one goes to a paywalled, Stück–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.

Quick-Links:

MyGene2: http://www.mygene2.org

Folgen Sie ihnen auf twitter: https://twitter.com/MyGene2

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

(Das Genetik in der Medizin piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)

Referenzen:

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

Chong, J., Yu, J., Lorentzen, P., Park, 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 Genetik in der Medizin DOI: 10.1038/gim.2015.161

Genomics England is responsible for the 100,000 Genomes Project

Video Tipp der Woche: PanelApp, aus dem 100000 Genome Projekt

Genomics England is responsible for the 100,000 Genomes Project

Genomics England is responsible for the 100,000 Genome Projekt

Last week I talked about the 100,000 Genome Projekt in the UK. That video tip was an introduction and overview of the project. Diese Woche, obwohl, 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 (grün, Gelb, rot) 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 oder 4 Quellen.
  • Amber = intermediate; a gene from 2 Quellen.
  • Red = lowest level of confidence; 1 der 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. Sie haben detailed instructions and guidelines available to help. Allerdings, the first round of review ended already (Oktober 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. Auch, 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, der Decipher DDD project, HGNC, ClinVar, UniProt, NCBI Nucleotide, und 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. (Warten Sie, Farbe, Recht? UK variation). Check it out yourself, obwohl, with the link below. You can hear more in this podcast as well.

Quick-Links:

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

100,000 Genome Projekt: http://www.genomicsengland.co.uk/

Referenzen:

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 (Abgerufen: Oktober 8 2015)
SNPpets_2

Freitag SNPpets

This week’s SNPpets includes updates to existing tools, wie Reactome und IMG, the biggest JBrowse display I ever saw, various tidbits from #ASHG15 as word clouds, Gen-Bearbeitung, slices through personalized medicine and rare diseases, und ein Virtual Machine catalog. Most unusual thing this week: recent evolutionary genomics work gets onto The Big Bang Theory. Und mehr….


SNPpets_2Herzlich Willkommen auf unserer Friday Feature Linksammlung: SNPpets. Während der Woche kommen wir auf eine Vielzahl von Links und liest, dass wir denken, sind interessant, sondern machen es nicht zu einem Blog-Eintrag. Hier sind sie für Ihr Vergnügen…


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

Biostars

Was ist die Antwort? (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 ist ein Ort für die Nachfrage, Beantwortung und Diskussion Bioinformatik Fragen und Probleme. Wir sind Mitglieder der Biostars_logo Gemeinde und finde es sehr nützlich. Oft Fragen und Antworten ergeben sich bei Biostars, die relevant für unsere Leser (Endanwender von Genomik Ressourcen). Thursdays we will be highlighting one of those items or discussions here in this thread. Sie können Fragen in diesem Thread fragen, oder kann man immer mitmachen bei Biostars.


Forum: For the general public seeking advice from this community

Hallo Leute,–

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 (Ich denke,), 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.

Allerdings, my point is more general. This may become increasingly an issue here as more people have (or hear about) Sequenz-Information, 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, möglicherweise. 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: Antworten.

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, oder etwas? 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, vielleicht? 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

Freitag 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. Es gibt eine BLASTX alternative, a helpful tip in workshop teaching, quack DTC tests, handy errors (wirklich), 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, und mehr. The best item this week, obwohl, was a story of a family with a rare disease situation that found genomics researchers via Reddit, and that gave them answers and hope.


Herzlich Willkommen auf unserer Friday Feature Linksammlung: SNPpets. Während der Woche kommen wir auf eine Vielzahl von Links und liest, dass wir denken, sind interessant, sondern machen es nicht zu einem Blog-Eintrag. Hier sind sie für Ihr Vergnügen…


Tipp der Woche: Orphanet for Rare Disease information

Als ich umsah auf einige der Links zu verwandten Ressourcen aus dem neuen OMIM site, Ich bemerkte, dass es Links zu Orphanet. Ich habe von Orphanet gehört–nach ihren Angaben haben sie rund seither 1997, aber noch nicht sah es eng. Also für diese Woche Tipp der Woche werden wir erkunden Orphanet.

Ich fing an, am Hauptfahrwerk Seite erkunden, http://www.orpha.net/. Von der Landingpage können Sie Zugang zu einer Vielzahl von Such-Typen und Datensammlungen. Ein Tabbed Navigation in der Nähe des Top-Angebote Einstiegspunkte aus zahlreichen Perspektiven: Seltene Krankheiten, Orphan Drugs, Expert-Center, Diagnostische Tests, Forschung und klinische Studien, Selbsthilfe, ein Verzeichnis, und mehr. Es ist eine gut organisierte Portal für Informationen über seltene Krankheiten.

In dem Film Tipp werde ich nicht die Zeit, in all diesen Komponenten gehen, Ich ermutige Sie, um sich selbst schauen. Ich werde auf die Suche nach einer seltenen Erkrankung konzentrieren, und Blick auf die verfügbaren Funktionen auf dieser Seite. Zu der Zeit, wenn diese schriftlich, gibt es fast 6000 seltene Krankheiten mit Informationen aufgezeichnet, die am Standort gelagert werden (5954).

Ein Feature, das ich wirklich mochte, war vor kurzem hinzugefügt–Klinischer Nutzen Gene Cards (CUGCs). Eines der Dinge über den Wilden Westen von DNA-Tests, dass wir befinden uns jetzt in ist, dass manchmal die Nützlichkeit des Tests nicht ersichtlich ist,. Im Fall dieser Krankheiten, Dienstprogramm ist wichtig, und sie bieten Leitlinien für die Prüfung von diesen Seiten. Und es beschreibt viele Aspekte des Nutzens–sie sind eine nette allgemeines Modell für die Prüfung, wie nützlich ein Test sein könnte, Ich denke,, und Auswertung von Tests, was wirklich bieten Menschen. Als ein Beispiel, Sehen Sie sich diese eine für Huntington-Krankheit (PDF).

Ich mag, um eine Referenz für die Ressourcen, die wir erkunden bieten, aber ich war unfähig, eine über Orphanet lokalisieren. Allerdings, Sie können sich mit ihrer Hilfe-Bereich zu erfahren, wie die Nutzung der Seite, und über ihre Mission und Finanzierungsquellen. Eine Sache, die sie referenzieren es ist ihre Beziehung zu EuroGenTest, eine Website, die mich an die erinnert GeneTests Ressource bei NCBI. Durchführen einer Suche nach einem Testlabor in EuroGenTest gelangen Sie zurück zum Orphanet sowieso, mit der Diagnostik Suche.

Quick-Links:

Orphanet: http://www.orpha.net

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

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