Tag Archives: rare disease

Mygene2_vid

Video Tip of the Week: 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, and so on. 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, I went to have a look: Families Isolated By Rare Genetic Conditions Find New Ways To Reach Out.

The site is 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.

There is a “welcome” video that they’ve made, but it’s light on the software details. Still, though, 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, though, 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 (below) that provide some further information about the project [Note: the Genetics in Medicine one goes to a paywalled, piece–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

Follow them on twitter: https://twitter.com/MyGene2

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

(The Genetics in Medicine piece also notes My46.org, “a web-based tool for managing return of genetic test results”.)

References:

Panko, B. (2016). Six finalists to compete for Open Science Prize Science 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 Genetics in Medicine DOI: 10.1038/gim.2015.161

Genomics England is responsible for the 100,000 Genomes Project

Video Tip of the Week: PanelApp, from the 100000 Genomes Project

Genomics England is responsible for the 100,000 Genomes Project

Genomics England is responsible for the 100,000 Genomes Project

Last week I talked about the 100,000 Genomes Project in the UK. That video tip was an introduction and overview of the project. This week, though, 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 (green, yellow, red) 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 or 4 sources.
  • Amber = intermediate; a gene from 2 sources.
  • Red = lowest level of confidence; 1 of the 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. They have detailed instructions and guidelines available to help. However, the first round of review ended already (October 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. Also, 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, the Decipher DDD project, HGNC, ClinVar, UniProt, NCBI Nucleotide, and 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. (Wait, colour, right? UK variation). Check it out yourself, though, 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 Genomes Project: http://www.genomicsengland.co.uk/

References:

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 (Accessed: Oct 8 2015)
SNPpets_2

Friday SNPpets

This week’s SNPpets includes updates to existing tools, like Reactome and IMG, the biggest JBrowse display I ever saw, various tidbits from #ASHG15 as word clouds, gene editing, slices through personalized medicine and rare diseases, and a Virtual Machine catalog. Most unusual thing this week: recent evolutionary genomics work gets onto The Big Bang Theory. And more….


SNPpets_2Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


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

Biostars

What’s the Answer? (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 is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the Biostars_logo community and find it very useful. Often questions and answers arise at Biostars that are germane to our readers (end users of genomics resources). Thursdays we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at Biostars.


Forum: For the general public seeking advice from this community

Hello folks–

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 (I think), 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.

However, my point is more general. This may become increasingly an issue here as more people have (or hear about) sequence 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, possibly. 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: Answers.

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, or something? 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, maybe? 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

Friday 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. There’s a BLASTX alternative, a helpful tip in workshop teaching, quack DTC tests, handy errors (really), 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, and more. The best item this week, though, was a story of a family with a rare disease situation that found genomics researchers via Reddit, and that gave them answers and hope.


Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…


Tip of the Week: Orphanet for Rare Disease information

As I was looking around at some of the links to related resources from the new OMIM site, I noticed that there were links to Orphanet. I’ve heard of Orphanet before–according to their information they’ve been around since 1997, but hadn’t looked at it closely. So for this week’s Tip of the Week we’ll explore Orphanet.

I began to explore at the main landing page, http://www.orpha.net/. From the landing page you can access a wide range of search types and data collections. A tabbed navigation area near the top offers entry points from numerous perspectives: Rare diseases, Orphan drugs, Expert centers, Diagnostic tests, Research and trials, Patient organizations, a directory, and more. It is a nicely organized portal for information about rare diseases.

In the movie tip I won’t have time to go into all of these components, I encourage you to look around yourself. I’ll be focusing on a search for a rare disease, and looking at the features available on that page. At the time if this writing, there are nearly 6000 rare diseases recorded with information that are stored at the site (5954).

One feature I really liked was recently added–Clinical Utility Gene Cards (CUGCs). One of the things about the wild west of DNA testing that we now find ourselves in is that sometimes the utility of the testing isn’t apparent. In the case of these diseases, utility is important, and they offer guidance on the testing from these pages. And it describes many aspects of the utility–they are a nice general model for considering how useful a test might be, I think, and evaluating what testing will really offer people. As an example, check out this one for Huntington’s disease (PDF).

I like to provide a reference for the resources we explore, but I was unable to locate one about Orphanet. However, you can explore their Help section to learn about how to use the site, and about their mission and funding sources. One thing they reference there is their relationship with EuroGenTest, a site that reminded me of the GeneTests resource at NCBI. Performing a search for a testing lab at EuroGenTest takes you back to Orphanet anyway, using the Diagnostic tests search.

Quick links:

Orphanet: http://www.orpha.net

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

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