Tag Archives: personalized medicine

Friday SNPpets

This week was a busy and diverse week. From Bioinformatics as an Amusement Park, to the very serious FDA approval of 23andMe’s reports. From Lenski’s April Fool’s post to cancer databases. From diagnosing children with genomics details, to CRISPR sci-fi. We live in interesting times. But at least now we will be able to see everybody citing everybody else.


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…


Friday SNPpets

This week we find that all biology is computational biology. And that coding is missing. And I loved the knitted example of chromosomes–knitting is code. Also, some new misuse of data, and new appropriate uses. Get a fungus mug. Patients are going to be getting data, but nobody in the public knows about it. It’s a secret.


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…


check that one for embedded tweet too

Friday SNPpets

This week I gave a pub talk on the UCSC Genome Browser. It was the first time I’d tried a more general-public version of this. It was huge fun. And it was great timing to have this example of 5000+ samples from autism families to make the case about how hard it is to visualize all this data we are getting. But I also talked about microbes. I even mentioned to goat genome. The benefits and the trip-wires of misuse of personalized data were covered. We touched on restoration of extinct species. So it was a lot like this post, actually…. But I didn’t have the threat to GINA until today. Alas–I would like to have included that. I can’t believe we’re back there.


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…


SNPpets_2

Friday SNPpets

This week’s SNPpets have a pretty typical list of both new and updated sites and tools. The wheat genome (not gluten-free). A couple of key bits for folks who are scripting calls to NCBI (need to use https soon), or for folks in Asia who could use a UCSC Genome Browser mirror site closer to their location: http://genome-asia.ucsc.edu/. But my favorite thing this week was the best postdoc ad on twitter evah–see the snake one.


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…


https://twitter.com/Sara_and_Snakes/status/742891484064546816

SNPpets_2

Friday SNPpets

This week’s SNPpets offer a rather eclectic collection. Visualization with PanViz, LepBase for lepidopterans, a simulated data generator, and a new collection of community-curated phylogenetic estimates. But the big noise was the cancer “moonshot” data commons and the clinical trial for NCI-MATCH and precision medicine. Also newborn genome sequencing. Funniest thing: passive-aggresive bioinformatics. Coolest thing: Paul Simon and CRISPR (scroll to the bottom of the list).


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…


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

ga4gh_vid

Video Tip of the Week: Your DNA, Your Say. GA4GH wants to hear from you. And you.

The Global Alliance for Genomics and Health (GA4GH) has come up a few times on our blog. The last time we highlighted them for a tip, it was about their Beacon tool. The idea of the Beacon is that it could interrogate a database but in a very subtle way, without needing access to the entire sequence information of a patient. It would ask a simple yes/no question about a given sequence variant–and if a “yes” came back, then a researcher could go through the process of getting proper access to protected patient data.

So it was a way to keep people from pawing through data that they don’t need. And yet it could still connect people who might benefit from research, with researchers who need information.

But certainly issues of patient or donor privacy are hot topics. More and more data will come in from large projects, or from diagnostic samples, and cancer vs normal tissue comparisons, and we are going to struggle with the access vs. privacy matters for a while. The general public is only now becoming aware of the impacts. But we certainly need people to understand and we’ll want them to contribute to expanding our knowledge about health and disease.

That’s why the folks associated with GA4GH, the Wellcome Trust, and the Wellcome Genome Campus are eager to engage the public on their feelings on use of genomic sequence data. They have launched a project called “Your DNA Your Say”[PDF], in the form of a survey with videos to help understand where people are on this issue. Here’s the intro video to entice you to answer the survey:

I answered the survey because I do have concerns about access to information that will help us drive the science forward, as well as about the potential for misuse of the information. But I would like them to hear from as many people as possible, so that we can understand the barriers to research and donation that are looming. Have your say. And spread the word.

You can learn more about their ideas in a variety of publications–I’ll link to one below, but there are other publications and more details about the overall projects and individual tools at the GA4GH web site.

Quick links:

Survey site: YourDNAYourSay.org

GA4GH: http://genomicsandhealth.org/

References:

Lawler, M., Siu, L., Rehm, H., Chanock, S., Alterovitz, G., Burn, J., Calvo, F., Lacombe, D., Teh, B., North, K., Sawyers, C., & , . (2015). All the World’s a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health Cancer Discovery, 5 (11), 1133-1136 DOI: 10.1158/2159-8290.CD-15-0821

SNPpets_2

Friday SNPpets

This week’s SNPpets consist of a lot more social and general public genomics tidbits than usual. I don’t know why–I don’t feel I was particularly looking for those over the week. There was a GINA-related ruling: a company fined for misuse of testing. Myriad was spanked for not giving patients’ information back. On the good news side, there’s educational opportunities for teachers on “personal genetics” too. As always, more software, more data. Some humor. Some head-shaking.


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…


SNPpets_2

Friday SNPpets

This week’s SNPpets include items just posted to bioRxiv–which is lately where I see all the really intriguing tools. Including the awesomely-named “Clusterflock”. In a popular related item, someone responds to the Biostar question, “why are there errors in bioinformatics software?”. We have bat and bean genomics. And conch and lobster DNA. There’s at least 2 efforts to coordinate/wrangle human public genomes. 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…


SNPpets_2

Friday SNPpets

This week’s SNPpets include new and updated resources, the CRISPR zoo,  jokes, and even a job opportunity. But if there’s one thing to read this week, it’s the last tweet. It’s a sad story of what went wrong with a young patient’s sequencing results. This week I was talking about how curation of quality information matters for patient treatments as we move further with personalized medicine. This illustrates exactly why.


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…