Tag Archives: personalized medicine

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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

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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…


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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…


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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…


 

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Video Tip of the Week: Introduction to Biocuration and the career path

ISB_biocuration

The ISB is a professional organization for biocurators

At OpenHelix, we’ve long sung the praises of curators. Some of us have been curators and worked with curation and database development teams. All of us have relied on quality information in the databases for research and teaching. But I think there are a lot of people who don’t understand the value of quality curation, how it’s done, and who curators are. They are widely taken for granted.

A recent talk by Claire O’Donovan of EBI-EMBL helps to explain the roles and the importance of biocurators. So although this talk isn’t a typical software talk, I think understanding this is crucial to everyone’s appreciation of how information you rely on gets into the databases you use. And if you find yourself in situations where you are guiding students, knowing about this career is also worthwhile.

Claire O’Donovan has had a front row seat to the development of this field, and has great enthusiasm for the future. And going forward, in your doctor’s office as precision medicine and treatments become a thing–how much do you want correct information in the databases? Mining data, standardizing language for descriptions of features, and sharing this information is crucial for all of us.

Here’s what’s covered in this video, from the agenda slide:

  • Introduction to the concept of biocuration.
  • The different kinds of biocurators, and the skill set needed.
  • Our community: Biocuration Society and conference.
  • The future of biocuration and career paths.

Specific examples of what curators do are illustrated (~6:30min). A sample UniProt entry illustrates what kind of information is captured and where it appears. She also touches on their work with Gene Ontology. And a bit about the ecosystem of curation, how teams at different resources help each other but don’t wish to duplicate work, using HGNC nomenclature as an example.

About 8min, the skill sets for biocuration are covered: data basics, curation skills, programming and database concepts, ontologies, and usability of the data collected. This also includes data access and management, as well as dissemination and outreach. This includes user training (yay!) and the concepts of data analysis for users.

There’s no formal degree path for curation practitioners at this point, and different groups will have different needs. But the community is begining to think about this, and about professional qualifications. She also mentioned a recent report from the National Academy of Sciences press on the topic of the future workforce skills and needs (linked below). This is an alternative career route for people with science training, and it’s important to understand not only the science but computational pieces. And it should be taken seriously as a discipline. There is now a journal that reflects this (also linked below).

Claire also takes a look at the future of biocuration, using the Center for Target Validation (CTTV) as an example. And she talks about the importance of quality information in medical records as we increasingly have genomic details in diagnosis and treatment situations. If we want precision medicine to work, we have to have the precise and correct information in the databases. So respect and value the curators. They are worth it. And if you know anyone that deserves special recognition–nominate!

Quick links:

International Society for Biocuration:  http://biocuration.org/

Preparing the Workforce for Digital Curation: http://www.nap.edu/catalog/18590/preparing-the-workforce-for-digital-curation 

References:

COMMITTEE ON FUTURE CAREER OPPORTUNITIES AND EDUCATIONAL REQUIREMENTS FOR, & DIGITAL CURATION (2015). PREPARING THE WORKFORCE FOR DIGITAL CURATION National Academies Press : 10.17226/18590

Holliday, G., Bairoch, A., Bagos, P., Chatonnet, A., Craik, D., Finn, R., Henrissat, B., Landsman, D., Manning, G., Nagano, N., O’Donovan, C., Pruitt, K., Rawlings, N., Saier, M., Sowdhamini, R., Spedding, M., Srinivasan, N., Vriend, G., Babbitt, P., & Bateman, A. (2015). Key challenges for the creation and maintenance of specialist protein resources Proteins: Structure, Function, and Bioinformatics, 83 (6), 1005-1013 DOI: 10.1002/prot.24803

Gaudet, P., Munoz-Torres, M., Robinson-Rechavi, M., Attwood, T., Bateman, A., Cherry, J., Kania, R., O’Donovan, C., & Yamasaki, C. (2013). DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration Database, 2013 DOI: 10.1093/database/bat077

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Friday SNPpets

This week’s SNPpets have a range of resources–from food crops to public health to personal genomics. Really, it’s touching everything we do now. A resource filling a gap–digenic diseases–was new to me: DIDA.  A nice collection of miRNA resources. And a popular item about NGS can go “horribly wrong”. An awesome FAQ. The final JABBA award. There’s a lot more too–great week for fascinating reads.


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/ACGT_blog/status/696816305945632768

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Friday SNPpets

This week’s SNPpets explore the past and the future. There’s the effect of climate on human population movements. And a correction to another ancestry paper. We have retro bioinformatics hardware. The creator of the ribbon protein diagrams appears. Top stories from last year, and from this year (so far). And Neil DeGrasse Tyson and Anne Wojcicki on a “future without disease” (oh, please–but that was the headline writer’s fault, the interview isn’t that pollyanna-ish). There’s also the future of genetic discrimination and GINA. And future disease outbreak tools. Have a look.


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…


 

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Friday SNPpets

This week’s SNPpets cover a range of issues. Attempting to community-curate bioinformatics tools, a new paper on UCSC Genome Browser‘s features, iPlant now reborn as CyVerse, errors in databases, personalized diagnosis from the UK 100000 Genomes project and the re-launch of their PanelApp, and some new plant tools: AgroPortal and 30 plants going into OrothoDB. Also, read those thesis submissions carefully. There may be an easter egg.


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…


Thanks for joining us

Video Tips of the Week, Annual Review 2015. Part II

As you may know, we’ve been doing these video tips-of-the-week for eight years now. We have completed or collected around 400 little tidbit introductions to various resources through this past year, 2015. At first we had to do all of our own video intros, but as the movie technology became more accessible and more teams made their own, we were able to find a lot more that were done by the resource providers themselves. So we began to collect those as well. At the end of the year we’ve established a sort of holiday tradition: we are doing a summary post to collect them all. If you have missed any of them it’s a great way to have a quick look at what might be useful to your work.

You can see past years’ tips here: 2008 I, 2008 II, 2009 I, 2009 II, 2010 I, 2010 II, 2011 I, 2011 II, 2012 I, 2012 II, 2013 I, 2013 II, 2014 I, 2014 II, 2015 I.

July
July 1: MorphoGraphX, morphogenesis in 4D
July 8: PhenomeCentral
July 15: Introduction to the UCSC Genome Browser
July 22: PathWhiz for graphical appeal and computational readability
July 29: PathWhiz for Pathways, Part II

August
August 5: Araport, Arabidopsis Portal
August 12: World Tour of Genomics Resources, part II
August 19: gene.iobio for genome and variation browsing
August 26: Human Metabolome Database, HMDB

September
September 2: ENCODE Data Coordination Center, phase 3
September 9: UCSC features for ENCODE data utilization
September 16: BANDAGE for visualization of de novo assembly graphs
September 23: UCSC Xena System for functional and cancer genomics
September 30: Global Biotic Interactions database, GloBI

October
October 7: Weave, Web-based Analysis and Visualization Environment
October 14: 100,000 Genomes Project
October 21: PanelApp, from the 100000 Genomes Project
October 28: New Reactome Pathway Portal 3.0

November
November 4: RNACentral, wrangling non-coding RNA for simplifying access
November 11: UCSC Table Browser and Custom Tracks
November 18: Explore Gene Pages at NCBI with Variation and Expression Information
November 25: iDigBio for access to historical specimens and more

December
December 2: KBase, DOE’s Systems Biology Knowledgebase
December 9: Send UCSC Genome Browser sequence to external tools
December 16: Plant Reactome at Gramene
December 23: Video Tips of the Week, Annual Review 2015 (part 1)
December 30: [this post]

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Friday SNPpets

This week’s SNPpets offer both science and humor. I think people get a little punchy around the holidays/end of semester. There’s software for assembly, a bioinformatics network for African topics, bioethics of gene editing, cancer and personalized medicine,  Dilbert comments on big data and health, interesting tools for open- and evidence-based medicine, microbiome concepts and a metagenomic journey. Most curious thing this week: the mouse poem constructed entirely from paper titles.


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…