Tag Archives: personal genomics

SNPpets_2

Friday SNPpets

This week was yummy. Apple epigenome and a new corn assembly, in time for your northern hemisphere summer picnics. Marine protists for you to think about during your walks on the beach. The return of the Venn, and a guide to PCA plots. A very cool set of human protein complexes. Synbio tools.

My favorite this week, though, was the sequencing of different parts of a 200+ year old oak tree. That is a cool idea.


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/CSHL/status/874282809761910784

https://twitter.com/nekton4plankton/status/874357230866317313

dtc_testing

Video Tip of the Week: Direct to Consumer Genetic Testing and Genetic Counselling

At OpenHelix, we remember the days when people didn’t even barely have documentation with their software when they put it out (yah, I know, it still varies). But outreach really is getting better. There are journals now that are also enforcing more reader-friendly ways to describe the research, with non-jargon summaries and some terrific visual aids.

Increasingly, there are also videos associated with papers. I just came across this one, and thought it was a nice example of an important issue for non-scientists to access.

So this looks at direct-to-consumer (DTC) services available in Europe, but some of the same ones are available in the US. Of course, in the US, as we muck around with health care again and what is/is not a pre-existing condition, the advice might be different. Sigh.

Hat tip:

Reference:

Middleton, A., Mendes, Á., Benjamin, C. M., & Howard, H. C. (2017). Direct-to-consumer genetic testing: where and how does genetic counseling fit?. Personalized Medicine, (14:3) , Pages 249-257 , DOI 10.2217/pme-2017-0001.

 

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 a popular slide deck that illustrates roads that go to bioinformatics; questions of what to do with your own genome data (assuming you aren’t a PhD in bioinformatics); fast identification of bacterial strains with StrainSeeker; and the epigenomic landscape of prokaryotes;  the ancestors of cultivated peanuts sequenced; a cancer tool with proteomics coactivation pairs; very cool detailed visualization of tissue-level data that offers new insights; and microbiomes abound.


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 quite a range of things. New species genomes projects (pineapple is out, bauhinia being crowdfunded). I dare you to resist a tool called “Time Curves“.  The pre-print on over 60k protein coding human variations. Updates via FlyBase and discussed for QIIME. Best quip of the week: You can buy a DNA test on Amazon and it costs less than the textbook about it. A couple of items on bioinformatics pain. Some new solutions. 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 a lot of back-and-forth on the artist formerly known as personal genomics (now personalized medicine). We got the EU mucking up access, we have privacy issues unearthed, we have the cost of variant calling–and the uncounted cost of other analyses. But we also have the importance of genome sharing. There’s a follow-up story on the kid who was the “first child saved by genome sequencing”. Also some cool research on “essential” human genes. New databases or updates, as usual (dbGaP is one I need to go deeper on). 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…


 

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 include stories about the FlyBase memoriam for Bill Gelbart, Phenolyzer for gene discovery from phenotypes, tissue- and tumor-PPI comparison, Beacon, shotgun metagenomics, the future decade in genomics, no-so-scary personal genome sequencing and apps for it, DNA-barcoded beer, and more.


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…


dna_cutting_with_scissors_hr-150x150

Friday SNPpets

This week’s SNPpets include free passes for Phil Bourne’s keynote talk in Boston next week, software for analysis of the effects of protein variants, interpreting your own genome, a book review of a tome on bioinformatics that’s getting very good chatter among the practitioners, free image analysis tools for microscopy, and more….


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…

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Note: We might need to change the format of FridaySNPpets, since Twitter just made it harder to capture the text format for pasting. But embedded tweets may not be searchable, which is one reason we’ve done these this way. Anyway, stay tuned.

What’s The Answer? (23andMe to other formats)

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). Every Thursday 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.

This week’s highlighted question was from someone with personal genomics data in their hands, but doesn’t know what to do next.

Question: How to I convert 23andMe Raw Genome to GenBank or FASTA?

I used 23andMe to download my raw genome. I have it in a .txt file but you can’t use the format for real bio programs. i want to make my own library for further analysis. Does anyone know how i can convert .TXT to FASTA, GenBank, or any other usable file type?

someashole

Although Biostar usually hosts questions from folks who are a bit more advanced in their grasp of file formats, this question struck me as interesting for a couple of reasons. The needs of folks who are not practitioners, but who find themselves with data in their hands, will only increase going forward. And although the companies will offer some tools, there’s a niche for some lighter-weight public tools. I discussed this before on the issue of genome browsers, which are currently too much heavy lifting for intro-level users. I know there are some open data communities forming around this data too, but so far what I’ve seen has been more sophisticated early adopter types.

But I imagine it would be difficult to get funding for such intro-level tools. They probably wouldn’t score well on “innovation” and some of the other traditional grant criteria because–well, because that’s not what the system does.

Maybe it would make some good class projects for some coders who are learning to build tools, and to work with this type of data. Make some gentle 23andme to X-format converters. A browser that’s not too hard to load your data up and look around without too many tracks. These folks are going to need more hand-holding. They don’t know what formats they need, or what is available for them to do.

But have a look at the answers, and if you have other guidance for this newbie, drop some comments over there.