Tag Archives: 23andme

SNPpets_2

Friday SNPpets

This week I left the “call to action” tweet at the top–you can vote for GenBank every day in August. And I know it’s September now, but I wanted to go and check–and they made it to the final four! So go vote for GenBank some more. Same link works fine. Other things this week: NYTimes shows more stories of people whose recreational genomics endeavors reveal family secrets. One of them is what’s in the reference genome? I don’t think the answer came up completely clearly, but it reminds me I want to look into that again. The breakthrough cancer diagnostics kit is approved. The girlfriend meme. And one more example of how far ahead agriculture is on genomics.


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…


This seems to be the answer:

SNPpets_2

Friday SNPpets

I stayed up late last night to see if I’d have health care this morning, and I got off schedule. But off we go–still insured!

This Friday includes the first ever tardigrade protein structure! It’s bigger on the inside–wait, no, wrong thing. Human wise, we have recreational genomics apps, and we have recreational genomics consequences. Epigenetic shampoo (seriously). Students and biotechnology issues, how are they thinking about the topics? Maize and Mars. Dead bovine DNA. Live cheese microbes. Hungry yet?


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 I’m taking a different tack. There was something bothering me about misuse of genomics, and I’m going to rant on that. Recently a friend pointed me to something that I hadn’t seen before: cranks are misusing 23andMe-type of data to “diagnose” kids as being likely to suffer “vaccine injury”. As you might recognize from the dog-whistle, this means that anti-vaccine cranks are taking their message to a new front: personalized genomics. They are misusing data to convince parents that vaccinating their kids is dangerous.

This is a very, very disturbing direction as vaccine fears already have led to tragic outcomes as kids get vaccine-preventable diseases at increasing rates.

In addition, cranks are coming together around “personalized medicine” to pitch their terrible ideas to people and sell them “detox” potions and supplements. They are out talking to the public on these things. We need to step up our game and get people better information. There will be serious consequences–misuse of genomics on many topics–with the potential for public health outcomes.

So below are a few links to illustrate this. It’s time to raise awareness of this in the legit genomics community. I expect others didn’t know this was going on, too.


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…


This week there was some mainstream communication on genomics as well. I’m not sure it helped. Sigh.

 

SNPpets_2

Friday SNPpets

This week, DNA was indicted and decades later led to a conviction. Genomes of birch trees and shape-shifting butterflies. And the most interesting stuff to me is non-human, but dbSNP will stop accepting non-human species info. Sigh. Well, I do think alternative splicing is interesting too, and we have some of that this week. Human gene editing, tumors, and various types of personalized genomics were out and about this week as well. It’s not that I dislike humans (all the time), but I’m sort of agnostic on species.


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 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…


dna_cutting_with_scissors_hr-150x150

Friday SNPpets

A pretty typical week, lots of great software and fascinating data. Methylation analysis, 7-set Venn, a new genomics comic strip, some personal genomics, some clinical genomics.  Gosh, I love my life. But the most amusing and unexpected snippet: misuse of a Circos image of caught the eye of the developer, and he found that Jurassic Park dinosaurs are made of corn.


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…


https://twitter.com/vahidaidun/status/619550732518342656

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.

What’s The Answer? (23andMe bioinformatics)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar 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 BioStar.

This week’s highlighted Biostar item is an incarnation of the 23andMe drama. I’ve seen people take on the legal, medical practice, and social aspects. But this thread takes on the underlying bioinformatics as an issue. I thought that was interesting.

Forum: FDA sends a warning letter to 23andMe – Personal Genomics Service marketing to be discontinued

There has been an interesting development in the world of personal genomics. The FDA sent what may be interpreted a cease and desists order:

Therefore, 23andMe must immediately discontinue marketing the Personal Genome Service (PGS) until such time as it receives FDA marketing authorization for the device.

Read more here: http://www.fda.gov/ICECI/EnforcementActions/WarningLetters/2013/ucm376296.htm

This seems to put bioinformaticians at the forefront of deciding what constitutes credible evidence that the PGS does indeed work as advertised.

Istvan Albert

I added my favorite additional pieces over there, which haven’t got much airplay among the genoscenti. But go have a look at the wider discussion among bioinformatics practitioners, which I thought was interesting.

SNPTips update (1.1)

I did a tip of the week on SNPTips a few months ago (more information there). It’s a great addon to view your genomic data while browsing databases and web sites. They’ve moved to version 1.1. There are two nice new features and some bug fixes. The features are:
*You can now use your deCODEme data, in addition to the 23andme support they started with.
*You can use SNPTips even without raw data to view SNPs on a page.
*and it’s been updated for Firefox 4.x.

You can check our our previous tip here (which still applies :).

SNPTips landing page at 5am Solutions.

The cost of genomics, revisited

1,000 dollars to sequence the entire 3 billion ‘basepair’ long human genome is the holy grail. Last year, on this blog, I predicted that we’d reach that goal ‘within a year’. Well, it’s been a year and we aren’t there. I did hedge a bit in the comments later, but the main point was that the cost was plummeting and headed for $1,000 for an entire genome. The graph at the left is cost of a single genome from 2003 to 2010… 300 million, to 10 thousand.

The cost is still plummeting. Illumina* has lowered the cost of sequencing the genome to $5,000. Half.Complete Genomics* today announced that their first quarter revenue was 6.8 million, up from 300 thousand last year. They have 2,000 complete genomes to sequence in their backlog. They charge < 10,000 for small orders, down to $5,000 for bulk orders (in research groups). The cost of sequencing large groups for research is getting much smaller.

So the price plummets still.

The price for genomic scans also plummets. 23andMe, which scans about 1 million variable sites in your genome (most of the human genome is not variable from person to person), cost 400 dollars last year, in December they price went to 200. After a one-day free sale, it’s now $100.

Of course, the question remains how expensive will it be to analyze that data.

 

*full disclosure, I own a (very) small amount of stock in both Illumina and Complete Genomics.