Tag Archives: GINA

Friday SNPpets

This week’s tips contain quite a range of things, from patent battles to drying tardigrades (probably somebody patented this?). I put in the goat genome again because I like goats. We have precision medicine, and mutants asking to not be discriminated against. Some interesting tools this week 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…


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 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…


Friday SNPpets

This week’s SNPpets include a range of tools and genomics studies, from microbial to planaria to salmon to humans, as usual–as well as some that are species-agnostic.  Also stuff that is aimed at drug targets and pharmacology, including the Open Targets project Target Validation Platform. There’s a new DNA privacy bill under discussion in the US that I found interesting. Also–next Monday April 25 is #DNADay! Participate in community outreach with a number of strategies.


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 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 include stories about how DNA gets into the databases, network visualizations, historical genome browsers, CVS doing personalized medicine, fungal genome resource issues, mouse, dog, plant and human data stories, free data, 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…


https://twitter.com/timknut/status/628194770649804800

https://twitter.com/howplantswork/status/628198284658475008

Friday SNPpets

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…

  • Nice video on RNA interference by Nature Reviews Genetics. You can access all of the featured RNAi multimedia links from this page, or go straight to the video on this page. [Jennifer]
  • Interesting, The Repertoire 10K (R10K) Project: RT @deannachurch: CG: go to http://t.co/rekf2Gkd for more information on joining the project! #AGBT [Mary]
  • And it’s not in the papers anymore… RT @genome_gov: Pachter: “My worst nightmare: the curse of deep sequencing” aka too much data. #AGBT [Mary]
  • Read a Nature Outlook on allergies from Nov. 2011 – lot of new philosophies & theories that I wasn’t aware of. Currently free full access is available to the Nature Allergy Outlook [Jennifer]
  • RT @andrewsu: Word cloud of NAR 2012 Database issue abstracts via http://t.co/TMtefZ0k http://t.co/2zRzZkEG [Mary]
  • Cool new option for PDB submissions: Volunteer Structures For Foldit [Jennifer]
  • RT @LouWoodley NYC tweeps – the next Science Online NYC is on March 20th on keeping the research record straight http://bit.ly/xwziUb #sonyc [Jennifer]
  • RT @GeneSherpas: “@GeneticsUpdate: Can You Be Fired for Your Genes?  http://t.co/fDaOriU” Hopefully our future doesn’t come down to this!” [Mary]
  • Ha! That was unexpected… RT @edyong209: Bizarre SNP study on genetics of choral singing. Abstract takes surprising turn in final lines. http://t.co/VkSU4fd0 [Mary]
  • RT @jacksonlab: Facing a rare #genetic disease together, the Wentzell family doesn’t let anything slow them down. #raredisease http://t.co/bscdUXoN [Mary]

Friday SNPpets

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…

  • RT @BGI_Events: Important question, & great primer RT @deannachurch: From @kbradnam:. ‘When is a genome finished?’ http://tinyurl.com/7rypaxe  //nice! [Mary]
  • Because of meeting @papermantis at @scio12 conference, today I am checking out PATRIC (or Pathosystems Resource Integration Center) which describes itself as “providing rich data and analysis tools for all bacterial species in the selected NIAID category A-C priority pathogens list.” So far I am impressed & looking forward to digging into it deeper as I have time. [Jennifer]
  • @OpenHelix: DNA Day essay contest announced! Via @DNAday Also teaching+learning resources from @GeneticsSociety http://t.co/PMEOyQt1 ht @geneticmaize [Mary]
  • Things that make you go hmmmm….. RT @phylogenomics: Am wondering – will GINA cover studies of microbes living in and on people http://t.co/JaWuFTKN #UCDCitSci [Mary]
  • Interesting example of why integration of data across resources is hard. Chemistry issue, but true of all sorts of bio and gene related things. Hat tip Antony Williams on G+. See the post Challenges of data integration. [Mary]
  • FYI, from ExPASy News: “Due to maintenance work, many ExPASy proteomics services will be unavailable from Sunday January 29th to Wednesday February 1st, 2012. These services include PROSITE, ENZYME, Protein Spotlight, World-2DPAGE, Swiss-2DPAGE and proteomics tools such as ProtParam, Compute pI/MW.” [Jennifer]
  • The watermelon map! Woot! @francfue: A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome http://t.co/PkNQIcY0 [Mary]
  • Testify! @KamounLab: “Given proper training and demystification biologists are perfectly capable of working their own #bioinformatics” http://t.co/OJ9IWMgV [Mary]
  • RT @mary_carmichael: Start of the Human Circuit Project? @broadinstitute launches effort to catalog all biochemical wiring in human cells: http://t.co/tm8wnMDa” [Mary (not Carmichael)]
  • More #scio12 goodies: @genome_gov: Check out ‘science online’ genomic medicine session on wiki: http://t.co/sKjbjfml Thanks @MishaAngrist [Mary]
  • RT @yokofakun: [delicious] miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3′UTRs of human genes #t… http://t.co/Ccq1seEL [Mary]

 

I hate to suggest a Nobel Prizewinner is wrong…but…

He is. But it’s not his fault. A lot of people have this wrong.

There’s an article in the Australian press that is getting some buzz. Nobel Laureate Barry Marshall (of ulcer-causing bacteria identification fame) is talking about the personal genomics wave that’s coming our way. It’s been picked up and re-tweeted quite a bit, including by the followers of Kurzweil, who are tech early adopters in a big way.

Sample tweet:

RT @EdwinRankin: Genome power is about to sweep world: Nobel laureate | KurzweilAI http://bit.ly/jM8slS via @kurzweilainews

I have no quibble with the fact that “genome power is about to sweep the world”. But I have issue with a tidbit within the story. Now, it’s not a direct quote so it may be a mis-characterization of what was actually said. But here it is:

What’s right: Australia should legislate against discriminatory practices based on genetics. Everyone should.

What’s wrong: The US did not legislate against discriminatory practices like higher life insurance premiums. Aussies should aim higher than our current legislation.

I have been a giant fan of the GINA legislation since I saw Louise Slaughter introduce it while I was in her district in grad school. OpenHelix actively supported the lobbying for that legislation–despite knowing that it was only a baby-step towards the protections we really need. And we celebrated wildly when it actually passed and was signed into law. It definitely is a major advance in US policy.

But: it does NOT protect you from discrimination for life or long-term care insurance.

The Genetic Fairness coalition assembled a nice guide to GINA.  What does GINA mean? A guide to the Genetic Information Nondiscrimination Act. From this page we find this statement, which couldn’t be clearer:

“The protections of GINA do not include protections from genetic discrimination in life, disability, or long-term-care insurance.”

Now, if you find yourself with some unfortunate Alzheimer alleles, would you be interested in some of that insurance potentially?

Even a lot of American biomedical researchers I know aren’t aware of the limitations of GINA. And people who come from places where there is a public health care system may not grasp the real problem with this situation.

I wish we did have more protection. And I wish we had universal health care rendering this a non-issue. But wishing doesn’t make it true.

I’m delighted that Barry Marshall has the level of financial and medical security to release his full genome data to the world. I wish we all did. He is right that this wave is coming for us all. He is wrong that we in the US are safe from misuse of the data by life insurers. But it’s nice to have powerful allies who understand the importance of not discriminating based on these data.

You can follow Marshall on twitter: @barjammar

Reference:

McGuire, A., & Majumder, M. (2009). Two cheers for GINA? Genome Medicine, 1 (1) DOI: 10.1186/gm6

Personal Genomics, tipping points and a personal perspective

ResearchBlogging.org Please indulge a long post from a personal perspective, what genomics is about to do for _me_. This is information that many, if not all, of our readers already know. I’ve been researching and working in either experimental biology or genomics for over 20 years. Ever since the beginning of the Human Genome Project , which coincidently started the same year I started my Ph.D. program, into my postdoctoral research at EMBL and now my work at OpenHelix, I’ve known that someday personal genomics was going to impact me, and millions of others, in a big way. Yet, it has always felt that it was one of those things that would be a decision I and we as a society didn’t have to make until we turned that corner that seemed always “just ahead.”

But now I think we’ve turned a corner. It feels, to mix metaphors, that we’ve hit a tipping point. The Human genome project, the mapping and sequencing of the/a human genome from 1990 to 2003, cost approximately 2,700,000,000 dollars (that’s 2.7 billion, I wanted to get all the zeros in). Celera did the genome for 300,000,000. The cost of sequencing an entire human genome has been plummeting ever since. In 2007, the cost of sequencing the genome of James Watson (co-discoverer of DNA) was about 2,000,000. The today cost is about 10,000. Complete Genomics and other companies are on the march to quickly reducing the cost of sequencing a genome under 1,000.

Let me graph the last 8 years for you, mind you, this is starting from the 300,000,000 number, not the 2.7billion, because that graph would be a straight line down.

So, within a year, the cost of sequencing your, my, genome will reach 1,000. If not less. We’ve seen this coming for years now, and it’s upon us. But what does it mean?  A lot of data. But data means nothing without context and analysis. Sequencing my genome would be a waste of 1,000 dollars if I gleaned nothing from it.

Yet, even that seems to have turned the corner from a few tidbits of genetic information to a steady steam and the beginning of a flood.

You know you’ve turned a corner when a genomics testing company begins to offer genetic tests to the mass market through Walgreens. There’s enough context in that data to make money from it, or so they hope. You can be sure the corner is safely behind you when the FDA tells Pathway Genomics and Walgreens that they will need to hold off while they make sense of the regulatory implications. Genomic ancestry test are are also gaining is usability… and scrutiny.

It was the recent Lancet paper on the clinical analysis that seemed to be a tipping point, not for me or those in the field. Genomics has been on my radar since 1988, but for society. I blogged about the paper and it’s use of genomics resources such as GVS, dbSNP and others. In the paper, the researchers did a thorough clinical assessment of an individual’s genome. We’ve brought down the cost of sequencing, now we are learning how much it’s going to take to assess that data from a medical point of view, and importantly, what we can learn from it.

What can we learn from it? I read this paper again from a personal perspective now. Could I learn something from sequencing and analyzing my genome, and if so what. My answer came to this: yes, I could learn something and in fact enough that I’m not convinced that as soon as that sequencing gets down to a 1,000 or lower (and is a high quality sequence :), I’m going to do it.

There are three things I see from this paper that one could learn from assessing their genome: prevention, early detection and therapy. I believe the former will be, for most people, something they already know and their genome sequence will tell them nothing new. The other two could be a wealth of information they will want, even need, to know. You’ll notice I left off ‘cure.’ I saw nothing in this paper, and nothing on the near horizon, that suggests to me that our genome sequence data will help with curing anything. Perhaps, just not much. Yet, the possibilities of early detection of disease and personalized drug treatment are tantalizing. Continue reading