Tag Archives: GINA


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…



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…



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…



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


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

What would you do with your genome?

So last week I treated myself to my first vacation in a long time.  It was my birthday, and I wanted to disconnect a bit and recharge.  Mostly it worked, although the hundreds of emails I’m facing this morning are a bit daunting.  But just before I left I got an email from a colleague who asked me a really great question:

….I would love to know where you would start when you get back a personal genome sequence….

And I couldn’t shake this out of my head.  I was sitting on a bridge outside Windsor Castle thinking about it as the sun set on my first day.  (On subsequent days I found that the far superior ciders in the UK were able to push this question out of my head for some periods of time. And also pie.)

I’ve spent some significant time thinking about the onslaught of personal genomics, of course.  It’s all been very theoretical, because I would have refused to even begin the process of obtaining my personal genome sequence until the GINA legislation fully kicked in.  But now that barrier is down.  I’m still not ready to get mine done for a variety of reasons (cost, quality, informative value).  But it’s still worth thinking about what I would do with it if it was handed to me–in specific terms, with concrete actions.  So here’s what I decided I would do.  Your mileage may vary.  And I’d love to hear what others might do with theirs.  Follow the link for the specific actions I’d take.

Continue reading

"Genetic Town Halls" report is available

I’m very interested in public policy and genetics. There are a number of threads that I was following along those lines. On the actual legislation I was watching the GINA efforts, and participating where I could. I was reading an article on the downstream effects of that today (Two Cheers for GINA, by McGuire and Majumder, Genome Med 2009, 1:6 doi:10.1186/gm6).  One sentence sums up my feeling on GINA–we absolutely needed some protection, but other problems in our health care and insurance systems will persist…

If significant sections of the public focus on these gaps in US policy, reluctant to enter the genomic era without a blanket guarantee against harm, GINA may fail to live up to the hopes of its supporters.

There was also a series of public meetings about biobanking and genetics research that I was following (Town hall meetings on genes + environment studies).  I wish I could have participated in these town halls to get a sense of the room full of people interested in this topic–but none of them were near me.  However, the report on these was just released and you can get the summary of the outcomes from the sessions:

Center releases report on genetic town hall series

….Most participants felt that the biobank should go forward, and more than half indicated they were likely to participate in it if asked. Among the issues participants weighed in on were privacy protections for participants and concerns about possible misuse of information collected, the nature of the proposed study’s consent agreement, and the ability to get individual research results back from the study….

If you go to the DNApolicy.org site you can download the report in PDF form.  It is clear that the participants were concerned about discrimination based on the information–especially by insurers, but also law enforcement.  And this is despite the passage of GINA during this timeframe.  There are privacy concerns in general, too.  And the potential for misuse for “nefarious” purposes.  They also saw the benefits–research and new knowledge, new medications, increased precision for treatments.

Thanks to the Genetics & Public Policy Center folks for the report.  Thanks to the Genetic Alliance Policy Bulletin mailing list for the heads-up.