Tag Archives: genetics

Tip of the Week: Creating an Electronic Informed Consent


Informed consent has been a foundation of research, and especially genetics research, in that last few decades though it’s taken quite some time to right past wrongs. And with genomics research and personal genomics generating huge amounts of data, informed consent becomes both more important and more complex. The National Human Genome Research Institute has a pretty good selection of information and regulations surrounding informed consent including the regulations, guidelines, specific NHGRI guidelines and applicable federal legislation. If you are doing human genetics and genomics research it would behoove you to make sure you understand the guidelines and issues. A good paper to read to understand would be the article, “Tailoring the process of informed consent in genetic and genomic research” in Genome Medicine cited below.

Depending on your institution and support, you might not have to ever write up or administer informed consent documentation, but often smaller institutions or projects must. So, let’s get to the nitty gritty logistics of actually creating an informed consent survey and document.

Today’s Tip of the Week is the 4 minute first part of a five part series from iDASH at UCSD on creating an electronic informed consent using LimeSurvey and then using iCONS, iDASH’s Informed Consent Management Tool. iDASH:

“is one of the National Centers for Biomedical Computing (NCBC) under the NIH Roadmap for Bioinformatics and Computational Biology. Founded in 2010, the iDASH center is hosted on the campus of the University of California, San Diego and addresses fundamental challenges to research progress and enables global collaborations anywhere and anytime. Driving biological projects motivate, inform, and support tool development in iDASH. iDASH collaborates with other NCBCs and disseminates tools via annual workshops, presentations at major conferences, and scientific publications.”

There are many ways to create an electronic survey, but this set of tutorials makes it straight forward using LimeSurvey and iCONS. The other short sections are here: Part two, three, four and five.

… and while I have you at iDASH, I suggest you watch this hour talk by Philip Bourne (at UCSD) titled “In the future, will a biological database really be different than a biological journal.” The talk was given just over a month ago and an update to something Dr. Bourne said in 2005. It’s a good corollary to Mary’s (apt and true) oft-repeated mantra: “The data is not in the papers any more.”

(we’ve mentioned iDASH before and a lecture about the cost curation that was interesting)

Quick links:

iDASH: http://idash.ucsd.edu
iCONS: http://idash.ucsd.edu/electronic-informed-consent
iDASH Tutorials: http://www.scivee.tv/user/17631

Reference:

Charles N Rotimi and Patricia A Marshall (2010). Tailoring the process of informed consent in genetic and genomic research Genome Medicine, 2 (3) : doi:10.1186/gm141

Virus-resistant cassava (and some software used to get there)

I’ve been very interested in plant genomics projects and it’s been great to see them yield so many interesting papers lately–most recently on the tomato genome and even more on corn analysis. As much as it’s fun to navel-gaze about the human genome for personal genomics, and it is important to get to medical treatments on human diseases–plant genomics projects can help huge numbers of people with basic nutrition. And these are not just the well-insured Westerners. I wish plant genomics was better funded and not under threat…alas.

So it’s nice to see some outreach on projects of this sort. My CLCBio newsletter linked to a nice story and video of the virus-resistant cassava project (VIRCA). Teams from the US and Africa are working on a plant that’s under major threat right now–but is a major source of food for smallholder farmers. This article at the NYT from a couple of years ago provides some background on that issue, and shows photos of the terrible result of a virus infection: Virus Ravages Cassava Plants in Africa. In the video you’ll note that they stress that this is not a project of corporate agriculture–it’s going to be freely available for farmers.

And they mention that they use the CLCBio software to help with that–rarely does anyone highlight the software in these projects, and that made me smile!

Watch the video for some nice views of what plant genomics projects look like, but be sure to check out the additional project details over at the CLCBio page. And if this doesn’t format right, you can watch the video over there too.

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]

Mining the World News: Michael Pollan has alien genes?

As Mary pointed out last week, we had an alien DNA upgrade about 1,000 years which lead to the blast furnace, among other necessary modern accoutrements, according to recent research reported in the Weekly World News (still no original paper found in PubMed).

Well, apparently current genomics research has shown  that those meddlesome  aliens are still tinkering. In our deep digging into that bastion of truth and scientific fact, the World Weekly News we found 1 in four Americans have alien genes, a set of genes that started showing up in 1978 it seems.

One of the symptoms is the overwhelming love and cravings for green vegetables, so I suspect Michael Pollan might be one of those 25% of Americans with the new version 2.1 genes from Molganis. Though I couldn’t be sure, other symptoms include an impatience with crying people and using too much dish soap, so perhaps he doesn’t have those?

I haven’t been able to track down “Dr.”  Kornblum to clarify. I’d love to talk to him about setting up an annotation track in the UCSC Genome Browser so we can all determine whose genome carries these recently introduced genes, we can call it MorganiGene (2.1).

The Weekly World News is a wealth of genomics information!  The article:

New Feature: Mining the World News

Well, I’ve been behind on some of my reading.  That arsenic DNA stuff from NASA really got me thinking that my astrobiology was not up to snuff. So I decided to put some deliberate effort into catching up on that.

Good thing. I found a report that I had totally missed before. I’m not sure how I could have missed it, but it was around the time we were starting OpenHelix and I must have just been busy.  Anyway, here’s the publication:

Aliens Altered our Genes 1000 Years Ago, by Vincenzo Sardi.

You can access this masterpiece from Google books here.

Reportedly a team from France had discovered that during the Middle Ages there was a major alteration of human DNA. They found a segment of DNA that did not conform to the known “language” of DNA….sound familiar??? They claim it has all the earmarks of a splicing event.

Dr. Sedeaux, the lead researcher, suggests that this is the basis for all the advances humans made after the Dark Ages.  There’s a very helpful inset that lists human inventions since this upgrade was performed. It’s certainly impressive.  Check out the larger view of the story image, or go to Google books for the original.

The researchers are now using this sequence to see if they can markedly increase the intelligence of monkeys. I’ll have to see if the follow-up work has been published on this.

I’m unable to locate the original paper in PubMed, I can’t imagine why. So I can’t get a DOI and do a ResearchBlogging post on this. If anyone has the original work, or contacts at the Foundation–send them to me. And NASA.

The OpenHelix team will be offering a new feature–Mining the World News, with periodic offerings that we unearth from that paragon of sciency-ness, The Weekly World News. It’s how the cranks spread pseudo-science and anti-science before the intertubz….

“Why genes are leftwing,” or not

Why genes are leftwing , by Oliver James is wrong. He posits that because we have found that much of our behavior hasn’t shown a genetic basis, it supports the general ‘left’ view that society and environment are the culprits for much of our individual and societal disfunction. It thus contradicts the ‘right’ view that it’s human nature and no amount of government action will change things, or as he  puts it:

The political right believes that genes largely explain why the poor are poor, as well as twice as likely as the rich to be mentally ill. To them, the poor are genetic mud, sinking to the bottom of the genetic pool.

As someone left-of-center (most of the time), you’d think I’d like to agree with this. I don’t. Never mind that this is a simplified caricature of the more complex reality of political ideologies, it’s wrong on the science. In fact, it reads much like the satire science article in the same paper (I think that satirical article should be required reading of all journalists writing about science, especially those in the Guardian). The only thing it’s missing is a random graphic.

What is wrong with this piece?

This is another round in the tired ‘nature vs. nurture’ debate. Genes and environment interplay in such a complex manner that teasing them apart is a sisypean task at best. What is true for one individual, isn’t true of another genetically. One individual’s genetic makeup might give them more or less plasticity in behavioral responses to environment, than another. Environmental influences can cause behaviors with little plasticity or none later in life. Genetics affect our response to environment, environmental influences can have profound affects on some genetic backgrounds and little on others. Just because something is ‘genetic’ doesn’t make it ‘rigid’ and just because something is environmental doesn’t make it ‘plastic.’ Nature vs. Nurture is a false dichotomy.

The science quoted is misread and misreported. To quote:

That was illustrated recently in a heavily publicised study by Anita Thapar, of Cardiff University. Although she claimed to have proved that ADHD is a “genetic disease”, if anything, she proved the opposite. Only 16% of the children with ADHD in her study had the pattern of genes that she claimed causes the illness. Taken at face value, her study proved that non-genetic factors cause it in 8 out of 10 children.

This is indeed wrong. What this is saying is that 16% of the children had the genetic cause to ADHD she had uncovered. What did not say was that the other 84% of children had non-genetic factors that caused their ADHD. In fact, if one would read the article he linked to above (not to mention, the actual research report), they’d find this quote:

Although this finding was limited to 16% of all the children with ADHD, they say it is highly likely the rest have other genetic variants that have not yet been identified.

The reality is that much ADHD has a genetic basis, much of it doesn’t and much of it is affected strongly by both. But that doesn’t fit the thesis of the article, so that nuance is thrown out. (Pharyngula has a few good words to say about that ADHD paper btw and the article about it)

Again, he misunderstands the science and the scientists he quotes:

This result had been predicted by Craig Venter, one of the key researchers on the project. When the map was published, he said that because we only have about 25,000 genes psychological differences could not be much determined by them. “Our environments are critical,”he concluded.

Yes, environments are critical. So are genes. Both are necessary to explain our behaviors, neither sufficient alone.

He builds a straw man soon after this quote. What we are learning, which the author has glossed over, is that so is the regulatory environment of these genes, and epigenomics, and splice variants, and structural variations  can create a very complex space of genetic foundations with ‘only’ 25,000 genes.  There were very few scientists who believed that ‘one gene’ was ever the cause for more than a minute handful of behavior and mental conditions. I knew none in the early 90′s. And yet he vaguely mentions, unreferenced,

…, after only a few years of extensive genome searching, even the most convinced geneticists began to publicly admit that there are no individual genes for the vast majority of mental health problems.

I think most geneticists were admitting this decades ago, but he makes it sound as if this is a new revelation.

Sexuality, one example of many, gives a counter-example to the nature vs. nurture/right vs. left dichotomy he posits. Many conservatives (to generalize) would dismiss the scientific evidence that sexuality is genetically hard-wired, while many on the left (definitely not all) would side with the nature argument. Even there, the picture is more complex. Sexuality has a strong genetic component and in some individuals (most men?) it is quite rigid and in some individuals (some women?) it’s quite plastic.

The author falls into the age-old trap of using science to back up a political ideology. A dangerous proposition at best. Indeed, knowing the science and facts behind issues can help inform the best courses of action to take to alleviate problems, but they don’t necessarily support or refute a political ideology.

Let’s take climate science. If we accept that the science is valid that the earth is warming and much of that warming is caused by human activity (which is quite scientifically a solid fact at this point), this does not mean one would necessarily have to accept either a left or right solution. One could argue that market forces would be the best solution, or that coordinated regulation of carbon markets, or doing nothing would be better than something. The science doesn’t necessarily inform on solution over the other, one ideology over the other.

The same is true for genetics. Let’s assume that much of the population differences in IQ are mainly (but not solely) due to nutrition or disease in early developmental years (as the research seems to be pointing) and not genetics, do we allow market forces to help level those differences, or social programs? Or we find that, all environmental things being equal, individual differences in IQ are largely genetic. What does that tell us about the ‘correct’ ideology? If our sexuality differences are rigid and unchangeable, do we allow for the free expression and social acceptance of those differences, do we regulate and suppress them? Or, as several have suggested, are there conservative responses to this that don’t suppress those differences? Or returning to ADHD, let’s assume we find that ADHD has a large genetic component. Does this invariably mean that environmental changes can’t affect the expression of that genetic foundation? No, to answer my rhetorical question. In fact, I would assume ADHD has both major genetic and environmental influences and the ‘solution’ to this is probably found to be everything from parenting, therapy, societal change, to drugs.

The article is yet another in a long line of poor science reporting. Sad, because there is so much that is fascinating in modern science that doesn’t need political embellishment.

Here is a growing roundup of responses to Oliver James’ poor piece:

Genes are Political Agnostics

Friday SNPpets

Welcome to our Friday feature link dump: 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…

  • A bit of a dust-up at ScienceBlogs as they added a corporate blog (Pepsi writing about nutrition science) and several of the bloggers left or threatened to leave. The Pepsi blog is no more. I hope that’s resolved, ScienceBlogs is an excellent collection of science writing. [Trey]
  • Pathway Tools Workshop 2010 held by the folks from BioCyc announced for October 21-25: http://bioinformatics.ai.sri.com/ptools10/ [Mary]
  • Animal portraiture against a white background. It’s been done before, this time with birds. It always reminds me how amazingly beautiful life can be. [Trey]
  • VectorBase announces that they have moved to the new style Ensembl browser with their current release–Yeah!  If you are interested in “Invertebrate Vectors of Human Pathogens”, this database may have species you want to know about. [Mary]
  • A good discussion about the recent ‘longevity gene’ study and it’s possible flaws by Razib Khan of Gene Expression [Trey]
  • Bandwidth-heavy, but really neat movies of tumor angiogenesis. You can open the Navigator menu to see the various movies listed, or you can migrate around the tumor yourself.  Hat tip to Jill!  [Mary]
  • On the GBrowse mailing list people were looking for examples of GBrowse 2.0 in action. WormBase indicated they are up to that version, and there was another research group with a species I never heard of before that also has it running: Gardnerella vaginalis.  They have compared 2 strains: one from a healthy woman, one suffering from infection. They show divergence, interestingly.  You can check out their recent publication on it from their publication tab.  A nice demonstration of how to use GBrowse for your species of interest. [Mary]

Updated Online Tutorial for GeneTests

Comprehensive tutorial on the publicly available GeneTests resource enable researchers to quickly and effectively use this invaluable resource.

Seattle, WA (PRWEB) May 25, 2010 – OpenHelix today announced the availability of an updated tutorial suite on GeneTests.

GeneTests is an integrated resource designed to provide access to current genetic testing and other clinical genetics information. The GeneTests resource includes the Laboratory Directory database, an international directory that identifies the location of clinical laboratories offering genetic testing; and GeneReviews, a collection of up-to-date, comprehensive disease-specific overviews which include clinical descriptions, diagnosis, management, molecular genetics, current genetic testing, and genetic counseling. This tutorials, in conjunction with OpenHelix tutorials on OMIM, dbSNP, GVS, HapMap and many others will give the medical researcher or clinician a set of training resources to help be efficient and effective at accessing and analyzing genomic variation and biomedical data.

The tutorial suites, available through an annual OpenHelix subscription, contain an online, narrated, multimedia tutorial, which runs in just about any browser connected to the web, along with slides with full script, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. The scripts, handouts and other materials can also be used as a reference or for training others.

This tutorials will teach users:
*to perform disease-specific searches and navigate the GeneTests site
*to understand the GeneReviews and Laboratory Directory Displays
*to access additional searches to query the GeneReviews and Laboratory Directory databases by disease feature, gene and protein specific searches, and more
*to identify U.S. and international laboratories offering molecular genetic testing for specific disorders, use the Clinical Directory to locate genetics professionals and services, and investigate additional educational and other resources

To find out more about these and over 90 other tutorial suites visit the OpenHelix Catalog and OpenHelix. Or visit the OpenHelix Blog for up-to-date information on genomics and genomics resources.

About OpenHelix
OpenHelix, LLC, (www.openhelix.com) provides a bioinformatics and genomics search and training portal, giving researchers one place to find and learn how to use resources and databases on the web. The OpenHelix Search portal searches hundreds of resources, tutorial suites and other material to direct researchers to the most relevant resources and OpenHelix training materials for their needs. Researchers and institutions can save time, budget and staff resources by leveraging a subscription to nearly 100 online tutorial suites available through the portal. More efficient use of the most relevant resources means quicker and more effective research.

Learn.Genetics (TM)

There are some great sites out there to learn the basics. Most of our readers might not need to learn those themselves, but they might need to teach them or at least give out resources to people who need (or should learn) them. The University of Utah has a great site: Learn.Genetics (TM).

And the “Cell Cize and Scale” interactive flash is cool.

And while I’m at it there is a good intro to Essentials of Genetics at Scitable (and we’ve had a tip of the week on Scitable Classrooms before you might to check out so you can create a class on Genetics if you so desire).

Stuff read over the weekend…

Just a few links for your reading pleasure from the last week.

While the mainstream news is reporting on the demise (redefinition) of the ‘gene‘, some high schools kids are doing amazing things with ‘genes.’

Oh, and if, like us, you can’t wait till the annual NAR database is published officially, you can always check out the advanced online publication of the articles to find new and updated databases (like the SpBase, sea urchin, database that went public earlier this year and SuperToxic, a database of over 60,000 toxic compounds) and genome resources! :D