It is a very nice post about some exciting prospects for the future.  The idea of planning “explicitly for sustainable exponential growth” is wise.  There will be no abatement of the flow of data at this point–it’s no longer a big bolus of one species data, or one type of project.  The taps are wide open now, and we just keep adding more taps.

I also love the idea of “democratization“.  In part, it includes:

….To enable individual investigators to make effective use of large datasets, we must create an effective infrastructure of data, hardware, and software. NHGRI has extensive experience in big data, and can lead and catalyze across the NIH….

Now, I know this is a snippet of some thoughts–there may be more to it in the actual planning meetings on this.  But it pushed my buttons because it sounds a lot like what we always hear about big data projects: build it and they will come.

It got a little better in another segment:

Spur better software development. Traditional academia and funding mechanisms do not reward the development of robust, well-documented research software; at the same time, the history of commercial software viability in a narrow, rapidly-moving research area like computational genomics is not at all encouraging….

Well-documented research software.  Sigh.  We probably read more documentation than most people. And even the good documentation can be brutal. Dated. And not particularly effective. But still–if nothing else, please reward time spent on documentation….

But what is missing for me from this–and not just this, but most of these big data types of projects–is a real commitment to outreach and support for end users.  Formal, organized, supported, rewarded, outreach.  Sometimes there is a place to write to with questions.  But we probably send in more questions to projects than most people too–and the success rate for answers varies widely.  But even when we get good answers–that’s not enough.

I know funding is hard.  We can’t fund everything.  Databases and software project have to struggle to even persist.  Curation is frequently not valued enough.  And often curators are expected to do outreach as just one of their tasks…which pushes outreach even further down the priority list.  But without dedicated outreach–formal, quality, active outreach–databases and software projects won’t have so many users, and not many effective users.   Which will make funding agencies wonder if they should keep supporting them.  Which…well, you can see where this spiral goes….

What bugs me, I guess, is essentially this: Nobody speaks for the end users. There’s really no one in these types of meeting that really speaks for the consumers of this software and this data.  I mean people who aren’t directly attached to the data production and management.   The project teams think they are thinking about the users.  They really want users.  But ur not doin’ it rite.

I would like to see outreach and end user support valued, required, and really done right.  No matter how  much hardware and documentation you throw at these projects, if people 1) don’t know it exists, and 2) have no idea how to use it, the project will not yield all the results that it could. A marker paper is nice.  But it’s not sufficient, folks. And it’s nice to have the high-end team members talk at conferences. But that reaches only a tiny subset of the users or potential users.  And another thing about that: a lot of times people are hesitant to ask what sound like naive questions to the high-end representatives of these projects.  I’m jes’ sayin.

Yes, this is fairly self-serving for me to say.  But we see the users when we do outreach.  They crave it.  They love it.  We’ve been lucky to be a part of some great projects that do outreach right.  We have seen it work.  It should be Standard Operating Procedure on software and database projects.  Not an afterthought.

So,you ask, what made me think of that long-passed sweet dog that tripped over it’s too-long ears with it’s too-short legs? It turns out that they found out what genetic cause there was for those short legs in Basset Hounds (and Dachshunds and other breeds).

As NHGRI’s press release states:

In a study published in the advance online edition of the journal Science, the researchers led by NHGRI’s Elaine Ostrander, Ph.D., examined DNA samples from 835 dogs, including 95 with short legs. Their survey of more than 40,000 markers of DNA variation uncovered a genetic signature exclusive to short-legged breeds. Through follow-up DNA sequencing and computational analyses, the researchers determined the dogs’ disproportionately short limbs can be traced to one mutational event in the canine genome – a DNA insertion – that occurred early in the evolution of domestic dogs.

The insertion turns out to be a retrogene, which of course I also find interesting in that I studied retrotransposable elements. Reverse transcriptase has this habit of reverse transcribing RNA into DNA which can get reinserted back into the genome (hence processed pseudogenes of course).

The study is interesting for two reasons (other than because I had a Basset Hound and studied the evolution of retroelements , it gives us a further clue into evolutionary events that lead to large changes in morphology and the role of retrotranscription and it gives us a clue into possible human conditions.

For more about dog genome, you can read our several posts about the dog genome, go to NCBI’s dog genome home site (or UCSC or Ensembl and other browsers) and read the paper (needs a subscription of course, it’s in Science). It’s an interesting read so far (I want to find some time to read it more fully, perhaps Useless doesn’t live up to his name.. he didn’t really even then ).

Today’s tip is on a new resource brought to you by the National Human Genome Research Institute, or NHGRI. The resource is PhenX Toolkit version 2.1, which was released on May 22 2009. The PhenX Toolkit provides protocols for taking standardized measurements of research subjects’ physical characteristics and their environmental exposures. You can browse for protocols by domain or measurement type, or search for protocols. If you register, you are also able to collect sets of reports. These can be save for each of your projects, or for later modification. I’ll introduce you (briefly) to all of this and more in this tip.

I learned about this new resource from a GenomeWeb Daily News article in which they published NHGRI’s press release.

NHGRI recently pointed out

And it gives me the opportunity to again point out that we do indeed have seven publicly available tutorials and training materials (slides, exercises, etc) on model organism databases including SGD, RGD, MGI, WormBase, FlyBase and ZFIN… and a seventh on GBrowse, a generic genome browser used by some of these and other genome databases.

Check them out (and fill out the new poll to the left .

You can go here for a page devoted to the festivities: http://genome.gov/27529500

You can launch the video there if it doesn’t work here:

My favorite part of the video is when Leslie Biesecker takes us from Darwin–>software, of course.  Later on he also talks about how important evolutionary concepts are to our interpretation of health and disease.  I mean, I know you guys get this–but I think it is the piece that makes me craziest about the people who want to deny evolution and its relevance today.

Couldn’t they have found at least 1 woman to interview, though?  I saw them in the background….I know they were there…

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.

Dear Colleagues,

The National Human Genome Research Institute has embarked on a long-range planning process focused on the future of human genome research. To kick-start a conversation among our community, we have posted three white papers on our website to start the conversation on the following topics: diagnostics, preventive medicine, and pharmacogenomics; therapeutics; and education and community engagement.

These white papers are available for viewing and comment at http://www.genome.gov/About/Planning. We invite your review and comment in two phases. Phase 1, open now, will collect community thoughts solely on the questions posed in the white papers, aimed at ensuring we are asking the right questions. Phase 1 will continue through January 30, 2009. Once the questions are refined, Phase 2 will commence and collect community input regarding how best to answer the questions, probably starting in mid-February 2009 and continuing through mid-April 2009. Other white papers on other topics may be added as the process continues.

To stimulate discussion, comments received will be anonymously posted for viewing. Comments received through this white-paper process will be used to generate topics for further planning activities and workshops, which will be held in 2009 and 2010.

We encourage you to participate in this important discussion and look forward to your input. Since we would like this to be an inclusive process, please share this announcement with any colleagues who may be interested in participating.

Sincerely,

Alan E. Guttmacher, M.D.

Acting Director

National Human Genome Research Institute, NIH

“As of 11/24/08, this table includes 202 publications and 435 SNPs.” according to the Catalog of Published Genome-Wide Association Studies.

So if you are interested in GWAS data this is a nice collection of that literature. It also comes as an Excel doc you can download.

The traits they cover are quite a range–from freckles to diabetes to bipolar disorder and many more. I think I would like to take some of these data over to the UCSC Genome Brower’s Genome Graphs feature where you can visualize the data on a handy genome graphic. To get this figure, here’s what I did:

1. Took the GWAS excel file.

2. Pulled out the rs IDs for the SNPs. Some cells had to be fixed because the data within it is a series of comma delimited SNPs. Moved each to a single cell.

3. Cleaned up any non rsIDs. I end up with 480 SNPs. I left the duplicates for now.

4. Created a plain text file of these SNPs. I gave each one a value of 1 just for the purposes of the genome graphs software. I just wanted to see all these SNPs on the genome in one graphic. Genome graphs tool tells me:

Loaded 12351941 elements from snp126 table for mapping.
Mapped 479 of 480 (99.8%) of markers
These data are now available in the drop-down menus on the main page for graphing

Off we go…Here are my SNPs on the genome graph–the SNPs are teeny blue dots. Ok, I don’t know what it means either. I just wanted a sense of what was coming out of all the GWAS studies and where they actually were on the genome. I would like to take another look at the data, this was just a quick pass–I’m intrigued by the SNPs that come up in multiple studies and I’m curious about what those genes do. Hmmm…..

It was posted on the webinar I attended yesterday on GWAS studies so I took a screen shot of it.

If this is a topic that interests you, watch the webinar website. You do need to register ahead of time for these, and an email comes with login information specific for you.

I’ll have more thoughts on the GWAS one later, but I wanted you to be able to put this on your calendar and save the date if it something you might want to see.

I just got an email announcement that they have scheduled that GWAS one for Nov. 20, 2pm ET, and the email has a bit more content description:

The upcoming webinar is entitled, “Genome-Wide Association Studies: The Basics of the science and related policies”. Laura Rodriguez, Acting Director of the Office of Policy, Communications, and Education at NHGRI, will host the webinar and also speak about data sharing policies related to GWAS studies. Teri Manolio, Director of the Office of Population Genomics will report the latest on GWAS results, and what they can tell us about genomics and health. We will then take questions from participants.

I’m curious about the recent removal of GWAS data from the public sphere, and to see what they expect will happen afterwards.

They’ll have sign up information posted soon, they say. Keep an eye out if you are interested because you do have to shoot them an email to get registered.