Tag Archives: autism

SNPpets_2

Friday SNPpets

This Friday includes a range of topics, as usual. Interesting assessments of the state of autism genomic architecture–and read the piece on the “ghettoization” of genetic disease after that (Laura Hercher’s tweet). Horizontal gene transfer in cheese bacteria. Traits in crops. CRISPR for insects. Deep time in human DNA, and evolutionary history of tumors. There are so many great things around right now…. Off we go!


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…


UCSC Genome Brower on TV

Sometimes I complain about my Tivo.  It thinks I like to cook and that I speak Portuguese.  Neither of these things are correct (not that there’s anything wrong with that).  But it must also know that I like science because it does find some nuggets that are suitable.  And when I got back from a recent road trip of trainings on the UCSC Genome Browser it cracked me up to see the browser on my TV!

The segment is about finding genes related to autism.  As a popular press sort of story it doesn’t quite get all the science right.  There’s some phrasing of the description of autism that I think is incorrect–or misleading as it was described.  But they talk about the importance of collections of DNA from affected families, they interview Mark Daly and Rudy Tanzi, and they show some software that identfies CNVs (copy number variations) and Rudy shows genes on the UCSC Genome Browser.

I like to see working scientists doing this kind of outreach.  I think it is something we need more of.  Click the image to go to the site and watch the piece (about 15 minutes long).

pbs_now_ucsc

Specific episode and segment link:  http://www.pbs.org/wgbh/nova/sciencenow/0402/04.html

Oh, could you take a look at this? Browser sessions.

Have you found yourself wanting your colleagues to look at some region of the genome, the way you have it set up on your browser at that moment? Yes, you changed some colors and customized the display a bit. You picked exactly the stretch you want to show. But thisthey have to see this!

I found myself wanting my colleagues to look at that stretch of genes implicated in that autism research from the other day. So I went to the paper and found figure 1 where they have the list of genes and the region indicated, and went over to the UCSC Genome Browser to look for myself. And I could just tell you to go over to UCSC. Or I could show you my saved session–where I put that region in focus and could have set up the display any way I wanted. Follow me over the flip to learn more, and to view my session. Those duplications at the end are really apparent here–check out the BOLA2 on each end. Same with SULT1A3. And others. Isn’t that curious and intriguing?

As we were doing trainings around the country on the UCSC Genome Browser and explaining to people how great it was to be able to customize their view with filters and track choices, people were asking if they could save all that. And yes–the browser remembers where you were last, so it is still there. But if there was one view you wanted to create regularly and go back to, or you wanted to share that particular view with your colleagues, UCSC created the Sessions mechanism to enable this.

When you start working around in the Genome Viewer, you will find yourself in a genomic region like this one. At the top of the browser page, in the blue navigation line, you can see the option for Session. If you click that you will be able to save your current exact view, and you will have the option of loading that in the browser or generating an email with that link. The sessions are stored and you can go in and use them later, and other people can load them later. This is much easier than dragging your colleague over to your computer at exactly the moment you need them. Especially if your colleague is not in your department, or even your country! It might also be handy for teaching or training like we do–you can set up a specific region that you know everyone is on at the same time. And for those of you who are the local help desk–answering questions from your colleagues about how to look at stuff in the genome browser–voilà. You look great!

It will require a login and password for the UCSC Genome Wiki. But once you have that you are ready to go.

This feature was described in the 2007 news, [edit: and in the paper below] and the details are:

16 February 2007 – New Browser Session-Sharing Function Available

We are pleased to announce the release of a new session management functionality in the Genome Browser, which allows users to save and share browser sessions.

Users are now able to configure their browsers with specific track combinations, including custom tracks, and save the configuraton options. Multiple sessions may be saved for future reference, for comparison of scenarios or for sharing with colleagues. Saved sessions persist for one year after the last access, unless deleted. Custom tracks persist for at least 48 hours after the last time they are viewed.

The new feature may be accessed via the “Sessions” link in the top blue bar in any assembly. To ensure privacy and security, users must login to the genomewiki site and create a username and password. Individual sessions may be designated by the user as either “shared” or “non-shared” to protect the privacy of confidential data.

To avoid having a new shared session from someone else override existing Genome Browser settings, users are encouraged to open a new web-browser instance or to save existing settings in a session before loading a new shared session.

The Sessions feature was written by Angie Hinrichs of the UCSC Genome Bioinformatics Group and released with the assistance of Kayla Smith and Robert Kuhn.

Edited to offer citations for the research components:

1. Autism research paper: Weiss, L.A., Shen, Y., Korn, J.M., Arking, D.E., Miller, D.T., Fossdal, R., Saemundsen, E., Stefansson, H., Ferreira, M.A., Green, T., Platt, O.S., Ruderfer, D.M., Walsh, C.A., Altshuler, D., Chakravarti, A., Tanzi, R.E., Stefansson, K., Santangelo, S.L., Gusella, J.F., Sklar, P., Wu, B., Daly, M.J. (2008). Association between Microdeletion and Microduplication at 16p11.2 and Autism. New England Journal of Medicine DOI: 10.1056/NEJMoa075974 .

2. UCSC Genome Browser paper: Karolchik, D., Kuhn, R.M., Baertsch, R., Barber, G.P., Clawson, H., Diekhans, M., Giardine, B., Harte, R.A., Hinrichs, A.S., Hsu, F., Kober, K.M., Miller, W., Pedersen, J.S., Pohl, A., Raney, B.J., Rhead, B., Rosenbloom, K.R., Smith, K.E., Stanke, M., Thakkapallayil, A., Trumbower, H., Wang, T., Zweig, A.S., Haussler, D., Kent, W.J. (2007). The UCSC Genome Browser Database: 2008 update. Nucleic Acids Research, 36(Database), D773-D779. DOI: 10.1093/nar/gkm966

Autism: regional duplications and deletions?

I was reading my local newspaper just now and spotted this intriguing information:

Boston researchers find genetic trigger for 1 percent of autism

….The discovery, reported on-line in the New England Journal of Medicine this afternoon, stems from the most extensive genome scanning for autism done so far. The scans found that in just over 1 percent of people with autism, a chunk of about 25 genes had been either duplicated or deleted, mainly in spontaneous mutations not carried by their parents….

The team was led by Mark Daly. I saw him recently at MGH giving a talk to students on genome-wide association studies. He is also responsible for developing great software, including HaploView and other tools. We have used HaploView to examine the HapMap data–you can pull data from the HapMap browser and load it right in to HaploView for a more detailed look at it.

I want to check out that paper: Association between Microdeletion and Microduplication at 16p11.2 and Autism

Fascinating information.