SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Exome sequencing: a transformative technology. Newsbot! Literature Watch 0 09-24-2011 05:21 AM
Confirmation sequencing technology gendxdoc General 7 08-05-2011 05:18 AM
Tech Summary: Animated video explaining Helicos tSMS Next-gen Technology apfejes Helicos / Direct Genomics 8 06-17-2011 10:10 AM
Question and Answer Format: http://I.SEQanswers.com ECO Site Announcements 33 10-05-2010 06:07 AM
Amplicon sequencing using Titanium technology sacha 454 Pyrosequencing 2 04-23-2009 05:08 AM

Reply
 
Thread Tools
Old 05-07-2008, 12:22 PM   #1
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default If you could use next-gen sequencing technology to answer any question....

...what small study would you do?

This is intended as a bit of fantasy, but a serious question, as I've often considered this question:

If you could do one small set of focused samples what would they be and what platform would you use to answer the question?

Cost/labor/your ability to analyze the data is not to be considered...we're talking pure scientific curiousity. Let's limit it to say one run on a GA/SOLiD, or 2-3 runs on 454, or a combination of short/long reads. But no more than 8-16 samples.

Moon rocks? Environmental mining? The fauna scraped off your windshield after a cross country drive? Swabs from a subway seat?
ECO is offline   Reply With Quote
Old 05-07-2008, 03:51 PM   #2
cariaso
Member
 
Location: Wageningen, the Netherlands

Join Date: Jan 2008
Posts: 31
Default

N timepoints for 3 patients from birth to death. Patients are triplets (twins+1) . The first two would be raised in the same environment, the third would be separated at birth. Sequence the epigenome. No clear platform preference.

No triplets were harmed in the making of this fantasy.

Last edited by cariaso; 05-07-2008 at 04:01 PM.
cariaso is offline   Reply With Quote
Old 06-18-2008, 10:21 PM   #3
apfejes
Senior Member
 
Location: Oakland, California

Join Date: Feb 2008
Posts: 236
Default

I like cariaso's study, though I'd also do gene expression studies:

I'd take N drug therapies, and test the whole transcriptome shotgun expression on each of M cell types, on X people, where N, N and X are impossibly large numbers. And, of course, each of the X people would also have a complete genome reference assembled.

You'd be able to figure out what parts of the genome cause drug interactions (successful, no effect or adverse side effect) if M,N and X were large enough.

For people who develop resistance, ie. cancer drugs no longer work, I'd also WTSS those tissues before and after resistance occurs to identify mechanisms.

What fun!
__________________
The more you know, the more you know you don't know. —Aristotle
apfejes is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:55 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO