SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
Ion Torrent $1000 Genome!? Benchtop Ion Proton Sequencer aeonsim Ion Torrent 88 10-28-2012 04:50 AM
ion torrent herrroaa Introductions 5 07-25-2011 05:36 AM
interpretation insertion/deletion file SAMTOOL labmtl Bioinformatics 0 03-28-2011 07:39 AM
How do you find the insertion, deletion and translocation? Chien-Yuan Chen Bioinformatics 2 06-02-2009 10:43 AM

Reply
 
Thread Tools
Old 09-22-2011, 03:34 PM   #1
arrayprofile
Junior Member
 
Location: california

Join Date: Jan 2011
Posts: 2
Default Ion torrent for insertion/deletion

Hi, I have a question: because Ion torrent doesn't do paired end sequencing, does this mean the technology cannot be used for insertion/deletion detection?

Thanks

John
arrayprofile is offline   Reply With Quote
Old 09-22-2011, 07:24 PM   #2
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

What size insertions & deletions are you looking for?

For 1-2nt indels, IT is very difficult due to the homopolymer counting issue

For longer small indels, IT can work -- except there will be noise from the homopolymer counting issue. In some recent data, we definitely spotted a known 5nt deletion -- except in some reads it is called as a 4nt deletion due to the counting issue.

Paired ends are not magical indel detectors, but do enhance your sensitivity for indels of certain sizes. Reads from any platform can detect an indel by crossing the indel boundary; paired ends (and mate pairs or strobes) simply enhance sensitivity by scanning a larger region.

It is surprising that ABI hasn't retrofitted all of their SOLiD mate pair protocols to the Ion. Perhaps they need longer reads to make it work.
krobison is offline   Reply With Quote
Old 09-22-2011, 10:46 PM   #3
arrayprofile
Junior Member
 
Location: california

Join Date: Jan 2011
Posts: 2
Default

Thank you K! If I understand correctly, you don't really need paired end to detect indels if there is no homopolymer issue. But IT had serious issue with small indels because of homopolymer.

For Illumina platform, am I correct that paired end reads only help indel detection for large indels because the fragment size is only approximate (~300 bp), a few nt indel won't be identified by checking the size between the 2 paired reads?

Thanks
arrayprofile is offline   Reply With Quote
Old 09-23-2011, 06:34 AM   #4
epistatic
Senior Member
 
Location: Dronning Maud Land

Join Date: Mar 2009
Posts: 129
Default

Mate-pair libraries are a bit painful and expensive to produce. With the template on the bead, Ion would need to have a way to melt off the strand and reprime, or do a mate-pair bidirectional read. I'm sure this is an application being developed, the Paired-End ability of the MiSeq is seen to be a benefit over the PGM.
epistatic is offline   Reply With Quote
Old 09-28-2011, 03:11 AM   #5
nickloman
Senior Member
 
Location: Birmingham, UK

Join Date: Jul 2009
Posts: 356
Default

As other commenters have stated, looking for 1/2 base indels is not the easiest task on Ion Torrent because of homopolymer counting issues which will produce false positives. If you restrict your hunt to regions away from homopolymers you may find the false positive rate goes down.
nickloman 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 10:40 AM.


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