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Old 07-18-2012, 04:14 AM   #7
Location: Guilford, CT and S.F., CA

Join Date: Jan 2010
Posts: 64

Hi slm1816,

Thanks for reporting the issue with the KRAS G12D exon number in Ion Reporterô Software. We confirmed this error recently and have identified a solution. You can expect an update early next week that will resolve this issue; we'll send out an announcement to users when the update is complete. Please let us know if we can help further.

Also worth pointing out is that if you ever have an urgent question or suspect an issue I'd recommend the following paths: 1) as a US customer, for fastest response call 1-87-SEQUENCE to reach one of our Technical Applications Scientists [other regions have their own customer support phone numbers], or 2) contact your local Field Applications Scientist (who I understand is already working with you on the initialization issues you reported here and in another thread). For less urgent matters, or general inquiries, consider the Ion Community.

Originally Posted by slm1816 View Post

I have run the Ion Torrent AmpliSeq Panel and the Illumina TruSeq Panel.

Starting with the Illumina TruSeq Panel:
-Much easier setup. The machine might run longer but the ease of setup and the "walk away" time is much more. It allows you to walk away and complete other experiements you are working on.

I have run 3 samples with barcoding so far. I have plans to do a much larger batch soon. I got satisfactory results.

-After the run is complete, the MiSeq reporter does all the demultiplexing, aligment, etc which is wonderful! You can view results in MiSeq Reporter and Amplicon Viewer. There are great tools from Illumina, however, they are not useful in catching indels. They are great for point mutations. I am still trying to find a good third party software that will catch indels. Any suggestions?

-coverage is much better with the Illumina Platform.
-Working on adjusting the input for better cluster densities.
-Having issues with the company is getting answers to some of my questions and some of the excel sheets they have given me, such as the list of genes and the exons covered have been wrong. Just have to scrutinize everything

Ion Torrent Ampliseq:

-Lots of hands on time.
-have had major problems with initializing the machine
-Only run one sample at a time on a 316 chip.
-Ion Reporter is similar to the MiSeq reporter but some of the columns of data output are wrong. For instance, a G12D mutation of the KRAS gene is not on exon 3. That's what the reporter is telling us. So it looks like you have to scrutinize all of that as well.

That's all I can think of off the top of my head right now.

This is all such a major experiement. I learn something new everyday and sometimes it gets very frustrating!
I would appreciate it if we can all help each other out!
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