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Old 05-20-2015, 10:11 PM   #1
rjones89
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Default Compare samples sequenced on Ion Proton and Illumina platform

Is it possible to compare exome data generated on an Ion Proton with exome data generated on an Illumina platform? I have sequenced germline samples on the proton and have sequenced tumour samples using Illumina and I am wondering if it will be at all possible to compare?
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Old 05-20-2015, 10:41 PM   #2
Brian Bushnell
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It's certainly possible to generate useful data in this case, but there will be a lot more noise than if everything was the same platform. The biggest issue will probably be not the difference in platforms, but the difference in baits/kits; if the tumor sample has 0 coverage for some gene that has 50x coverage in the control, you won't really know if that's because the gene got deleted, or because the capture was ineffective in that area.

I suggest you calculate the cost of person-hours spent analyzing this data versus the cost of rerunning on or the other so that all data is from the same platform. It does not make sense to spend $50k chasing down and validating spurious differences that could be wiped out en masse with $1k of sequencing. The alternate platform's data is not wasted in this case, either, as it can increase confidence in variations found (or not found) in the other platform.
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Old 05-20-2015, 10:42 PM   #3
rjones89
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Yes, that is what I am wondering - would it be much better to sequence both on the same platform?
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Old 05-20-2015, 11:18 PM   #4
kushald
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Hi rjones89. You could compare the data from 2 platforms, but for the INDELS. The SNP variants called could be compared. Let me know if you need help with this, if you are interested in analysis of only the SNP variants.

We (Genotypic Technology - www.genotypic.co.in) are a Genomics services provider based in India. Write to me at kushal.dinodia@genotypic.co.in with your query and we can discuss more on this. I will work out the best possible price for analysis work.

Thanks.
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Old 05-21-2015, 08:29 AM   #5
NextGenSeq
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Ion Torrent just released the HiQ chemistry for the Ion Torrent. They claim that the indel problem has been resolved.
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Old 05-21-2015, 09:15 AM   #6
Brian Bushnell
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Quote:
Originally Posted by rjones89 View Post
Yes, that is what I am wondering - would it be much better to sequence both on the same platform?
Yes, it would.
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Old 05-22-2015, 05:54 PM   #7
ECO
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Hey there...we keep commercial activities in the Vendor Forum and discourage overt commercial posting...please contact me if you want permission to post in the Vendor Forum. Thanks.

Quote:
Originally Posted by kushald View Post
Hi rjones89. You could compare the data from 2 platforms, but for the INDELS. The SNP variants called could be compared. Let me know if you need help with this, if you are interested in analysis of only the SNP variants.

We (Genotypic Technology - www.genotypic.co.in) are a Genomics services provider based in India. Write to me at kushal.dinodia@genotypic.co.in with your query and we can discuss more on this. I will work out the best possible price for analysis work.

Thanks.
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