cancer panel on miseq

bartekd · 11-18-2012, 03:18 AM

hi there
I am clnical oncologist looking for a way to improve diagnostics department in my cancer center and I was wondering
what is more cost effective for doing cancer research only ? miseq or hiseq?
is illumina providing end to end expierence or is there any additional software needed ?
last but not least ? what kind of personel would be inexpensable to run hiseq/miseq platform ?

thanks in advance

Bukowski · 11-19-2012, 01:38 AM

I'm not sure that there is an end to end solution for the HiSeq. The TruSeq Amplicon Cancer Panel seems to be designed to run on the MiSeq, with some on machine data analysis.

As someone who analyses cancer panel data from HiSeq and MiSeq (we have designed our own panels for running) the MiSeq per-base costs are higher, but to make the HiSeq cost effective you have to make sure it is running at capacity (or that you are sharing a machine that is operating close to capacity).

Additional software could be anything from aligners, to variant callers to automated annotation. Clinical interpretation of the results are something else entirely.

I work for a company that would allow you to outsource such a service, obviously this means you don't then have the equipment/setup/staff costs associated with the service. We have HiSeq/MiSeq and experience in cancer profiling on a number of capture technologies. Message me if you're interested in knowing more.

kwaraska · 11-19-2012, 12:49 PM

Qiagen just released a product that is 124 genes with subsets available-specifically cancer panels-that generate PCR products that can then be made into libraries for MiSeq or HiSeq.

I have not used it myself as it just released last week.

You would need someone and/or robot to construct libraries.
Then a Technician to run the MiSeq or HiSeq. The MiSeq is very user friendly while the HiSeq takes some cajoling to work right. Also, you need 7 (or 8 if you don't run a control lane) samples to run a HiSeq flow cell. Probably your best bet would be a HiSeq 2500 which runs a "single" lane flow cell. It is actually 2 lanes but there are ways around that. They run with the speed of a MiSeq but the density of a HiSeq lane.
Then you would need an informatics person to determine what all the data means.

bartekd · 01-29-2013, 01:56 PM

hey bukowski if you're still interested in helping me please enable msg link so i can email you or msg me yourself

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11-18-2012, 03:18 AM	#1
bartekd Junior Member Location: poland Join Date: Nov 2012 Posts: 4	cancer panel on miseq hi there I am clnical oncologist looking for a way to improve diagnostics department in my cancer center and I was wondering what is more cost effective for doing cancer research only ? miseq or hiseq? is illumina providing end to end expierence or is there any additional software needed ? last but not least ? what kind of personel would be inexpensable to run hiseq/miseq platform ? thanks in advance

11-19-2012, 12:49 PM	#3
kwaraska Senior Member Location: Boston,MA Join Date: Nov 2008 Posts: 122	Qiagen new product Qiagen just released a product that is 124 genes with subsets available-specifically cancer panels-that generate PCR products that can then be made into libraries for MiSeq or HiSeq. I have not used it myself as it just released last week. You would need someone and/or robot to construct libraries. Then a Technician to run the MiSeq or HiSeq. The MiSeq is very user friendly while the HiSeq takes some cajoling to work right. Also, you need 7 (or 8 if you don't run a control lane) samples to run a HiSeq flow cell. Probably your best bet would be a HiSeq 2500 which runs a "single" lane flow cell. It is actually 2 lanes but there are ways around that. They run with the speed of a MiSeq but the density of a HiSeq lane. Then you would need an informatics person to determine what all the data means.

11-19-2012, 01:38 AM	#2
Bukowski Senior Member Location: UK Join Date: Jan 2010 Posts: 390	I'm not sure that there is an end to end solution for the HiSeq. The TruSeq Amplicon Cancer Panel seems to be designed to run on the MiSeq, with some on machine data analysis. As someone who analyses cancer panel data from HiSeq and MiSeq (we have designed our own panels for running) the MiSeq per-base costs are higher, but to make the HiSeq cost effective you have to make sure it is running at capacity (or that you are sharing a machine that is operating close to capacity). Additional software could be anything from aligners, to variant callers to automated annotation. Clinical interpretation of the results are something else entirely. I work for a company that would allow you to outsource such a service, obviously this means you don't then have the equipment/setup/staff costs associated with the service. We have HiSeq/MiSeq and experience in cancer profiling on a number of capture technologies. Message me if you're interested in knowing more.

01-29-2013, 01:56 PM	#4
bartekd Junior Member Location: poland Join Date: Nov 2012 Posts: 4	hey bukowski if you're still interested in helping me please enable msg link so i can email you or msg me yourself