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Old 07-20-2010, 05:45 PM   #1
HICORE
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Default Illumina IIe sample processing cost

I am hoping someone can help me out.

My facility is getting an Illumina IIe sequencer. I am new to this technology. Currently I have only had sequencing experience with the ABI 3730 and 3130xl.

How do other labs charge their customers for processing samples? Do you base prices from total GB, number of samples, number of cycles, etc?

Any input would be greatly appreciated!

Aloha
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Old 07-20-2010, 07:17 PM   #2
jgibbons1
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We've sequenced at 4 different places now and all seem to have the same schema.

Library prep: $500-600
Cost per lane:
36se: $1000-1300
36pe: $1400-1700
72se: $1300-1600
72pe: $1600-2000

Hope that isn't too vague.

-John
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Old 07-20-2010, 07:18 PM   #3
jgibbons1
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Oh one more thing...some places charge a bit extra when multiplexing samples in a single lane. I think this is ridiculous but I've seen $50 per sample, up to 12.
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Old 07-20-2010, 11:24 PM   #4
simonandrews
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Quote:
Originally Posted by jgibbons1 View Post
Oh one more thing...some places charge a bit extra when multiplexing samples in a single lane. I think this is ridiculous but I've seen $50 per sample, up to 12.
It depends what you want doing. In our facility no one has used the official Illumina multiplexing protocols, but have made their own adapters with barcodes on the front. This means you can't separate them using the normal Illumina pipeline. We'd therefore make an additional charge if you wanted these separating and mapping. This would probably be somewhere around an additional $200, so $50 per sample doesn't seem too unreasonable.
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Old 07-30-2010, 05:31 AM   #5
nasobema
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Quote:
Originally Posted by simonandrews View Post
It depends what you want doing. In our facility no one has used the official Illumina multiplexing protocols, but have made their own adapters with barcodes on the front. This means you can't separate them using the normal Illumina pipeline. We'd therefore make an additional charge if you wanted these separating and mapping. This would probably be somewhere around an additional $200, so $50 per sample doesn't seem too unreasonable.
I'm interested in these custom made barcodes.
You would still have to make a full library (including the full cost) for each sample, or wouldn't you?
I'm thinking about a way to use a barcoding method that would only result in one library with a mix of samples to save the 400,- Eur for each single sample.
But that's not what you are doing, if I get that right (?).
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Old 07-30-2010, 01:13 PM   #6
cbrennan
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Originally Posted by simonandrews View Post
This means you can't separate them using the normal Illumina pipeline.
Actually, with Casava-1.7.0 you can use the Illumina pipeline to demultiplex & map barcoded samples even if you don't use the Illumina kits - you just need to manually generate a SampleSheet.csv file.
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Old 08-02-2010, 02:01 PM   #7
epistatic
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If a Core facility uses the standard Illumina multiplexing kit, it costs ~$30 sample + more time. They have to buy the kit and add different adapters so the user should expect to pay more than standard prep.

PE-400-1001, Multiplexing Sample Preparation Oligonucleotide Kit $2,880.00

Last edited by epistatic; 08-02-2010 at 06:36 PM.
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Old 08-02-2010, 03:55 PM   #8
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Default Multiplexing kit

The description of the kit on-line says there are 12 oligonucleotides included. Generally I would think that one oligonucleotide could be used per sample, making it an extra $240 per sample. How are you able to only charge $30 per sample?
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Old 08-02-2010, 06:33 PM   #9
epistatic
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The kit can index 96 libraries, up to 12 per lane. This does come out to $30/library.

"The Multiplexing Sample Preparation Oligonucleotide Kit contains 12 unique oligonucleotides to "tag" libraries for pooling in a single lane of a flow cell. Using this kit, up to 96 samples can be sequenced on a single flow cell..."
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Old 09-09-2010, 06:55 AM   #10
clr28
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I'm in Boston and the queues for 2x72 on GAII are excruciatingly long (about two months now and cost closer to $3600, even through academic cores). We only need to run one lane. Could you please refer me to any cores that have a quick turn around for 72bp PE? Thanks so much for letting me know!
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Old 09-09-2010, 11:33 AM   #11
NextGenSeq
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A 72bp PE run takes 8 days, that's why the queues are long.
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Old 11-27-2010, 11:44 PM   #12
lry198010
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For one lane with 12 sample using Multiplexing scheme in 72pe mode, is it the cost will calculate as follow?
Multiplexing: 12 * $50 = $600
Library prep: $600
72pe: $2000

So the total Cost is about $600 + $600 + $2000 = $3200. Is this right?
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Old 11-28-2010, 11:26 PM   #13
nasobema
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Quote:
Originally Posted by lry198010 View Post
For one lane with 12 sample using Multiplexing scheme in 72pe mode, is it the cost will calculate as follow?
Multiplexing: 12 * $50 = $600
Library prep: $600
72pe: $2000

So the total Cost is about $600 + $600 + $2000 = $3200. Is this right?
No, you have to generate one library per sample, so with your prices, it will sum up to:
12 * ($600 + $50) + $2000 = $7800
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