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Old 03-05-2009, 03:54 AM   #1
Patrick
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Default Question and Confuse about Complete Genomics

Hi, I just saw this company recently. I feel very exciting and interesting about the technique that they used for sequencing human genome. But I faced some problem and can't understand some technique used behind this company.
1. Can anybody explained the technique that used by Complete Genomics?
2. I also confused about the Read length of bases that Complete Genomics can sequence. Is it 35 bp? 70 bp? or 80 bp? I feel quite confuse when read through their paper. Can anybody explain it in detail?
3. I also confused about the expected throughput MB (million bases)/day by this company. As I know, 454 Life Science is 96 MB per day and Solexa is about 500 MB per day. Is the Complete Genomics faster than them?

Thanks a lot for all of the advises and explanation.
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Old 03-05-2009, 12:20 PM   #2
thondeboer
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Hi,

Great to hear you are excited about our genome sequencing service...I hope I can answer your question here (Also check the thread here:
http://seqanswers.com/forums/showthread.php?t=644

1) We use a technique called Combinatorial Probe Anchored Ligation that reads each individual base from a DNA Nano Ball that contains the genomic sequence in a library construct. Our base reads are independent of each other, that will ensure that each base is read with the most possible accuracy.

2) The read structure of our technology is two times 5+10+10+10 = 2 x 35 = 70 bp. We use a mate paired structure, where each half of the pair consists of 35 bp and each half is separated by a larger gap of about 400 bp. The mate paired read structure is pretty common in the short read technologies and not specific to our technology. Due to the library construction, we only read 5 bases from one of the adapters, since there are only 12-14 nucleotides between the Ad1 and Ad2 adapters. We actually read some bases twice, once from each side, hence our notation of negative gaps. So technically, we have two times [32-34 bp] = [64-68] unique reads for a sequence, separated by a gap of about 400 bp. See our whitepaper here for more information about our library constructs.

3) The throughput of our service is indeed quite high, but since we don't sell machines but a sequencing service, the throughput per machine is not that relevant. For our first genome that we recently released (See our website here: http://www.completegenomics.com/dataRelease/) we sequenced 630 Giga bp on 9 machines in 8 days, so that is a throughput of about 9 GBP per day. Mind you that was one of our earlier machines and when you know we have announced we will do 20,000 genomes per year very soon at 40x coverage, you can calculate from that we will have a throughput of 6500 GBP per day! Scary, isn't it!

Hope this helped...Let me know if you have any more questions...

Thon
Complete Genomics
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Old 10-06-2009, 03:10 PM   #3
vasvale
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Default yeld

so one run produces 70 gbp andf 70 bp reads?
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Old 10-06-2009, 04:24 PM   #4
NextGenSeq
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DNA Nano Balls?
No comment besides a chortle.
I'm sure your marketing team will have a challenge with that technological description.

Good Luck!
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Old 10-12-2009, 12:50 PM   #5
kentnf
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I also confused?
9 GBP per day = ?? mb (million bases)
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Old 10-13-2009, 08:19 AM   #6
krobison
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1 gigabasepairs = 1000 megabasepairs, so 9 gigabasepairs per day = 9,000 megabasepairs per day
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