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Old 01-27-2014, 09:09 AM   #1
GW_OK
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Default Quantum Biosystems

A new single-strand sequencer emerges!

Quantum Biosystems
Like a nanopore, but pulling the DNA through a 2D gate instead of through a membrane.

Company website here:
http://www.quantumbiosystems.com/?lang=en

Raw data download (WHAAAT?!) here:
http://www.quantumbiosystems.com/get/index.html?lang=en
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Old 01-27-2014, 11:14 AM   #2
GenoMax
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Any bets if this or MinION can actually be seen in action next month at AGBT?
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Old 01-30-2014, 05:46 PM   #3
ymc
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Nicely done website.

In particular, am impressed by their claim that it can detect methylation during sequencing. I think this can help greatly when doing tumor-normal comparions.

The only thing missing is some hard number claims about the throughput. read length and cost.
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Old 01-30-2014, 06:11 PM   #4
ymc
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wow. The data is really "raw". Only rows of floats within the range of 0 and 0.025

According to the accompanying pdf, you need to write your own HMM to call the bases. I don't see that the HMM has a state for methylated C though...
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Old 01-30-2014, 06:19 PM   #5
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From the pdf: I hope this is not the read length of the final product or the read length here is not the same thing as the read length I know...

"4 Read length distribution
GATGAT GTGATG TATAG TGAGTAGTAGTGTATA ATGATG GAGT GAGT TGTGATGAT
Figure 6: Data set with reads of four or more bases highlighted.
After collapsing homopolymer subsequences, the reference sequence contains 18 bases. This data set contains 23 reads,
of which the longest is 16 bases (again treating homopolmers as single bases). Events in the signal that most likely
represent a read of single base were ignored in these counts.
The average read length was 3.95, for a total of 91 bases over 0.2 seconds. The 8 reads of 4 or more bases are shown
in Figure 5."
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Old 01-31-2014, 07:43 AM   #6
ajthomas
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I looks like their technology might turn into something useful at some point, but it's far from ready for prime time.
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Old 02-01-2014, 12:28 AM   #7
ymc
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http://www.quantumbiosystems.com/abo....html?lang=eng

Interesting. Nava Whiteford and Johnathan Teutenberg jumped ship from Oxford Nanopore.
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Old 02-03-2014, 01:25 AM   #8
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ymc/ajthomas: yes quite early days. We've been going for about a year and have received a relatively low level of financing. Hopefully we'll be able to talk about larger datasets in the near future, but we wanted to start engaging with the community at this, relatively early, stage.
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