Quantum Biosystems

GW_OK · 01-27-2014, 09:09 AM

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

GenoMax · 01-27-2014, 11:14 AM

Any bets if this or MinION can actually be seen in action next month at AGBT?

ymc · 01-30-2014, 05:46 PM

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.

ymc · 01-30-2014, 06:11 PM

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...

ymc · 01-30-2014, 06:19 PM

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."

ajthomas · 01-31-2014, 07:43 AM

I looks like their technology might turn into something useful at some point, but it's far from ready for prime time.

ymc · 02-01-2014, 12:28 AM

http://www.quantumbiosystems.com/abo....html?lang=eng

Interesting. Nava Whiteford and Johnathan Teutenberg jumped ship from Oxford Nanopore.

new299 · 02-03-2014, 01:25 AM

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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01-27-2014, 09:09 AM	#1
GW_OK Senior Member Location: Oklahoma Join Date: Sep 2009 Posts: 408	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

01-27-2014, 11:14 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 6,854	Any bets if this or MinION can actually be seen in action next month at AGBT?

01-30-2014, 05:46 PM	#3
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	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.

01-30-2014, 06:11 PM	#4
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	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...

01-30-2014, 06:19 PM	#5
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	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."

01-31-2014, 07:43 AM	#6
ajthomas Senior Member Location: Utah Join Date: Mar 2010 Posts: 162	I looks like their technology might turn into something useful at some point, but it's far from ready for prime time.

02-01-2014, 12:28 AM	#7
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	http://www.quantumbiosystems.com/abo....html?lang=eng Interesting. Nava Whiteford and Johnathan Teutenberg jumped ship from Oxford Nanopore.

02-03-2014, 01:25 AM	#8
new299 Junior Member Location: Japan Join Date: Feb 2014 Posts: 2	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.