Any use for a 20 base sequencer?

bios90 · 08-24-2013, 09:51 AM

Any use for it?

SNPsaurus · 08-24-2013, 02:11 PM

Sequencing of medically-relevant SNPs. Each target is one or a few nucleotides, so a quick PCR and read-out would have a use. Maybe still not competitive if other platforms can do more at the same cost and speed.

Expression analysis... just need a short tag of the transcript. miRNAs are short anyway. Local assembly could convert short reads into longer pseudoreads (see RAD PE assembly or Moleculo).

austinso · 08-24-2013, 03:33 PM

Probably not the best idea to publicize your PhD before it is complete...you don't want to get scooped.

krobison · 08-27-2013, 09:40 AM

A key question to ask of your technology is how it will perform in the presence of a non-clonal DNA sample. Simplest case is an essentially 50:50 mixture (heterozygote), but for other applications could it detect either an infrequent allele or many mixed alleles.

SNPsaurus · 08-27-2013, 10:03 AM

Yes, you could screen cell-free blood DNA for tumor alleles (at less than 1% frequency) if you had an excellent error rate and reduced the time for turning sample -> data.

BBoy · 09-12-2013, 10:45 PM

And more importantly, how is this better than established array technology. FET sensing of hybridization has been published time and again over the past 10 years.

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08-24-2013, 09:51 AM	#1
bios90 Junior Member Location: MA Join Date: Aug 2013 Posts: 8	Any use for a 20 base sequencer? Any use for it? Last edited by bios90; 02-24-2014 at 09:04 PM. Reason: Could be proprietary information

08-24-2013, 02:11 PM	#2
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	Sequencing of medically-relevant SNPs. Each target is one or a few nucleotides, so a quick PCR and read-out would have a use. Maybe still not competitive if other platforms can do more at the same cost and speed. Expression analysis... just need a short tag of the transcript. miRNAs are short anyway. Local assembly could convert short reads into longer pseudoreads (see RAD PE assembly or Moleculo). __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

08-27-2013, 10:03 AM	#5
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	Yes, you could screen cell-free blood DNA for tumor alleles (at less than 1% frequency) if you had an excellent error rate and reduced the time for turning sample -> data. __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

08-24-2013, 03:33 PM	#3
austinso Member Location: Bay area Join Date: Jun 2012 Posts: 77	Probably not the best idea to publicize your PhD before it is complete...you don't want to get scooped.

08-27-2013, 09:40 AM	#4
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	A key question to ask of your technology is how it will perform in the presence of a non-clonal DNA sample. Simplest case is an essentially 50:50 mixture (heterozygote), but for other applications could it detect either an infrequent allele or many mixed alleles.

09-12-2013, 10:45 PM	#6
BBoy Member Location: Pacific Northwest Join Date: Oct 2010 Posts: 52	And more importantly, how is this better than established array technology. FET sensing of hybridization has been published time and again over the past 10 years.