Spike-in controls

GenoMax · 08-09-2016, 07:53 AM

Spike-in controls is one of the oft discussed topics on SeqAnswers.

Researchers at the Garvan Institute of Medical Research have just published two papers in Narure Methods about synthetic DNA and RNA standards that can be used as spike-in controls.

Deveson et al: http://www.nature.com/nmeth/journal/...meth.3957.html

Quote:

DNA Controls

Sequencing reads derived from sequins align exclusively to an artificial in silico reference chromosome, rather than the human reference genome, which allows them them to be partitioned for parallel analysis.

Hardwick et al: http://www.nature.com/nmeth/journal/...meth.3958.html

Quote:

RNA Controls

Sequins have an entirely artificial sequence with no homology to natural reference genomes, but they align to gene loci encoded on an artificial in silico chromosome. The combination of multiple sequins across a range of concentrations emulates alternative splicing and differential gene expression, and it provides scaling factors for normalization between samples.

nucacidhunter · 08-09-2016, 11:28 PM

It will be good if they can design longer DNA Sequins for PacBio or 10x Genomics Chromium platform.

tedwong · 08-14-2016, 05:52 PM

Hi nucacidhunter,

DNA sequins can be used with any sequencing platform. An application where the combination of long-read sequencing (eg PacBio) and Sequins will be particularly powerful is in the detection of structural variation (which we all know is a major challenge). Our current generation of Sequins includes longer standards that emulate large deletions, inversions, tandem duplications, novel sequence insertions and mobile element insertions, all based on real instances of human variation.

Cheers

Ira Deveson (on behalf of the Sequins team)

tedwong · 08-14-2016, 06:57 PM

We have started a formal thread for current and future users to discuss DNA sequins:

http://seqanswers.com/forums/showthr...786#post197786

or RNA sequins:

http://seqanswers.com/forums/showthread.php?t=70843

Enjoy!

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08-09-2016, 11:28 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,248	It will be good if they can design longer DNA Sequins for PacBio or 10x Genomics Chromium platform.

08-14-2016, 05:52 PM	#3
tedwong Member Location: Sydney Join Date: Mar 2015 Posts: 13	Hi nucacidhunter, DNA sequins can be used with any sequencing platform. An application where the combination of long-read sequencing (eg PacBio) and Sequins will be particularly powerful is in the detection of structural variation (which we all know is a major challenge). Our current generation of Sequins includes longer standards that emulate large deletions, inversions, tandem duplications, novel sequence insertions and mobile element insertions, all based on real instances of human variation. Cheers Ira Deveson (on behalf of the Sequins team)

08-14-2016, 06:57 PM	#4
tedwong Member Location: Sydney Join Date: Mar 2015 Posts: 13	We have started a formal thread for current and future users to discuss DNA sequins: http://seqanswers.com/forums/showthr...786#post197786 or RNA sequins: http://seqanswers.com/forums/showthread.php?t=70843 Enjoy!