Thursday, 25 June 2015

Sequencers for sale

Back in 2010 a HiSeq 2000 cost $690,000 - you'll be lucky to get anything today. A V4 2500 might get you $100+k, but your V4 capable V3 just $20k. Depreciation sucks!




In accountancy, depreciation refers to the decrease in value of an asset over time. Most of us come across this when buying a car - for me that's usually on the nice side where I'm wondering why someone is selling a car they bought five years ago for so little!

But no asset lasts forever, and certainly not in the world of NGS. That "faster than Moore's law" graph you see at almost every NGS conference has a dark-side, and instrument depreciation is part of that. If this depreciation were accounted for properly thent sequencing costs in most labs would jump due to the relatively low number of runs performed.

Incidentally if you have a MiSeq sitting idle then these are pretty hot right now - I can probably put you in touch with someone who wants to buy one if you are interested!

Wednesday, 24 June 2015

King of the hill: which journal is best?

A paper on the BioArxiv describes a new metric to measure scientific journals by based on their efficiency of information distribution (citations) within the network of journals. It provides a providing together a complex picture of the intricate relations between scientific journals; but basically Science, Nature and PNAS are the top 3 journals!

Monday, 22 June 2015

Even more microfulidic RNA-seq: Drop-seq

I realised I'd not covered the recent droplet sequencing papers (the post was sitting in my draft blogs pile) and wanted to make sure I did after posting on single-cell RNA-seq last week. The use of droplets has some benefits over microfluidics where the current leader of the field was, until recently, limited to 96 cells per run. Droplets seem to offer almost unlimited numbers of cells but realistically going past 1000 seems to be beyond the needs of many experiments (do you agree?). And with the release of the upgraded C1 offering 800 cell capacity, the off-the-shelf ease of Fluidigm's sytem is likely to make it popular for a while to come. However the Fluidigm chips are biased in the cells they capture as evidenced by the chips for differently sized cells and the droplet methods lower bias may ultimately win people over.

Droplets are also likely to be much more cost-effective, for the labs that can build their own systems. Drop-seq is around $0.10 cents per cell, compared to $10.00 on the 800 cell C1 chip (according to GenomeWeb). We've also been testing the Cellular Research technology which gets to somewhere in-between with the resolve system. However for ultimate spatial information in situ sequencing is likely to be difficult to beat.



Monday, 15 June 2015

More microfluidic single-cell RNA-seq

A team from Columbia University present a microfluidic device that can capture single-cell lysates in picotire plates and produce single-cell 3' tag RNA-Seq library prep at $0.10 cents per cell: Scalable microfluidics for single cell RNA printing and sequencing. They discuss two methods - RNA “printing” on glass and RNA capture on beads, but the paper focuses on the second of these. This is an early paper with two experiments each of which could be improved by another round or two in the lab. However in this fast moving field I can’t help but wonder if this is a method that will never be commercialised and if the authors simply want to make their mark? I think the fact that single-cell methods are appearing thick and fast shows how much this space there still is to innovate into. And for the investment pundits looking to Fluidigm et al, there is a danger that a clever molecular biology approach could allow single cell without any hardware - imagine library prep inside a cell?

Thursday, 11 June 2015

RNA-seq contextualised: what's possible in 2D and in situ RNA sequencing

When George Church talks about something it often turns out to be a good idea to listen. He's been talking about in situ sequencing for many years and the technology looks to be ready for take off. It could be a niche method used by a few very skilled groups, but if companies like Spatial Transcriptomics get their way we'll be using it routinely. I think in situ sequencing could be a massive, but we'll see over the next eighteen months or so if I'm right. A big question remains over how easily the technology can move from sequencing RNA in the cytoplasm to DNA in the nucleus. Being able to call mutations in cells from a tissue biopsy would be great, but the inaccessibility of DNA might mean we'll stick to expressed mutations for now.

A simplified workflow of the Spatial Transcriptomics technology

Tuesday, 9 June 2015

Nanopore library prep kit anyone?

A year ago I surveyed the costs of Illumina library prep and found over 15 providers; they offer generally the standard Illumina library prep method but with prices ranging from £15-£60 per sample. There was some real innovation amongst some of these kits too, enabling methods and applications not supported by Illumina (in the way of TruSeq kits). Illumina have created an ecosystem for other companies to feed on.


With the developments coming thick and fast from ONT and the people taking part in the MinION access program I wonder when the first nanopore kit might be released by a 3rd party? I'm sure a similar ecosystem will be created as MAPpers release protocols and the system becomes more widely adopted.

Saturday, 6 June 2015

Chromosome linkage to disease

I'm often trying to find an image for a post and it can be tough trying to find something that can be used freely. The U.S. DOE has an image gallery from the Genomic Science program, which includes archived images from the Human Genome Project. Many of the images do not need permissions, simply credit the DOE Genomic Science program (http://genomicscience.energy.gov).I love their 2006 poster showing the numerous genetic disorders and traits mapped to specific chromosomes.


But I want more: Unfortunately I often can't find the kind of image I'm looking for...please let me know of good sites to use?

Update: I was contacted by Anna Hupalowska about her work, some wonderful stuff, take a look.

If anyone else gets in touch I'll start a list here of scientific illustrators for hire!

Wednesday, 3 June 2015

Exomes from a spot of blood

Michael Snyder has a great paper published in AJRCCM: Exome Sequencing of Neonatal Blood Spots Identifies Genes Implicated in Bronchopulmonary Dysplasia (BPD). BPD is a lung disease of premature babies which appears to have a strong genetic component and was investigated using exome sequencing. The neat twist was they used the blood spot taken from a heel-prick to extract DNA for exome library prep. In the paper they report finding over 250 rare nonsynonymous mutations after comparing 50 affected and unaffected twin pairs. Many of these were enriched for, and up-regulated in, a murine model of BPD.
 
Image from : http://en.wikipedia.org/wiki/Robert_Guthrie

Thursday, 28 May 2015

Book Review: Next-Generation DNA Sequencing Informatics 2nd ed.

Next-Generation DNA Sequencing Informatics (2nd edition), edited by Stuart M. Brown (blogger) is a book to get you well and truly started in NGS Bioinformatics. The twelve chapters cover QC, sequence alignment, assembly, transcriptome and ChIP-seq analysis, visualisation, and much else besides. For this review I read the chapters on QC, RNA-seq and emerging technologies and applications.