Friday, 29 January 2016

System biology provides a magic wand for cell reprogramming

This is not exactly genomic, but it is based on genomic data and so fascinating that I had to report about it!

In a letter appeared recently on Nature Genetics, Rackham et al. proposed the Mogrify tool, a web-based interface that can predict the minimum set of trancription factors (TF) needed for a specific cell type reprogramming. The idea that somatic cells can be reprogrammed across different cell types has been around for a while, but a systematic assessment of the conditions needed for each conversion has never been carried out, mainly due to the amount of time and effort needed to test the various combination of TFs experimentally.

The authors took advantage of the huge amount of data produced by the FANTOM project to calculate the specific transcriptional landscape of different cell types and then developed a method that could predict which TFs should be overexpressed to move a specific cell type to another one.

With Mogrify it could be now much easier to perform reprogramming experiments, an approach with a potential great impact for regenerative medicine.

The idea behind this interesting tool is summarized in Figure 1 from the paper as you can see below

The Mogrify algorithm for predicting transcription factors for cell conversion.

Thursday, 28 January 2016

Illumina get small with new miniSeq and FireFlight

After bullying the NGS market a couple of years ago with its new large sequencing platforms able to deliver thousands of human genomes per year, now Illumina decided to further expand its offer with also small solutions.

Few days ago at JP Morgan the company revealed a new benchtop sequencer aiming at small labs and clinical application based on gene panels. The new machine, called miniSeq, can produce up to 8 Gb per run with 25M reads, costs "only" ~50k$ and promise a cost per run between $200 and $300.
With this move Illumina try to challenge Ion Torrent PGM and the Thermo Fisher good position in the area of small, rapid an cheap sequencing. The new sequencer is based on the two-color technology developed for the NextSeq and HiSeq X sequencers allowing to reduce machine cost and speed up the sequencing runs.

Look how it compares to the existing Illumina benchtop sequencers:

In its try to fill all the space in the market Illumina has also annunced an even smaller sequencer, developed under the name of "project FireFlight". The details released included a 1.2Gb output, one "colour" SBS and patterned flowcells. It also has a digital fluidics library prep module. The machine alone might cost just $15,000, with under $200 cost per run. The new machine will be based on semiconductor technology with CMOS sensor collecting light data from multiple simultaneous reactions. Project Firefly will be developed through 2016 and expect to deliver in 2017.

More details and interesting consideration have been provided on the Illumina website and other omics blogs, like CoreGenomics and OmicsOmics.