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.

Thursday, 1 October 2015

1000G and UK10K publish results of large scale human genome sequencing

Risultati immagini per human genetic variability

Both 1000G and UK10K consortia have recently published the results of their analysis on the variability of human genomes, based on their large scale genomics projects.

In the 1000G papers appeared on Nature the consortium described SNV and structural variants findings based on the phase 3 dataset. 
Citing the abstract, they have analyzed "2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries."

You can find the papers here:
A global reference for human genetic variation (Nature, 2015)

An integrated map of structural variation in 2,504 human genomes (Nature, 2015)

UK10K LogoThe UK10K consortium also published a detailed description of the human genetic variability based on around 10,000 samples, partially low coverage WGS of control samples and partially deep covered WES focused on various complex and rare diseases.
Citing the abstract, "Here we describe insights from sequencing whole genomes (low read depth, 7×) or exomes (high read depth, 80×) of nearly 10,000 individuals from population-based and disease collections. In extensively phenotyped cohorts we characterize over 24 million novel sequence variants, generate a highly accurate imputation reference panel and identify novel alleles associated with levels of triglycerides (APOB), adiponectin (ADIPOQ) and low-density lipoprotein cholesterol (LDLR and RGAG1) from single-marker and rare variant aggregation tests. We describe population structure and functional annotation of rare and low-frequency variants, use the data to estimate the benefits of sequencing for association studies, and summarize lessons from disease-specific collections."
By the way, they published also an improved haplotype reference panel that can be used to improve imputation of low-frequency and rare variants also developed an online tools to explore their association results.
The third paper is a first example of the disease-oriented results obtained by the consortium: they identified EN1 as a gene involved in reduced bone density and recurrent fracture.

You can find the papers here:
The UK10K project identifies rare variants in health and disease (Nature, 2015)

Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel (Nature Communications, 2015)

1000$ genome finally broken?

Risultati immagini per 1000$ genome

From the introduction of Illumina X Ten about an year ago, the goal of 1000$ genome seems at grasp. As I see it, this milestone will be reached when a personal genome could be provided to consumer for 1000$ or less overall price, including at least library, sequencing and variant identification.
From my recent experience, we can get all this stuff delivered now for a 30X human genome paying about 1500$ for normal sized project or 1200$ for large ones.

Risultati immagini per personal genome projectHowever, recent new from Veritas Genomics (a genomic service company founded by George Church) and the PGP (Personal Genome Project) promise to finally break the barrier, pushing the price down to 999$. The two groups have announced a collaboration that will initially provide the service only for the partecipant enrolled in PGP, but Veritas has promised that they will open this service to common customers soon.

link to home
So it may be a good time for a full genome sequence Xmas gift!