1000$ genome finally broken?

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.

However, 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.



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

PubMed Highlights: In a recent special issue Science discuss recent advances in human genomics, their impact for human health and future perspectives

Science Magazine has just published a special issue on the recent advances in genomics, as well as the promise and challenges of the new technologies for human health. The special issue is composed by a set of reviews discussing the main topics in the field:

• the use of new sequencing technologies for the identification of genetic mutations causing human disease and the improvements in our ability to interpret the consequences of such mutations.
• the state of the art in somatic variant detection and the impact of the new technology on cancer research
• the genetic and genomics of psychiatric diseases, reporting the difficulties in understanding the interplay of inherited genetics and spontaneous mutations in complex diseases
• the impact on mitochondrial disease research

In addition there are some commentary on ethical and privacy related challenges emerging from the wide adoption of the new genomics technologies and their use for preimplantation screens and human health care. Finally, there is a report on the recent effort from NIH to deliver personalized medicine.

A must read issue!

New Ion S5 sequencher announced

It's been a while since Life Technologies, now part of Thermo Fisher, has announced major improvements on its semiconductor sequencing platforms.

Now the company announced this new entry in its NGS sequencers portfolio: the Ion S5.
The Ion S5 looks similar to the Ion Proton and represents a compromise solution between the Proton and the PGM. The new machine will be available in two versions, standard and XL, with the XL version having more computational power.
The Ion S5 works with three different sequencing chips. As reported in the official brochure, the 3 new chips are named Ion 520, resembling the PGM 318 chip with up to 1 Gb throughput; Ion 530, up to 4 Gb; and Ion 540, similar to the Proton PI chip with 15 Gb.

The idea is clearly to offer an instrument that combines the speed and low cost of gene panel analysis with the ability to deliver human exomes and RNA-Seq data.
In this way the machine became an interesting choice to perform both cost-effective diagnostic panels based on the AmpliSeq technology, but maintaining also a research flavor with exome sequencing and counting applications.
The sequencing kits have been reconfigured and are now sold as prepacked cartridges and bottles that combines with a barcode scan system to simplify operations. Ideally the Ion S5 has to be integrated with the Ion Chef System for automated template preparation and chip loading. Moreover, thanks to a recent software upgrade, this system will also allow to prepare AmpliSeq libraries. In this way all the diagnostic (or research) AmpliSeq panels could be prepared in automated fashion from DNA to ready-to-sequence chip with minimal hand-on time, increasing standardization and performances.

It has been clear in the past few years that Ion technology delivers its best, and has more commercial opportunities, on fast and low cost targeted sequencing applications, with an expanding range of solutions available in terms of diagnostic gene panels and targeted panels for cancer research.Going this new machine in this direction, it seems clearly aimed at diagnostic applications.

With a price tag of $65K ($150K for the XL model) the Ion S5 sequencer represents a new interesting competitor in the field!

Main new technologies from AGBT15

Ion Torrent

• The new avalanche chemistry.

This new chemistry based on isothermal amplification will provide longer reads up to 600bp on PGM an 400bp on Proton PI with lower costs for template preparation. 

• New protocols for Ampliseq library preparation on Ion Chef system. 

The company aims to transfer all the processing steps on the new Ion Chef that will beacm the all-in-one solution from library prep to chip loading, minimizing hand on time. Take a look to the video on you tube.

• News on the PII chip.

They finally reported about a full working version of the PII chip producing up to 300M reads with 100bp length. However an official release date was not announced

Illumina

• NeoPrep, the new automated system for library preparation. 

Having already presented some new sequencers few months ago, Illumina come to the stage with this new equipment that will provide fast and accurate library preparation and can prepare 16 libraries at with as little as 30 minutes of hands-on time. NeoPrep is based on the electrowetting microfluidic technology and use A cartridge with reagents and your sheared DNA. The instrument generate and quantify each library, ready for pooling. Roughly is required per run. All this stuff at the price of $49K ($39K introductory pricing for the first 6 months). More details at the Illumina page or on Omics Omics blog.

10X Genomics

10X Genomics is the real innovation this year. They revealed their new GemCode technology to reconstruct long reads and haplotypes from standard short reads sequencing. The new instrument will integrate in the standard Illumina based library preparation, thus configuring as an add-on for already equipped laboratories. Using dedicated pen source software and genome browsers from 10X Genomics one can then generate standard file formats (such as phased VCF or BAM with phase tags) and visualize the reconstructed haplotypes. 

Take a look at this nice video or read more details from Omics Omics. 

AGBT 2015 is here!!

Here it is another edition of the exciting conference AGBT (advances in genome biology an technology).

As usual there are a lot of new technologies announced and hundreds of interesting talks touching every aspects of genomics and presenting the latest technologies and methods!

In this first day one there is a lot of talking about the new platform from 10X Genomics that promise to use massive fragment labeling to assemble long reads from standard short reads produce by Illumina technology. The new instrument will thus be an add-on for seqeucning labs instead of a completely new sequencing technologies with the ability to deliver long haplotypes.

Let see what they will reveal at the official presentations

Don't forget to follow the conference in real-time on twitter #AGBT15

If you want an overview of what is going on take a look to the official agenda and to the full list of posters and software presented on site.

Exome Aggregation Consortium release its data on 63,000 exomes!

On October 29th, the Exome Aggregation Consoritum as released its browser based on the impressive number of 63,000 human exomes.
This database is the larger collection of human exome data so far and provide both a web base interface to retrieve variants in your gene of interest or the download of a VCF file containing the list of all the annotated variants.

The final dataset is based on sequences from several consortia working on complex disorders and also includes 1000G and ESP6500 data.

The first aim of the Consortium is to study the distribution of "human knockout", that is people having both copies of a given gene inactivated by severe mutations. The analysis of associated phenotype data promise to reveal lot of interesting information of the actual role of single human genes. Moreover, the study of subjects carrying inactivating mutations on known disease genes but not showing the expected phenotype could lead to identification of new therapeutic targets.

See more information on Nature News and Genome Web!