Thursday, 23 May 2013

Illumina Scientific Summit "Cancer Genomics" breakout

This years Illumina Scientific Summit was a great meeting, lots of great talks and great people to talk to at dinner and the bar. I already posted about a collaboration Geoff Smith presented and this post is some rough notes on the "Cancer Genomics" breakout that took part today.

Wednesday, 22 May 2013

Moleculo data presented at Illumina Scientific Summit

Geoff Smith from Illumina presented a great piece of work his group have been collaborating on with Jill Banfield’s research group at the University of California Berkely, Department of Earth and Planetary sciences. Geoff included a discussion on their use of Moleculo.

NGS forensics might require unique barcodes

The use of NGS in forensics is likely to supplant current STR profiling. One issue that has been discussed is the need to robustly determine that the correct sample has been analysed and reported on. With NGS almost all sequencing today is being done in a multiplex fashion using indexing barcode reads of generally around 6-10bp.

Current barcoding uses sets of up to 96 or 384 barcodes which is fine for many research applications. However there are reports of carry-over of barcodes from one run to another  on the kinds of instruments that are likely to be used in forensic labs. This is likely to make courts nervous about bringing this technology in.

One way to remove some of the problems would be to create significantly longer index oligos that are unique. I can see a market for a consumable kit where each is truly unique. The indexes included would be single-use only and no-one else in the world would get the same index oligo. Oligos can be made in very small synthesis scales today and in high-throughput. Given a long enough read even lower quality synthesis should allow confident discrimination of contamination allowing users to be confident about the final results.

A 25bp barcode read should be as unique as we might ever need and on HiSeq today would not add much time to a sequencing run.

Thursday, 16 May 2013

Using SPRI beads to improve Nextera

We have been running Nextera in my lab for a while now and had some great success e.g. 600x C. elegans genomes. With the release of Illumina's rapid exome kits Nextera is proving to be a versatile and useful addition to our lab tools. Unfortunately it has at least one significant weakness; the need to accurately quantify dilute DNA.

Wednesday, 15 May 2013

Automating Illumina library preparation

Illumina's just announced a partnership with major automation vendors so their s-bot looks like it has been killed as a project. We've got a Tecan Evo in our lab and would like to use it for library prep but a major headache has been the rapid development of library prep methods. There just does not seem time to program and validate a method before the next one comes out.

Monday, 13 May 2013

Make a DNA diffraction with a laser pointer

I came across this blog recently and thought you'd like to read it too.

Try this at home is a blog written by Mark Lorch, a chemistry lecturer at the University of Hull. He has some great stuff to try at home with the kids, check out his Knex DNA model. My son and I made the DNA replication fork with Okazaki fragments, Mark points to at Mount Sinai!

The DNA diffraction post tries to demonstrate the physics behind the data that allowed Watson and Crick to work out the famous molecule's structure. The X-ray diffraction image taken by Rosalind Franklin was crucial to the discovery. Read Watson's book for a history of the discovery, and his addendum to Rosalind Franklin.

Wednesday, 8 May 2013

New York Times piece on personalised medicine

The New York Times recently published an article on Foundation Medicine and their approach to personalised cancer genomics (targeted sequencing of 236 cancer genes). The test costs $5800 and is covered by some insurers in the USA. And the reports from the test have caused doctors to change patient therapy. 

So far so good. A personalised test a cancer patient might be able to afford (and they may not have to pay anyway). 

The article also refers to the My Cancer Genome web site, which offers a gene-by-gene portal into Cancer genomics. The site lists different diseases and points users to some of the literature supporting the impact of a particular gene on cancer. For examples a user can search for melanoma and BRAF to find mutations that might affect prognosis. At the same time they can check for clinical trials that might be ongoing.

Targeted sequencing is getting loser and closer to reality in the clinic. The technology we are using in my lab (and others like it) is becoming pretty robust. All that is needed is a good way to make doctors aware of what's possible and get the results into their hands in a way that means they can focus on medicine and not bioinformatics.