Thursday 29 August 2013

Targeted RNA-seq methods are here

Illumina and Life Technologies are both launching targeted RNA-seq applications which are likely to become standard tools for many labs; if the price is right.

The ability to target a portion of the genome has revolutionised next-generation sequencing experiments. The analysis of exomes has exploded, custom panels for exome-style pull-down are being used to great effect in 1000’s of samples and amplicon analysis is making it possible to run 10,000’s of samples in a single experiment (we’ve run a HiSeq flowcell with 12288 samples on it, 1536 per lane using Fluidigm – currently unpublished).

The next frontier looks like it could be using the same techniques to target a portion of the transcriptome, again allowing many 1000’s or 10,000’s of samples to be analysed in a single experiment. These technologies are likely to replace real-time PCR for mid- to high-plex studies. Anyone that has tried to run a few 100 TaqMan or SYBR assays on their 96-well qPCR machine will see the potential. And users with BioMark, TLDA, Wafergen, and other high-throughput qPCR systems will see the potential of using just one analysis method (NGS) as their primary data collection tool.

Tuesday 27 August 2013

Back from my holidays

Two weeks away from the lab, from papers, from email and from Core Genomics - I’ve just got back from Finland’s wilderness: wood-fired sauna, lakes to swim in, fish to catch and no-one for miles; and all with fantastic 4G connection! Holidays are great and I think cutting yourself off from work is important if you’re truly going to relax and unwind. On my return to work there was the usual mass of email to work through. I thought I’d summarise the things that happened in the world of Genomics that I thought were interesting while I was away.