Wednesday 21 May 2014

What should we call an overlapping read-pair from a paired-end fragment run?

HiSeq rapid is going to be getting paired-end 250bp reads. Assuming you can sequence with a 500bp insert (+/-50bp) then we can expect to get perhaps 200-300M pairs of overlapping reads that can be merged to create 200-300M 500bp sequences. I suspect this is going to have a transformative effect on genome assembly and transcript isoform detection and the development of novel methods is likely to come from longer and longer reads on the Illumina platforms.

Sunday 18 May 2014

NASA's NextSeq?

A wonderful story appeared on BBC news website today about the company Planet Labs who are using a similar idea Illumina implemented in designing NextSeq - borrow from consumer electronics to advance science. Rather than building sequencers Planet Labs have built and launched a flock of 28 shoebox-sized "cubesats" - cheap, miniature imaging satellites. This is GoogleMaps satellite images with super-high resolution.

Saturday 17 May 2014

DNA technology symposium at Illumina's headquarters in Cambridge

I've just returned from Illumina's 2014 scientific summit in Prague which was a great meeting with loads of interesting speakers, great food (check out this restaurant if you're ever in Prague) and lots of opportunity for engagement with other users as well as Illumina executives. Illumina do put on a good show, so here's details of an event in September.

Saturday 10 May 2014

Say no to DMSO: and remember make your materials and methods clear

DMSO is used in many protocols as a ‘universal solvent’, it’s great for solublising small molecules and you've almost certainly used DMSO when freezing cells or in PCR. Unfortunately it’s relative ubiquity of use in research labs means it’s negative impacts on some compounds can be forgotten. A recent paper in Cancer Research by Michael Gottesman’s lab at NCI highlights one of these: that DMSO inactivates platinum drugs like cisplatin. They demonstrated that DMSO inhibits the cytotoxicity of platinum therapy, and reported that a literature review found up to one third of researchers are using DMSO and make the claim that this may render “a substantial portion of the literature on cisplatin uninterpretable”. Up to 50% of papers did not report the solvent that was used to dissolve cisplatin, making reproducibility of their results potentially impossible.

DMSO inhibits platinum therapy cytotoxicity