Archive for January, 2012

What’s Driving Roche’s $5.7 Billion Bid for Illumina – 01/27/2012 – The Burrill Report

January 30, 2012 Leave a comment

What’s Driving Roche’s $5.7 Billion Bid for Illumina – 01/27/2012 – The Burrill Report.

Interesting read (or ‘hear’, since it’s an audio report). What’s your take on Roche’s move? Is it just another merger (think 454 and ion torrent), or is it a turn-point of some sort for the sequencing industry?

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How far is whole genome sequencing from the clinics

January 21, 2012 3 comments

A few weeks ago, I cam across a comment by an FDA official regarding the clinical utility of next generation whole genome sequencing. According to the official, current sequencing technologies need to improve its accuracy by a few orders of magnitude before they’re any useful in the clinics. Really?

I have a different opinion. The FDA’s view is well known to be, for a good reason, very conservative. For a full genome with 6G bases, with Complete Genomics’ technology, you can already achieve a precision where there’re only some ~3000 – 10000 errors. Is this good enough? It depends.

Take the post-natal diagnostic market for example. Majority of the hereditary diseases that cytogeneticists are trying to diagnose have copy number changes (gains and losses) rather than point mutations, and they’re big events: >10kb in almost all cases. For traditional methods (let’s not go back to “ancient” times where karyotyping is used) say SNP arrays, this presents a challenge, but not so much for sequencing. In fact, whole genome sequencing is already being evaluated in the post-natal space. Knowingly, in a space where the reimbursement level is only ~$1500, next-gen sequencing at the current price point is not viable. Therefore, here what’s preventing NGS to enter the clinical labs is the cost, not the current precision level.

The cancer market? It’s kind of a mixed bag at the moment. NGS, even at the current precision level, provides a whole slew of useful information that can help with diagnosis, prognosis and therapeutic decisions, but it also presents challenges. Aside from the cost (which is more tolerated in cancer), the vastly unknown nature of cancer and the boat load of information that NGS generates do not lead to an easy solution. There’s also a general lack of pharmacogenomics links with mutations vs drugs to use. Admittedly, we have a long way to go there.

Here the focus has been on whole genome NGS. If we move to targeted sequencing, there are far more applications one can use it for (not necessarily market size wise: cancer is still the single biggest one out there!), and many are indeed being commercialized (check out companies like Sequenom, Aria Dx and Verinata etc.).

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