Friday, 17 September 2010

The Broad’s Approach to Genome Sequencing (part I)

In Part I of a two-part exclusive interview, Nicol and Nusbaum share some of the keys to the Broad’s sequencing success with Bio-IT World chief editor Kevin Davies. 

NUSBAUM: The cost of storage is coming down very slowly [compared to sequencing costs]. It’s not very hard to foresee a time when storage is half the [total] cost [of sequencing].
NICOL: Or we store it as DNA – and resequence it!
NUSBAUM: It’s been a couple of years since we saved the primary [raw image] data. It is cheaper to redo the sequence and pull it out of the freezer. There are 5,000 tubes in a freezer. Storing a tube isn’t very expensive. Storing 1 Terabyte of data that comes out of that tube costs half as much as the freezer! People [like Ewan Birney at EBI] are working on very elaborate algorithms for storing data, because you can’t compress bases any more than nature already has. The new paradigm is, the bases are here, only indicate the places where the bases are different . . . In 2-3 years, you’ll wonder about even storing the bases. And forget about quality scores.
The cost of DNA sequencing might not matter in a few years. People are saying they’ll be able to sequence the human genome for $100 or less. That’s lovely, but it still could cost you $2,500 to store the data, so the cost of storage ultimately becomes the limiting factor, not the cost of sequencing. We can quibble about the dollars and cents, but you can’t argue about the trends at all.

My comments:
It seems terribly weird that DNA is more 'efficient' than HDD (or archival tapes) for storing data. Granted cost wise, it might be cheaper to store DNA but they neglected to factor in the time required to find that tube, process it. And the cost to implement a LIMS so that you CAN find that tube, and the man hours used to seq the DNA.
Looking forward to Part II of the interview!
what are your thoughts?

1 comment:

  1. With a cancer sample, for example, you only get one shot at sequencing; there is not enough DNA!


Datanami, Woe be me