To the editor:

A news story by Jim Kling that appeared in the November issue is timely and well researched (Nat. Biotechnol. 23, 1333–1335, 2005); however, two points merit clarification.

Kling suggests that the 'polony' sequencing method developed by my group at Harvard and collaborators at Washington University1 “avoids potentially costly PCR.” In fact, our method does not completely 'avoid' PCR; it merely attempts to use less of the costly PCR enzymes by using beads 20,000 times smaller in volume than those used in the method of the 454 group (ref. 2).

The article also states that “454 estimates that it achieved a 100-fold decrease in cost compared with the Sanger method.” This is quite different from “100-fold increase in throughput,” which is what they reported in their Nature paper. The 454 cost was $5,000 for a 580-kbp genome or $9 per consensus kbp (at an error rate of 4.0 × 10−5). Sanger/ABI is $7/kbp (at an error rate of 4 × 10−6). Both methods can achieve trade-offs between cost and accuracy, but published data does not yet indicate any point where 454 is less costly than Sanger for a given accuracy goal. We estimate polony sequencing at $0.8 per consensus bp ($0.11/raw-bp, ref. 1). More detailed cost-accuracy trade-off analyses are to be encouraged and a possible start point is available here: http://arep.med.harvard.edu/Polonator/speed.html.