NGS by the Numbers

By Laurie Sullivan

November 15, 2011 | Insights Outlook | Insight Pharma Reports conducted a user market survey as part of its latest report focused on next-generation sequencing (NGS), which describes innovations in this field and analyzes their impact on what can only be described as an extremely dynamic technology and market sector. Partial survey results are shared here.

Respondents were asked to rate sequencer attributes on a scale of 1–5 (with 5 being most important; see Table). Average response ratings are proportional to the relative importance of an attribute. Results show a great deal of bunching in the 3–4-point range, which indicates that those attributes are considered well above average in importance. However, a few points stand out. “Instrument size” rates considerably lower in importance than any other factor within this survey population, which is weighted strongly toward modest-sized, academic core labs. Also noteworthy are raw data accuracy and consensus accuracy, both of which have the highest importance ratings.

This observation is not surprising given the predominance of genetic variation studies among user applications. It is interesting in this respect that, in our PacBio interview (excerpted in the September/October issue of Bio•IT World), Dr. Steven Turner claims that long-read tails in repetitive SMRT sequencing of single-molecule fragments can compensate for relatively low raw read accuracy and generate very high consensus accuracy.

Selling Points

We also asked whether a respondents’ organization had purchased a low-cost NGS system or planned to do so by the end of 2011. In fact, more than half (56%) answered positively.

In terms of system selection among the three such systems available, Ion Torrent’s PGM came in first (59.2%), the new Illumina MiSeq second at 26.5%, and the 454 GS Junior at 14.3%.

Next we asked whether organizations are currently doing single-molecule sequencing using one of the two commercially available systems. Only one-fifth of those surveyed responded to this question, and nearly three-quarters of those use Pacific Biosciences’ RS system compared to one-quarter using Helicos’.

When asked whether their organization planned to purchase a Pacific Biosciences’ sequencer in the coming year, a surprisingly-high 20% of the 71 respondents answered affirmatively.

An additional query along this same line asked about degree of interest in performing single-molecule sequencing. Given five degrees of interest, 85% of the 68 responses fell in the top three categories, with roughly equivalent numbers for ‘very much,’ ‘quite a lot,’ and ‘moderately.’

The next two queries dealt with nanopore-based single-molecule sequencing. The first asked respondents’ opinion on the likelihood that a nanopore system would hit the market by the end of 2012, given four levels of response covering ‘very likely,’ ‘somewhat likely,’ ‘possible,’ and ‘unlikely.’ The largest number of responses fell in the ‘possible’ category, although about one-quarter fell in each of the two more likely categories. Only 13% thought it unlikely. The result reflects somewhat more optimism than conclusions drawn by individuals whom we interviewed, who tended to believe that once feasibility for sequencing was made public, several more years would need to elapse before commercial introduction.

Respondents’ were then asked to rate attributes of a putative nanopore system on an attractiveness scale of 1–5, with 5 reflecting most important. Again, the average score is proportional to attractiveness. Read length and accuracy both led with scores exceeding 4, followed closely by speed and consumables cost. Instrument cost and size fell last in the attractiveness scale, both with scores less than 3.4.

For complete survey results, as well as transcripts of interviews conducted with individuals highly knowledgeable in diverse aspects of NGS, please refer to the full Insight Pharma Report: Next-Generation Sequencing Generates Momentum: Markets Respond to Technology and Innovation Advances. July 2011.

This article also appeared in the November-December 2011 issue of Bio-IT World magazine. Subscribe today!