Genomics


state of flux. Continual technological evolution is driving the transfer of sequencing into new envi- ronments, while allowing sequencing to become routine in many areas of traditional research. Around two-thirds of sequencing activity is no longer carried out in the labs of survey respon- dents, indicating a shift away from conventional routes of access to sequencing technology. Respondents are able to access a multiplicity of sequencing platforms and purchasing decisions are based on multiple factors. These survey findings reflect how individual respondents match their own specific requirements to the unique character- istics of each instrument. This diversity is paral- leled by the wide range of applications currently being employed to conduct research in a variety of areas in biology.


One noticeable trend is the shift to targeted rese- quencing, which has overtaken de novo sequencing as the most widely-investigated NGS application. In contrast to de novo sequencing, in which the genome sequence of an organism is discovered for the first time, targeted resequencing involves com- parison with a previously generated reference sequence. This allows the variation within the sam- ple sequence to be determined, enabling detection of genetic variants known to play a role in disease, a prerequisite for genomics-based diagnostics. Sequencing vendors are directing their efforts towards improving system performance and extend- ing read lengths. More chemistry kits are available to support target enrichment, an expanding menu of amplicon assays (Roche 454), targeted human DNA sequencing and targeted RNA sequencing (Ion Torrent). Furthermore, some vendors (Illumina) are developing novel IT platforms to expand the range of analytical tools available to users.


Many labs are currently operating under consid- erable financial constraints, with the economic downturn affecting all aspects of biomedical research. These unrelenting pressures are leading to demands for cheaper instruments and reduced running costs. As a result, there has been increased emphasis on improving aspects of sample prep and increasing ease of workflow in order to realise greater efficiency (QIAGEN).


The launch of desktop personal sequencers rep- resents another response of the industry to the financial situation and aims to take NGS beyond the centralised facility to a wider diversity of small- er labs. The advent of third-generation sequencing instruments, able to reach rapid test times while maintaining precision and low costs, has the poten- tial to greatly improve diagnosis of cancer and many inherited diseases.


Drug Discovery World Spring 2013


Sequencing is set to become even more accessi- ble, with single molecule real-time sequencing, semi-conductor technology and simpler chemistry already in use. Nanopore technology is expected to deliver the first fully miniaturised systems, as well as the next big leap in sequencing performance and cost. The launch of the Ion PIITM chip from Ion Torrent raises the possibility that the milestone fig- ure of $1,000 for human-scale genome sequence in a single day will become a reality.


These exciting advances suggest that the current trajectory of technological progress in DNA sequenc- ing is likely to continue, extending the sequencing revolution from the lab into the clinic.


DDW


References 1 Next Generation Sequencing Trends 2012 Report, published by HTStec Limited, Cambridge, UK, December 2012.


Andrew Szopa-Comley prepared the NGS Trends 2012 market report discussed in this article while gaining work experience as a market analyst at HTStec. A recent graduate in Natural Sciences from Cambridge University, Andrew is hoping to pursue a research career in biological research and is particularly interested in how genomics can pro- vide insights into questions in evolutionary biolo- gy. HTStec Limited is an independent market research consultancy whose focus is on assisting clients delivering novel enabling platform tech- nologies (liquid handling, laboratory automation, detection instrumentation and assay reagent tech- nologies) to drug discovery and the life sciences. Since its formation nine years ago, HTStec has published more than 80 market reports on enabling technologies and more than 40 review articles in Drug Discovery World. Please contact info@htstec.com for more information about HTStec reports.


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