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BioPortfolio | HTStec | Next-Gen Sequencing Trends 2009

Next-Gen Sequencing Trends 2009

HTStec's Next-Gen Sequencing Trends 2009 report was published on 3 August 2009. This 51 page report summarizes the results of HTStec’s industry-wide global web-based benchmarking survey on next-generation sequencing carried out in July 2009. The main objectives were to document current user experiences, practices, assay metrics and preferences obtained using next-gen sequencing instruments and to understand future requirements. The report is based on 106 responses, obtained primarily from University, Research Institute or Not-for-Profit Facilities in both Europe and North America.

Executive Summary

• This market report summarizes the results of HTStec’s industry-wide global web-based benchmarking survey on next-generation (next-gen) sequencing carried out in July 2009.

• The study was initiated by HTStec as part of its ongoing tracking of emerging life science technologies and marketplaces. The main objectives were to document current user experiences, practices, assay metrics and preferences obtained using next-gen sequencing instruments and to understand future requirements. Equal emphasis was given to soliciting opinion from all organizations where next-gen sequencing is being undertaken, with no geographic bias in the distribution of persons contacted.

• The survey looked at the following aspects of next-gen sequencing as practiced today (2009) and in some cases as predicted for the future (2011): sequencing platforms respondents use or have access to; applications run on sequencing platforms; current bottlenecks; main bottleneck in sample prep; sample prep methods used to shear DNA; aspect of sample prep most in need of automation; typical cost per mappable base sequenced; mappable bases typically read per run; sequencing throughput achieved; biggest restriction to improving sequencing throughput; how frequently systems have broken down; experience of vendor service support; whether any publishable data has been generated; platforms most associated with desirable characteristics/attributes; what is used for data analysis and storage; biggest bottleneck in data analysis and storage; where respondents plan future growth in data analysis and storage; how long raw data is retained; future expectations for cost per genome; improvements most wanted in next-gen sequencers; whether a ‘gold standard method’ will emerge; thoughts on achieving a $1,000 genome; what has impacted respondent’s ability to purchase/implement a next-gen sequencing capability; plans to purchase new next-gen sequencing systems; thoughts on 3rd generation sequencing solutions; interest in outsourcing next-gen sequencing, providers used/considered; budget allocated and its breakdown; and unmet needs in the next-gen sequencing process.

• The main questionnaire consisted of 29 multi-choice questions and 2 open-ended questions. In addition, there were 5 questions related solely to the administration and demographics of the survey.

• The survey collected 172 responses. Approximately 40% (68) of these responses were subsequently excluded as they did not meet the initial respondent selection criteria, or provided minimal input, or came from vendor companies active in the area. This left 106 survey respondents that met our selection criteria (i.e. were currently undertaking or involved in next-gen sequencing), provided verifiable details of their lab origin and gave input in a significant part of the questionnaire.

• Survey responses were geographically split: 53% Europe; 27% North America; 11% Asia (Excluding Japan); 5% Japan; and 4% Rest of World.

• Respondents came from 72 University, Research Institute or Not-for-Profit Facilities; 10 Biotechs; 7 Other; 5 Not-For-Profit Sequencing Centers; 5 Government/Military/Defense; 4 Commercial Fee-For-Service Providers; 1 Pharma; 1 Diagnostics Company; and 1 Hospital/Clinic.

• Most survey respondents had a senior job role or position which was in descending order: 15 Lab/ Research/Facilities Manager; 15 Professor/Assistant Professor; 13 Research Scientist; 11 Department Head; 8 Principal Investigator; 7 Director; 6 Section/Group Leader; 5 Senior Scientist/Research Associate; 4 Post-doc; 3 Vice President; and 19 Other Roles.

• Survey results were expressed as an average of all survey respondents. In addition, were appropriate the data was reanalyzed after sub-division into the following 4 survey groups: 1) University or Research Institute; 2) Other Organizations; 3) Europe; and 4) North America.

• Survey respondents use in their labs or have access to (e.g. via collaborating centers) the following next-gen sequencing platforms: 82% to 454 FLX/Roche, 79% to Solexa/Illumina, and 56% to SOLiD/ABI.

• The application most run on a next-gen sequencer was mutation/SNP discovery.

• Data processing was the most limiting bottleneck in next-gen sequencing today.

• The main bottleneck in sample preparation for next-gen sequencing reported was library construction.

• The most used method for DNA shear in next-gen sequencing sample prep was nebuliser for both short and medium/long fragments, and sonication for fragmentation for ChIP.

• The aspect of sample prep for next-gen sequencing most in need of automation was DNA fragmentation.

• The median typical cost per billion mappable bases sequenced was <$25K for 454 FLX/Roche; <$2.5K for SOLiD/ABI; and <$2.5K for Solexa/Illumina.

• The median typical number of mappable bases read per run today was <0.5 billion for 454 FLX/Roche; <5 billion for SOLiD/ABI; and <5 billion for Solexa/Illumina.

• The median throughput reported for next-gen sequencing operations today was <0.5Gb/day for 454 FLX/Roche; <1Gb/day for SOLiD/ABI; and <1Gb/day billion for Solexa/Illumina.

• Data analysis (quality of software tools) was rated the biggest restriction to improving throughput.

• The highest incidence of frequent breakdowns was reported for Solexa/Illumina.

• The median time interval between system failures on all next-gen sequencing platforms was 1-3months.

• The service support experience related to 59 next-gen sequencing platforms used by survey respondents are reported with respect to overall satisfaction, faults rectified on first visit and geographic location.

• The highest incidence of very happy with overall service support experience was reported for SOLiD/ABI.

• The highest incidence of >99% of faults rectified on first visit was reported for 454 FLX/Roche.

• The highest incidence of generating publishable data was reported for 454 FLX/Roche.

• The next-gen sequencing platform most associated with the following desirable characteristics/attributes was: 454 FLX/Roche for system reliability, ease of integration with LIMS, and understanding sequencing/user requirements; SOLiD/ABI for good after-sales support & service, and innovative software; and Solexa/Illumina for highest accuracy, cutting-edge technology, and value for money.

• The majority of respondents used in house bioinformatics for data analysis and storage.

• The biggest bottleneck for next-gen sequencing data analysis and storage was software.

• The median time respondents plan to retain raw data (unprocessed image files) was 3-6 months.

• The future requirements (i.e. where they expect be by the end of 2011) of 52 respondents for the cost per genome sequenced are reported with respect to base pair read length (fragment size) processed.

• The median cost per genome most expected was <$10K for short fragment applications of >100kb and long fragment applications of 1.5-3kb.

• Read length accuracy (irrespective of the definition) was rated what respondents most wanted to see improved in the next-gen sequencing offerings.

• Most respondents do not believe that any of the 3 established next-gen sequencing platforms will become ‘the gold-standard method’ in the next few years.

• The majority of respondents believe a $1,000 genome is achievable, within a median time frame of <3 years, and will most likely to be achieved using a PacBio platform.

• Infrastructure requirements were ranked what had most impacted respondent’s ability to purchase and/or implement a next-gen sequencing capability in their organization.

• A total of 62 purchasing plans for next-gen sequencers spread over the next 3 years were identified from 32 different labs. Greatest interest was for purchasing Solexa/Illumina. The majority of labs planned to purchase more than 1 unit, mainly from a single instrument manufacturer.

• Most respondents are not delaying initiating sequencing and putting off the purchase of a sequencing platform until 3rd generation sequencers come to the market.

• Opinion on 3rd generation sequencers was that the need for instrument upgradeability is absolutely essential and the importance of a common infrastructure is desirable.

• Most respondents are currently outsourcing at a not-for-profit collaborating lab, only a small minority use commercial fee-for-service providers, and a list of the providers used to date was collated.

• The median outsourcing budget for next-gen sequencing at a fee-for-service provider was $10K-$25K.

• The breakdown of the budget for outsourced next-gen sequencing at a fee-for-service provider was projected with the biggest proportion spent on transcriptome analysis, small RNA analysis and mutation/SNP discovery.

• A simple bottom-up model was made to estimate the market for outsourced next-gen sequencing at a fee-for-service provider. This model used data derived from this survey on respondent’s involvement in outsourcing and their mean budgets allocated or estimated per lab for this activity.

• The global 2009 market estimate for outsourced next-gen sequencing at a fee-for-service provider was around $30million. The full report details the 2011 estimate, % CAGR, and its breakdown into services.

• Respondent’s feedback on the biggest unmet needs in next-gen sequencing was documented.

• The full report provides the data, details of the breakdown of the responses for each question, mean and median values for the assay metrics, and the estimates for the future (2011). It also highlights a few interesting differences between the survey groups.

August 2009

Format: PDF

Pages: 51
Table of Contents
Price: $2,475.00 / €1,654.29

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