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Next-Generation Sequencing Trends 2012

Date Published: December 2012
Format: PDF
Pages: 54
Publisher: HTStec
Product Code: jc09091314
Availability: In Stock
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Next-Generation Sequencing Trends 2012

• This market report summarizes the results of HTStec’s 3rd industry-wide global web-based benchmarking survey on next-generation sequencing (NGS) carried out in November 2012.
• The study was initiated by HTStec as part of its ongoing tracking of emerging life science technologies and marketplaces. This subject was last surveyed by HTStec in March 2011.
• The main objectives were to comprehensively document current end-user experiences, practices, preferences and metrics in NGS and to understand future requirements. The survey also examined interest in amplicon sequencing, purchasing new instruments, alternative purchasing scenarios and expectations for 3rd generation sequencing platforms.
• Equal emphasis was given to soliciting opinion from all organizations where NGS is currently being investigated, with no geographic bias in the distribution of persons contacted.
• The survey looked at the following aspects of NGS as practiced today (2012) and in some cases as predicted for the future (2014): where respondents undertake their sequencing today; NGS instrument systems used to generate sequencing data in the past year; how many NGS instrument systems (sequencer units) are in respondent’s lab/sequencing facility; applications investigated on NGS platforms; primary focus of investigations which use applications of NGS technology; current bottlenecks in NGS; aspects of library construction procedures for NGS that currently negatively impact upon sequencing reliability and data quality; whether standard vendor protocols have been modified in library preparation steps; whether NGS-related sample prep techniques have been automated; satisfaction with the performance of vendor’s platforms used for the automation of NGS sample prep; importance of potential benefits and attributes of automation applied to NGS sample prep; use of amplicon sequencing systems; factors considered to be most important in determining use of amplicon sequencing systems; performance of existing sequencing platforms with respect to typical cost per mappable Gb sequenced, mappable Gb typically read per run, average duration of sequencing run and throughput achieved; biggest limitations to improving sequencing throughput; factors most likely to influence a decision to purchase an NGS instrument; plans to purchase new NGS systems over the coming years; openness to consider alternative sequencer purchasing scenarios; attractiveness of a range of alternative sequencer purchasing strategies; whether respondents are experiencing any budgetary constraints affecting the operation of their sequencing laboratory; whether the amount of money available to purchase NGS-related consumables, reagents or services has changed relative to previous years; annual budget for NGS-related consumables, reagents or services; plans to use 3rd generation sequencing instruments; use of 3rd generation sequencing technologies in a clinical setting; features of 3rd generation sequencing instruments that are more appealing than their next-generation counterparts; most serious potential errors of 3rd generation sequencing technologies impacting upon data quality; areas where respondents most want to see improvements when considering 3rd generation sequencing technologies; future NGS expectations in terms of cost/genome and base pair read length processed; and any unmet needs in the NGS process.
• The main questionnaire consisted of 30 multi-choice questions and 2 open-ended questions. In addition, there were 5 questions related solely to the administration and demographics of survey.
• The survey collected 109 validated responses, of these 52% provided comprehensive input.
• Survey responses were geographically split: 37% North America, 33% Europe, 21% Asia (excluding Japan) and 8% Rest of World.
• Respondents originated from 59 University, Research Institute or Not-for-Profit Facilities; 12 Hospitals/ Clinics; 9 Biotechs; 9 Government/Military/Defense Labs; 5 Other; 5 Diagnostics; 4 Not-For-Profit Sequencing Centres; 4 Agri Biotech/Plant Genomics Centres; 1 Pharma and 1 Commercial Fee-For-Service Provider.
• Most survey respondents had a senior job role or position which was in descending order: 21 research scientists; 17 professors/assistant professors; 14 lab/research/facilities managers; 13 principal investigators; 9 directors; 7 department heads; 9 senior scientist/research associates; 7 post-docs; 7 graduate/PhD students; 3 section/group leaders; 3 others and 1 vice president.
• Survey results were expressed as an average of all survey respondents. In addition, where appropriate the data was re-analyzed after sub-division into the following 4 survey groups: 1) University or Research Institute; 2) Other Organisations; 3) Europe; and 4) North America.
• Most sequencing was carried out in respondent’s own lab or using NGS instruments belonging to their organisation. The most prevalent NGS machine reported was the Illumina HiSeq 2000/1000.

Executive Summary .................................. 2
Table of Contents ..................................... 4
Survey Methodology ................................. 5
Respondent’s Organisational Origin and Response to Survey....................... 6
Respondent’s Company or Organisational Origin ......................... 7
Respondent’s Geographic Origin .............................. 8
Respondent’s Job Role .................................. 9
Location of NGS Activities ............................... 10
Use of NGS Instruments to Generate Sequencing Data ....................... 11
Current Composition of Next-Gen Sequencers Used by Respondents.................... 12
Access to Sequencing Units ................................ 13
NGS Applications Run by Respondents ........................... 14
Primary Focus of Investigations Using NGS Technology ......................... 15
Current Bottlenecks in NGS ................................ 16
Library Construction ................................... 17
Modification of Library Construction Protocols........................... 18
Summary of Survey Findings (1) ............................. 19
NGS Sample Prep Automation ................................. 20
Automation Platforms Used for NGS Sample Prep & Satisfaction .................... 21
Key Aspects of NGS Sample Prep Automation......................... 22
Amplicon Sequencing Systems ............................... 23
Factors Determining Use of Amplicon Sequencing Systems ....................... 24
Cost Per NGS Mappable Bases Today (2012) .......................... 25
Expected Future Cost Per NGS Mappable Bases (2014)....................... 26
Mappable Bases Read Per NGS Run Today (2012) ........................... 27
Expected Future Mappable Bases Read Per NGS Run (2014) ....................... 28
Typical Duration of a NGS Run Today (2012).......................... 29
Expected Future Typical Duration of a NGS Run (2014) ...................... 30
NGS Throughput Today (2012) - Mappable Bases Read Per 24h .................... 31
Expected Future (2014) NGS Throughput - Mappable Bases Read Per 24h ................ 32
Biggest Hurdle to Improving Sequencing Throughput ........................ 33
Summary of Survey Findings (2) ............................. 34
Factors Influencing NGS Instrument Purchase ............................ 35
Purchasing Plans for Next-Gen Sequencers (1) .......................... 36
Purchasing Plans for Next-Gen Sequencers (2) .......................... 37
Alternative Purchasing Scenarios ................................ 38
Attractiveness of Alternate Sequencer Purchasing Strategies ..................... 39
Budgetary Constraints Affecting NGS Operations ........................... 40
Changes in Money Available for Purchase of NGS-Related Consumables ................... 41
2012 Annual Budget for NGS-Related Consumables, Reagents or Services ................ 42
NGS-Related Consumables, Reagents or Services Market Estimate .................... 43
Plans to Use 3rd Generation Sequencers ............................. 44
Use of 3rd Generation Sequencing Technologies in a Clinical Setting ..................... 45
Appeal of 3rd Generation Sequencing ............................. 46
Potential Errors Associated with 3rd Generation Sequencers ....................... 47
Areas for Improvement in 3rd Generation Sequencing ........................ 48
Future Requirements/Expectations for NGS (1) .......................... 49
Future Requirements/Expectations for NGS (2) .......................... 50
Cost Per Genome Expectation in Relation to Base Pair Read Length ................... 51
Awareness of Unmet Needs ................................ 52
Summary of Survey Findings (3) ............................. 53