Sample preparation and library preparation are important steps in the DNA sequencing process with specialized products and companies. Based on a survey of labs worldwide conducted by Kalorama’s biotech analyst Justin Saeks, this report provides detailed information on the current state of DNA sequencing sample preparation and library preparation for next-generation systems, as well as sample preparation, cycle sequencing and sequencing reaction cleanup with capillary systems. The report’s perspective is demand-side, focusing on what labs are doing today.
The information in the report from survey results includes:
- Number of Sequencers and Models Owned
- Typical Applications and Libraries Run (by percentage)
- How Often or How Many Samples (runs, samples, slides, flow cells, plates, multiplexed or not) and Typical Output (reads, read length)
- Changes Sought in Sequencer Features, or Steps in the Sequencing Process
- Main Bottlenecks in Sequencing Process
- Sources of the Samples (human, bacteria, plant)
- Types of Targeted Enrichment Products Used
- Systems Used for Checking Concentration, Size, and/or Quality
- Importance of Cost, Throughput, Flexibility, Reproducibility, Robustness, User-Friendliness, Accuracy and other factors
- Brands Used for DNA or RNA Extraction and Purification
- Brands Used for Fragmentation and Library Preparation
- Brands Used for Amplification/ Polymerases, Dyes, and Sequencing Cleanup
- Third Party Liquid Handlers Used
- Barriers to 2nd- and 3rd-generation Sequencer Use
- Analyst Findings
The study focuses on a survey of 120 laboratories which was carried out from July to September of 2010, with the majority in the latter portion. Along with questions about the specific sequencers used in the labs, the respondents were asked about the sample preparation and library preparation kits, reagents, and other consumables used for sequencing.
The survey effort targeted any lab that uses sequencing for any application, but with the goal of achieving as close as possible a representative breadth of labs. Due to the increasing importance of 2nd- and 3rd-generation systems in the market, the scope leans towards these types of sequencers.
However, the market inevitably also includes capillary sequencers, as 47 of the 87 surveyed labs with next-generation systems also have capillary sequencers. Around a third of the systems in the respondents’ labs overall are capillary systems. The mix of labs reached in the survey provides both diverse industry segments, as well as groups of labs with both types of systems, only capillary systems, or only next-generation systems.
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