The SOLiD 4hq system, originally manufactured by Applied Biosystems, is a next-generation genetic analysis system that gives great cost effectiveness per sample run. For analysis, the system executes massive parallel sequencing that utilizes short reads of 75 bp to analyze sequences up to 300 Gb. Sequencing technology is derived from ligation-based chemistry for the sequencing of clonally-amplified DNA fragments. In order to ensure accuracy upwards of 99.99%, the system integrates a two-base encoding method to execute error checking. Altogether, the features of this instrument are designed to provide labs working in genetics a platform for improved accuracy, throughput, and cost effectiveness.
The foundation of cost effectiveness is based on the reduction of a relationship between cost, accuracy and throughput ((Accuracy x Throughput)/Cost). Without sacrificing accuracy and throughput, sample runs on this instrument can be conducted for as low as $3,000 per 30X coverage of the genomes analyzed. Improved accuracy allows for several advantages, including the ability to detect variants in sequences run at low coverage. Variants can be detected when studied as pooled or heterogeneous samples. Because errors such as false positives are reduced, the costs of downstream validations are similarly reduced. Accuracy and efficiency are aided by an automated error-checking workflow. Quality values (QV), which are highly correlated with error rates, are automatically reported by the system for each base read. With this system, a QV of at least 30 is reported in more than 80% of bases. Greater accuracy and less cost facilitate larger projects due to the cost efficiency per sample run.
This system can be scaled to meet the requirements of any application, and is modular enough to readily do so. Flexibility in sample formats is established with an open slide format and bead densities. With this flexibility, slides can be modified to adjust throughput with minimal optimization. Adjusting throughput creates more uniform coverage across the tested genome concurrently with more samples being tested. This slide format flexibility is based on a range of slide segmentations for the two independent flowcells. Multiple options for slide segmentation â€“ single, quad, and octo formats â€“ enable a variety of experimental setups. As another option, the support of sample multiplexing allows up to 96 samples with corresponding barcodes to be run simultaneously on a slide. This range of options not only enables user flexibility, but also reduces the cost per sample.
The SOLiD platform, with all components included, permits the execution of complete genomic workflows. This includes:
- Isolation of Nucleic Acid - Preparation of Genomic Library - Amplification and Sequencing - Data analysis - Validation of Results
The incorporation of the optional EZ Bead System, for example, can reduce the time spent on manual labor by 80% due to automated bead preparation solutions. Such an integrated system will also result in increased experimental control in part due to implementing quality control checkpoints. Ultimately, the modularity of the SOLiD system accommodates varied applications while still forming an extremely accurate and efficient analytical unit.
Library Preparation Sub-System:
- Covaris S2 Ultrasonic Sample Processor
- VWR 612 Chilling Recirculator
EZ Bead Preparation Sub-System:
- (3) Dell Laptop computers (for control)
- SOLiD EZ Bead Emulsifier
- SOLiD EZ Bead Amplifier
- SOLiD EZ Bead Enricher
- SOLiD 4 Analyzer
- SOLiD software suite version 4.0
- Reagent Delivery System
- Computer Rig w/ (3) computing nodes, analyzer controller, head node, and gigabit switch
- (2) APC Smart-UPS RT 3000 uninterruptible power supplies
- IKA Ultramax Tube Drives w/ Kit
- Slide storage/depo chambers
- Various tubing, cables, accessories and tools