Benchtop sequencing refers to compact DNA and RNA sequencing machines small enough to fit on a laboratory bench. These instruments have made genetic analysis more accessible, allowing individual labs to perform it in-house rather than outsourcing to large, costly facilities. This shift from older, time-consuming methods provides faster access to sequence data. The availability of these smaller, more affordable systems has accelerated discovery and diagnostics across numerous fields.
Understanding Benchtop Sequencing Technology
The core of most benchtop platforms is a method called “sequencing by synthesis” (SBS). In this approach, a DNA sample is broken into fragments, which are then amplified to create clusters of identical DNA strands. The sequencer adds nucleotides—the A, C, G, and T building blocks of DNA—one at a time. Each nucleotide type has a unique fluorescent tag, and when one binds to a DNA strand, it releases a flash of light that a camera records to determine the sequence.
Another method is nanopore sequencing, which passes a single strand of DNA through a microscopic pore. As the DNA molecule moves through, each base disrupts an electrical current in a distinct way. A sensor measures these changes, which are decoded to determine the sequence in real-time. This technique is notable for its ability to read very long strands of DNA.
The innovation that makes these technologies “benchtop” is their miniaturization. Complex fluidic systems are scaled down to microfluidic chips, while high-resolution cameras and sensors are integrated into a compact design. This integration eliminates the need for the extensive equipment required by older systems. The result is a self-contained instrument combining chemistry, optics, and computing into one machine.
Common Uses in Science and Medicine
In clinical settings, benchtop sequencing allows for the rapid identification of pathogens. During an outbreak, public health labs can sequence the genome of a virus or bacterium to track its spread and identify mutations, as was done for the virus causing COVID-19. In hospitals, sequencing can quickly identify the cause of a serious infection. This helps doctors choose the most effective antibiotic treatment and combat antimicrobial resistance.
Benchtop systems are also used in cancer treatment through the targeted sequencing of genes from a patient’s tumor. This information helps oncologists identify the specific mutations driving the cancer. This guides the selection of therapies designed to attack cancer cells with those alterations. This approach, known as precision medicine, moves away from a one-size-fits-all model.
Beyond human health, benchtop sequencers are used in many scientific fields. Microbiologists sequence the genomes of bacteria and viruses to understand their biology and evolution. Environmental scientists analyze DNA from soil or water to study microbial communities and ecosystem health. The systems are also used for quality control in research, such as confirming the identity of cell lines or verifying genetically engineered organisms.
Forensic science is another area applying benchtop sequencing. The technology is used for mitochondrial DNA sequencing to help identify human remains. The ability to perform sequencing on-site with a quick turnaround is advantageous in certain forensic investigations.
Distinctive Features and Practical Considerations
A main feature of benchtop sequencers is their rapid turnaround time. Because they are designed for lower to medium throughput, labs can run samples on demand instead of batching them for a large-scale machine. This speed is beneficial for time-sensitive applications like clinical diagnostics. The lower purchase price also makes the technology accessible to smaller labs and institutions with limited budgets.
This accessibility provides operational flexibility, giving researchers direct control over their workflow and data. However, this control requires bioinformatics expertise. While many systems include user-friendly software, interpreting the raw data to draw biological conclusions requires data analysis skills.
A practical consideration is that benchtop systems have a lower data output, or throughput, than their larger counterparts. This makes them less suitable for sequencing a massive number of samples or very large genomes, such as in population-level studies. For these large-scale efforts, high-throughput sequencing centers are more efficient. Researchers must match the instrument’s capacity to their research goals.
Overview of the Benchtop Sequencing Process
The process of turning a biological sample into genetic data involves four main stages.
- Sample preparation: DNA or RNA is extracted from its source material, such as blood, tissue, or a microbial culture.
- Library preparation: The genetic material is fragmented, and special DNA sequences called adapters are attached to the ends. These adapters allow the fragments to attach inside the sequencer and act as starting points for the sequencing reaction.
- Sequencing run: The prepared library is loaded into the instrument, often onto a consumable flow cell or chip. The user initiates the automated run, which can take from a few hours to a day to complete.
- Bioinformatics analysis: After the run, the raw data files are processed using specialized software. This analysis assembles the short sequences, compares them to a reference genome, and identifies genetic variations or other features of interest.