Automation of Exome Sequencing

Automating exome sequencing involves using specialized technologies and systems to streamline the process:

• Sample Preparation Robotic systems handle the extraction of DNA from biological samples (e.g., blood, tissue). Automated liquid handling platforms ensure precise pipetting and mixing of reagents for DNA isolation.
• DNA Fragmentation DNA is mechanically or enzymatically fragmented into smaller pieces. Automated systems precisely control fragmentation, ensuring uniform sizes for sequencing.
• Exonic Region EnrichmentAutomated systems use hybridization-based methods (e.g., capture probes) to selectively enrich the exonic regions of the DNA. Magnetic beads or other solid-phase technologies are used to isolate the enriched exonic fragments.
• Library Preparation  DNA fragments are converted into sequencing libraries. Automated systems such as the Opentrons Flex NGS Workstation can handle the steps of end-repair, adapter ligation, and PCR amplification, ensuring consistency and reproducibility.
• Sequencing High-throughput sequencing platforms automatically process and sequence the enriched exonic regions, generating raw data.
• Data Analysis Computational pipelines automatically process the sequencing data to align sequences, call variants, and perform quality control checks. Automated bioinformatics tools identify potential mutations or variants related to specific conditions.

Automate Exome Sequencing with Opentrons:

Interested in automating your lab’s sample and library prep processes? Enter the Opentrons Flex, a walk up, no-code pipetting robot that scales with your lab. Let us handle the pipetting while you spend more time on science.

Benefits of Automation Over Manual Methods

• Increased Speed: Automation speeds up tasks like pipetting, digestion, and ligation, reducing overall process time.
• Improved Reproducibility:Machines ensure consistent protocols, minimizing human error and delivering reliable results.
• Higher Throughput: Automation allows for handling larger sample volumes simultaneously, ideal for high-throughput projects.
• Better Accuracy and Precision: Robots perform tasks with higher precision, reducing contamination and errors.
• Cost Savings: Though the upfront cost is high, automation reduces labor and reagent waste in the long run.

Methods of Exome Sequencing

Capture-Based Exome Sequencing

This is the most common method for exome sequencing, using hybridization techniques to selectively capture the exonic regions. DNA is fragmented, and capture probes (oligonucleotides complementary to the exonic regions) are used to bind and isolate these regions. The captured DNA is then sequenced.

PCR-Based Exome Sequencing

This method uses polymerase chain reaction (PCR) to selectively amplify the exonic regions of interest before sequencing. Specific primers are designed for each exonic region to amplify them, and then the amplified regions are sequenced.

Targeted Exome Sequencing (Amplicon Sequencing)

This method focuses on sequencing specific exonic regions of interest using targeted primers. DNA is amplified using primers that target specific exonic regions, and then sequencing is performed on those targeted regions.

Exome Sequencing Using Long-Read Technologies

Long DNA fragments are sequenced to directly capture and analyze exonic regions. Longer read lengths can improve accuracy in identifying complex variants, structural variants, and phasing of mutations.