Welcome to the wild world of genomics, where science meets serious problem-solving—and plenty of innovation. The Center forAdvanced Technology (CAT) at UCSF, led by Dr. EricChow, Associate Professor, Biochemistry and Biophysics, is at the forefront of providing cutting-edge sequencing services and technology access to researchers. In a recent interview, Eric shared insights into the facility’s operations, the challenges they faced in high-throughput sequencing, and how adopting the n6 iconPCR has significantly improved their workflow.
WhatDoes the CAT Facility Do?
The CAT facility serves as a core resource for the UCSF campus, offering both short and long-read sequencing on high-throughput platforms. Beyond sequencing, the facility provides access to essential equipment for sample preparation, extraction, quality control, and quantitation—resources that are often too expensive or inaccessible for individual labs. The CAT also offers training and 24/7 access, ensuring researchers can prepare their samples efficiently. Additionally, the facility has an R&D arm focused on developing new technologies and methods in next-generation sequencing (NGS), including bulk, single-cell, and spatial applications.
The Challenge: Variability and Inefficiency in PCR Amplification
One of the main pain points for the CAT team was handling metagenomic sequencing from clinical samples, which often have highly variable and sometimes unquantifiable input amounts. This variability made it difficult to choose the optimal number of PCR cycles, leading to some samples being over-amplified (causing issues like adapter dimers) and others under-amplified (resulting in insufficient library for sequencing). For precious or limited samples, this risk was especially acute—if a sample was under-amplified and there wasn’t enough material left to try again, that data could be lost for good. Traditional methods for monitoring and adjusting amplification were labor-intensive and not scalable for large sample sets, compounding the risk and inefficiency.
The Solution: iconPCR
The introduction of iconPCR brought a game-changing level of automation and precision. With iconPCR, each sample can be amplified to its optimal amount automatically, without manual intervention.The software determines the right threshold, and researchers can process a full96-well plate in one run, with each sample perfectly amplified. This not only saves time but also ensures consistency and quality across all samples.
Workflow Improvements and Cost Savings
iconPCR has streamlined the CAT facility’s workflow in several ways:
- Automated Quantification: The system provides quantification data immediately after PCR, eliminating the need for separate quantitation steps and reducing consumable costs.
- Simplified Pooling by Volume: With iconPCR, samples are amplified to similar levels, so pooling can often be done using a single pipette setting or multichannel pipette—saving time and ensuring balanced sample representation.
- Reduced Labor and Consumables: The need for individual cleanups, quantitation runs, and extra sequencing pilots is greatly reduced, saving both time and money.
- Higher Sequencing Efficiency: By minimizing over-amplification and adapter dimer formation, more samples can be included in each sequencing run, maximizing throughput.
Ensuring Sample Quality and Reducing Dropouts
Eric emphasized that, in genomics, some samples are truly irreplaceable—whether due to limited availability, cost, or the unique nature of the material. Losing such a “precious sample” to dropout isn’t just a minor setback; it can mean the permanent loss of critical data.With iconPCR, the CAT facility can amplify each sample just enough to ensure success, dramatically reducing the risk of dropout. This precise control is especially vital when working with limited or valuable material, providing peace of mind that every sample—no matter how precious—gets the best possible chance at success.
Looking Ahead
The CAT facility continues to explore new ways to leverage iconPCR’s capabilities, excited by the unique data and workflow improvements it offers. As genomic applications scale up, tools like iconPCR will be essential for maintaining high quality, efficiency, and cost-effectiveness in sequencing workflows.
Final Thoughts
Eric Chow’s experience and journey with iconPCR is proof that science doesn’t have to be all pipettes and paperwork—it can be a playground for innovation, too. By tackling the age-old headaches of sample prep and amplification, iconPCR lets researchers spend less time troubleshooting and more time geeking out over their discoveries. The CAT facility’s story is a reminder that with the right tools, even the trickiest workflows can be tamed. Here’s to more breakthroughs, fewer dropouts, and enabling researchers to focus on discovery rather than troubleshooting technical hurdles.
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