Rare Access: DNA Operations and Sequencing Pipelines

Rare Access: DNA Operations and Sequencing Pipelines

DNA Operations at Demetrix

Our Rare Access interview this month features Anna Lee, scientist on the DNA operations team at Demetrix. Anna focuses on building genotype strains at a high throughput, with the goal of making processes more efficient and robust.

Click below to view her interview

Welcome Anna thanks for joining us! So Anna would you mind just letting people know your background and current role at the Demetrix?

Sure, my background is in synthetic biology and I was very interested in engineer back to behaviors and using computational models for optimizing and predicting their behaviors. After my studies I moved to the Bay Area, and I’ve been working in the biotech industry for about three years now. Currently as a scientist in the DNA operations team, I’m responsible for maintaining, troubleshooting, and optimizing our automated R&D pipelines.

So what are some of the main goals and objectives for your team in DNA operations?

We strive to make new strain development process both time and cost efficient. To do so the main goal of our team is to make R&D activities more efficient and at a higher throughput by providing the tools. For that, we have multiple pipelines that support R&D activities at Demetrix and we also actively communicate with other teams to find different ways to help and to provide new tools as necessary. We aim to ensure that each process is robust and scalable so that we can support the increase in R&D activities as Demetrix grows.

So what are some of these different pipelines that you’re currently working on?

 We have three main pipelines. Each one has a DNA sequencing component, but each one is also very unique. We have a DNA sequencing pipeline, a Colony PCR sequencing pipeline, and a Whole Genome Sequencing pipeline. The first pipeline is used for high throughput DNA building. To continuously build and test new strains we need to build a large number of synthetic DNA parts with different promoters, genes and so on. Our DNA building pipeline integrates software tools and automation so that the process is streamlined and we can build large number of DNA parts in a relatively short period of time. Newly engineered strains using those synthetic DNA parts can be diagnosed with another pipeline which is called colony PCR sequencing pipeline. It allows quick assessment of whether intended genetic modification was successful. We implemented unique barcoding and design strategies so that we can have a standardized method for quickly assessing the new strains when there are strains of a particular interest from screening process either from micro fermentation or large scale fermentation. We use whole genome sequencing to determine the DNA sequences over our strains genome. By checking the strains with whole genome sequencing, scientists can get the full picture about the strain, detect any intended or unintended mutations, and also find correlations between the strain’s behaviors and their genetic background.

What can people expect from the DNA operations team this year as well as next year?

 As we are growing rapidly we want to make sure that we have capacity to support the increased demand in R&D activities. We continuously look for ways to improve each pipeline, making it more accurate and make it higher throughput so that we can make our research process more efficient.

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