Tue 23rd January 2018
Join Rachel Rubinstein in this Knowledge Exchange to learn:
- How to use "WIMP" for non-traditional sequencing analysis
- General extraction methods for success in Nanopore Sequencing
- How an industrial biotech company incorporates Nanopore sequencing for many applications
Rachel Rubinstein is a member of Team NGS at Ginkgo Bioworks, Inc. located in Boston MA. At Ginkgo, she works on the operation and development of highly automated, high-throughput next-generation sequencing pipelines, as well as handling nanopore sequencing for multiple parts of the company. Rachel graduated from Tufts University with a BS in Biology and Spanish, where she wrote her Honors Thesis on nanopore sequencing of secondary-structure-forming DNA sequences.
Large-scale fermentation is a critical process in the successful deployment of Ginkgo Bioworks’ products such as fragrances, flavors, and speciality enzymes. As such, rapid identification of contamination that occurs at this scale is imperative to ensuring successful deployment of the product as well as maintaining high quality and industry standards. Often, the identification of contaminants using traditional methods such as next-generation Illumina sequencing and NCBI BLAST is too time consuming, with results being returned much too late for tangible action. However, the Oxford Nanopore MinION, along with the WIMP (What’s in my pot) real-time analysis workflow, allows for sequencing and rapid identification of potential bacterial and fungal contaminants in less than one day. Using extracted DNA from an offsite fermentation sample, we at Ginkgo Bioworks were able to identify a bacterial contaminant in approximately eight hours from receipt of sample. This quick identification allowed for significant decisions to be made about the fermentation run before it was finished, in turn protecting the product, saving thousands of dollars, and influencing decisions for the post-processing of the sample.
If you miss the event it will be posted on this page for on-demand viewing.
Time: 3pm (GMT)
Other timings: 4pm CET, 10am EST, 7am PST, 11am EET
Rachel Rubinstein i
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