PAG 2023, San Diego, CA
Low Pass Sequencing in Animals: Element Biosciences AVITI as a Useful Platform
Jacky Carnahan1, Ryan Ferretti1, Chuanyu Sun1, Tracee Stucky1, Mathias Schulte1, Lindsay Ridlen1, Benjamin Krajacich2, Junhua Zhao2, Isaku Tanida2, Jesse Hoff3, Niraj Patel1, and Rich Tait Jr.1
1Neogen Genomics, Lincoln, NE 68504
2Element Biosciences, San Diego, CA 92121
3Gencove, New York, NY 10016
Low pass sequencing combined with imputation is becoming a widely adopted tool for agricultural and companion animal applications. Combining the two yields more genotypes per dollar than other genetic screening platform. To provide high-quality data and rapid turnaround times for a multitude of applications, high throughput sequencing must be dynamic. Instead of using a production scale sequencer, which requires thousands of samples per run, we explored leveraging a benchtop sequencer which requires hundreds of samples to achieve these objectives.
In this study we compared data quality and consistency from a production scale sequencer to a benchtop sequencer. Libraries were prepared utilizing a miniaturized library preparation method, normalized, and pooled for sequencing. The library pool was divided with one portion being sequenced at Neogen Genomics, and the other processed using the Element Adept Compatibility workflow before sequencing on the Element AVITITM System. All libraries were sequenced to a target of less than 1x coverage.
Demultiplexed fastqs were adapter trimmed, imputed using the Gencove imputation platform, and analyzed for concordance. Analysis showed comparable sequencing performance metrics between the two platforms (91% >Q30 with AVITITM vs 90% on the production sequencer). Overall data consistency was high when compared across the two platforms with >99% concordance for imputed genotypes. Because fewer samples are needed to fill sequencing runs, faster turnaround times can be achieved with the Element AVITITM System while maintaining data quality and consistency at a price point similar to production level sequencers.