Cost-Effective Trio Sequencing - Semyon Kruglyak, PhD

Semyon Kruglyak, PhD - VP of Informatics at Element Biosciences

  • AVITI™ System enabled benchtop trio sequencing, on a single flow cell, for $1,680 in sequencing reagent costs
  • Element Elevate Library Prep is simple and effective for whole genome sequencing
  • DeepTrio from Google enables high-quality variant calling when parental genome coverage is reduced
  • Franklin by Genoox efficiently identifies variants likely to be causal for the phenotype
  • All components above have been integrated to analyze a previously undiagnosed rare eye disease case

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Transcript of Q&A Session

Q: In regards to library prep, is this closer to HyperPlus?

A: We work with HyperPlus and HyperPrep, but we are fairly agnostic. There’s a long list of supported third party providers that we are compatible with. View full list here.

Q: Is there a way to compare the same genomes that you can run on, for example, Illumina? It seems like there are similar workflows.

A: Yes, we use our Elevate™ library prep workflow with Roche KAPA. But if you want to do a transposon-based prep, that will be OK too.

Q: In regards to the rate of switching from one spot to another between Read-1 and Read-2 — how have you dealt with getting the optics realigned exactly in the right place?

A: We generate our feature set based on Read-1 and then the features don’t really move. You can correct for the various optics and you can map. Because this is a random flow cell, there’s only one unique mapping — so you take the images of Read-2 and very accurately map them back onto the Read-1 map that was previously generated. From what we have seen, switching spots between Read-1 and Read-2 is extremely rare.

Q: Looking to the future, where is Element Biosciences heading?

A: It’s relatively new technology, so there’s a lot of headroom in all dimensions. We promise 800 million read pairs but the run shown here is 1.1 billion. We are working to determine which improvement directions would be of greatest value to the customer.