Somatic and Germline sequencing of SureSelect Libraries on the Element AVITI System

Felicia Hawthorne, PhD Explains Somatic and Germline sequencing of SureSelect Libraries on the Element AVITI System

Summary Transcript

This is a brief overview of our experience sequencing germline and somatic samples with Agilent's SureSelect Library Prep on our AVITI system.

This study was done on a pre-release early version of AVITI, and the results of the study were made available as a data sheet by Agilent. SureSelect library prep kits were used for both somatic tumor and germline normal samples.

For the normal samples, the all human exon panel was used and a custom cancer panel was used for tumor samples. This collaborative study demonstrated the ability to leverage the current Agilent SureSelect catalog and their custom workflows without the need to develop new library prep solutions or protocols for the AVITI system.

The AVITI sequencing system can run independent flow cells on either side of it. So on one side, you could run your germline exome samples while the other runs your somatic targeted samples. Using the 2X150 sequencing kit each flow cell can generate up to a billion reads in under 48 hours. So you can run 60 paired germline and somatic samples and yield 5G per sample. To assess the sequencing quality we looked at the percent passing filter and Q30.

And as you can see in the table with the germline exome panels and the targeted panels, deeper sequencing of somatic samples yielded high percent passing filter and high Q30. Now again, remember, this was done using a prerelease version of the product.

So you'll find the data published from studies on the launch version of the product have even better data quality. Next variant calling performance for germline samples shown in the top table were evaluated by looking at the recall or percent known variants called correctly and precision or percent of calls that were known variants.

While for somatic samples shown in the bottom table, we assessed their accuracy of detected versus expected frequency for variants. And as you can see, a high alignment was demonstrated even for variants with 5% and lower frequency. Additionally, key sequencing metrics such as fold 80, duplication rate, and coverage demonstrated robust sequencing data generated from germline exome samples and deeper somatic samples where higher duplication rates are expected.

I hope this overview is helpful to highlight how easily the AVITI system can enable you to do more as you plan your next project. I would also like to extend our thanks to our partners at Agilent for their collaboration and support.

For more details on the performance of the AVITI with SureSelect Library Prep for germline and somatic samples, please feel free to download the datasheet from the Element website and look for new products using the AVITI system. Thank you.