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Updated: Jul 9, 2025
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Rare Event Detection Using Error-corrected DNA and RNA Sequencing
Published on: August 3, 2018
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Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by
Jeremiah H Li1, Karrah Findley1, Joseph K Pickrell1
1Gencove, NewYork, NY 11101USA.
G3 (Bethesda, Md.)
|December 1, 2023
Summary
Avidity sequencing offers a cost-effective alternative for low-pass sequencing and genotype imputation. This novel method shows lower duplication rates and comparable imputation accuracy to standard sequencing by synthesis (SBS).
Area of Science:
- Genomics
- Next-Generation Sequencing Technologies
Background:
- Low-pass sequencing combined with genotype imputation is a cost-effective genotyping strategy.
- Sequencing by synthesis (SBS) is the predominant short-read sequencing technology.
Purpose of the Study:
- To compare the performance of avidity sequencing against SBS for low-pass sequencing and genotype imputation.
- To evaluate imputation accuracy across diverse genetic ancestries using both sequencing methods.
Main Methods:
- Low-pass libraries from biological samples of varied ancestries were sequenced using Element AVITI (avidity sequencing) and Illumina NovaSeq 6000 (SBS).
- Optical duplication rates and effective coverage were analyzed.
- Genotype imputation accuracy was assessed for both platforms.
Main Results:
- Avidity sequencing on the AVITI system exhibited significantly lower optical duplication rates compared to SBS on the NovaSeq 6000.
- Lower duplication resulted in higher effective sequencing coverage for a fixed number of bases.
- Imputation accuracy was comparable between avidity sequencing and SBS across different genetic ancestries.
Conclusions:
- Avidity sequencing is a viable and effective alternative to SBS for low-pass sequencing applications.
- This technology provides comparable genotype imputation accuracy with improved data quality metrics.
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