Low-pass sequencing plus imputation using avidity sequencing displays comparable imputation accuracy to sequencing by synthesis while reducing duplicates.

Low-pass sequencing with genotype imputation has been adopted as a cost-effective method for genotyping. The most widely used method of short-read sequencing uses sequencing by synthesis (SBS). Here we perform a study of a novel sequencing technology-avidity sequencing. In this short note, we compare the performance of imputation from low-pass libraries sequenced on an Element AVITI system (which utilizes avidity sequencing) to those sequenced on an Illumina NovaSeq 6000 (which utilizes SBS) with an SP flow cell for the same set of biological samples across a range of genetic ancestries. We observed dramatically lower optical duplication rates in the data deriving from the AVITI system compared to the NovaSeq 6000, resulting in higher effective coverage given a fixed number of sequenced bases, and comparable imputation accuracy performance between sequencing chemistries across ancestries. This study demonstrates that avidity sequencing is a viable alternative to the standard SBS chemistries for applications involving low-pass sequencing plus imputation.
Competing Interests: Conflicts of interest JHL, KF, and JKP were all employees of Gencove Inc., a private company that develops and markets software for the analysis of low-pass sequencing data, at the time of the experiment. KB, JZ, and SK were all employees of Element Biosciences, a private company that develops and markets sequencing instruments.
(© The Author(s) 2023. Published by Oxford University Press on behalf of The Genetics Society of America.)