Publication Highlights: Accuracy of Element Biosciences Avidity Sequencing
Arslan, Sinan, Francisco J. Garcia, Minghao Guo, et al., “Sequencing by avidity enables high accuracy with low reagent consumption,” Nature Biotechnology (May 2023).
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#1. Accuracy of Element Biosciences Avidity Sequencing
To evaluate the accuracy of avidity sequencing, 20 sequencing runs were performed using a well-characterized human genome. Combined over reads 1 and 2, 96.2% of base calls were >Q30 (an average of one error per 1,000 bp) and 85.4% >Q40, with a maximum of Q44, or approximately one error in 25,000 bases.
Fig. 3 | Predicted and observed quality scores for a 2 × 150-bp sequencing run of human genome HG002. a, Read 1 (R1). b, Read 2 (R2). Points on the diagonal indicate that predicted scores match observed scores. The histograms show that the majority of the data points are >Q40.
#2. Substantial improvements in accuracy across difficult-to-sequence regions compared to Illumina.
Sequencing through long homopolymers has posed challenges for multiple sequencing technologies. Figure 4 shows the results comparing avidity sequencing with SBS, averaged across the ~700,000 homopolymer loci of length 12 or more. Average error rate of avidity sequencing remained stable following a long homopolymer (controlling for the fact that post-homopolymer stretch occurs in later cycles of a read). By contrast, the error rate of SBS reads increased by more than a factor of five following homopolymer stretches. The avidity sequencing error rate outperformed SBS in >97% of cases and the magnitude of difference is correlated with homopolymer length (Fig. 5).
Fig. 4 | Post-homopolymer performance across platforms. Mismatch percentages of AVITI, NovaSeq 6000 and NextSeq 2000 reads before and after homopolymers of length 12 or greater.
Fig. 5 | Comparison of mismatch rate following homopolymers of length between four and 29. Mismatch percentage difference between avidity sequencing and SBS increases with homopolymer length. The box plot shows median, quartiles and whiskers, which are 1.5× interquartile range.
Carroll, Andrew, Alexey Kolesnikov, Daniel E. Cook, et al., “Accurate human genome analysis with Element Avidity sequencing,” bioRxiv (August 2023)
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Element data achieves greater variant calling accuracy over a range of coverages, with especially improved accuracy in the 20x-30x coverage range. We identify certain sequence contexts in which Element outperforms Illumina reads, including in tandem repeats and homopolymers, as measured by soft-clipping rates.
Proportion of soft-clipped bases in Element and Illumina reads across the genome and in repetitive regions.
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