Cost-efficient whole genome-sequencing using novel mostly natural sequencing-by-synthesis chemistry and open fluidics platform

Abstract

We introduce a massively parallel novel sequencing platform that combines an open flow cell design on a circular wafer with a large surface area and mostly natural nucleotides that allow optical end-point detection without reversible terminators. This platform enables sequencing billions of reads with longer read length (~300bp) and fast runs times (<20hrs) with high base accuracy (Q30 > 85%), at a low cost of $1/Gb. We establish system performance by whole-genome sequencing of the Genome-In-A-Bottle reference samples HG001-7, demonstrating high accuracy for SNPs (99.6%) and Indels in homopolymers up to length 10 (96.4%) across the vast majority (>98%) of the defined high-confidence regions of these samples. We demonstrate scalability of the whole-genome sequencing workflow by sequencing an additional 224 selected samples from the 1000 Genomes project achieving high concordance with reference data.

Pseudoalignment facilitates assignment of error-prone Ultima Genomics reads

“…In the Ultima Genomics preprint (Almogy et al 2022), the company discusses the challenges of sequencing homopolymers with their non-terminating chemistry, but touts an accuracy of 90% for homopolymers of length 8, and characterizes this as "good accuracy up to length 8-10 bases". We find that in the Ultima Genomics single-cell RNA-seq reads, the homopolymer challenge presents as more acute than what may be imagined from summary statistics.…”

“…The TMSB4X example demonstrates that Ultima Genomics displays poor performance not only in regions with long homopolymer runs, extreme GC content, or highly repetitive sequences. While the genome-wide accuracy of Ultima Genomics technology is likely to be better than for the TMSB4X gene, a comprehensive assessment of the error profiles was not possible because at the time of writing of this preprint, the data in (Almogy et al 2022) has not been released (the preprint states that “the data will be made available in the near future”). However, regardless of the genome-wide performance of Ultima Genomics technology, it is worth noting that improvement of sequencing technology is best guided by understanding worst-case performance.…”

“…Hopefully Ultima Genomics will eventually find a way to reduce error rates so they can be competitive with existing technologies. The “many degrees of freedom” provided by their architecture design (Almogy et al 2022) is possibly reason for optimism. The genomics community is already benefiting from cost reductions following the introduction of BGI sequencers (Drmanac et al 2020; Hahn et al 2021; LeMieux 2020), and will benefit even further if Ultima Genomics can similarly reduce sequencing costs.…”

“…Despite numerous improvements in DNA sequencing technology and dramatic reductions in the price of sequencing over the past fifteen years (LeMieux 2019; Goodwin, McPherson, and McCombie 2016), the cost of sequencing can limit the scope of projects for biology labs (Haichao Li et al 2019), and is a barrier to adoption of routine sequencing in the clinic (Schwarze et al 2020). The recently unveiled Ultima Genomics sequencing technology (Almogy et al 2022) has been advertised as providing a solution to these challenges by way of delivering high-throughput sequencing at a small fraction of the cost of current technologies (“Ultima Genomics Delivers the $100 Genome” 2022) 1 .…”

Ultra high-throughput whole-genome methylation sequencing reveals trajectories in precancerous polyps to early colorectal adenocarcinoma

“…The Ultima Genomics (UG) sequencing platform utilizes a new sequencing architecture that combines an open flow cell design on a circular wafer with large surface area, utilizing rotational reagent delivery, optical end-point detection, and mostly natural nucleotides without reversible terminators. This platform enables sequencing billions of reads with high base accuracy (Q30 > 85%), at significantly reduced cost versus conventional sequencing platforms 24 , thereby allowing efficient generation of comprehensive WGMS data. In this study we used the UG platform to sequence 44 WGMS samples along the FAP tumor progression from normal mucosa to adenocarcinoma at high coverage (30-60X).…”