This presentation provides a comprehensive update on Stratogenomics' Sequencing by Expansion (SBX) technology, detailing recent advancements across its duplex (SBXD) and simplex (SBXS/SL) platforms. Key achievements include reducing whole-genome sequencing (WGS) time to under five hours from sample to variant call (SBXFAST), significant improvements in accuracy with Q40+ average duplex base quality and enhanced F1 scores for SNVs, indels, and homopolymer regions (up to 21 bases). The video introduces the successful generation of first-ever data for Formalin-Fixed Paraffin-Embedded (FFPE) tumor profiling, demonstrating superior performance against Illumina in terms of error rates and GC coverage uniformity, and for Minimal Residual Disease (MRD) detection at an estimated 10^-6 tumor fraction with Q50-type accuracy. The SBX platform, founded on expandomer chemistry and an 8-million nanopore array with sophisticated translocation control, also showcases high throughput (e.g., 14 billion valid reads/hour for 10xFlex) and robust long-read capabilities (averaging over 1000 bp), enabling advanced genomic phasing and Variable Number Tandem Repeat (VNTR) resolution. The company emphasizes continuous optimization, concurrent data analysis, and plans for a 2026 launch, with future applications including target enrichment and methylation.
Exploring Stratogenomics' SBX Technology: Breakthroughs in Speed, Accuracy, and Applications
0:00 Introduction & Context: The presentation updates on Stratogenomics' Sequencing by Expansion (SBX) technology, referencing prior webinars, a preprint, and an AGBT launch, emphasizing flexibility, performance, and cost efficiency.
0:49 Agenda & Key Improvements: The agenda covers updates on SBX duplex and fast sequencing, new data for FFPET and MRD, and simplex applications for RNA and DNA, highlighting continuous improvements in data accuracy.
1:26 Core Technology & Performance Goals: The SBX approach aims for flexible single-molecule sequencing (e.g., 4 minutes to several hours), high accuracy (Q20 for simplex, higher for duplex), and throughput (500 million bases/second), targeting sample-to-VCF in under 5 hours at cost-efficient rates.
3:17 SBX Technology Foundation: The technology combines Stratogenomics' SBX chemistry with the Genia high-throughput sensor array, using an "expandomer" molecule as a DNA surrogate to improve signal-to-noise for nanopore sequencing.
4:41 Expandomer Design & Synthesis: The core is the expandable nucleotide (XNTP), featuring a reporter tether, cleavable bond, translocation control, and incorporation enhancers. Synthesis occurs on a chip, converting DNA templates into clean expandomers.
7:07 Nanopore Translocation Control: A critical element for efficiency and quality is a "translocation control" mechanism that holds the expandomer in the nanopore for statistical sampling, then rapidly advances it using microsecond pulses.
8:41 High-Throughput Array & Reuse: The system scales to an 8 million nanopore array. The sequencing instrument allows cyclical reuse of the sensor module, which is vital for cost reduction. Initial runs yield over 7 million sequence-quality pores.
11:37 Duplex Sequencing (SBXD) for Accuracy: SBXD utilizes Y-adapters and hairpin structures to generate intramolecular consensus reads, achieving very high accuracy. It is applied to MRD, rapid Whole Genome Sequencing (WGS), and FFPET.
13:45 SBXD Performance Update: Recent data from Genome-in-a-Bottle samples show 5 billion duplex reads in a 1-hour run, achieving Q40 average duplex base quality and 99.9% coverage at >10X, with significantly improved F1 scores for SNVs and indels.
15:22 Homopolymer & GC Coverage in SBXD: Achieves F1 scores >99% for homopolymers up to 17 base pairs. Demonstrates good coverage uniformity across the GC spectrum, performing particularly well in high GC regions.
16:18 SBX Fast Workflow for Rapid WGS: This amplification-free SBXD variant (using 2 micrograms of DNA) has reduced sample-to-VCF time to 4 hours 23 minutes (from 6h 25m in February), aided by concurrent data analysis and aiming for trio sequencing within a workday.
21:24 First-Ever FFPE Data: A new SBXD-like workflow, including DNA repair steps, demonstrates lower SNV/indel error rates, higher homopolymer accuracy, and better coverage uniformity in high GC regions for 18 matched normal-tumor FFPE samples compared to Illumina, showing ~10% better recall in non-difficult regions.
26:12 First-Ever MRD Data: The SBXD protocol, applied to 15 cancer samples (4 ng DNA), successfully detected positive Minimal Residual Disease (MRD) at an estimated tumor fraction of 1 to 10^-6, achieving Q50-type accuracy through super consensus collapsing.
28:00 Simplex Sequencing (SBXS/SL) for Throughput & Long Reads: SBX-S (reads <500bp) and SBX-SL (reads >500bp) offer higher throughput and the potential for longer reads. Example throughputs include 14 billion CellRanger valid reads/hour for 10xFlex and 4 billion reads/hour with a 500 bp average length for 10x 5' mRNA.
29:46 Simplex for Genomic DNA Phasing & VNTRs: SBXSL enables the detection of Variable Number Tandem Repeats (VNTRs) and complex allele phasing (e.g., a pathogenic compound heterozygous variant in hyperphenylalanemia) that shorter reads cannot resolve. A 1-hour run yielded a billion reads with an average length of almost 1,000 bases.
33:08 Conclusion & Future Outlook: Stratogenomics is rapidly advancing SBX FAST (sub-5hr WGS), FFPE, and MRD applications, emphasizing continuous optimization. The technology is slated for launch in 2026, with plans to expand into new areas like target enrichment and methylation.