In high-throughput genomics laboratories, the pressure to run more samples per instrument at lower cost falls upstream: on library preparation, sample batching logistics, and the indexing strategies that determine how many distinct libraries a single sequencing run can reliably separate. As clinical and research demand for next-generation sequencing (NGS) grows across oncology, rare disease diagnostics, and reproductive health testing, indexing capacity has become a practical bottleneck between sample volume and instrument utilization.
OGT expanded its SureSeq Universal NGS Unique Dual Index (UDI) range to support multiplexing of up to 384 uniquely indexed samples per sequencing run, a fourfold increase from the prior ceiling of 96. The expansion slots into existing SureSeq workflows and software, so laboratories can scale throughput without redesigning library preparation protocols or data analysis pipelines.
Index count sets the hard ceiling on NGS multiplexing capacity
Index count determines how many distinct libraries can coexist in a single sequencing pool: each library receives a short, distinctive nucleotide sequence attached before pooling, and those sequences sort reads back to their source samples during a computational step called demultiplexing. The number of available unique index combinations sets an absolute cap on per-run sample capacity. Increasing that number directly lifts the cap.
Indexing architecture also affects data quality. On Illumina platforms using patterned flow cells and exclusion amplification (ExAmp) chemistry, including the HiSeq 4000, NovaSeq 6000, and NextSeq 2000, a phenomenon called index hopping causes reads from one library to be misassigned to another. Estimates suggest index hopping affects up to 2 percent of reads on ExAmp-based platforms, a small proportion that becomes consequential in sensitive applications such as low-frequency variant detection or measurable residual disease monitoring.
Unique dual indexing resolves the misassignment problem by giving each library a combination of i7 and i5 index sequences used nowhere else in the pool. Any index-hopped read carries a barcode pair absent from the sample sheet and gets discarded automatically during demultiplexing. Benchmarking data show that UDI cuts cross-contamination 100-fold relative to combinatorial dual indexing, from above 1 percent down to below 0.01 percent even on ExAmp-based systems.
What does the SureSeq UDI expansion include?
The expanded range raises indexing capacity from 96 to 384 unique dual indexes while matching the performance of the validated UDI 1-96 index sets, with no changes to established SureSeq library preparation or data analysis workflows. Key specifications include:
- 384 uniquely indexed samples per sequencing run, up from 96
- Drop-in compatibility with existing SureSeq library preparation workflows and data analysis software
- UDI architecture on all index pairs, enabling automatic flagging and removal of index-hopped reads at demultiplexing
- Performance matched to the validated UDI 1-96 index sets across the SureSeq NGS panel range
- Designed for use with high-capacity Illumina sequencing systems
Gareth Thomson, Executive Vice President of Commercial Operations at OGT, described the expansion as a response to a specific operational constraint. "As sequencing demand continues to grow, laboratories need practical ways to increase throughput without adding complexity," Thomson said. "By expanding SureSeq Universal NGS indexing capacity to 384 samples per run, we're helping laboratories reduce batching constraints and costs per sample to maximise the value of their existing sequencing infrastructure."
Higher multiplexing directly lowers per-sample sequencing costs
Pooling four times as many samples per run distributes fixed instrument costs across more libraries, lowering per-sample reagent spend without purchasing additional sequencers or altering validated protocols. Industry analysts identify ultra-high multiplexing as a primary mechanism through which labs cut upstream preparation costs, driven by the declining cost of sequencing itself, which sharpens scrutiny of library preparation expenditure. The global NGS market was valued at approximately $10.44 billion in 2025 and forecast to reach $11.79 billion in 2026, with the clinical application segment holding the largest share of demand.
The table below summarizes the UDI indexing landscape by supplier category.
| Supplier category | Typical max samples per run | Index architecture | Regulatory status |
|---|---|---|---|
| OGT SureSeq Universal NGS UDI (expanded) | 384 | Unique dual index (UDI) | Commercial kit |
| Established NGS reagent suppliers | Up to 384 (in sets of 96) | Unique dual index (UDI) | Commercial kit |
| Specialist RNA-seq indexing systems | 384+ (nested, error-correcting designs) | Unique dual index (UDI) | Commercial kit |
| Laboratory-developed indexing approaches | Variable | Combinatorial or unique dual index | In-house validated |
Across the market, 384-sample UDI capacity has become the emerging standard for laboratories running high-output Illumina instruments, with most commercial kit suppliers converging on that ceiling. SureSeq now matches that benchmark while retaining compatibility with established workflows.
SureSeq UDI expansion and the hematology panel portfolio
The 384-plex UDI capacity matters most in applications where a single misassigned read at low allele frequency can generate a false positive call. OGT's hematological malignancy panel portfolio supplies exactly those use cases. In November 2025, OGT launched the SureSeq Myeloid MRD Plus NGS Panel, covering 16 biomarkers associated with acute myeloid leukemia (AML), including FLT3 internal tandem duplications (ITDs) and NPM1, with variant detection as low as 0.01 percent allele frequency.
AML cohorts that require measurable residual disease (MRD) monitoring generate repeated sequencing samples across multiple patient time points, placing high demand on both per-run capacity and per-sample data fidelity. A 384-plex UDI system addresses both constraints simultaneously: it processes more samples per run while the UDI architecture ensures reads are correctly attributed to their source library at the sensitivity levels MRD monitoring requires.
Expanding the SureSeq multiplexing platform
The SureSeq platform has moved from 96-plex to 384-plex indexing in step with a growing hematology-focused panel menu, reflecting the increasing NGS sample volumes that laboratories in oncology, rare disease diagnostics, and reproductive health programs are managing. For laboratories where the 96-sample ceiling forced multi-batch workflows, the expansion reduces instrument run time, hands-on preparation, and per-sample reagent spend in a single product change. The trajectory of the platform points toward continued throughput scaling as the clinical adoption of NGS broadens across Europe and North America.
This article is based on a press release issued by OGT and was produced under Drug Discovery News' AI Editorial Guidelines.
