Illumina’s Constellation and 5-Base Unlock New Depths of DNA Insights

Constellation offers long-range genomic insights that are enabled by loading long, unfragmented DNA directly into the flow cell. Since the DNA is not fragmented until it’s captured on the flow cell, new bioinformatic algorithms can use the location of the fragments to work out their position in the original sequence, creating the kind of long-distance insights previously not possible with short-read sequencing. This approach also has the benefit of eliminating the traditional library preparation process, which can reduce both turnaround and hand-on time, to create operational efficiencies and reduce the total cost of workflows. Constellation will initially run on Illumina's existing NovaSeq X platforms, part of Illumina's ongoing commitment to unlocking deeper biological insights on the platforms our customers already rely on for accurate, cost-effective insights.

Long-read approaches are often used today to supplement regions of the genome that are not well interrogated with standard short-read sequencing. With constellation-mapped read technology, most of those difficult regions can now be accessed by researchers sequencing on NovaSeq X. Long reads are also useful in assigning reads to parental haplotypes, especially in the absence of both parents. Constellation provides the ability to phase large haplotype blocks from standard short-read sequencing, removing the necessity to utilize a long-read technology to address these issues that routinely come up within molecular genetics labs. Additionally, long-read approaches have been historically used to detect large structural variant rearrangements. Short-read methods to detect these variants have improved greatly with advanced informatics, and constellation has now made these technologies comparable in performance.

We’re just beginning to scratch the surface on the utility of this breakthrough technology. Constellation is a powerful tool for detecting structural variants, ultra-long phasing and improving detection of large, complex structural rearrangements. We expect that constellation can resolve the genes tied to the rare and ultra-rare diseases caused by these difficult-to-detect regions.

A recent preprint in MedRXiv showed the technology’s ability to uncover complex regions such as compound heterozygous events, phased de novo mutations and structural variants within medically relevant genes. Some of these samples would have been incompatible with long-read methods due to insufficient input material.

Additionally, at ASHG, Illumina’s R&D team shared the results of combining constellation technology with DRAGEN algorithms to resolve pathogenic variants across 14 complex cell lines. We correctly resolved pathogenic variants of PMS2 in four confirmed Lynch Syndrome cases, and fully reconstructed two variants tied to congenital adrenal hyperplasia that exceeded the resolution of standard-of-care testing.

One year ago, at our strategy update, we began sharing a view into technologies in development on our innovation roadmap. Together, these technologies create the most comprehensive set of multiomic applications available on a single platform.

Constellation represents Illumina’s ongoing commitment to unlock deeper genomic insights. The speed and scalability of the technology make it optimal for translational research. Constellation’s unique combination of workflow simplicity and comprehensive view of the genome will be incredibly powerful.

We’ve since launched three multiomic solutions: Illumina Protein Prep, Illumina Single-Cell 3’ RNA, and most recently, our 5-base solution – offering the full breadth of genetic variation and methylation profiling from a single assay. With these tools available on our trusted, leading platforms, we are empowering our customers to go further in biological understanding and discovery.

Over the next several years, we will begin to see an acceleration in biological discovery fueled by multiomic analyses. These discoveries will quickly drive translational research and become the basis for future clinical applications. As we helped pave the way for clinical genomic testing, Illumina is committed to partnering with our customers and across the broader health ecosystem to generate the evidence needed to enable novel ‘omic solutions to create a transformative impact on patient lives and human health.

Illumina’s 5-base solution provides expanded insights with more complete genome and methylome detection. 5-base achieves DNA methylation detection accuracy that is comparable to traditional WGBS, with high methylation accuracy and high conversion rates. It is also has high genetic variant calling accuracy, comparable to standard whole genome sequencing, which is not achievable with WGBS. 

Illumina 5-base achieves high accuracy for both genomic variants and methylation status, outperforming other dual-omic assays, which compromise on data quality for 5mC (methylated cytosine) or small variants.

The 5-base solution is an end-to-end workflow solution that offers dual genetic variant calling and methylation profiling, eliminating the need for running multiple assays, sequencing runs or analysis pipelines. This reduces reagent and labor costs, and reduces the complexity of consolidating separate data sets. Sequencing results are processed through custom DRAGEN analysis pipelines with interpretation and visualization through Illumina Connected Multiomics. The automated secondary and tertiary analysis for data insights reduces the need for advanced bioinformatics expertise.