Illumina Launches TruPath Genome in Taiwan: Proximity Mapped Read Technology Brings the Genome’s “Dark Regions” into the Light

On April 30, 2026, Illumina hosted the “Unlocking Deeper Biology Conference” in Taiwan to officially introduce its new TruPath™ Genome whole-genome sequencing solution to the local medical and biotech communities. Built around proximity mapped read technology—previously known internally as constellation mapped read technology—the platform was presented during the event. Illumina General Manager for Taiwan, Hong Kong and Macau, Jerry Cheng opened the conference, followed by talks from Dr. Vincent Hsieh, Dr. Ian Chang, and Dr. Niu Dao-ming of Taipei Veterans General Hospital, who shared the latest in multiomics advances and real-world clinical research applications.

The meeting centered on solving long-standing bottlenecks in traditional short-read sequencing, particularly in the genome’s “dark regions” and complex structural variants. By simplifying sample preparation, adding AI-assisted interpretation, and delivering long-fragment positioning information, TruPath™ Genome offers a true end-to-end solution from sample to clinical insight. Attendees from major medical centers and biotech companies showed strong interest, underscoring Taiwan’s growing focus on next-generation precision medicine tools.

Multiomics Innovations Align with Global Trends from AGBT and ACMG

Dr. Vincent Hsieh detailed how Illumina is expanding from traditional genomics into full multiomics. He highlighted the company’s 5-Base methylation technology, which produces whole-genome sequencing (WGS) data plus methylation information at 28 million CpG sites in a single run—delivering roughly 30 times more data density than conventional methylation arrays. Using an enzyme-based conversion method instead of traditional bisulfite treatment, the approach minimizes DNA damage and is well-suited for early cancer detection and tracking molecular residual disease.

Through the acquisition of Fluent BioSciences, Illumina now offers a single-cell RNA sequencing solution that scales easily from about 2,000 to one million cells without needing expensive instrumentation. This makes it a practical tool for drug development, immune microenvironment analysis, and treatment response stratification. On the proteomics front, the SomaLogic acquisition brings Illumina Protein Prep 9.5K technology, which can detect nearly 9,500 proteins from a single drop of blood with excellent stability and low coefficient of variation—enabling more objective disease assessment and the discovery of new protein biomarkers.

Dr. Hsieh noted that integrating these multiomics datasets with the richer genomic signals from TruPath™ Genome will create a more complete picture of biology. He also updated the audience on Illumina’s AI progress, led by scientist Dr. Kyle Farh. The team has developed tools such as PrimateAI-3D, SpliceAI, and PromoterAI, which have been published in leading journals including Nature, Cell, and Science, with plans to integrate them further into research and clinical workflows.

TruPath™ Genome Brings Long-Range Mapping to the NovaSeq X Platform

TruPath™ Genome uses long-range mapping capabilities to run up to 16 whole-genome sequencing samples per day on the NovaSeq™ X series. Sample preparation takes just 10 minutes of hands-on time, skipping the traditional library prep steps of fragmentation and size selection. At a cost of only $395 per sample (excluding tariffs and shipping).

Speakers emphasized that the technology continues Illumina’s “one instrument, many applications” approach while giving the field a practical path from raw data generation to meaningful biological insights.

DRAGEN™ and Emedgene Get Major Upgrades for Faster, Smarter Analysis

Dr. Ian Chang focused on the backend bioinformatics side. The newly enhanced DRAGEN™ algorithm includes dedicated mapping and phasing modules for TruPath™ Genome. By linking physical coordinates on the flow cell with genomic coordinates, it creates phase blocks spanning millions of base pairs and dramatically reduces false-positive structural variant (SV) calls. The system also generates intuitive colocation plots—similar to Hi-C contact maps—that help researchers quickly spot and pinpoint complex events such as deletions, duplications, inversions, and translocations.

Meanwhile, the Emedgene platform uses explainable AI to cut interpretation time from 7–8 hours down to just 60 minutes for WGS and 30 minutes for exome sequencing. In Illumina’s internal validation of 1,395 cases, Emedgene achieved 98.7% accuracy, with 97% of correct answers landing in the top three candidates.

Emedgene now integrates phasing, STR analysis, and TruPath-specific features, plus new modules like PromoterAI that evaluate how promoter variants affect downstream gene expression. It can also prioritize variants based on phenotype keywords. Together, DRAGEN™ and Emedgene create a seamless automated workflow from FASTQ files to customized reports. These tools are especially powerful for medically important but challenging genes like PMS2 and SMN1/SMN2, as well as previously hard-to-resolve dark regions, offering a more reliable single-test solution for rare disease research.

Real-World Cases: Dr. Niu Dao-ming Shares how TruPath Genome Helps Explore Complex Genetic Disease Research

Dr. Niu Dao-ming, a pediatric rare disease specialist at Taipei Veterans General Hospital, shared three clinical research cases that highlight the practical impact of TruPath™ Genome in structural variant analysis.

In one case, a 10-year-old boy with short stature and multiple skeletal abnormalities had a prenatal chromosomal test indicating a balanced translocation, but standard WGS and SHOX-related testing couldn’t provide clear answers. Using TruPath™ Genome’s colocation plots, the team zoomed in and precisely located the t(1;5) translocation breakpoint inside an intron of the DNM3 gene. The finding potentially affects DNM3OS long non-coding RNA and related microRNAs (miR-214 and miR-199a) involved in bone regulation, opening new directions for mechanistic research.

In another case, a newborn with severe hypertriglyceridemia—commonly called “strawberry milk” blood—had no diagnosis after gene panel and whole-exome sequencing. TruPath™ Genome combined with Emedgene AI identified a homozygous deletion in the APOC4–APOC2 region as the top candidate, with phasing data also suggesting possible uniparental disomy (UPD) mechanisms.

Dr. Niu stressed that TruPath™ Genome can clearly visualize complex structural variants while providing supporting SNP pattern evidence, bringing hidden clues to light. It delivers near-long-read positioning and phasing power without the higher costs typically associated with true long-read sequencing, and when paired with DRAGEN™ and Emedgene, it forms a complete sample-to-answer solution.

Building Taiwan’s Precision Medicine Ecosystem Through Collaboration

Illumina General Manager for Taiwan, Hong Kong and Macau, Jerry Cheng pointed out that Taiwan’s excellent healthcare system and rich clinical data make it fertile ground for population genomics efforts. The next step, he said, is connecting scattered resources into a true ecosystem so data can be turned into insights faster and drive meaningful collaborations.

Illumina continues to move from genomics into multiomics and AI-driven insights, delivering end-to-end solutions that create added value for biotech companies, medical centers, and academia. The company also plans to work with global pharmaceutical partners to advance clinical research, translational medicine, and companion diagnostics.

From Sequencing to Interpretable Insights: The Next Step

Overall, the launch event showcased TruPath™ Genome as a true end-to-end platform: from streamlined lab workflows and resolution of dark regions and complex structural variants to AI-assisted interpretation and multiomics integration. Discussions also covered practical topics around clinical adoption, workflow integration, and reimbursement in Taiwan, laying the foundation for broader real-world use in the coming years.

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Author

Oscar Wu

Fostering knowledge sharing to create a more fluid and transparent information landscape.