Benthic Genomics Adds Mako to the Benthic Analysis Platform for High-Resolution Immune-Region Analysis From Short-Read Sequencing Data

New analysis module expands Benthic’s commercial portfolio with support for short-read sequencing workflows

Palo Alto, CA — April 16, 2026 — Benthic Genomics today announced the launch of Mako, a short-read immunogenomics analysis module on the Benthic Analysis Platform. Mako is designed to reconstruct phased haplotypes across the major histocompatibility complex (MHC) and generate high-resolution HLA typing and immune-region variant calls from standard short-read sequencing datasets. Its outputs include phased MHC haplotypes, high-resolution HLA typing, and broader immune-region variant calls from whole-genome sequencing data.

The launch marks Benthic’s second product release and expands the company’s commercial portfolio on the Benthic Analysis Platform. Angler Imputation supports immunogenomics analysis from SNP array data, while Mako extends that offering to short-read sequencing workflows, giving customers a broader immunogenomics capability across common research data types.

Short-read sequencing is ubiquitous, but the MHC remains one of the hardest regions of the genome to analyze — extreme polymorphism, structural variation, and paralogous genes mean most standard pipelines leave significant immune-region signals on the table. Mako is designed to recover it, delivering phased haplotypes, high-resolution HLA calls, and broader MHC variant calls from data research teams are already generating.

Unlike tools that focus narrowly on classical HLA loci, Mako is designed for broader immune-region analysis. Mako delivers four-field HLA typing across 45 genes in the MHC and goes beyond classical HLA genes to recover dense variant calls across the region, including immune genes such as MICA/B and TAP1/2. Mako reconstructs haplotypes before calling variants and HLA alleles, which enables clearer downstream interpretation for applications such as fine-mapping, association studies, and translational immunology research.

“Researchers have no shortage of sequencing data. The bottleneck is extracting the immune-region signals that standard pipelines routinely miss,” said Liza Huijse, Cofounder and Head of Computational Genomics and Engineering at Benthic Genomics. “Mako gives teams a practical way to recover phased haplotypes, high-resolution HLA calls, and broader MHC variation from NGS data. That matters for biomarker discovery, fine-mapping, and studies where immune genetics may influence the result.”

Mako’s commercial launch also expands Benthic’s product portfolio beyond array-based immunogenomics. With Angler for genotyping cohorts and Mako for short-read sequencing datasets, Benthic now offers a broader immunogenomics platform strategy for organizations working across mixed data modalities.

In an early collaboration with Sequence Bio, Mako was applied to a family-based whole-genome sequencing study of multiple sclerosis — a disease where HLA associations are well-established but had remained analytically out of reach in this cohort. Mako generated phased, four-field HLA allele calls directly from short-read WGS data, surfaced a recurring signal tied to a known MS-risk haplotype, and integrated cleanly with the team’s existing rare-variant analysis. The result was a more complete picture of immune-region risk than the study had previously been able to capture.

“Using Mako, we attained a new threshold of confidence in our HLA risk haplotype calls,” said Tom Barber, Chief Scientific Officer at Sequence Bio. “This complemented our family-based rare variant analysis and helped reveal the interplay of rare and common variants in MS genetic aetiology in our cohort.”

Benthic is launching Mako with a structured pilot model in which research teams run Mako on their own sequencing data and evaluate outputs within weeks. Initial focus is on translational immunology groups in biopharma, population genomics cohorts and biobanks, and genomics service providers looking to expand their immunogenomics capabilities for clients.

“Mako is an important commercial milestone for Benthic. It’s our second product on the platform and the first purpose-built for short-read sequencing workflows,” said Solomon Endlich, CEO, Benthic Genomics. “We’re already in early deployments with biopharma and population genomics teams, and we see significant demand from organizations that need a more complete immunogenomics capability across the data types they already work with.”

Mako is available now for research use. To learn more or discuss a pilot, visit www.benthic.bio/mako or contact info@benthic.bio.

About Benthic Genomics

Benthic Genomics was founded to address critical gaps in the precision and usability of current genomic solutions, particularly in immunogenomics. The company's mission is to master the most complex genomic challenges through pioneering computational tools and molecular methods, empowering researchers and clinicians to advance human health. Their hope is to be a catalyst in an era where previously inaccessible genomic information is readily understood and applied, leading to profound advancements in personalized medicine and global health.

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