Beyond the HLA Call: Resolving MHC Risk Haplotypes in a Family-Based Multiple Sclerosis Study
See how Sequence Bio added phased HLA and MHC-wide context to a family-based rare variant analysis using existing short-read whole genome sequencing data and Mako Analysis from Benthic Genomics.
Webinar Date:
📆 Thursday, September 3, 2026 at 9:00am PT / 12:00 pm ET
The HLA/MHC region contains variants that are known risk factors for numerous autoimmune diseases, but it remains one of the most difficult regions of the genome to analyze accurately.
Sequence Bio encountered this challenge while conducting family-based whole genome analysis in a founder population from Newfoundland and Labrador. The study aimed to identify rare inherited variants associated with the autoimmune disease multiple sclerosis, but standard short-read workflows could not provide the phased haplotypes and broader MHC context needed to interpret variation across families.
In this webinar, Cam Nugent, Lead Bioinformatician at Sequence Bio, will discuss the study, the analytical gap, and how phased HLA and MHC outputs added common immune-risk context to the familial rare variant analysis. Solomon Endlich, CEO of Benthic Genomics, will explain why the HLA/MHC is difficult to resolve from short-read data, how Mako reconstructs phased MHC haplotypes, and why phasing matters in family-and population-based studies.
Together, they will cover how Sequence Bio:
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Generated phased, four-field HLA calls from existing short-read WGS data
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Examined HLA and broader MHC variation across families
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Identified a recurring, strongly suggestive signal involving a known MS-risk haplotype
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Connected common immune-region risk with a broader rare variant analysis
Featured Speakers
Cam Nugent
Lead Bioinformatician, Sequence Bio
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Cam Nugent, PhD, is Lead Bioinformatician at Sequence Bio, a Newfoundland and Labrador based organization dedicated to discovering the genetic causes underlying rare and complex diseases within the province’s unique founder population. Cam and the rest of the Sequence Bio Research Team draw upon extensive genomics, software engineering, and data science experience to build production-level bioinformatics workflows, advance large-scale genomics research, and provide biological insights that help discover the genetic signals of disease.
Solomon Endlich
CEO, Benthic Genomics
Solomon Endlich is CEO of Benthic Genomics, which develops purpose-built analysis and sample prep solutions for complex genomic regions. Benthic’s Mako software reconstructs phased MHC haplotypes and generates high-resolution HLA and MHC-wide variant calls from standard sequencing data.
