Enabling Down Syndrome Research through a Knowledge Graph-Driven Analytical Framework

Madan Krishnamurthy; Surya Saha; Pierrette Lo; Patricia L. Whetzel; Tursynay Issabekova; Jamed Ferreris Vargas; Jack DiGiovanna; Melissa A Haendel

arXiv · 2509.01565

Enabling Down Syndrome Research through a Knowledge Graph-Driven Analytical Framework

Madan Krishnamurthy·Surya Saha·Pierrette Lo·Patricia L. Whetzel·Tursynay Issabekova·Jamed Ferreris Vargas·Jack DiGiovanna·Melissa A Haendel

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Abstract

Trisomy 21 results in Down syndrome, a multifaceted genetic disorder with diverse clinical phenotypes, including heart defects, immune dysfunction, neurodevelopmental differences, and early-onset dementia risk. Heterogeneity and fragmented data across studies challenge comprehensive research and translational discovery. The NIH INCLUDE (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE) initiative has assembled harmonized participant-level datasets, yet realizing their potential requires integrative analytical frameworks. We developed a knowledge graph-driven platform transforming nine INCLUDE studies, comprising 7,148 participants, 456 conditions, 501 phenotypes, and over 37,000 biospecimens, into a unified semantic infrastructure. Cross-resource enrichment with Monarch Initiative data expands coverage to 4,281 genes and 7,077 variants. The resulting knowledge graph contains over 1.6 million semantic associations, enabling AI-ready analysis with graph embeddings and path-based reasoning for hypothesis generation. Researchers can query the graph via SPARQL or natural language interfaces. This framework converts static data repositories into dynamic discovery environments, supporting cross-study pattern recognition, predictive modeling, and systematic exploration of genotype-phenotype relationships in Down syndrome.

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q-bio.QM cs.AI cs.DB cs.LG

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Madan Krishnamurthy, Surya Saha, Pierrette Lo, Patricia L. Whetzel, Tursynay Issabekova, Jamed Ferreris Vargas, Jack DiGiovanna, Melissa A Haendel. 2025-09-01. Enabling Down Syndrome Research through a Knowledge Graph-Driven Analytical Framework. https://arxiv.org/abs/2509.01565

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