Data overview

The Saudi cohort v1 release, available through Enigma Clinical Platform, includes data exclusively from whole-exome sequencing (WES), focusing on both healthy individuals and those affected by childhood-onset genetic disorders. This dataset represents a foundational step toward building a high-resolution genomic reference for the Saudi and Indigenous Arab populations.

The current cohort was originally published as the Saudi Genomics Platform. Rebranding the application does not change its population, source data or release.

• Analyses were performed using variant call format (VCF) files provided by participating laboratories.
• Plans are in place to reanalyze the dataset from raw sequencing data (FASTQ/CRAM) in future releases to enhance consistency and enable deeper genomic insights.

To ensure high-quality, reliable variant data, the following steps were applied:

• All variants were mapped to the GRCh38 human genome build, enabling compatibility with the most up-to-date variant databases and clinical annotations.
• Variants with genotype quality (GQ) scores below 20 were excluded from all analyses to maintain confidence in reported findings.
• Genomic sites identified as low quality (LQ) were flagged, allowing users to exclude or annotate these regions in downstream analyses.
• Variant annotations reflect the most recent database version parsed at the time of processing, ensuring alignment with current clinical knowledge and guidelines.

• Phenotypic data was standardized using the Human Phenotype Ontology (HPO).
• Curated HPO terms were harmonized from clinical reports and linked to individual variants, allowing for genotype-phenotype correlation and enabling more precise variant interpretation.