Table 1.

Query modules available on the platform

Query domain	Query name	Description	Example
Clinical	queryDomain	Query based on OMOP concept ID with date and/or value	Build cohort of patients diagnosed with diabetes and on metformin since 2015
	queryPerson	Query based on person ID(s) with date and/or concept and/ or value	Find all medications taken by patient(s) before 2018
Genetic	queryVariant	Query based on genomic coordinate and genotype with MAF and sequencing/technical analysis metadata filter	Find all patients with rare variants (MAF < 0.05) in chromosome 8 with variants called using GATK
	queryPerson	Query based on person ID(s) and genomic location with MAF filter	Find all variants with MAF < 0.1 for specific patient(s) in chromosomes 11 and 12
	queryVariantGene	Query based on variants associated with particular gene	Find all patients with rare variants (MAF < 0.05) in gene BRCA1
	queryVariantAnnotations	Query based on variants with a particular clinical annotation	Find all patients with rare variants (MAF < 0.05) that are ClinVar annotated in chromosome 6
Analysis	querySamplePCA	Query based on person IDs that returns population stratification PC scores	Retrieve the top 20 PC scores for specific patient(s)
	queryKinship	Query based on person IDs that determines relatedness between samples	Find level of relatedness between specific patient(s) in the network
	queryMetadata	Query based on sequencing and technical analysis metadata	Find all patients sequenced on Illumina NovaSeq, aligned using HISAT2, and variant called with GATK
Combination	queryClinicalVariant	Query based on clinical cohort definition and gene of interest	Find all patients with rare variants in the SOD1 gene and a specific age of onset for ALS
	queryVariantClinical	Query based on variants of interest returning patient clinical characteristics	Find all diseases for patients with a particular rare variant