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Individuals diagnosed with certain ICD10 codes in the UKB are herein referred to as cases and all remaining individuals as controls for that ICD10. Both cases and controls can have QVs, such as protein truncating variants, in a given gene. The objective of rare-variant collapsing analysis is to identify genes in which QVs are enriched in either cases or controls. Some controls may not yet be diagnosed with a given ICD10 code or are incorrectly classified. MILTON aims to identify these individuals by checking if they share similar biomarker profiles to known cases (represented by the shades of green). The predicted cases are eventually merged with the known cases to form an augmented case cohort (ranging from L0 to L3), which is analyzed along with a revised control set in an updated PheWAS on whole-genome sequencing (WGS) data.

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