Genetic Screening of a nonsyndromic amelogenesis imperfecta patient cohort using a custom smMIP reagent for selective enrichment of target loci

Amelogenesis is the process of tooth enamel formation, and genetic variants disrupting it cause the Mendelian inherited disorder amelogenesis imperfecta (AI). AI patients have weak, discoloured or brittle enamel, caused by reduced enamel quantity or mineralisation. AI can occur in isolation or, less commonly, as part of a syndrome. Pathogenic variants in at least 38 genes have been shown to cause AI. Current genetic screening studies typically use exome sequencing, but this is expensive and involves complex data analysis workflows. Target enrichment using smMIPs (single molecule molecular inversion probes) provides a flexible alternative, allowing the creation of a disease-specific reagent for low cost, robust, high-throughput screening. Here, we describe the development of an smMIP reagent targeting 19 genes implicated in isolated AI and assess its use in screening a cohort of 181 UK probands with nonsyndromic AI. While this was intended only as a prescreen to prioritise exome sequencing more efficiently, it nevertheless led to molecular diagnoses for 63 probands (35%). Cost per sample screened was approximately £40. Variants in three genes, COL17A1, FAM83H (both dominant) and MMP20 (recessive), accounted for approximately half of solved cases. There is scope to further improve the smMIP reagent by adding additional probes targeting regions of low coverage or additional genes, including those involved in syndromic AI, as well as accommodating new information about the genetic basis of AI. The smMIP reagent provides a robust, flexible, high-throughput, low-cost approach to AI screening, and it is available as a resource to the international AI research community.