Avinash Dharmadhikari
Abstract
Avinash Dharmadhikaria, Dejerianne Ostrowa, Dennis Maglintea, Moiz Bootwallaa, Ankit Sharmaa, Vandana Mehtaa, Cindy Fonga, Arupa Gangulyb, Jaclyn Biegela, Matthew Deardorffa
aChildren’s Hospital Los Angeles, Los Angeles, CA, United States; bUniversity of Pennsylvania, Philadelphia, PA, United States
Vascular anomalies and some overgrowth disorders are typically caused by mosaic variants. Due to the frequent selection against these variants in blood, sensitive assays are required to detect them in affected tissues. The Vascular Anomalies and Mosaic Disorders (VMD4Kids) panel was developed using a Twist custom capture design with Unique Molecular Indexes (UMIs) targeting the coding sequence and intron/exon junctions of 218 genes. These genes are associated with capillary/lymphatic/ venous/arteriovenous malformations, lymphedema, vascular tumors, generalized body overgrowth, Noonan syndrome, skin pigmentary mosaicism and dermal hypoplasia, focal sclerotic bone lesions, and focal cortical dysplasia. Forty-five samples, previously clinically tested for single nucleotide variants (SNVs) and insertion/deletions (INDELs) were used to determine clinical accuracy (100%) and sensitivity (100%). The specimen types included formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissue, skin fibroblasts and blood. Using a compressed average read depth of 1000X coverage; the limit of detection was determined to be 1% for both SNVs and INDELs at a minimum depth of coverage of 200X. Initial clinical testing has identified clinically relevant variants in the genes PIK3CA, KRAS, KDR, RHOA and TEK in a variety of vascular and overgrowth phenotypes. Variant allele frequencies ranged from 4.9%-32.6%. In conclusion, this test addresses the need for detection of low-level mosaic variants in an overlapping set of disorders and provides necessary molecular diagnoses for gene and variant specific therapies, including MEK, MTOR and PIK3CA inhibitors.