Casey Brewera, Kristen Sundb, Xinjian Wanga, Jie Liua, Qiaoning Guana, Wenying Zhanga, Brian Dawsona, Yaning Wua
aCincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; bEmedgene at Illumina, San Diego, CA, USA
Biallelic disease-causing variants in the SBDS gene account for over 90 percent of Shwachman-Diamond Syndrome, a congenital autosomal recessive disorder characterized by pancreatic insufficiency, hematological malfunction, and skeletal abnormalities. Molecular genetic tests of SBDS include single-gene Sanger sequencing or next generation sequencing (NGS) panels. The detection of SBDS variants by either method, however, is complicated by the pseudogene, SBDSP1. In fact, common disease variants in SBDS are created by gene conversion events between SBDS and SBDSP1, making it difficult to determine whether a variant affects the functional gene or the pseudogene. We evaluated the performance of SBDS sequencing tests offered at our institution and determined if additional test strategies are needed for accurate variant detection. Sanger sequencing of SBDS identified the 2 known, common disease variants (c.183_184delinsCT and c.258+2T>C), as well as several less common disease variants. NGS testing of SBDS detected the common c.183_184delinsCT as 2 separate variants, such that those 2 variants had to be flagged and manually inspected when they were present. NGS also identified the second common disease variant, c.258+2T>C, and could determine the phase of the 2 common disease variants in individuals carrying them both. It remains possible to miss a rare gene conversion event by both sequencing methods. Extra attention should be given to patients negative by sequencing that are a strong phenotypic match for Shwachman-Diamond Syndrome. A reflex Sanger test can be considered for such patients, as well as analysis of low allele fraction NGS variants that might be constitutively heterozygous.