Design of a multiplex ligation-dependent probe amplification assay for SLC20A2: identification of two novel deletions in primary familial brain calcification

Elisa Giorgio, Emanuela Garelli, Adriana Carando, Stefania Bellora, Elisa Rubino, Paola Quarello, Fabio Sirchia, Federico Marrama, Salvatore Gallone, Enrico Grosso, Barbara Pasini, Roberto Massa, Alessandro Brussino, Alfredo Brusco

Research output: Contribution to journalArticle

Abstract

Primary familial brain calcification (PFBC) is a rare disease characterized by brain calcifications that mainly affect the basal ganglia, thalamus, and cerebellum. Among the four autosomal-dominant genes known to be associated with the disease, SLC20A2 pathogenic variants are the most common, accounting for up to 40% of PFBC dominant cases; variants include both point mutations, small insertions/deletions and intragenic deletions. Over the last 7 years, we have collected a group of 50 clinically diagnosed PFBC patients, who were screened for single nucleotide changes and small insertions/deletions in SLC20A2 by Sanger sequencing. We found seven pathogenic/likely pathogenic variants: four were previously described by our group, and three are reported here (c.303delG, c.21delG, and c.1795-1G>A). We developed and validated a synthetic Multiplex Ligation-dependent Probe Amplification (MLPA) assay for SLC20A2 deletions, covering all ten coding exons and the 5′ UTR (SLC20A2-MLPA). Using this method, we screened a group of 43 PFBC-patients negative for point mutations and small insertions/deletions, and identified two novel intragenic deletions encompassing exon 6 NC_000008.10:g.(42297172_42302163)_(423022281_42317413)del, and exons 7–11 including the 3′UTR NC_000008.10:g.(?_42275320)_(42297172_42302163)del. Overall, SLC20A2 deletions may be highly underestimated PFBC cases, and we suggest MLPA should be included in the routine molecular test for PFBC diagnosis.

Original languageEnglish
Pages (from-to)1083-1090
Number of pages8
JournalJournal of Human Genetics
Volume64
Issue number11
DOIs
Publication statusPublished - Nov 1 2019

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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    Giorgio, E., Garelli, E., Carando, A., Bellora, S., Rubino, E., Quarello, P., Sirchia, F., Marrama, F., Gallone, S., Grosso, E., Pasini, B., Massa, R., Brussino, A., & Brusco, A. (2019). Design of a multiplex ligation-dependent probe amplification assay for SLC20A2: identification of two novel deletions in primary familial brain calcification. Journal of Human Genetics, 64(11), 1083-1090. https://doi.org/10.1038/s10038-019-0668-3