1. In-house multiplex ligation-dependent probe amplification assay for citrin deficiency: analytical validation and novel exonic deletions in SLC25A13
- Author
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Y K Chong, Y P Yuen, Chloe Miu Mak, C C Shek, Candy Wai Yan Ng, Mei Tik Leung, Chor Kwan Ching, Sammy Pak-Lam Chen, Hencher Han Chih Lee, Nike Kwai Cheung Lau, and Tammy Tsz Yan Tong
- Subjects
0301 basic medicine ,DNA Copy Number Variations ,Biology ,Mitochondrial Membrane Transport Proteins ,Pathology and Forensic Medicine ,03 medical and health sciences ,Exon ,symbols.namesake ,0302 clinical medicine ,medicine ,Humans ,Multiplex ,Genetic Testing ,Multiplex ligation-dependent probe amplification ,Copy-number variation ,Gene ,Sequence Deletion ,Genetic testing ,Genetics ,Sanger sequencing ,Citrullinemia ,medicine.diagnostic_test ,Infant, Newborn ,Exons ,medicine.disease ,030104 developmental biology ,Inborn error of metabolism ,030220 oncology & carcinogenesis ,symbols ,Multiplex Polymerase Chain Reaction - Abstract
Citrin deficiency is one of the most common inborn errors of metabolism in East Asians, which may manifest as neonatal cholestasis, failure to thrive and dyslipidaemia, or recurrent hyperammonaemic encephalopathy. Its molecular diagnosis requires confirmation of the presence of biallelic pathogenic variants in SLC25A13 gene by sequencing, and analysis for a common insertion IVS16ins3kb. However, patients with compatible biochemical features but only one monoallelic pathogenic variant have remained a diagnostic challenge. Here we report the development, validation and application of a multiplex ligation-dependent probe amplification (MLPA) assay using an in-house oligonucleotide probemix and a customised Coffalyer.NET worksheet for detection of exonic copy number variations in SLC25A13. With this MLPA assay, we successfully identified the presence of a heterozygous exonic deletion in SLC25A13 in three of 15 (20%) unrelated individuals with only one monoallelic pathogenic variant detected using conventional methods. Three exonic deletions, two novel involving exon 14 and one reported involving exon 5, were subsequently confirmed with Sanger sequencing. In summary, we developed, evaluated, and demonstrated the clinical utility of an in-house MLPA assay to look for exonic deletions in SLC25A13 in patients with citrin deficiency. With the discovery of novel deletions, MLPA should be considered a test of choice for molecular diagnosis of citrin deficiency when the sequencing result is inconclusive.
- Published
- 2021