Long-read sequencing to resolve the parent of origin of a de novo pathogenic <i>UBE3A</i> variant.

Abstract

<b>Background</b> The ever-increasing capacity of short-read sequencing instruments is driving the adoption of whole genome sequencing (WGS) as a universal approach to the diagnosis of rare genetic disorders. However, many challenging genomic regions remain, for which alternative technologies must be deployed in order to address the clinical question satisfactorily. <b>Methods</b> Here we report the use of long-read sequencing to resolve ambiguity over a suspected diagnosis of Angelman syndrome. <b>Results</b> Despite a normal chromosomal microarray result and methylation studies at the imprinted 15q11q13 locus, the continued clinical suspicion of Angelman Syndrome prompted trio WGS of the proband and his parents. A de novo heterozygous frameshift variant, c.2370_2373del (NM_130838.2) p.(Asp790Glufs*7), in <i>UBE3A</i> was identified. To determine the parental allele on which this variant arose, long-read sequencing of the flanking genomic region was performed. Comparison of the resulting haplotypes allowed us to determine that the pathogenic frameshift variant arose on the maternal allele, confirming a diagnosis of Angelman syndrome in this case. <b>Conclusion</b> Long-read nanopore sequencing provides significant clinical utility when assessing the parental origin of de novo variants.