ESPE Abstracts (2018) 89 FC15.1

The Diagnostic Yield of a Targeted Next Generation Sequencing Panel in Children with Short Stature of Undefined Aetiology

Reena Percharda, Philip G Murrayb, Georgina L Hightona, Andrew J Whatmorea & Peter E Claytona,b

aFaculty of Biology, Medicine and Health, School of Medical Sciences, University of Manchester, Manchester, UK; bPaediatric Endocrinology Department, Royal Manchester Children’s Hospital, Manchester, UK

Background: Currently, data on the diagnostic yield of targeted gene panels using next generation sequencing (NGS) in children with short stature of undefined aetiology (SSUA) are limited. EPIGROW ( ID NCT00710307) was a prospective European epidemio-genetic study in which a targeted NGS panel including 69 genes associated with short stature (e.g. primordial growth disorders and skeletal dysplasias) was performed in 263 patients and 263 controls. In these patients, there were no clinical features suggestive of a given disorder.

Aim: To determine the diagnostic yield from a targeted NGS panel in children with SSUA.

Methods: NGS was performed on genomic DNA (exons, exon–intron junctions, and promoter regions) using the Agilent SureSelect (Agilent Technologies, Inc., Santa Clara, CA) platform for target enrichment and Illumina TruSDefault (Illumina Inc., San Diego, CA) for sequencing. To identify potentially pathogenic variants, we selected those which were present in cases but not controls, were exonic, had a minor allele frequency <2% and where carriage of the variant allele fitted the mode of inheritance of the known short stature disorder. For missense variants only those predicted to be potentially damaging by Polyphen2 were included. To identify known mutations a combination of Ensembl and Leiden Open Variation Database (to access a range of gene specific databases) were used. Variants identified through this strategy were classified as probably pathogenic where they had previously been reported to be associated with the condition or if they were nonsense/frameshift (loss of function) mutations. Where the variant did not fit these criteria they were classified as possibly pathogenic.

Results: We identified 43 variants of interest in 37 patients. 13 of these were classified as probably pathogenic – 11 were previously known mutations in FANCB, IGF1R, MMP13, NPR2, OBSL1 and PTPN11 (all missense) and 2 in ACAN were nonsense mutations. An additional 30 possibly pathogenic mutations were identified in these genes and in others, including GH1, GNAS, HRAS and LHX4. 9 were insertions or deletions and 21 were missense variants predicted as damaging.

Conclusion: This gene panel led to a potential diagnostic yield of 5% (13/263) to 14% (37/263) in a cohort of pre-pubertal children with SSUA. Therefore, the use of such panels may improve diagnosis in SSUA.

We would like to acknowledge the EPIGROW Investigator Group for their participation and contributions.

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