A custom gene panel for interrogating pediatric overgrowth disorders and tumour predisposition.

Abstract

The Genetics and Molecular Pathology laboratory at Monash Health is the predominant Australian testing laboratory for pediatric overgrowth disorders associated with increased cancer risk in childhood, including Beck with Wiedemann syndrome (BWS) and hemihypertrophy (HH). Cascade testing typically involves SNP microarray, methylation analysis of imprinting centres on 11p15.5 and CDKN1C (P57) mutation screening. Rare point mutations in NSD1, NLRP2, DNMT1 and ZFP57 have been described in BWS and like disorders as well as deletions and insertions within the 11p15.5 imprinting centres IC1 (H19/IGF2) and IC2 (KCNQ1OT1/CDKN1C). Tumor risk is increased in most genetic and epigenetic subtypes of BWS and HH however degree of risk and tumor type varies between groups. Parents of affected children are often understandably anxious to know the recurrence risk for these conditions and as the number of childhood cancer survivors increases, the possibility for transmission of a causative mutation is becoming an increasingly important issue. To improve our capacity to detect predisposing mutations in BWS, HH and in the pediatric tumors that have been described in these conditions, we have designed a gene panel comprising 37 genes as well as intergenic regions spanning imprinting centres on 11p15.5 and 11p13. We have used the Haloplex target enrichment system with sequences run on an Illumina MiSeq. We have performed pilot testing to show that the panel has clinical utility and demonstrates excellent sequence coverage of the 11p imprinting centres. Analysis of results to date has revealed novel mutations including OCT-4 binding site disruption in IC1 and subregions of homozygosity.