METHODOLOGY
Whole-Genome Sequencing Whole genome sequencing was performed on NovaSeq 6000 instruments (Illumina), generating paired 101-nt reads with an average coverage of 55× and 42x for proband 1 and 2 respectively. Alignment and single nucleotide polymorphisms (SNV) calling were performed using the DRAGEN processor (Illumina). Copy number variant (CNV) calling was performed with CNVnator and Manta (Abyzov et al. 2011; Chen et al. 2016). Variant call format (VCF) files incorporating SNV and CNV calls were annotated and analyzed using Fabric Enterprise version 6.2.8 (Fabric Genomics) according to standard guidelines (Coonrod et al. 2013; Richards et al. 2015). The Human Phenotype Ontology terms used during analysis are listed below. Parental samples for were available for targeted variant analysis and inheritance determination.
Human Phenotype Ontology terms used for Patient 1: Neonatal hypotonia (HP:0001319), Feeding difficulties in infancy (HP:0008872), Arthrogryposis multiplex congenital (HP:0002804), Hip dysplasia (HP:0001385), Overlapping fingers and toes (HP:0010557).
Human Phenotype Ontology terms used for Patient 1: Small for gestational age (HP:0001518), Apnea (HP:0002104), Arthrogryposis multiplex congenital (HP:0002804), Bilateral talipes equinovarus (HP:0001776) , Abnormality of limb bone morphology (HP:0002813).RESULTS
Patients 1 and 2 were each found to have a heterozygous, de novo, pathogenic frameshift variant, c.1996dupC; p. Gln666ProfsTer47 in theMAGEL2 gene (Table 1. rWGS Results of Patient 1 and 2 ). This is also referred to as the c.187dupC; p.Gln63ProfsTer47 (NM_019066.4) in the literature based on the transcript used. This variant is expected to create a frameshift in the protein coding sequence, leading to a truncated protein. This variant has been previously reported in individuals with Schaaf-Yang syndrome and has been classified as pathogenic in ClinVar (Variation ID: 190122).
Patient 1 also had a heterozygous, maternally inherited, pathogenic variant, c.3130_3149delACCCCTGC; p. Thr1044LeufsTer63, in theABCC8 gene. This variant is expected to create a frameshift in the protein sequence, leading to a truncated protein. This variant has been classified as pathogenic in ClinVar and Human Gene Mutation Database (HGMD). Pathogenic variation in the ABCC8 gene has been associated with autosomal dominant/recessive familial hyperinsulinemic hypoglycemia-1 (HHF1, MIM: #256450). LONG TERM CLINICAL OUTCOMES AFTER DIAGNOSIS