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