P777: Genome sequencing detects transposable element (TE) insertions in two diagnostic challenging cases

Treatment and Management: Case #1: Patient follows a low carbohydrate diet with added cornstarch, protein powder, and vitamin D, and has not had recent hypoglycemia.His hypotonia has resolved.He is monitored for portal hypertension, esophageal varices, and his echocardiograms show left ventricular hypertrophy.Case #2: A ventriculoperitoneal shunt was placed at day 5 of life, anti-epileptic drugs were started at 1 month of age, and a g-tube was required due to oral aversion at 6-weeks of age.Outcome and Follow-Up: Case #1: Patient is doing very well and is rarely hypoglycemic.A paternal first cousin who was diagnosed with GSDIII and also had a missing second variant was updated with this finding.Case #2: Patient is deceased.Discussion: The two case reports presented here address the challenges and value of detecting TEs as part of routine diagnostic pipelines to maximize diagnostic yield.In each case, a focused interrogation of the cGS data was performed to elucidate a molecular diagnosis in the presence of a single hit in a gene associated with an autosomal recessive disorder with strong phenotypic overlap.Additionally, long read sequencing and RNA-seq studies were used as complementary approaches to confirm TEs with splice-altering activity.Conclusion: Patients with a suspected genetic diagnosis may benefit from additional genomic approaches to reduce the diagnostic odyssey and bypass invasive testing and provide recurrence risk information for reproductive planning.As illustrated here, we provide evidence to support the use of cGS as a first-tier test.This is, in part, due to the detection of various types of genetic variants, including SVs, that may have been otherwise missed by other tests.Introduction: Transposable elements (TEs) are mobile repetitive DNA sequences that comprise a significant fraction of eukaryotic genomes, thus contributing to genetic diversity.Due to their mobile nature, they can cause disease.Here, we present two cases wherein clinical genome sequencing (cGS), in conjunction with other genomic testing approaches, led to the identification of disease-causing TE insertions.Case Presentation: Case #1: The patient presented at age 14 months with hepatomegaly and elevated liver functions.Liver biopsy was consistent with glycogen storage disease.Left ventricular hypertrophy, esophageal varices, and ketotic hypoglycemia were noted.The patient was diagnosed with glycogen storage disease type III (GSDIII), and molecular testing was pursued.An external lab identified a heterozygous variant in the AGL gene, c.100C>T (p.Arg34Ter).Case #2: The patient presented with hydrocephalus, macrocephaly, seizures, dysmorphic facial features, retinal hemorrhage, ventriculomegaly, hypothermia, tube feeding, apneic episodes in infancy, abnormal TSH hormone level, gastroesophageal reflux, hypospadias, and micropenis.Previous genetic testing reported a heterozygous POMT1 c.793C>T (p.Arg265Ter) variant in association with POMT1-related myopathies.cGS was pursued to further evaluate the underlying genetic etiology of both patients' clinical presentations.Diagnostic Workup: Trio cGS was performed by Illumina Laboratory Services (ILS).For case 1, a structural variant (SV) that appeared to disrupt the AGL gene was identified in the proband.Research testing was pursued to further evaluate the SV.Karyotyping and optical genome mapping (OGM) were normal.Longread sequencing confirmed an Alu insertion at the end of exon 32 of the AGL gene that is predicted to disrupt splicing.RNA-seq on blood confirmed the insertion in the proband and father, resulting in skipping of exon 32, which is predicted to cause frameshift-induced premature termination, AGL c.4259+2_+3insN[?] (p.Asp1420GlufsTer20).For case 2, a TE insertion in exon 3 of POMT1 was detected in the proband and a parent via cGS.This insertion was confirmed by orthogonal testing (Invitae) and is predicted to result in a frameshift and loss of normal protein function, POMT1 c.160_161ins?(p.Tyr54fs).