Genome Sequencing for Cases Unsolved by Exome Sequencing: Identifying a Single-Exon Deletion in TBCK in a Case from 30 Years Ago

Abstract

In patients with neurodevelopmental disorders (NDDs), exome sequencing (ES), the diagnostic gold standard, reveals an underlying monogenic condition in only approximately 40% of cases. We report the case of a female patient with profound NDD who died 30 years ago at the age of 3 years and for whom genome sequencing (GS) now identified a single-exon deletion in TBCK previously missed by ExomeDepth, the copy number variation (CNV) detection algorithm in ES.

Deoxyribonucleic acid (DNA) was extracted from frozen muscle tissue of the index patient and the parents' blood. Genome data were analyzed for structural variants and single nucleotide variants (SUVs)/indels as part of the Bavarian Genomes consortium project.

Biallelic variants in TBCK, which are linked to the autosomal recessive disorder TBCK syndrome, were detected in the affected individual: a novel frameshift variant and a deletion of exon 23, previously established as common but underrecognized pathogenic variant in individuals with TBCK syndrome. While in the foregoing ES analysis, calling algorithms for (SNVs)/indels were able to identify the frameshift variant, ExomeDepth failed to call the intragenic deletion.

Our case illustrates the added value of GS for the detection of single-exon deletions for which calling from ES data remains challenging and confirms that the deletion of exon 23 in TBCK may be underdiagnosed in patients with NDDs. Furthermore, it shows the importance of “molecular or genetic autopsy” allowing genetic risk counseling for family members as well as the end of a diagnostic odyssey of 30 years.

Keywords

TBCK - genome sequencing - molecular autopsy - neurodevelopmental disorder

• References

• 1 Brunet T, Jech R, Brugger M. et al. De novo variants in neurodevelopmental disorders-experiences from a tertiary care center. Clin Genet 2021; 100 (01) 14-28
• 2 Coutelier M, Holtgrewe M, Jäger M. et al. Combining callers improves the detection of copy number variants from whole-genome sequencing. Eur J Hum Genet 2022; 30 (02) 178-186
• 3 Sumathipala D, Strømme P, Gilissen C, Corominas J, Frengen E, Misceo D. TBCK encephaloneuropathy with abnormal lysosomal storage: use of a structural variant bioinformatics pipeline on whole-genome sequencing data unravels a 20-year-old clinical mystery. Pediatr Neurol 2019; 96: 74-75
• 4 Dai H, Zhu W, Yuan B. et al; Undiagnosed Diseases Network. A recurrent single-exon deletion in TBCK might be under-recognized in patients with infantile hypotonia and psychomotor delay. Hum Mutat 2022; 43 (12) 1816-1823
• 5 Chong JX, Caputo V, Phelps IG. et al; University of Washington Center for Mendelian Genomics. Recessive inactivating mutations in TBCK, encoding a Rab GTPase-activating protein, cause severe infantile syndromic encephalopathy. Am J Hum Genet 2016; 98 (04) 772-781
• 6 Bhoj EJ, Li D, Harr M. et al. Mutations in TBCK, encoding TBC1-domain-containing kinase, lead to a recognizable syndrome of intellectual disability and hypotonia. Am J Hum Genet 2016; 98 (04) 782-788
• 7 Durham EL, Angireddy R, Black A. et al. TBCK syndrome: a rare multi-organ neurodegenerative disease. Trends Mol Med 2023; 29 (10) 783-785
• 8 Köhler S, Gargano M, Matentzoglu N. et al. The human phenotype ontology in 2021. Nucleic Acids Res 2021; 49 (D1): D1207-D1217
• 9 Plagnol V, Curtis J, Epstein M. et al. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics 2012; 28 (21) 2747-2754
• 10 Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res 2011; 21 (06) 974-984
• 11 Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol 2014; 15 (06) R84
• 12 Fan X, Abbott TE, Larson D, Chen K. BreakDancer: identification of genomic structural variation from paired-end read mapping. Curr Protoc Bioinformatics 2014; 45: 6.1-11
• 13 Chen X, Schulz-Trieglaff O, Shaw R. et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 2016; 32 (08) 1220-1222
• 14 Kronenberg ZN, Osborne EJ, Cone KR. et al. Wham: identifying structural variants of biological consequence. PLOS Comput Biol 2015; 11 (12) e1004572
• 15 Richards S, Aziz N, Bale S. et al; ACMG Laboratory Quality Assurance Committee. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med 2015; 17 (05) 405-424
• 16 Karczewski KJ, Francioli LC, Tiao G. et al; Genome Aggregation Database Consortium. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 2020; 581 (7809) 434-443
• 17 Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the human genome. Nat Rev Genet 2015; 16 (03) 172-183
• 18 Manheimer KB, Patel N, Richter F. et al. Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors. Hum Mutat 2018; 39 (06) 870-881
• 19 Carmichael N, Tsipis J, Windmueller G, Mandel L, Estrella E. “Is it going to hurt?”: the impact of the diagnostic odyssey on children and their families. J Genet Couns 2015; 24 (02) 325-335
• 20 Shamseldin HE, AlAbdi L, Maddirevula S. et al; Molecular Autopsy Consortium. Lethal variants in humans: lessons learned from a large molecular autopsy cohort. Genome Med 2021; 13 (01) 161