Diagnostic Utility of Whole Exome Sequencing in the Neuromuscular Clinic

Abstract

Next-generation sequencing is a powerful diagnostic tool, yet it has proven inadequate to establish a diagnosis in all cases of congenital hypotonia or childhood onset weakness. We sought to describe the impact of whole exome sequencing (WES), which has only recently become widely available clinically, on molecular diagnosis in the Nationwide Children's Hospital Neuromuscular clinics. We reviewed records of all patients in our clinic with pediatric onset of symptoms who had WES done since 2013. Patients were included if clinical suspicion was high for a neuromuscular disease. Clinical WES was performed in 30 families, representing 31 patients, all of whom were seen for hypotonia, weakness, or gait disturbance. Probands had between 2 and 12 genetic diagnostic tests prior to obtaining WES. A genetic diagnosis was established in 11 families (37%), and in 12 patients (39%), with mutations in 10 different genes. Five of these genes have only been associated with disease since 2013, and were not previously represented on clinically available disease gene panels. Our results confirm the utility of WES in the clinical setting, particularly for genetically heterogeneous syndromes. The availability of WES can provide an end to the diagnostic odyssey for parents and allow for expansion of phenotypes.

Keywords

whole exome sequencing - neuromuscular - hypotonia - diagnostic odyssey

• References

• 1 Savarese M, Di Fruscio G, Torella A. , et al. The genetic basis of undiagnosed muscular dystrophies and myopathies: Results from 504 patients. Neurology 2016; 87 (01) 71-76
• 2 Boycott KM, Rath A, Chong JX. , et al. International cooperation to enable the diagnosis of all rare genetic diseases. Am J Hum Genet 2017; 100 (05) 695-705
• 3 Maggi L, Scoto M, Cirak S. , et al. Congenital myopathies--clinical features and frequency of individual subtypes diagnosed over a 5-year period in the United Kingdom. Neuromuscul Disord 2013; 23 (03) 195-205
• 4 Ghaoui R, Cooper ST, Lek M. , et al. Use of whole-exome sequencing for diagnosis of limb-girdle muscular dystrophy: outcomes and lessons learned. JAMA Neurol 2015; 72 (12) 1424-1432
• 5 Colombo I, Scoto M, Manzur AY. , et al. Congenital myopathies: natural history of a large pediatric cohort. Neurology 2015; 84 (01) 28-35
• 6 Witting N, Werlauff U, Duno M, Vissing J. Phenotypes, genotypes, and prevalence of congenital myopathies older than 5 years in Denmark. Neurol Genet 2017; 3 (02) e140
• 7 Todd EJ, Yau KS, Ong R. , et al. Next generation sequencing in a large cohort of patients presenting with neuromuscular disease before or at birth. Orphanet J Rare Dis 2015; 10: 148
• 8 Kuperberg M, Lev D, Blumkin L. , et al. Utility of whole exome sequencing for genetic diagnosis of previously undiagnosed pediatric neurology patients. J Child Neurol 2016; 31 (14) 1534-1539
• 9 Fattahi Z, Kalhor Z, Fadaee M. , et al. Improved diagnostic yield of neuromuscular disorders applying clinical exome sequencing in patients arising from a consanguineous population. Clin Genet 2017; 91 (03) 386-402
• 10 Ankala A, da Silva C, Gualandi F. , et al. A comprehensive genomic approach for neuromuscular diseases gives a high diagnostic yield. Ann Neurol 2015; 77 (02) 206-214
• 11 Monroe GR, Frederix GW, Savelberg SM. , et al. Effectiveness of whole-exome sequencing and costs of the traditional diagnostic trajectory in children with intellectual disability. Genet Med 2016; 18 (09) 949-956
• 12 Haskell GT, Adams MC, Fan Z. , et al. Diagnostic utility of exome sequencing in the evaluation of neuromuscular disorders. Neurol Genet 2018; 4 (01) e212
• 13 Reddy HM, Cho KA, Lek M. , et al. The sensitivity of exome sequencing in identifying pathogenic mutations for LGMD in the United States. J Hum Genet 2017; 62 (02) 243-252
• 14 Wright CF, FitzPatrick DR, Firth HV. Paediatric genomics: diagnosing rare disease in children. Nat Rev Genet 2018; 19 (05) 325
• 15 Johnson K, Bertoli M, Phillips L. , et al. Detection of variants in dystroglycanopathy-associated genes through the application of targeted whole-exome sequencing analysis to a large cohort of patients with unexplained limb-girdle muscle weakness. Skelet Muscle 2018; 8 (01) 23
• 16 Harris E, Topf A, Barresi R. , et al. Exome sequences versus sequential gene testing in the UK highly specialised Service for limb girdle muscular dystrophy. Orphanet J Rare Dis 2017; 12 (01) 151
• 17 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
• 18 Byrne S, Jansen L, U-King-Im JM. , et al. EPG5-related Vici syndrome: a paradigm of neurodevelopmental disorders with defective autophagy. Brain 2016; 139 (Pt 3): 765-781
• 19 Byrne S, Dionisi-Vici C, Smith L, Gautel M, Jungbluth H. Vici syndrome: a review. Orphanet J Rare Dis 2016; 11: 21
• 20 Waldrop MA, Gumienny F, Boue D. , et al. Low-level expression of EPG5 leads to an attenuated Vici syndrome phenotype. Am J Med Genet A 2018; 176 (05) 1207-1211
• 21 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
• 22 Alazami AM, Patel N, Shamseldin HE. , et al. Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. Cell Reports 2015; 10 (02) 148-161
• 23 Bailey AG, Bloch EC. Malignant hyperthermia in a three-month-old American Indian infant. Anesth Analg 1987; 66 (10) 1043-1045
• 24 Horstick EJ, Linsley JW, Dowling JJ. , et al. Stac3 is a component of the excitation-contraction coupling machinery and mutated in Native American myopathy. Nat Commun 2013; 4: 1952
• 25 Waldrop MA, Boue DR, Sites E, Flanigan KM, Shell R. Clinicopathologic Conference: a newborn with hypotonia, cleft palate, micrognathia, and bilateral club feet. Pediatr Neurol 2017; 74: 11-14
• 26 Ravenscroft G, Miyatake S, Lehtokari VL. , et al. Mutations in KLHL40 are a frequent cause of severe autosomal-recessive nemaline myopathy. Am J Hum Genet 2013; 93 (01) 6-18
• 27 Hackman P, Udd B, Bönnemann CG, Ferreiro A. ; Titinopathy Database Consortium. 219th ENMC International Workshop Titinopathies International database of titin mutations and phenotypes, Heemskerk, The Netherlands, 29 April-1 May 2016. Neuromuscul Disord 2017; 27 (04) 396-407
• 28 Chauveau C, Rowell J, Ferreiro A. A rising titan: TTN review and mutation update. Hum Mutat 2014; 35 (09) 1046-1059
• 29 Laing NG, Clarke NF, Dye DE. , et al. Actin mutations are one cause of congenital fibre type disproportion. Ann Neurol 2004; 56 (05) 689-694
• 30 Clarke NF. Congenital fiber-type disproportion. Semin Pediatr Neurol 2011; 18 (04) 264-271
• 31 Weedon MN, Hastings R, Caswell R. , et al. Exome sequencing identifies a DYNC1H1 mutation in a large pedigree with dominant axonal Charcot-Marie-Tooth disease. Am J Hum Genet 2011; 89 (02) 308-312
• 32 Grohmann K, Schuelke M, Diers A. , et al. Mutations in the gene encoding immunoglobulin mu-binding protein 2 cause spinal muscular atrophy with respiratory distress type 1. Nat Genet 2001; 29 (01) 75-77
• 33 Cottenie E, Kochanski A, Jordanova A. , et al. Truncating and missense mutations in IGHMBP2 cause Charcot-Marie Tooth disease type 2. Am J Hum Genet 2014; 95 (05) 590-601
• 34 Schottmann G, Jungbluth H, Schara U. , et al. Recessive truncating IGHMBP2 mutations presenting as axonal sensorimotor neuropathy. Neurology 2015; 84 (05) 523-531
• 35 van der Lei HD, van Berkel CG, van Wieringen WN. , et al. Genotype-phenotype correlation in vanishing white matter disease. Neurology 2010; 75 (17) 1555-1559
• 36 Schofield D, Alam K, Douglas L. , et al. Cost-effectiveness of massively parallel sequencing for diagnosis of paediatric muscle diseases. NPJ Genom Med 2017; 2: 2
• 37 Córdoba M, Rodriguez-Quiroga SA, Vega PA. , et al. Whole exome sequencing in neurogenetic odysseys: an effective, cost- and time-saving diagnostic approach. PLoS One 2018; 13 (02) e0191228
• 38 van Nimwegen KJ, van Soest RA, Veltman JA. , et al. Is the $1000 genome as near as we think? A cost analysis of next-generation sequencing. Clin Chem 2016; 62 (11) 1458-1464
• 39 Zurynski Y, Deverell M, Dalkeith T. , et al; APSU Rare Diseases Impacts on Families Study group. Australian children living with rare diseases: experiences of diagnosis and perceived consequences of diagnostic delays. Orphanet J Rare Dis 2017; 12 (01) 68
• 40 Lochmüller H, Badowska DM, Thompson R. , et al; RD-Connect consortium; NeurOmics consortium; EURenOmics consortium. RD-Connect, NeurOmics and EURenOmics: collaborative European initiative for rare diseases. Eur J Hum Genet 2018; 26 (06) 778-785