Yield of clinically reportable genetic variants in unselected cerebral palsy by whole genome sequencing

Cerebral palsy (CP) is the most common cause of childhood physical disability, with incidence between 1/500 and 1/700 births in the developed world. Despite increasing evidence for a major contribution of genetics to CP aetiology, genetic testing is currently not performed systematically. We assessed the diagnostic rate of genome sequencing (GS) in a clinically unselected cohort of 150 singleton CP patients, with CP confirmed at >4 years of age. Clinical grade GS was performed on the proband and variants were filtered, and classified according to American College of Medical Genetics and Genomics–Association for Molecular Pathology (ACMG-AMP) guidelines. Variants classified as pathogenic or likely pathogenic (P/LP) were further assessed for their contribution to CP. In total, 24.7% of individuals carried a P/LP variant(s) causing or increasing risk of CP, with 4.7% resolved by copy number variant analysis and 20% carrying single nucleotide or indel variants. A further 34.7% carried one or more rare, high impact variants of uncertain significance (VUS) in variation intolerant genes. Variants were identified in a heterogeneous group of genes, including genes associated with hereditary spastic paraplegia, clotting and thrombophilic disorders, small vessel disease, and other neurodevelopmental disorders. Approximately 1/2 of individuals were classified as likely to benefit from changed clinical management as a result of genetic findings. In addition, no significant association between genetic findings and clinical factors was detectable in this cohort, suggesting that systematic sequencing of CP will be required to avoid missed diagnoses.


Case ID
Clinical summary on the left side. Diffuse and generalised cortical volume loss. Thin and hypoplastic right MCA. MRI, 5 years -Gliotic change in the left periventricular region surrounding the encephalomalacic cavity has increased and evidence of wallerian degeneration has developed in the right thalamus. Extensive right middle artery territory cystic encephalomalacia and small right middle cerebral artery changes are stable. MRI, 11 years-Extensive cystic encephalomalacia and gliosis in the right middle cerebral artery territory does not show significant interval change. Wallerian degeneration involving the bilateral thalami and brainstem as described. Bilateral paranasal sinus disease.

P801
Female. Born 31/40. IUGR. Spastic triplegia with minimal effect on right leg. Visual problems. Grade 2 intraventricular haemorrhage at birth (VP shunt insertion in the newborn period).

P902
Female. Born 35/40. IUGR. Spastic hemiplegia. Dev. delay. MRI -regions of gliosis as demonstrated by T2 high signal and parenchymal volume loss are seen in the region of the right thalamus and basal ganglia.

P934
Male. Born 41/40. Spastic hemiplegia. MRI Brain -focal area of gliosis involving the posterior limb of the right internal capsule and right centrum semiovale.

Pathogenic/ Chr1q21.1 microdeletion (AD) (MIM 612474)
Risk factor. Event encompassing the recurrently deleted Chr1q21.1 region, reported to predispose to a range of neurological and cardiac phenotypes 29 . Forty-nine individuals had variants classified as pathogenic or likely pathogenic by ACMG criteria. For twenty-eight of these individuals, the clinically reportable variant was considered likely to be causative for cerebral palsy, while a further 9 individuals carried variants considered to be risk factors for cerebral palsy. Ten individuals carried at least one variant classified as likely pathogenic/pathogenic by ACMG criteria, but with uncertain clinical significance in the individual. A further four individuals carried ACMG pathogenic/likely pathogenic variants which were considered incidental findings likely contributing to other components of the clinical phenotype, but without a link to CP. # Additional high impact candidate variants identified in this individual (see Supplementary Table 4). + Additional compound heterozygous variants identified in this individual (see Supplementary  Table 6) *premature termination codon. Abbreviations: AD, autosomal dominant; APTT, activated partial thromboplastin time; AR, autosomal recessive; XLR, X-linked recessive; ASD, Autism spectrum disorder; ADHD, Attention-deficit/hyperactivity disorder; CADD phred, combined annotation dependent depletion scaled score; del, deletion; dup, duplication; EEG, electroencephalogram; fs, frameshift; GOF, gain of function; gnomAD, genome aggregation database; hemi, hemizygous; het, heterozygous; HSP, Hereditary spastic paraplegia; IUGR, intrauterine growth restriction; LOF, loss of function; MGRB, Medical Genome Reference Bank; MRI, magnetic resonance imaging; NDD, neurodevelopmental disorders; PVL, periventricular leukomalacia; VUS, variant of uncertain significance. Het, heterozygous; fs, frameshift; dup, duplication; del, deletion; *, premature termination codon; # , additional clinically reportable variant(s) identified in this proband (see Table 1); gnomAD, genome aggregation database; MGRB, Medical Genome Reference Bank; CADD phred, combined annotation dependent depletion scaled score; pLI, predicted loss-of-function intolerance; o/e, ratio of observed to expected number of variants; CI, confidence interval. Het, heterozygous; Hom, homozygous; fs, frameshift; dup, duplication; del, deletion; * premature termination codon; # additional clinically reportable variant identified in this proband (see Table 1); gnomAD, genome aggregation database; MGRB, Medical Genome Reference Bank; CADD phred, combined annotation dependent depletion scaled score; IBD, identical by descent; pLI, predicted loss-of-function intolerance; o/e, ratio of observed to expected number of variants; CI, confidence interval.