Abstract
SummaryBackgroundRepeat expansion disorders affect about 1 in 3000 individuals and are clinically heterogeneous diseases caused by expansions of short tandem DNA repeats. Genetic testing is often locus-specific, resulting in underdiagnosis of people who have atypical clinical presentations, especially in paediatric patients without a previous positive family history. Whole genome sequencing is increasingly used as a first-line test for other rare genetic disorders, and we aimed to assess its performance in the diagnosis of patients with neurological repeat expansion disorders.MethodsWe retrospectively assessed the diagnostic accuracy of whole genome sequencing to detect the most common repeat expansion loci associated with neurological outcomes (AR, ATN1, ATXN1, ATXN2, ATXN3, ATXN7, C9orf72, CACNA1A, DMPK, FMR1, FXN, HTT, and TBP) using samples obtained within the National Health Service in England from patients who were suspected of having neurological disorders; previous PCR test results were used as the reference standard. The clinical accuracy of whole genome sequencing to detect repeat expansions was prospectively examined in previously genetically tested and undiagnosed patients recruited in 2013–17 to the 100 000 Genomes Project in the UK, who were suspected of having a genetic neurological disorder (familial or early-onset forms of ataxia, neuropathy, spastic paraplegia, dementia, motor neuron disease, parkinsonian movement disorders, intellectual disability, or neuromuscular disorders). If a repeat expansion call was made using whole genome sequencing, PCR was used to confirm the result.FindingsThe diagnostic accuracy of whole genome sequencing to detect repeat expansions was evaluated against 793 PCR tests previously performed within the NHS from 404 patients. Whole genome sequencing correctly classified 215 of 221 expanded alleles and 1316 of 1321 non-expanded alleles, showing 97·3% sensitivity (95% CI 94·2–99·0) and 99·6% specificity (99·1–99·9) across the 13 disease-associated loci when compared with PCR test results. In samples from 11 631 patients in the 100 000 Genomes Project, whole genome sequencing identified 81 repeat expansions, which were also tested by PCR: 68 were confirmed as repeat expansions in the full pathogenic range, 11 were non-pathogenic intermediate expansions or premutations, and two were non-expanded repeats (16% false discovery rate).InterpretationIn our study, whole genome sequencing for the detection of repeat expansions showed high sensitivity and specificity, and it led to identification of neurological repeat expansion disorders in previously undiagnosed patients. These findings support implementation of whole genome sequencing in clinical laboratories for diagnosis of patients who have a neurological presentation consistent with a repeat expansion disorder.FundingMedical Research Council, Department of Health and Social Care, National Health Service England, National Institute for Health Research, and Illumina.
Highlights
Despite recent advances in our understanding of the genetic basis of rare neurological disorders, up to 70% of patients with such disorders remain genetically un diagnosed.[1–3] In part, this is due to the technical challenges of testing for complex and repetitive genetic variants, including repeat expansions; such expansions are estimated to affect about 1 in 3000 people, and are the leading cause of more than neurogenetic disorders,[4] including Huntington’s disease and fragile X syndrome
Added value of this study Here we report on the diagnostic accuracy and clinical validation of detection of repeat expansions by whole genome sequencing
Patients were identified from two sources: the 100 000 Genomes Project and the Genomic Laboratory based at Cambridge University Hospitals (Cambridge, UK). For both sets of patients, PCR testing had been performed on patient samples by laboratories in the National Health Service (NHS) as part of routine clinical assessment: for samples in the 100 000 Genomes Project, PCR tests were done before recruitment to the project by the University College London Hospital Neurogenetics Laboratory (London, UK); samples with PCR-confirmed repeat expansions were obtained from patients tested by the Genomic Laboratory based at Cambridge
Summary
Despite recent advances in our understanding of the genetic basis of rare neurological disorders, up to 70% of patients with such disorders remain genetically un diagnosed.[1–3] In part, this is due to the technical challenges of testing for complex and repetitive genetic variants, including repeat expansions; such expansions are estimated to affect about 1 in 3000 people (appendix p 1), and are the leading cause of more than neurogenetic disorders,[4] including Huntington’s disease and fragile X syndrome. Despite recent advances in our understanding of the genetic basis of rare neurological disorders, up to 70% of patients with such disorders remain genetically un diagnosed.[1–3] In part, this is due to the technical challenges of testing for complex and repetitive genetic variants, including repeat expansions; such expansions are estimated to affect about 1 in 3000 people (appendix p 1), and are the leading cause of more than neurogenetic disorders,[4] including Huntington’s disease and fragile X syndrome. The defining characteristic of these conditions is the expansion of short (3–6 bp) repetitive DNA sequences beyond a pathogenic threshold These disorders include well known conditions, such as Huntington’s disease, as well as C9orf72-associated frontal lobe dementia and amyotrophic lateral sclerosis. Repeat expansions have historically been undetectable by whole genome sequencing, contributing to underdiagnosis in patients with suspected genetic neurological disorders and limiting the benefit of genomic testing
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