Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study

Ibáñez, Kristina; Polke, James M.; Hagelstrom, R. Tanner; Dolzhenko, Egor; Pasko, Dorota; Thomas, E. R. A.; Daugherty, Louise C.; Kasperavičiūtė, Dalia; Smith, Katherine R.; Deans, Zandra C.; Hill, Sue; Fowler, Tom; Scott, Richard; Hardy, John; Chinnery, Patrick F.; Houlden, Henry; Rendon, Augusto; Caulfield, Mark J.; Eberle, Michael A.; Taft, Ryan J.; Tucci, Arianna

doi:10.1016/s1474-4422(21)00462-2

Cited by 112 publications

(79 citation statements)

References 37 publications

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“…Computational methods capable of detecting expanded STR loci from PCR-free WGS data (e.g. ExpansionHunter 63 ) provide an avenue to detect and report on clinically relevant STRs 64 , 65 ; however, existing algorithms have limitations in terms of sensitivity and specificity 63 , 66 , 67 .…”

Section: Discussionmentioning

confidence: 99%

Best practices for the interpretation and reporting of clinical whole genome sequencing

et al. 2022

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Whole genome sequencing (WGS) shows promise as a first-tier diagnostic test for patients with rare genetic disorders. However, standards addressing the definition and deployment practice of a best-in-class test are lacking. To address these gaps, the Medical Genome Initiative, a consortium of leading health care and research organizations in the US and Canada, was formed to expand access to high quality clinical WGS by convening experts and publishing best practices. Here, we present best practice recommendations for the interpretation and reporting of clinical diagnostic WGS, including discussion of challenges and emerging approaches that will be critical to harness the full potential of this comprehensive test.

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Section: Discussionmentioning

confidence: 99%

Best practices for the interpretation and reporting of clinical whole genome sequencing

et al. 2022

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“…However, the repeat expansion detected by the analysis of the WES data needs to be further validated and the number of repeats should be tested by PCR or TP PCR. A recent study showed that WGS was reliable for detecting repeat expansion with high sensitivity and specificity ( 13 ). WGS would be a promising diagnostic tool for the possibility to detecting repeat expansions and deep intronic variants regardless of the high expense.…”

Section: Discussionmentioning

confidence: 99%

“…However, some subtypes of hereditary cerebellar ataxia and spastic ataxia, such as spinocerebellar ataxia (SCA) type 1 ( ATXN1 ) ( 10 ) and type 3 ( ATXN3 ) ( 11 ) and Friedreich's ataxia ( FXN ) ( 12 ), have been reported to present as isolated spastic paraplegia and are caused by abnormal trinucleotide repeat (TNR) expansion. Although WGS has been certified to be reliable for detecting repeat expansion with high sensitivity and specificity ( 13 ), targeted gene sequencing or WES is incapable of detecting repeat expansion in routine. Triplet repeat primed PCR (TP PCR) is the usual chosen approach to screen for the abnormal TNR expansion and other dynamic mutations of known SCA genes.…”

Section: Introductionmentioning

confidence: 99%

Clinical Features and Genetic Spectrum of Patients With Clinically Suspected Hereditary Progressive Spastic Paraplegia

et al. 2022

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Background and PurposeA variety of hereditary diseases overlap with neurological phenotypes or even share genes with hereditary spastic paraplegia (HSP). The aim of this study was to determine the clinical features and genetic spectrum of patients with clinically suspected HSPs.MethodsA total of 52 patients with clinically suspected HSPs were enrolled in this study. All the patients underwent next-generation sequencing (NGS) and triplet repeat primed PCR to screen for the dynamic mutations typical of spinocerebellar ataxia (SCA). Multiplex ligation-dependent probe amplification (MLPA) was further conducted in patients with no causative genetic mutations detected to examine for large deletions and duplications in genes of SPAST, ATL1, REEP1, PGN, and SPG11. Clinical characteristics and findings of brain MRI were analyzed in patients with definite diagnoses.ResultsThe mean age of the patients studied was 36.90 ± 14.57 years. 75% (39/52) of patients manifested a phenotype of complex form of HSPs. A genetic diagnosis was made in 51.9% (27/52) of patients, of whom 40.3% (21/52) of patients had mutations in HSPs genes (SPG4/SPG6/SPG8/SPG11/SPG15/SPG78/SPG5A) and 11.5% (6/52) of patients had mutations in SCAs genes (SCA3/SCA17/SCA28). SPG4 and SPG11 were the most common cause of pure form of HSPs (5/6, 83.3%) and complex form of HSPs (5/15, 33.3%), respectively. Gait disturbance was the most common initial symptom in both the patients with HSPs (15/21) and in patients with SCAs (5/6). Dysarthria and cerebellar ataxia were detected in 28.5% (6/21) and 23.8% (5/21) of patients with HSPs, respectively, and were the most common symptoms in addition to progressive weakness and spasticity of the lower limbs. Cerebellar atrophy was seen on the brain MRI of patients with SPG5A, SCA3, and SCA28.ConclusionCausative genetic mutations were identified in 51.9% of patients with clinically suspected HSPs by NGS and triplet repeat primed PCR. A final diagnosis of HSPs or SCAs was made in 40.3% and 11.5% of patients, respectively. The clinical manifestations and neuroimaging findings overlapped between patients with HSPs and patients with SCAs. Dynamic mutations should be screened in patients with clinically suspected HSPs, especially in those with phenotypes of complex form of HSPs.

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“…To solicit feedback on REViewer and FlipBook and create training materials for new REViewer users, we performed a concordance study involving 12 scientists (analysts). We used a collection of whole-genome sequencing (WGS) samples described in a recent study of subjects with suspected neurological disorders [13] and additional samples with PCR-validated FMR1 and DMPK repeats from the 100,000 Genomes Project (Additional file 1: Supplementary methods; Additional file 2: Table S1). The HTT, TBP, AR, ATXN3, ATN1, ATXN2, ATXN7, ATXN1, CACNA1A, DMPK, PPP2R2B, FXN, FMR1, and C9orf72 STR loci were genotyped in these samples with ExpansionHunter (EH) and also tested with PCR.…”

Section: A Concordance Studymentioning

confidence: 99%

REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats

et al. 2022

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Background Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads. Results We implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions and FlipBook, a companion image viewer designed for manual curation of large collections of REViewer images. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in short tandem repeat research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically relevant repeat interruptions by comparing visual assessment results of 44 FMR1 repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR. Conclusions Read pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer and FlipBook to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions. REViewer and FlipBook are available under open-source licenses at https://github.com/illumina/REViewer and https://github.com/broadinstitute/flipbook respectively.

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Whole genome sequencing for the diagnosis of neurological repeat expansion disorders in the UK: a retrospective diagnostic accuracy and prospective clinical validation study

Cited by 112 publications

References 37 publications

Best practices for the interpretation and reporting of clinical whole genome sequencing

Best practices for the interpretation and reporting of clinical whole genome sequencing

Clinical Features and Genetic Spectrum of Patients With Clinically Suspected Hereditary Progressive Spastic Paraplegia

REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats

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