Whole exome sequencing in patients with white matter abnormalities
Open accessAbstract
Here we report whole exome sequencing (WES) on a cohort of 71 patients with persistently unresolved white matter abnormalities with a suspected diagnosis of leukodystrophy or genetic leukoencephalopathy. WES analyses were performed on trio, or greater, family groups. Diagnostic pathogenic variants were identified in 35% (25 of 71) of patients. Potentially pathogenic variants were identified in clinically relevant genes in a further 7% (5 of 71) of cases, giving a total yield of clinical diagnoses in 42% of individuals. These findings provide evidence that WES can substantially decrease the number of unresolved white matter cases. Ann Neurol 2016;79:1031–1037
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The percentage of leukodystrophy cases without a specific diagnosis has been estimated to be 20-30%.
“Nevertheless, the percentage of leukodystrophy cases without a specific diagnosis has been estimated to be 20–30% [7,39,40].”
From Identification of a Novel Non-Canonical Splice-Site Variant in ABCD1 (2023) · cites this paper as [7]
The Introduction estimates that nearly half of patients presenting with a possible leukodystrophy remain unresolved, rather than 20–30%. The Methods (Cohort description) also report 90 persistently unsolved cases among 191 identified cases, approximately 47%. (LLM, conf=0.87)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredNGS genetic testing, including gene panel testing, WES, or WGS, is the most successful approach for diagnosing rare diseases with the highest diagnostic yield.
“NGS genetic testing, including gene panel testing, WES, or whole genome sequencing (WGS), is the most successful approach for diagnosing rare diseases with the highest diagnostic yield [7,37].”
From Identification of a Novel Non-Canonical Splice-Site Variant in ABCD1 (2023) · cites this paper as [7]
The Results and Discussion support WES as a useful diagnostic approach for patients with unresolved white matter abnormalities: it yielded clinical diagnoses in 42% of the study cohort and increased diagnoses beyond standard approaches. The Discussion explicitly says further research is needed to compare WES, WGS, and targeted panels, so the paper does not establish that NGS is the most successful approach or has the highest yield across rare diseases. Page numbers are not provided in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredGenetic screening using next-generation sequencing is the most successful approach with the highest diagnostic yield in cases of underlying genetic disorders, such as CALD, and provides the fastest results.
“Genetic screening using next-generation sequencing (NGS) is the most successful approach with the highest diagnostic yield in cases of underlying genetic disorders, such as CALD, and provides the fastest results [7,8].”
From Identification of a Novel Non-Canonical Splice-Site Variant in ABCD1 (2023) · cites this paper as [7]
The Discussion (page unavailable) reports that whole-exome sequencing would increase diagnoses by about 20% in a cohort with genetic white matter disorders. It does not establish that NGS has the highest diagnostic yield or provides the fastest results, and says comparative effectiveness needs further study. The cited passages do not establish the claim specifically for CALD. (LLM, conf=0.87)
Experimental — accuracy not yet measuredTrio-WES has substantially increased the number of known leukodystrophies and improved diagnoses.
“Trio-WES has substantially increased the number of known leukodystrophies and improved diagnoses [7,8,39].”
From Identification of a Novel Non-Canonical Splice-Site Variant in ABCD1 (2023) · cites this paper as [7]
The Abstract reports that trio-or-larger WES yielded clinical diagnoses in 42% of 71 previously unresolved patients, and the Discussion estimates an approximately 20% diagnostic increase when WES is added to standard approaches. The paper does not show that WES substantially increased the number of known leukodystrophies; its Results describe diagnoses involving genes already associated with those disorders. (LLM, conf=0.88)
Experimental — accuracy not yet measuredIn a previously reported cohort of 191 families with suspected leukodystrophy, 71 were persistently unsolved despite targeted molecular and enzymatic testing and 19 were lost to follow-up.
“Previously, we reported on a cohort of 191 families with a suspected leukodystrophy, of which 71 were persistently unsolved despite targeted molecular and enzymatic testing and 19 were lost to follow‐up.1”
From Genome sequencing in persistently unsolved white matter disorders (2020) · cites this paper as [1]
The Methods (Cohort description; page not provided) report an initial 191 cases, of which 101 received diagnoses and 90 remained unsolved; 71 of the unsolved families had suitable samples for exome sequencing. The other 19 were excluded from that testing—not reported as lost to follow-up: nine obtained sequencing elsewhere, and ten lacked suitable samples despite collection attempts. (LLM, conf=0.90)
Experimental — accuracy not yet measured
Trio-or-greater exome sequencing analysis resolved 42% (30/71) of unsolved cases, which, in combination with standard of care approaches, yielded a 77% overall diagnostic rate from 172 families available for testing.
“Trio‐or‐greater exome sequencing analysis resolved 42% (30/71) of unsolved cases, which, in combination with standard of care approaches, yielded a 77% overall diagnostic rate from 172 families available for testing.”
From Genome sequencing in persistently unsolved white matter disorders (2020) · cites this paper as [1]
The Abstract (page unavailable) reports a 42% clinical diagnostic yield in 71 trio-or-greater WES cases, comprising 25 cases with diagnostic variants and five with potentially pathogenic variants. The Methods describe 101 diagnoses by standard approaches, but the Discussion reports an overall rate of approximately 72% across the initial 191 families—not 77% across 172 families. The claim also treats all 30 WES findings as resolved without preserving the distinction between diagnostic and potentially pathogenic variants. (LLM, conf=0.90)
Experimental — accuracy not yet measuredThirty cases were solved by exome sequencing, and in this study, genome sequencing established a diagnosis in an additional 14 families yielding a 20% improvement, and an overall diagnostic efficacy of NGS of genome or exome sequencing increased to 44/71 (62%) and in total resolution of 145/172 (84%) of the original testable cohort.
“Thirty cases were solved by exome sequencing,1 and in this study, genome sequencing established a diagnosis in an additional 14 families yielding a 20% improvement, and an overall diagnostic efficacy of NGS of genome or exome sequencing increased to 44/71 (62%) and in total resolution of 145/172 (84%) of the original testable cohort.”
From Genome sequencing in persistently unsolved white matter disorders (2020) · cites this paper as [1]
The GJC2 duplication was previously undetected by exome sequencing due to a lack of coverage as it lies in the middle of a 110 nucleotide block of a ~95% GC-rich region.
“The duplication was previously undetected by exome sequencing due to a lack of coverage as it lies in the middle of a 110 nucleotide block of a ~ 95% GC‐rich region (Fig. 1B).1”
From Genome sequencing in persistently unsolved white matter disorders (2020) · cites this paper as [1]
The Methods (Cohort description; page unavailable) describe exome-sequencing coverage in the cohort, but not coverage at a GJC2 duplication. Searches for GJC2, the duplication, and the 110-nucleotide, approximately 95% GC-rich region found no passage addressing why this variant was missed. (LLM, conf=0.75)
Experimental — accuracy not yet measuredStringent variant filtering performed during the prior exome sequencing analysis excluded this intronic variant and precluded a diagnosis.
“Stringent variant filtering performed during the prior exome sequencing analysis excluded this intronic variant and precluded a diagnosis.1”
From Genome sequencing in persistently unsolved white matter disorders (2020) · cites this paper as [1]
The Methods (Cohort description; page unavailable) describe variant filtering, but do not say that it excluded an intronic variant or prevented a diagnosis. A search for “intronic” found no passage in our copy establishing that event. (LLM, conf=0.73)
Experimental — accuracy not yet measured
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- Authors
- Vanderver, A., Simons, C., Helman, G., Crawford, J., Wolf, N. I., Bernard, G., Pizzino, A., Schmidt, J. L., Takanohashi, A., Miller, D., Khouzam, A., Rajan, V., Ramos, E., Chowdhury, S., Hambuch, T., Ru, K., Baillie, G. J., Grimmond, S. M., Caldovic, L., Devaney, J., Bloom, M., Evans, S. H., Murphy, J. L. P., McNeill, N., Fogel, B. L., the Leukodystrophy Study Group, Schiffmann, R., van der Knaap, M. S., & Taft, R. J.
- Affiliations
- Children's National (US)
- The University of Queensland (AU)
- Amsterdam Neuroscience (NL)
- Montreal Children's Hospital (CA)
- Illumina (United States) (US)
- Institute for Metabolic Disease Baylor Research Institute Dallas TX
- University of California, Los Angeles (US)
- Department of Child Neurology VU University Medical Center and Neuroscience Campus Amsterdam Amsterdam the Netherlands
- Corresponding author
- Vanderver, Adeline
- Simons, Cas
- ORCID
- Vanderver, Adeline
- Simons, Cas
- Helman, Guy
- Crawford, Joanna
- Wolf, Nicole I.
- Bernard, Geneviève
- Pizzino, Amy
- Schmidt, Johanna L.
- Takanohashi, Asako
- Ramos, Erica
- Chowdhury, Shimul
- Hambuch, Tina
- Baillie, Gregory J.
- Grimmond, Sean M.
- Caldovic, Ljubica
- Devaney, Joseph
- Evans, Sarah H.
- Murphy, Jennifer L. P.
- McNeill, Nathan
- Fogel, Brent L.
- Schiffmann, Raphael
- Taft, Ryan J.
- Venue
- Annals of Neurology
- Publisher
- Wiley
- Published
- 2016-05-09
- Volume
- 79
- Issue
- 6
- Pages
- 1031-1037
- ISSN
- 0364-5134 (ISSN-L)
- 1531-8249
- PMC
- PMC5354169
- OpenAlex
- W2346093359
- Cited by
- 145
- References
- 36
- Citations by year
- 2026: 4 · 2025: 9 · 2024: 12 · 2023: 17 · 2022: 13 · 2021: 21 · 2020: 16 · 2019: 17 · 2018: 22 · 2017: 11 · 2016: 2 · 2015: 1
- FWCI
- 14.00
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Licence
- Locations
- Annals of Neurology (publishedVersion)
- PubMed (publishedVersion)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion)
- Funders
- Santé
- Australian Research Council
- National Health and Medical Research Council (APP1068278)
- ZonMw (91211005)
- National Institute of Mental Health (K08MH086297)
- National Institute of Neurological Disorders and Stroke (R01NS082094)
- National Center for Advancing Translational Sciences (UL1TR000075)
- Myelin Project
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Hereditary Neurological Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Clinical Biochemistry › Metabolism and Genetic Disorders
- Keywords
- white matter abnormalities, leukodystrophy, pathogenic variants, trio exome sequencing, genetic diagnosis, hereditary leukodystrophy
- MeSH terms
- Adolescent, Adult, Child, Child, Preschool, DNA Mutational Analysis, Female, Humans, Male, Mutation, Young Adult, Leukoencephalopathies, Exome, White Matter
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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