Identification of false-negative mutations missed by next-generation sequencing in retinitis pigmentosa patients: a complementary approach to clinical genetic diagnostic testing

Huang, Xiu‐Feng; Wu, Juan; Lv, Ji‐Neng; Zhang, Xiao

doi:10.1038/gim.2014.193

Cited by 51 publications

(41 citation statements)

References 18 publications

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“…Huang et al determined that next-generation sequencing has the potential to miss causative variants in the RPGR gene, accounting for 70–75% of X-linked retinitis pigmentosa cases. 24 In the currently described exome approach, most of the RPGR gene had a coverage above 20 ×, but approximately 30% of the RPGR-ORF15 exon 15, a mutation hotspot region, had less than 10 × coverage. Nevertheless, the RPGR gene was the fourth most frequently mutated gene in our cohort, demonstrating that our approach is able to detect causative RPGR variants.…”

Section: Discussionmentioning

confidence: 99%

Diagnostic exome sequencing in 266 Dutch patients with visual impairment

et al. 2017

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Inherited eye disorders have a large clinical and genetic heterogeneity, which makes genetic diagnosis cumbersome. An exome-sequencing approach was developed in which data analysis was divided into two steps: the vision gene panel and exome analysis. In the vision gene panel analysis, variants in genes known to cause inherited eye disorders were assessed for pathogenicity. If no causative variants were detected and when the patient consented, the entire exome data was analyzed. A total of 266 Dutch patients with different types of inherited eye disorders, including inherited retinal dystrophies, cataract, developmental eye disorders and optic atrophy, were investigated. In the vision gene panel analysis (likely), causative variants were detected in 49% and in the exome analysis in an additional 2% of the patients. The highest detection rate of (likely) causative variants was in patients with inherited retinal dystrophies, for instance a yield of 63% in patients with retinitis pigmentosa. In patients with developmental eye defects, cataract and optic atrophy, the detection rate was 50, 33 and 17%, respectively. An exome-sequencing approach enables a genetic diagnosis in patients with different types of inherited eye disorders using one test. The exome approach has the same detection rate as targeted panel sequencing tests, but offers a number of advantages. For instance, the vision gene panel can be frequently and easily updated with additional (novel) eye disorder genes. Determination of the genetic diagnosis improved the clinical diagnosis, regarding the assessment of the inheritance pattern as well as future disease perspective.

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Section: Discussionmentioning

confidence: 99%

Diagnostic exome sequencing in 266 Dutch patients with visual impairment

et al. 2017

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“…29 As a result, genetic tests such as microarrays, metabolic screening, or traditional gene testing may still be more suitable for consideration given a clear diagnostic indication, 30 such as in cases 1 and 2 here that underwent panel or single gene testing. Interpretation of variants of unknown significance remains a significant challenge in diagnostic WES, and the issue of secondary (incidental) findings continues to evolve.…”

Section: Discussionmentioning

confidence: 99%

Potential Role of Genomic Sequencing in the Early Diagnosis of Treatable Genetic Conditions

Zahed

Sparks

et al. 2017

The Journal of Pediatrics

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“…First, highly GC-rich, highly repetitive and/or homologous regions could not be captured, sequenced, and aligned unambiguously by targeted capture NGS [47,48]. For example, the open reading frame 15 (ORF15) of RPGR gene, which is a RP mutational hotspot, contains a ~300 bp highly repetitive region that cannot be unambiguously analyzed by conventional capture NGS [12,49,50]. Long-range PCR followed by NGS may be used to identify variants in these regions.…”

Section: Discussionmentioning

confidence: 99%

Retinal Diseases Caused by Mutations in Genes Not Specifically Associated with the Clinical Diagnosis

Wang

Feng

et al. 2016

PLoS ONE

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PurposeWhen seeking a confirmed molecular diagnosis in the research setting, patients with one descriptive diagnosis of retinal disease could carry pathogenic variants in genes not specifically associated with that description. However, this event has not been evaluated systematically in clinical diagnostic laboratories that validate fully all target genes to minimize false negatives/positives.MethodsWe performed targeted next-generation sequencing analysis on 207 ocular disease-related genes for 42 patients whose DNA had been tested negative for disease-specific panels of genes known to be associated with retinitis pigmentosa, Leber congenital amaurosis, or exudative vitreoretinopathy.ResultsPathogenic variants, including single nucleotide variations and copy number variations, were identified in 9 patients, including 6 with variants in syndromic retinal disease genes and 3 whose molecular diagnosis could not be distinguished easily from their submitted clinical diagnosis, accounting for 21% (9/42) of the unsolved cases.ConclusionOur study underscores the clinical and genetic heterogeneity of retinal disorders and provides valuable reference to estimate the fraction of clinical samples whose retinal disorders could be explained by genes not specifically associated with the corresponding clinical diagnosis. Our data suggest that sequencing a larger set of retinal disorder related genes can increase the molecular diagnostic yield, especially for clinically hard-to-distinguish cases.

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Identification of false-negative mutations missed by next-generation sequencing in retinitis pigmentosa patients: a complementary approach to clinical genetic diagnostic testing

Cited by 51 publications

References 18 publications

Diagnostic exome sequencing in 266 Dutch patients with visual impairment

Diagnostic exome sequencing in 266 Dutch patients with visual impairment

Potential Role of Genomic Sequencing in the Early Diagnosis of Treatable Genetic Conditions

Retinal Diseases Caused by Mutations in Genes Not Specifically Associated with the Clinical Diagnosis

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