Targeted next-generation sequencing of the ATP7B gene for molecular diagnosis of Wilson disease

Poon, Kok-Siong; Tan, Karen; Koay, Evelyn Siew-Chuan

doi:10.1016/j.clinbiochem.2015.10.003

Cited by 21 publications

(10 citation statements)

References 28 publications

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“…In 23% of our patients, we could not identify two mutant alleles, although they showed the characteristic clinical and biochemical features of WD. Whole exome sequencing revealed good concordance with direct DNA sequencing and would be timely effective, 17 it also could not detect large deletion and duplications. It is possible that unknown molecular defects exist that are also be a cause of WD.…”

Section: Discussionmentioning

confidence: 99%

Multiplex Ligation-dependent Probe Amplification Analysis Subsequent to Direct DNA Full Sequencing for IdentifyingATP7BMutations and Phenotype Correlations in Children with Wilson Disease

et al. 2018

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BackgroundMutations in ATP7B cause Wilson disease (WD). However, direct DNA full sequencing cannot detect all mutations in patients with WD. Multiplex ligation-dependent probe amplification (MLPA) analysis is reportedly useful in increasing the diagnostic yield in other genetic disorders with large deletions or insertions. The aim of this study was to evaluate whether the detection rate of ATP7B mutations can be increased by using MLPA.MethodsWe enrolled 114 children with WD from 104 unrelated families based on biochemical tests and direct DNA full sequencing. The patients with one or zero mutant allele were investigated using MLPA. We analyzed phenotypic correlations.ResultsTotal allele frequency by full sequencing was 87.5%. Full sequencing revealed two mutant alleles in 80 of 104 unrelated children. One mutant allele was detected in 22 children, and no mutations were found in two children. Novel mutations including small deletions with frameshift mutations were identified by DNA sequencing. MLPA revealed no gross deletion or duplication in 24 children with one or zero mutant alleles. The number of detected mutations was not associated with hepatic manifestation, age of onset, Kayser-Fleischer ring, ceruloplasmin, and urinary Cu concentrations.ConclusionMLPA showed a limited role to increase the mutation detection rate in children who do not receive a definite genetic diagnosis of WD through DNA full sequencing. This finding suggests that large deletions or duplications might be extremely rare in WD. Further development is needed to improve the genetic diagnosis of WD.

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Section: Discussionmentioning

confidence: 99%

Multiplex Ligation-dependent Probe Amplification Analysis Subsequent to Direct DNA Full Sequencing for IdentifyingATP7BMutations and Phenotype Correlations in Children with Wilson Disease

et al. 2018

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“…However, this approach is labour-intensive, time-consuming and costly for a large gene like ATP7B . Recently, we developed an amplicon-based next-generation sequencing (NGS) assay to overcome the limitations of Sanger sequencing 11. We showed 100% concordance in detection of pathogenic variants with an additional advantage of the NGS assay being able to detect variants within the non-coding regions of the gene (deep intronic variants) 11.…”

Section: Wilson Diseasementioning

confidence: 99%

“…Recently, we developed an amplicon-based next-generation sequencing (NGS) assay to overcome the limitations of Sanger sequencing 11. We showed 100% concordance in detection of pathogenic variants with an additional advantage of the NGS assay being able to detect variants within the non-coding regions of the gene (deep intronic variants) 11. Although the NGS assay reduced labour intensiveness and cost per sample for a batch of 18 samples,11 the small number of sample requests in our laboratory did not make the NGS assay cost-effective in the routine clinical workflow.…”

Section: Wilson Diseasementioning

confidence: 99%

Challenges in molecular diagnosis of Wilson disease: viewpoint from the clinical laboratory

et al. 2019

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“…The instruments most often used in precision medicine programs performing WES/WGS of the human genome in clinical care settings are the HiSeq sequencers [ 30 ] that have the advantages of a relatively high sample throughput and a low sequencing error rate. However, all of the NGS technologies are being applied to health research [ 31 – 36 ]. The single-molecule, real-time sequencing technology generates the longest reads ( Table 2 ), making the PacBio RS II instrument well suited for de novo sequencing (by assembly of reads into long contiguous sequences) of the genomes of organisms that do not have a reference genome (e.g., many microbial genomes) [ 37 ].…”

Section: Genomic Data Generationmentioning

confidence: 99%

Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine

Carter

2016

Journal of Healthcare Engineering

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Advances in genomic medicine have the potential to change the way we treat human disease, but translating these advances into reality for improving healthcare outcomes depends essentially on our ability to discover disease- and/or drug-associated clinically actionable genetic mutations. Integration and manipulation of diverse genomic data and comprehensive electronic health records (EHRs) on a big data infrastructure can provide an efficient and effective way to identify clinically actionable genetic variants for personalized treatments and reduce healthcare costs. We review bioinformatics processing of next-generation sequencing (NGS) data, bioinformatics infrastructures for implementing precision medicine, and bioinformatics approaches for identifying clinically actionable genetic variants using high-throughput NGS data and EHRs.

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Targeted next-generation sequencing of the ATP7B gene for molecular diagnosis of Wilson disease

Cited by 21 publications

References 28 publications

Multiplex Ligation-dependent Probe Amplification Analysis Subsequent to Direct DNA Full Sequencing for IdentifyingATP7BMutations and Phenotype Correlations in Children with Wilson Disease

Multiplex Ligation-dependent Probe Amplification Analysis Subsequent to Direct DNA Full Sequencing for IdentifyingATP7BMutations and Phenotype Correlations in Children with Wilson Disease

Challenges in molecular diagnosis of Wilson disease: viewpoint from the clinical laboratory

Challenges of Identifying Clinically Actionable Genetic Variants for Precision Medicine

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