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Coffey A.J.,Wellcome Trust Sanger Institute | Durkie M.,Sheffield Diagnostic Genetics Service | Hague S.,University of Sheffield | McLay K.,Wellcome Trust Sanger Institute | And 26 more authors.
Brain | Year: 2013

Previous studies have failed to identify mutations in the Wilson's disease gene ATP7B in a significant number of clinically diagnosed cases. This has led to concerns about genetic heterogeneity for this condition but also suggested the presence of unusual mutational mechanisms. We now present our findings in 181 patients from the United Kingdom with clinically and biochemically confirmed Wilson's disease. A total of 116 different ATP7B mutations were detected, 32 of which are novel. The overall mutation detection frequency was 98%. The likelihood of mutations in genes other than ATP7B causing a Wilson's disease phenotype is therefore very low. We report the first cases with Wilson's disease due to segmental uniparental isodisomy as well as three patients with three ATP7B mutations and three families with Wilson's disease in two consecutive generations. We determined the genetic prevalence of Wilson's disease in the United Kingdom by sequencing the entire coding region and adjacent splice sites of ATP7B in 1000 control subjects. The frequency of all single nucleotide variants with in silico evidence of pathogenicity (Class 1 variant) was 0.056 or 0.040 if only those single nucleotide variants that had previously been reported as mutations in patients with Wilson's disease were included in the analysis (Class 2 variant). The frequency of heterozygote, putative or definite disease-associated ATP7B mutations was therefore considerably higher than the previously reported occurrence of 1:90 (or 0.011) for heterozygote ATP7B mutation carriers in the general population (P < 2.2 × 10-16 for Class 1 variants or P < 5 × 10-11 for Class 2 variants only). Subsequent exclusion of four Class 2 variants without additional in silico evidence of pathogenicity led to a further reduction of the mutation frequency to 0.024. Using this most conservative approach, the calculated frequency of individuals predicted to carry two mutant pathogenic ATP7B alleles is 1:7026 and thus still considerably higher than the typically reported prevalence of Wilson's disease of 1:30 000 (P = 0.00093). Our study provides strong evidence for monogenic inheritance of Wilson's disease. It also has major implications for ATP7B analysis in clinical practice, namely the need to consider unusual genetic mechanisms such as uniparental disomy or the possible presence of three ATP7B mutations. The marked discrepancy between the genetic prevalence and the number of clinically diagnosed cases of Wilson's disease may be due to both reduced penetrance of ATP7B mutations and failure to diagnose patients with this eminently treatable disorder. © 2013 The Author).


Young E.C.,Royal Devon and Exeter NHS Trust | Owens M.M.,Royal Devon and Exeter NHS Trust | Adebiyi I.,Institute of Medical Genetics | Bedenham T.,University of Oxford | And 24 more authors.
Diagnostic Molecular Pathology | Year: 2013

EGFR mutation testing of tumor samples is routinely performed to predict sensitivity to treatment with tyrosine kinase inhibitors for patients with non-small cell lung cancer. At least 9 different methodologies are employed in UK laboratories, and the aim of this study was to compare the sensitivity of different methods for the detection of EGFR mutations. Participating laboratories were sent coded samples with varying mutation loads (from 0% to 15%) to be tested for the p.Leu858Arg (p.L858R) missense mutation and c.2235-2249del exon 19 deletion. The p.L858R mutation and deletions within exon 19 of the EGFR gene account for ̃90% of mutationpositive cases. The 11 laboratories used their standard testing method(s) and submitted 15 sets of results for the p.L858R samples and 10 for the exon 19 deletion. The p.Leu858Arg (p.L858R) mutation was detected at levels between 1% and 7.5% by Sanger sequencing, pyrosequencing, real-time polymerase chain reaction (PCR), amplification refractory mutation system, and capillary electrophoresis single-strand conformation analysis. The c.2235-2249del mutation was detected at 1% to 5% by fragment size analysis, Sanger sequencing or real-time PCR. A mutation was detected in 24/25 (96%) of the samples tested which contained 5% mutated DNA. The 1% sensitivity claimed for commercial real-time PCR-targeted EGFR tests was achieved and our results show greater sensitivity for the Sanger sequencing and pyrosequencing screening methods compared to the 10% to 20% detection levels cited on clinical diagnostic reports. We conclude that multiple methodologies are suitable for the detection of acquired EGFR mutations. Copyright © 2013 by Lippincott Williams & Wilkins.


Loberg A.,Swedish University of Agricultural Sciences | Durr J.W.,Swedish University of Agricultural Sciences | Durr J.W.,Interbull Center | Fikse W.F.,Swedish University of Agricultural Sciences | And 3 more authors.
Journal of Animal Breeding and Genetics | Year: 2015

The amount of variance captured in genetic estimations may depend on whether a pedigree-based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree-based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population-trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree-based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree-based relationship matrix. The ratio of the genomic to pedigree-based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress. © 2015 Blackwell Verlag GmbH.


Balasubramanian M.,Sheffield Childrens NHS Foundation Trust | Parker M.J.,Sheffield Childrens NHS Foundation Trust | Dalton A.,Sheffield Diagnostic Genetics Service | Giunta C.,University of Zürich | And 6 more authors.
Clinical Dysmorphology | Year: 2013

Type V osteogenesis imperfecta (OI) presents with moderate-to-severe skeletal deformity and is characterized by hyperplastic callus formation at fracture sites and calcification of the interosseous membranes of the forearm and lower leg. The facial dysmorphism is not well characterized and has not been described in previous reports. Inheritance is autosomal dominant, although the genetic aetiology remained unknown until very recently. The aims of this study were to establish the genetic aetiology in patients with type V OI and further characterize patients with this condition, and to ascertain whether they have a similar clinical phenotype and facial dysmorphism. Three families (one mother-daughter pair and two singletons) were identified with the above features and further investigations (molecular genetic analysis and skin biopsy including electron microscopy, histology and collagen species analysis) were performed. Accurate phenotyping of patients with type V OI was performed. PCR amplification was performed using the Sheffield Diagnostic Genetics Service pyrosequencing assay for the interferon-induced transmembrane protein-5 (IFITM5) gene. All the patients had been confirmed to have a heterozygous variant, c.[-14C>T];[=], in the 5′-UTR of the IFITM5 gene, which is located in the transcribed region of this gene. This recurrent mutation, in IFITM5, also known as bone-restricted interferon-induced transmembrane protein-like protein or BRIL, encodes a protein with a function in bone formation and plays an important role in osteoblast formation. All four patients in this study appear to have similar clinical features and facial dysmorphism, including a short, up-turned nose, a small mouth, a prominent chin and greyish-blue sclerae. Skin biopsy in one patient showed clumping of elastic fibres and normal biochemical analysis of collagen. We have been able to characterize patients with type V OI further and confirm the genetic aetiology in this distinct form of OI. Accurate phenotyping (including describing the common facial features) before investigations is important to enable the useful interpretation of genetic results and/or target-specific gene testing. © 2013 Wolters Kluwer Health | Lippincott Williams & Wilkins.


PubMed | Swedish University of Agricultural Sciences and Sheffield Diagnostic Genetics Service
Type: Journal Article | Journal: Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie | Year: 2015

The amount of variance captured in genetic estimations may depend on whether a pedigree-based or genomic relationship matrix is used. The purpose of this study was to investigate the genetic variance as well as the variance of predicted genetic merits (PGM) using pedigree-based or genomic relationship matrices in Brown Swiss cattle. We examined a range of traits in six populations amounting to 173 population-trait combinations. A main aim was to determine how using different relationship matrices affect variance estimation. We calculated ratios between different types of estimates and analysed the impact of trait heritability and population size. The genetic variances estimated by REML using a genomic relationship matrix were always smaller than the variances that were similarly estimated using a pedigree-based relationship matrix. The variances from the genomic relationship matrix became closer to estimates from a pedigree relationship matrix as heritability and population size increased. In contrast, variances of predicted genetic merits obtained using a genomic relationship matrix were mostly larger than variances of genetic merit predicted using pedigree-based relationship matrix. The ratio of the genomic to pedigree-based PGM variances decreased as heritability and population size rose. The increased variance among predicted genetic merits is important for animal breeding because this is one of the factors influencing genetic progress.

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