Publications by authors named "Matthew Wakeling"

20 Publications

  • Page 1 of 1

Missense substitutions at a conserved 14-3-3 binding site in HDAC4 cause a novel intellectual disability syndrome.

HGG Adv 2021 Jan 14;2(1):100015. Epub 2021 Jan 14.

Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter EX2 5DW, UK.

Histone deacetylases play crucial roles in the regulation of chromatin structure and gene expression in the eukaryotic cell, and disruption of their activity causes a wide range of developmental disorders in humans. Loss-of-function alleles of , a founding member of the class IIa deacetylases, have been reported in brachydactyly-mental retardation syndrome (BDMR). However, while disruption of HDAC4 activity and deregulation of its downstream targets may contribute to the BDMR phenotype, loss of HDAC4 function usually occurs as part of larger deletions of chromosome 2q37; BDMR is also known as chromosome 2q37 deletion syndrome, and the precise role of HDAC4 within the phenotype remains uncertain. Thus, identification of missense variants should shed new light on the role of HDAC4 in normal development. Here, we report seven unrelated individuals with a phenotype distinct from that of BDMR, all of whom have heterozygous missense variants that affect a major regulatory site of HDAC4, required for signal-dependent 14-3-3 binding and nucleocytoplasmic shuttling. Two individuals possess variants altering Thr244 or Glu247, whereas the remaining five all carry variants altering Pro248, a key residue for 14-3-3 binding. We propose that the variants in all seven individuals impair 14-3-3 binding (as confirmed for the first two variants by immunoprecipitation assays), thereby identifying deregulation of HDAC4 as a pathological mechanism in a previously uncharacterized developmental disorder.
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http://dx.doi.org/10.1016/j.xhgg.2020.100015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7841527PMC
January 2021

Loss of MANF Causes Childhood-Onset Syndromic Diabetes Due to Increased Endoplasmic Reticulum Stress.

Diabetes 2021 Apr 26;70(4):1006-1018. Epub 2021 Jan 26.

Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland

Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-resident protein that plays a crucial role in attenuating ER stress responses. Although MANF is indispensable for the survival and function of mouse β-cells, its precise role in human β-cell development and function is unknown. In this study, we show that lack of MANF in humans results in diabetes due to increased ER stress, leading to impaired β-cell function. We identified two patients from different families with childhood diabetes and a neurodevelopmental disorder associated with homozygous loss-of-function mutations in the gene. To study the role of MANF in human β-cell development and function, we knocked out the gene in human embryonic stem cells and differentiated them into pancreatic endocrine cells. Loss of induced mild ER stress and impaired insulin-processing capacity of β-cells in vitro. Upon implantation to immunocompromised mice, the MANF knockout grafts presented elevated ER stress and functional failure, particularly in recipients with diabetes. By describing a new form of monogenic neurodevelopmental diabetes syndrome caused by disturbed ER function, we highlight the importance of adequate ER stress regulation for proper human β-cell function and demonstrate the crucial role of MANF in this process.
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http://dx.doi.org/10.2337/db20-1174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7610619PMC
April 2021

YIPF5 mutations cause neonatal diabetes and microcephaly through endoplasmic reticulum stress.

J Clin Invest 2020 12;130(12):6338-6353

Institute of Interdisciplinary Research (IRIBHM), ULB Neuroscience Institute, Université Libre de Bruxelles, Brussels, Belgium.

Neonatal diabetes is caused by single gene mutations reducing pancreatic β cell number or impairing β cell function. Understanding the genetic basis of rare diabetes subtypes highlights fundamental biological processes in β cells. We identified 6 patients from 5 families with homozygous mutations in the YIPF5 gene, which is involved in trafficking between the endoplasmic reticulum (ER) and the Golgi. All patients had neonatal/early-onset diabetes, severe microcephaly, and epilepsy. YIPF5 is expressed during human brain development, in adult brain and pancreatic islets. We used 3 human β cell models (YIPF5 silencing in EndoC-βH1 cells, YIPF5 knockout and mutation knockin in embryonic stem cells, and patient-derived induced pluripotent stem cells) to investigate the mechanism through which YIPF5 loss of function affects β cells. Loss of YIPF5 function in stem cell-derived islet cells resulted in proinsulin retention in the ER, marked ER stress, and β cell failure. Partial YIPF5 silencing in EndoC-βH1 cells and a patient mutation in stem cells increased the β cell sensitivity to ER stress-induced apoptosis. We report recessive YIPF5 mutations as the genetic cause of a congenital syndrome of microcephaly, epilepsy, and neonatal/early-onset diabetes, highlighting a critical role of YIPF5 in β cells and neurons. We believe this is the first report of mutations disrupting the ER-to-Golgi trafficking, resulting in diabetes.
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http://dx.doi.org/10.1172/JCI141455DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685733PMC
December 2020

Annotating high-impact 5'untranslated region variants with the UTRannotator.

Bioinformatics 2021 05;37(8):1171-1173

National Heart and Lung Institute and MRC London Institute of Medical Science, Imperial College London, London W12 0NN, UK.

Summary: Current tools to annotate the predicted effect of genetic variants are heavily biased towards protein-coding sequence. Variants outside of these regions may have a large impact on protein expression and/or structure and can lead to disease, but this effect can be challenging to predict. Consequently, these variants are poorly annotated using standard tools. We have developed a plugin to the Ensembl Variant Effect Predictor, the UTRannotator, that annotates variants in 5'untranslated regions (5'UTR) that create or disrupt upstream open reading frames. We investigate the utility of this tool using the ClinVar database, providing an annotation for 31.9% of all 5'UTR (likely) pathogenic variants, and highlighting 31 variants of uncertain significance as candidates for further follow-up. We will continue to update the UTRannotator as we gain new knowledge on the impact of variants in UTRs.

Availability And Implementation: UTRannotator is freely available on Github: https://github.com/ImperialCardioGenetics/UTRannotator.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa783DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8150139PMC
May 2021

Refinement of the critical genomic region for congenital hyperinsulinism in the Chromosome 9p deletion syndrome.

Wellcome Open Res 2019 4;4:149. Epub 2020 Aug 4.

Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.

Large contiguous gene deletions at the distal end of the short arm of chromosome 9 result in the complex multi-organ condition chromosome 9p deletion syndrome.  A range of clinical features can result from these deletions with the most common being facial dysmorphisms and neurological impairment. Congenital hyperinsulinism is a rarely reported feature of the syndrome with the genetic mechanism for the dysregulated insulin secretion being unknown.  We studied the clinical and genetic characteristics of 12 individuals with chromosome 9p deletions who had a history of neonatal hypoglycaemia. Using off-target reads generated from targeted next-generation sequencing of the genes known to cause hyperinsulinaemic hypoglycaemia (n=9), or microarray analysis (n=3), we mapped the minimal shared deleted region on chromosome 9 in this cohort. Targeted sequencing was performed in three patients to search for a recessive mutation unmasked by the deletion. In 10/12 patients with hypoglycaemia, hyperinsulinism was confirmed biochemically. A range of extra-pancreatic features were also reported in these patients consistent with the diagnosis of the Chromosome 9p deletion syndrome. The minimal deleted region was mapped to 7.2 Mb, encompassing 38 protein-coding genes. analysis of these genes highlighted and as potential candidates for the hypoglycaemia. Targeted sequencing performed on three of the patients did not identify a second disease-causing variant within the minimal deleted region. This study identifies 9p deletions as an important cause of hyperinsulinaemic hypoglycaemia and increases the number of cases reported with 9p deletions and hypoglycaemia to 15 making this a more common feature of the syndrome than previously appreciated.  Whilst the precise genetic mechanism of the dysregulated insulin secretion could not be determined in these patients, mapping the deletion breakpoints highlighted potential candidate genes for hypoglycaemia within the deleted region.
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http://dx.doi.org/10.12688/wellcomeopenres.15465.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7422856PMC
August 2020

Misannotation of multiple-nucleotide variants risks misdiagnosis.

Wellcome Open Res 2019 1;4:145. Epub 2019 Oct 1.

Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, Devon, EX2 5DW, UK.

Multiple Nucleotide Variants (MNVs) are miscalled by the most widely utilised next generation sequencing analysis (NGS) pipelines, presenting the potential for missing diagnoses that would previously have been made by standard Sanger (dideoxy) sequencing. These variants, which should be treated as a single insertion-deletion mutation event, are commonly called as separate single nucleotide variants. This can result in misannotation, incorrect amino acid predictions and potentially false positive and false negative diagnostic results. This risk will be increased as confirmatory Sanger sequencing of Single Nucleotide variants (SNVs) ceases to be standard practice. Using simulated data and re-analysis of sequencing data from a diagnostic targeted gene panel, we demonstrate that the widely adopted pipeline, GATK best practices, results in miscalling of MNVs and that alternative tools can call these variants correctly. The adoption of calling methods that annotate MNVs correctly would present a solution for individual laboratories, however GATK best practices are the basis for important public resources such as the gnomAD database. We suggest integrating a solution into these guidelines would be the optimal approach.
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http://dx.doi.org/10.12688/wellcomeopenres.15420.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6957021PMC
October 2019

De Novo Mutations in Affecting eIF2 Signaling Cause Neonatal/Early-Onset Diabetes and Transient Hepatic Dysfunction.

Diabetes 2020 03 27;69(3):477-483. Epub 2019 Dec 27.

Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K.

Permanent neonatal diabetes mellitus (PNDM) is caused by reduced β-cell number or impaired β-cell function. Understanding of the genetic basis of this disorder highlights fundamental β-cell mechanisms. We performed trio genome sequencing for 44 patients with PNDM and their unaffected parents to identify causative de novo variants. Replication studies were performed in 188 patients diagnosed with diabetes before 2 years of age without a genetic diagnosis. (encoding the eIF2B complex α subunit) was the only gene with novel de novo variants (all missense) in at least three patients. Replication studies identified two further patients with de novo variants. In addition to having diabetes, four of five patients had hepatitis-like episodes in childhood. The de novo mutations were found to map to the same protein surface. We propose that these variants render the eIF2B complex insensitive to eIF2 phosphorylation, which occurs under stress conditions and triggers expression of stress response genes. Failure of eIF2B to sense eIF2 phosphorylation likely leads to unregulated unfolded protein response and cell death. Our results establish de novo mutations as a novel cause of permanent diabetes and liver dysfunction. These findings confirm the importance of cell stress regulation for β-cells and highlight EIF2B1's fundamental role within this pathway.
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http://dx.doi.org/10.2337/db19-1029DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7100014PMC
March 2020

Balancing Bulkiness in Gold(I) Phosphino-triazole Catalysis.

European J Org Chem 2019 Sep 30;2019(31-32):5540-5548. Epub 2019 Jul 30.

School of Chemistry University of Birmingham Edgbaston B15 2TT Birmingham West Midlands UK.

The syntheses of a series of 1-phenyl-5-phosphino 1,2,3-triazoles are disclosed, within which, the phosphorus atom (at the 5-position of a triazole) is appended by one, two or three triazole motifs, and the valency of the phosphorus(III) atom is completed by two, one or zero ancillary (phenyl or cyclohexyl) groups respectively. This series of phosphines was compared with tricyclohexylphosphine and triphenylphosphine to study the effect of increasing the number of triazoles appended to the central phosphorus atom from zero to three triazoles. Gold(I) chloride complexes of the synthesised ligands were prepared and analysed by techniques including single-crystal X-ray diffraction structure determination. Gold(I) complexes were also prepared from 1-(2,6-dimethoxy)-phenyl-5-dicyclohexyl-phosphino 1,2,3-triazole and 1-(2,6-dimethoxy)-phenyl-5-diphenyl-phosphino 1,2,3-triazole ligands. The crystal structures thus obtained were examined using the web tool and percentage buried volumes determined. The effectiveness of these gold(I) chloride complexes to serve as precatalysts for alkyne hydration were assessed. Furthermore, the regioselectivity of hydration of but-1-yne-1,4-diyldibenzene was probed.
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http://dx.doi.org/10.1002/ejoc.201900850DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6774259PMC
September 2019

Trisomy 21 Is a Cause of Permanent Neonatal Diabetes That Is Autoimmune but Not HLA Associated.

Diabetes 2019 07 8;68(7):1528-1535. Epub 2019 Apr 8.

Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, U.K.

Identifying new causes of permanent neonatal diabetes (PNDM) (diagnosis <6 months) provides important insights into β-cell biology. Patients with Down syndrome (DS) resulting from trisomy 21 are four times more likely to have childhood diabetes with an intermediate HLA association. It is not known whether DS can cause PNDM. We found that trisomy 21 was seven times more likely in our PNDM cohort than in the population (13 of 1,522 = 85 of 10,000 observed vs. 12.6 of 10,000 expected) and none of the 13 DS-PNDM patients had a mutation in the known PNDM genes that explained 82.9% of non-DS PNDM. Islet autoantibodies were present in 4 of 9 DS-PNDM patients, but DS-PNDM was not associated with polygenic susceptibility to type 1 diabetes (T1D). We conclude that trisomy 21 is a cause of autoimmune PNDM that is not HLA associated. We propose that autoimmune diabetes in DS is heterogeneous and includes coincidental T1D that is HLA associated and diabetes caused by trisomy 21 that is not HLA associated.
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http://dx.doi.org/10.2337/db19-0045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6609990PMC
July 2019

Copy number variation of in familial dystonic tremor.

Neurol Genet 2019 Feb 4;5(1):e307. Epub 2019 Feb 4.

Medical Research (Level 4) (V.A., B.A.C., G.V.H., H.H., A.S.-N., J.K.C., E.L.B., A.H.C.), University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, United Kingdom; Reta Lila Weston Institute of Neurological Studies (V.A., T.T.W.), UCL Institute of Neurology, London, United Kingdom; Department of Neurology (T.I.), Government Medical College, Thiruvananthapuram, Kerala, India; Department of Anatomy and Microbiology (R.S.), Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India; Clinical Neuroscience (C.P.), Royal Free Campus, UCL Institute of Neurology, London, United Kingdom; Institute of Psychological Medicine and Clinical Neurosciences (K.P.), Cardiff University, Cardiff, United Kingdom; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (L.N.C.), Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY; Institute of Biomedical and Clinical Science (R.C., H.L.A., M.W.), University of Exeter Medical School, United Kingdom; and Departments of Neurology and Chronic Disease Epidemiology and Center for Neuroepidemiology and Clinical Neurological Research (E.D.L.), Yale School of Medicine and Yale School of Public Health, Yale University, New Haven, CT.

Objective: To elucidate the genetic cause of a large 5 generation South Indian family with multiple individuals with predominantly an upper limb postural tremor and posturing in keeping with another form of tremor, namely, dystonic tremor.

Methods: Whole-genome single nucleotide polymorphism (SNP) microarray analysis was undertaken to look for copy number variants in the affected individuals.

Results: Whole-genome SNP microarray studies identified a tandem duplicated genomic segment of chromosome 15q24 present in all affected family members. Whole-genome sequencing demonstrated that it comprised a ∼550-kb tandem duplication encompassing the entire gene.

Conclusions: The identification of a genomic duplication as the likely molecular cause of this condition, resulting in an additional gene copy in affected cases, adds further support for a causal role of this gene in tremor disorders and implicates increased expression levels of as a potential pathogenic mechanism.
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http://dx.doi.org/10.1212/NXG.0000000000000307DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6384021PMC
February 2019

An Amish founder variant consolidates disruption of CEP55 as a cause of hydranencephaly and renal dysplasia.

Eur J Hum Genet 2019 04 8;27(4):657-662. Epub 2019 Jan 8.

Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK.

The centrosomal protein 55 kDa (CEP55 (OMIM 610000)) plays a fundamental role in cell cycle regulation and cytokinesis. However, the precise role of CEP55 in human embryonic growth and development is yet to be fully defined. Here we identified a novel homozygous founder frameshift variant in CEP55, present at low frequency in the Amish community, in two siblings presenting with a lethal foetal disorder. The features of the condition are reminiscent of a Meckel-like syndrome comprising of Potter sequence, hydranencephaly, and cystic dysplastic kidneys. These findings, considered alongside two recent studies of single families reporting loss of function candidate variants in CEP55, confirm disruption of CEP55 function as a cause of this clinical spectrum and enable us to delineate the cardinal clinical features of this disorder, providing important new insights into early human development.
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http://dx.doi.org/10.1038/s41431-018-0306-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420058PMC
April 2019

NAD(P)HX dehydratase (NAXD) deficiency: a novel neurodegenerative disorder exacerbated by febrile illnesses.

Brain 2019 01;142(1):50-58

Institute of Human Genetics, Technische Universität München, Munich, Germany.

Physical stress, including high temperatures, may damage the central metabolic nicotinamide nucleotide cofactors [NAD(P)H], generating toxic derivatives [NAD(P)HX]. The highly conserved enzyme NAD(P)HX dehydratase (NAXD) is essential for intracellular repair of NAD(P)HX. Here we present a series of infants and children who suffered episodes of febrile illness-induced neurodegeneration or cardiac failure and early death. Whole-exome or whole-genome sequencing identified recessive NAXD variants in each case. Variants were predicted to be potentially deleterious through in silico analysis. Reverse-transcription PCR confirmed altered splicing in one case. Subject fibroblasts showed highly elevated concentrations of the damaged cofactors S-NADHX, R-NADHX and cyclic NADHX. NADHX accumulation was abrogated by lentiviral transduction of subject cells with wild-type NAXD. Subject fibroblasts and muscle biopsies showed impaired mitochondrial function, higher sensitivity to metabolic stress in media containing galactose and azide, but not glucose, and decreased mitochondrial reactive oxygen species production. Recombinant NAXD protein harbouring two missense variants leading to the amino acid changes p.(Gly63Ser) and p.(Arg608Cys) were thermolabile and showed a decrease in Vmax and increase in KM for the ATP-dependent NADHX dehydratase activity. This is the first study to identify pathogenic variants in NAXD and to link deficient NADHX repair with mitochondrial dysfunction. The results show that NAXD deficiency can be classified as a metabolite repair disorder in which accumulation of damaged metabolites likely triggers devastating effects in tissues such as the brain and the heart, eventually leading to early childhood death.
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http://dx.doi.org/10.1093/brain/awy310DOI Listing
January 2019

ICR142 Benchmarker: evaluating, optimising and benchmarking variant calling performance using the ICR142 NGS validation series.

Wellcome Open Res 2018 31;3:108. Epub 2018 Oct 31.

Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.

Evaluating, optimising and benchmarking of next generation sequencing (NGS) variant calling performance are essential requirements for clinical, commercial and academic NGS pipelines. Such assessments should be performed in a consistent, transparent and reproducible fashion, using independently, orthogonally generated data. Here we present ICR142 Benchmarker, a tool to generate outputs for assessing germline base substitution and indel calling performance using the ICR142 NGS validation series, a dataset of Illumina platform-based exome sequence data from 142 samples together with Sanger sequence data at 704 sites. ICR142 Benchmarker provides summary and detailed information on the sensitivity, specificity and false detection rates of variant callers. ICR142 Benchmarker also automatically generates a single page report highlighting key performance metrics and how performance compares to widely-used open-source tools. We used ICR142 Benchmarker with VCF files outputted by GATK, OpEx and DeepVariant to create a benchmark for variant calling performance. This evaluation revealed pipeline-specific differences and shared challenges in variant calling, for example in detecting indels in short repeating sequence motifs. We next used ICR142 Benchmarker to perform regression testing with DeepVariant versions 0.5.2 and 0.6.1. This showed that v0.6.1 improves variant calling performance, but there was evidence of minor changes in indel calling behaviour that may benefit from attention. The data also allowed us to evaluate filters to optimise DeepVariant calling, and we recommend using 30 as the QUAL threshold for base substitution calls when using DeepVariant v0.6.1. Finally, we used ICR142 Benchmarker with VCF files from two commercial variant calling providers to facilitate optimisation of their in-house pipelines and to provide transparent benchmarking of their performance. ICR142 Benchmarker consistently and transparently analyses variant calling performance based on the ICR142 NGS validation series, using the standard VCF input and outputting informative metrics to enable user understanding of pipeline performance. ICR142 Benchmarker is freely available at https://github.com/RahmanTeamDevelopment/ICR142_Benchmarker/releases.
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http://dx.doi.org/10.12688/wellcomeopenres.14754.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6234721PMC
October 2018

Correction: Homozygosity mapping provides supporting evidence of pathogenicity in recessive Mendelian disease.

Genet Med 2019 03;21(3):766

Institute of Biomedical & Clinical Science, University of Exeter, Exeter, UK.

The original version of this Article contained an error in the top left of Figure 2: the number 1 on the y-axis had been changed to 0 during the typesetting process. This has now been corrected in both the PDF and HTML versions of the Article.
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http://dx.doi.org/10.1038/s41436-018-0357-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6752275PMC
March 2019

Homozygosity mapping provides supporting evidence of pathogenicity in recessive Mendelian disease.

Genet Med 2019 04 3;21(4):982-986. Epub 2018 Oct 3.

Institute of Biomedical & Clinical Science, University of Exeter, Exeter, UK.

Purpose: One of the greatest challenges currently facing those studying Mendelian disease is identifying the pathogenic variant from the long list produced by a next-generation sequencing test. We investigate the predictive ability of homozygosity mapping for identifying the regions likely to contain the causative variant.

Methods: We use 179 homozygous pathogenic variants from three independent cohorts to investigate the predictive power of homozygosity mapping.

Results: We demonstrate that homozygous pathogenic variants in our cohorts are disproportionately likely to be found within one of the largest regions of homozygosity: 80% of pathogenic variants are found in a homozygous region that is in the ten largest regions in a sample. The maximal predictive power is achieved in patients with <8% homozygosity and variants >3 Mb from a telomere; this gives an area under the curve (AUC) of 0.735 and results in 92% of the causative variants being in one of the ten largest homozygous regions.

Conclusion: This predictive power can be used to prioritize the list of candidate variants in gene discovery studies. When classifying a homozygous variant the size and rank of the region of homozygosity in which the candidate variant is located can also be considered as supporting evidence for pathogenicity.
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http://dx.doi.org/10.1038/s41436-018-0281-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330071PMC
April 2019

Comprehensive screening shows that mutations in the known syndromic genes are rare in infants presenting with hyperinsulinaemic hypoglycaemia.

Clin Endocrinol (Oxf) 2018 11 20;89(5):621-627. Epub 2018 Sep 20.

Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.

Objective: Hyperinsulinaemic hypoglycaemia (HH) can occur in isolation or more rarely feature as part of a syndrome. Screening for mutations in the "syndromic" HH genes is guided by phenotype with genetic testing used to confirm the clinical diagnosis. As HH can be the presenting feature of a syndrome, it is possible that mutations will be missed as these genes are not routinely screened in all newly diagnosed individuals. We investigated the frequency of pathogenic variants in syndromic genes in infants with HH who had not been clinically diagnosed with a syndromic disorder at referral for genetic testing.

Design: We used genome sequencing data to assess the prevalence of mutations in syndromic HH genes in an international cohort of patients with HH of unknown genetic cause.

Patients: We undertook genome sequencing in 82 infants with HH without a clinical diagnosis of a known syndrome at referral for genetic testing.

Measurements: Within this cohort, we searched for the genetic aetiologies causing 20 different syndromes where HH had been reported as a feature.

Results: We identified a pathogenic KMT2D variant in a patient with HH diagnosed at birth, confirming a genetic diagnosis of Kabuki syndrome. Clinical data received following the identification of the mutation highlighted additional features consistent with the genetic diagnosis. Pathogenic variants were not identified in the remainder of the cohort.

Conclusions: Pathogenic variants in the syndromic HH genes are rare; thus, routine testing of these genes by molecular genetics laboratories is unlikely to be justified in patients without syndromic phenotypes.
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http://dx.doi.org/10.1111/cen.13841DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6283248PMC
November 2018

missense mutation causes familial insulinomatosis and diabetes mellitus.

Proc Natl Acad Sci U S A 2018 01 16;115(5):1027-1032. Epub 2018 Jan 16.

Institute of Biomedical and Clinical Science, University of Exeter Medical School, EX2 5DW Exeter, United Kingdom.

The β-cell-enriched MAFA transcription factor plays a central role in regulating glucose-stimulated insulin secretion while also demonstrating oncogenic transformation potential in vitro. No disease-causing variants have been previously described. We investigated a large pedigree with autosomal dominant inheritance of diabetes mellitus or insulinomatosis, an adult-onset condition of recurrent hyperinsulinemic hypoglycemia caused by multiple insulin-secreting neuroendocrine tumors of the pancreas. Using exome sequencing, we identified a missense mutation (p.Ser64Phe, c.191C>T) segregating with both phenotypes of insulinomatosis and diabetes. This mutation was also found in a second unrelated family with the same clinical phenotype, while no germline or somatic mutations were identified in nine patients with sporadic insulinomatosis. In the two families, insulinomatosis presented more frequently in females (eight females/two males) and diabetes more often in males (12 males/four females). Four patients from the index family, including two homozygotes, had a history of congenital cataract and/or glaucoma. The p.Ser64Phe mutation was found to impair phosphorylation within the transactivation domain of MAFA and profoundly increased MAFA protein stability under both high and low glucose concentrations in β-cell lines. In addition, the transactivation potential of p.Ser64Phe MAFA in β-cell lines was enhanced compared with wild-type MAFA. In summary, the p.Ser64Phe missense mutation leads to familial insulinomatosis or diabetes by impacting MAFA protein stability and transactivation ability. The human phenotypes associated with the p.Ser64Phe missense mutation reflect both the oncogenic capacity of MAFA and its key role in islet β-cell activity.
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http://dx.doi.org/10.1073/pnas.1712262115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5798333PMC
January 2018

Diagnosis of lethal or prenatal-onset autosomal recessive disorders by parental exome sequencing.

Prenat Diagn 2018 01 3;38(1):33-43. Epub 2017 Dec 3.

Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Vic, Australia.

Objective: Rare genetic disorders resulting in prenatal or neonatal death are genetically heterogeneous, but testing is often limited by the availability of fetal DNA, leaving couples without a potential prenatal test for future pregnancies. We describe our novel strategy of exome sequencing parental DNA samples to diagnose recessive monogenic disorders in an audit of the first 50 couples referred.

Method: Exome sequencing was carried out in a consecutive series of 50 couples who had 1 or more pregnancies affected with a lethal or prenatal-onset disorder. In all cases, there was insufficient DNA for exome sequencing of the affected fetus. Heterozygous rare variants (MAF < 0.001) in the same gene in both parents were selected for analysis. Likely, disease-causing variants were tested in fetal DNA to confirm co-segregation.

Results: Parental exome analysis identified heterozygous pathogenic (or likely pathogenic) variants in 24 different genes in 26/50 couples (52%). Where 2 or more fetuses were affected, a genetic diagnosis was obtained in 18/29 cases (62%). In most cases, the clinical features were typical of the disorder, but in others, they result from a hypomorphic variant or represent the most severe form of a variable phenotypic spectrum.

Conclusion: We conclude that exome sequencing of parental samples is a powerful strategy with high clinical utility for the genetic diagnosis of lethal or prenatal-onset recessive disorders. © 2017 The Authors Prenatal Diagnosis published by John Wiley & Sons Ltd.
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http://dx.doi.org/10.1002/pd.5175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5836855PMC
January 2018

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data.

Bioinformatics 2012 Dec 27;28(23):3163-5. Epub 2012 Sep 27.

Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.

Summary: InterMine is an open-source data warehouse system that facilitates the building of databases with complex data integration requirements and a need for a fast customizable query facility. Using InterMine, large biological databases can be created from a range of heterogeneous data sources, and the extensible data model allows for easy integration of new data types. The analysis tools include a flexible query builder, genomic region search and a library of 'widgets' performing various statistical analyses. The results can be exported in many commonly used formats. InterMine is a fully extensible framework where developers can add new tools and functionality. Additionally, there is a comprehensive set of web services, for which client libraries are provided in five commonly used programming languages.

Availability: Freely available from http://www.intermine.org under the LGPL license.

Contact: [email protected]

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bts577DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516146PMC
December 2012

FlyMine: an integrated database for Drosophila and Anopheles genomics.

Genome Biol 2007 ;8(7):R129

Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.

FlyMine is a data warehouse that addresses one of the important challenges of modern biology: how to integrate and make use of the diversity and volume of current biological data. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides web access to integrated data at a number of different levels, from simple browsing to construction of complex queries, which can be executed on either single items or lists.
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http://dx.doi.org/10.1186/gb-2007-8-7-r129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323218PMC
February 2008