المؤلفون: Jamie M. Ellingford, Joo Wook Ahn, Richard D. Bagnall, Diana Baralle, Stephanie Barton, Chris Campbell, Kate Downes, Sian Ellard, Celia Duff-Farrier, David R. FitzPatrick, John M. Greally, Jodie Ingles, Neesha Krishnan, Jenny Lord, Hilary C. Martin, William G. Newman, Anne O’Donnell-Luria, Simon C. Ramsden, Heidi L. Rehm, Ebony Richardson, Moriel Singer-Berk, Jenny C. Taylor, Maggie Williams, Jordan C. Wood, Caroline F. Wright, Steven M. Harrison, Nicola Whiffin

المصدر: Genome Medicine, Vol 14, Iss 1, Pp 1-19 (2022)

مصطلحات موضوعية: Variant interpretation, Non-coding variation, Gene regulation, Medicine, Genetics, QH426-470

الوصف: Abstract Background The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. Methods We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. Results We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. Conclusions These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1756-994XTest

الوصول الحر: https://doaj.org/article/592317068741464ab4f2701a8ccc78e4Test

المؤلفون: Charlie Rowlands, Huw B. Thomas, Jenny Lord, Htoo A. Wai, Gavin Arno, Glenda Beaman, Panagiotis Sergouniotis, Beatriz Gomes-Silva, Christopher Campbell, Nicole Gossan, Claire Hardcastle, Kevin Webb, Christopher O’Callaghan, Robert A. Hirst, Simon Ramsden, Elizabeth Jones, Jill Clayton-Smith, Andrew R. Webster, Genomics England Research Consortium, Andrew G. L. Douglas, Raymond T. O’Keefe, William G. Newman, Diana Baralle, Graeme C. M. Black, Jamie M. Ellingford

المصدر: Scientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)

مصطلحات موضوعية: Medicine, Science

الوصف: Abstract The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being ‘pathogenic’ or ‘benign’ is likely to have substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals carry rare variants expected to impact splicing that were not initially identified as ‘pathogenic’ or ‘likely pathogenic’; one in five of these cases could lead to new or refined diagnoses.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2045-2322Test

الوصول الحر: https://doaj.org/article/cff014b62747418fa2af4029a4e249c3Test

المؤلفون: Katherine A. Wood, Jamie M. Ellingford, James Eden, Huw B. Thomas, Raymond T. O’Keefe, Claire Hopton, William G. Newman

المصدر: Cardiogenetics, Vol 11, Iss 2, Pp 73-83 (2021)

مصطلحات موضوعية: hypertrophic cardiomyopathy, MYBPC3, splice variants, minigene assays, Diseases of the circulatory (Cardiovascular) system, RC666-701

الوصف: Genetic variants in MYBPC3 are one of the most common causes of hypertrophic cardiomyopathy (HCM). While variants in MYBPC3 affecting canonical splice site dinucleotides are a well-characterised cause of HCM, only recently has work begun to investigate the pathogenicity of more deeply intronic variants. Here, we present three patients with HCM and intronic splice-affecting MYBPC3 variants and analyse the impact of variants on splicing using in vitro minigene assays. We show that the three variants, a novel c.927-8G>A variant and the previously reported c.1624+4A>T and c.3815-10T>G variants, result in MYBPC3 splicing errors. Analysis of blood-derived patient RNA for the c.3815-10T>G variant revealed only wild type spliced product, indicating that mis-spliced transcripts from the mutant allele are degraded. These data indicate that the c.927-8G>A variant of uncertain significance and likely benign c.3815-10T>G should be reclassified as likely pathogenic. Furthermore, we find shortcomings in commonly applied bioinformatics strategies to prioritise variants impacting MYBPC3 splicing and re-emphasise the need for functional assessment of variants of uncertain significance in diagnostic testing.

وصف الملف: electronic resource

العلاقة: https://www.mdpi.com/2035-8148/11/2/9Test; https://doaj.org/toc/2035-8253Test; https://doaj.org/toc/2035-8148Test

الوصول الحر: https://doaj.org/article/5c46b773a2b144039d74397e5dc7663cTest

المؤلفون: D. Gareth Evans, Elke M. van Veen, Emma R. Woodward, Elaine F. Harkness, Jamie M. Ellingford, Naomi L. Bowers, Andrew J. Wallace, Sacha J. Howell, Anthony Howell, Fiona Lalloo, William G. Newman, Miriam J. Smith

المصدر: Cancers, Vol 13, Iss 16, p 4154 (2021)

مصطلحات موضوعية: breast cancer, BRCA1, BRCA2, PALB2, ATM, CHEK2, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

الوصف: Whilst panel testing of an extended group of genes including BRCA1/2 is commonplace, these studies have not been subdivided by histiotype or by a priori BRCA1/2 probability. Patients with a breast cancer diagnosis undergoing extended panel testing were assessed for frequency of actionable variants in breast cancer genes other than BRCA1/2 by histiotype and Manchester score (MS) to reflect a priori BRCA1/2 likelihood. Rates were adjusted by prior testing for BRCA1/2 in an extended series. 95/1398 (6.3%) who underwent panel testing were found to be positive for actionable non-BRCA1/2 breast/ovarian cancer genes (ATM, BARD1, CDH1, CHEK2, PALB2, PTEN, RAD51C, RAD51D, TP53). As expected, PALB2, CHEK2 and ATM were predominant with 80-(5.3%). The highest rate occurred in Grade-3 ER+/HER2− breast cancers-(9.6%). Rates of non-BRCA actionable genes was fairly constant over all likelihoods of BRCA1/2 but adjusted rates were three times higher with MS < 9 (BRCA1/2 = 1.5%, other = 4.7%), but was only 1.6% compared to 79.3% with MS ≥ 40. Although rates of detection of non-BRCA actionable genes are relatively constant across BRCA1/2 likelihoods this disguises an overall adjusted low frequency in high-likelihood families which have been heavily pre-tested for BRCA1/2. Any loss of detection sensitivity for BRCA1/2 actionable variants in breast cancer panels should lead to bespoke BRCA1/2 testing being conducted first.

وصف الملف: electronic resource

العلاقة: https://www.mdpi.com/2072-6694/13/16/4154Test; https://doaj.org/toc/2072-6694Test

الوصول الحر: https://doaj.org/article/ac2e30e983064b6895f92f36a899e14aTest

المؤلفون: David J. Green, Shalaw R. Sallah, Jamie M. Ellingford, Simon C. Lovell, Panagiotis I. Sergouniotis

المصدر: Genes, Vol 11, Iss 2, p 179 (2020)

مصطلحات موضوعية: inherited eye disease, inherited retinal disease, variable expressivity, incomplete penetrance, Genetics, QH426-470

الوصف: Inherited eye disorders (IED) are a heterogeneous group of Mendelian conditions that are associated with visual impairment. Although these disorders often exhibit incomplete penetrance and variable expressivity, the scale and mechanisms of these phenomena remain largely unknown. Here, we utilize publicly-available genomic and transcriptomic datasets to gain insights into variable penetrance in IED. Variants in a curated set of 340 IED-implicated genes were extracted from the Human Gene Mutation Database (HGMD) 2019.1 and cross-checked with the Genome Aggregation Database (gnomAD) 2.1 control-only dataset. Genes for which >1 variants were encountered in both HGMD and gnomAD were considered to be associated with variable penetrance (n = 56). Variability in gene expression levels was then estimated for the subset of these genes that was found to be adequately expressed in two relevant resources: the Genotype-Tissue Expression (GTEx) and Eye Genotype Expression (EyeGEx) datasets. We found that genes suspected to be associated with variable penetrance tended to have significantly more variability in gene expression levels in the general population (p = 0.0000015); this finding was consistent across tissue types. The results of this study point to the possible influence of cis and/or trans-acting elements on the expressivity of variants causing Mendelian disorders. They also highlight the potential utility of quantifying gene expression as part of the investigation of families showing evidence of variable penetrance.

وصف الملف: electronic resource

العلاقة: https://www.mdpi.com/2073-4425/11/2/179Test; https://doaj.org/toc/2073-4425Test

الوصول الحر: https://doaj.org/article/93f1e396c1694f9e85f18862910da17bTest

المؤلفون: Jamie M Ellingford, Ryan George, John H McDermott, Shazaad Ahmad, Jonathan J Edgerley, David Gokhale, William G Newman, Stephen Ball, Nicholas Machin, Graeme CM Black

المصدر: eLife, Vol 10 (2021)

مصطلحات موضوعية: SARS-CoV-2, genome, sequencing, healthcare worker, healthcare-associated, nosocomial, Medicine, Science, Biology (General), QH301-705.5

الوصف: Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.

وصف الملف: electronic resource

العلاقة: https://elifesciences.org/articles/65453Test; https://doaj.org/toc/2050-084XTest

الوصول الحر: https://doaj.org/article/ccd0a2e9674f422e9315dcf5926a5603Test

المؤلفون: Yanshan Liu, Siddharth Banka, Yingzhi Huang, Jonathan Hardman-Smart, Derek Pye, Antonio Torrelo, Glenda M. Beaman, Marcelo G. Kazanietz, Martin J. Baker, Carlo Ferrazzano, Chenfu Shi, Gisela Orozco, Stephen Eyre, Michel van Geel, Anette Bygum, Judith Fischer, Zosia Miedzybrodzka, Faris Abuzahra, Albert Rübben, Sara Cuvertino, Jamie M. Ellingford, Miriam J. Smith, D. Gareth Evans, Lizelotte J.M.T. Weppner-Parren, Maurice A.M. van Steensel, Iskander H. Chaudhary, D. Chas Mangham, John T. Lear, Ralf Paus, Jorge Frank, William G. Newman, Xue Zhang

المساهمون: Lee Kong Chian School of Medicine (LKCMedicine), Skin Research Institute of Singapore, A*STAR, RS: GROW - R3 - Innovative Cancer Diagnostics & Therapy, MUMC+: MA Dermatologie (9)

المصدر: British Journal of Dermatology, 187(6), 948-961. Wiley

مصطلحات موضوعية: Comparative Genomic Hybridization, Germ Cells, DNA Copy Number Variations, Carcinoma, Basal Cell, Microfilament Proteins, Humans, Follicular Atrophoderma, Medicine [Science], Dermatology, Hypotrichosis, Hair Follicle

الوصف: Background Bazex–Dupré–Christol syndrome (BDCS; MIM301845) is a rare X-linked dominant genodermatosis characterized by follicular atrophoderma, congenital hypotrichosis and multiple basal cell carcinomas (BCCs). Previous studies have linked BDCS to an 11·4-Mb interval on chromosome Xq25-q27.1. However, the genetic mechanism of BDCS remains an open question. Objectives To investigate the genetic aetiology and molecular mechanisms underlying BDCS. Methods We ascertained multiple individuals from eight unrelated families affected with BDCS (F1–F8). Whole-exome (F1 and F2) and genome sequencing (F3) were performed to identify putative disease-causing variants within the linkage region. Array comparative genomic hybridization and quantitative polymerase chain reaction (PCR) were used to explore copy number variations, followed by long-range gap PCR and Sanger sequencing to amplify the duplication junctions and to define the head–tail junctions. Hi-C was performed on dermal fibroblasts from two affected individuals with BDCS and one control. Public datasets and tools were used to identify regulatory elements and transcription factor binding sites within the minimal duplicated region. Immunofluorescence was performed in hair follicles, BCCs and trichoepitheliomas from patients with BDCS and sporadic BCCs. The ACTRT1 variant c.547dup (p.Met183Asnfs*17), previously proposed to cause BDCS, was evaluated with t allele frequency calculator. Results In eight families with BDCS, we identified overlapping 18–135-kb duplications (six inherited and two de novo) at Xq26.1, flanked by ARHGAP36 and IGSF1. Hi-C showed that the duplications did not affect the topologically associated domain, but may alter the interactions between flanking genes and putative enhancers located in the minimal duplicated region. We detected ARHGAP36 expression near the control hair follicular stem cell compartment, and found increased ARHGAP36 levels in hair follicles in telogen, in BCCs and in trichoepitheliomas from patients with BDCS. ARHGAP36 was also detected in sporadic BCCs from individuals without BDCS. Our modelling showed the predicted maximum tolerated minor allele frequency of ACTRT1 variants in control populations to be orders of magnitude higher than expected for a high-penetrant ultra-rare disorder, suggesting loss of function of ACTRT1 variants to be an unlikely cause for BDCS. Conclusions Noncoding Xq26.1 duplications cause BDCS. The BDCS duplications most likely lead to dysregulation of ARHGAP36. ARHGAP36 is a potential therapeutic target for both inherited and sporadic BCCs. What is already known about this topic? Bazex–Dupré–Christol syndrome (BDCS) is a rare X-linked basal cell carcinoma susceptibility syndrome linked to an 11·4-Mb interval on chromosome Xq25-q27.1.Loss-of-function variants in ACTRT1 and its regulatory elements were suggested to cause BDCS. What does this study add? BDCS is caused by small tandem noncoding intergenic duplications at chromosome Xq26.1.The Xq26.1 BDCS duplications likely dysregulate ARHGAP36, the flanking centromeric gene.ACTRT1 loss-of-function variants are unlikely to cause BDCS. What is the translational message? This study provides the basis for accurate genetic testing for BDCS, which will aid precise diagnosis and appropriate surveillance and clinical management.ARHGAP36 may be a novel therapeutic target for all forms of sporadic basal cell carcinomas.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce266f5315a5c98055d5aabca2e9efebTest
https://doi.org/10.1111/bjd.21842Test

المؤلفون: Jamie M. Ellingford, Robert B. Hufnagel, Gavin Arno

المصدر: Genes; Volume 11; Issue 11; Pages: 1274

مصطلحات موضوعية: n/a

جغرافية الموضوع: agris

الوصف: Inherited retinal diseases (IRDs) are a diverse and variable group of rare human disorders [.]

وصف الملف: application/pdf

العلاقة: Human Genomics and Genetic Diseases; https://dx.doi.org/10.3390/genes11111274Test

الإتاحة: https://doi.org/10.3390/genes11111274Test

المؤلفون: Charlie F Rowlands, Diana Baralle, Jamie M Ellingford

المصدر: Cells; Volume 8; Issue 12; Pages: 1513

مصطلحات موضوعية: Mendelian disease, diagnostics, variant interpretation, variant prioritization, RNA splicing, bioinformatics, machine learning, genomic medicine, effect prediction

الوصف: Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient’s variant landscape, the ability to characterize variants causing splicing defects has not progressed with the same speed. To address this, recent years have seen a sharp spike in the number of splice prediction tools leveraging machine learning approaches, leaving clinical geneticists with a plethora of choices for in silico analysis. In this review, some basic principles of machine learning are introduced in the context of genomics and splicing analysis. A critical comparative approach is then used to describe seven recent machine learning-based splice prediction tools, revealing highly diverse approaches and common caveats. We find that, although great progress has been made in producing specific and sensitive tools, there is still much scope for personalized approaches to prediction of variant impact on splicing. Such approaches may increase diagnostic yields and underpin improvements to patient care.

وصف الملف: application/pdf

العلاقة: https://dx.doi.org/10.3390/cells8121513Test

الإتاحة: https://doi.org/10.3390/cells8121513Test

المؤلفون: Malena Daich Varela, James Bellingham, Fabiana Motta, Neringa Jurkute, Jamie M Ellingford, Mathieu Quinodoz, Kathryn Oprych, Michael Niblock, Lucas Janeschitz-Kriegl, Karolina Kaminska, Francesca Cancellieri, Hendrik P N Scholl, Eva Lenassi, Elena Schiff, Hannah Knight, Graeme Black, Carlo Rivolta, Michael E Cheetham, Michel Michaelides, Omar A Mahroo, Anthony T Moore, Andrew R Webster, Gavin Arno

المصدر: Human molecular genetics, vol 32, iss 4

مصطلحات موضوعية: Patient Care Team, Genetics & Heredity, Whole Genome Sequencing, DNA Mutational Analysis, Human Genome, Membrane Proteins, Nerve Tissue Proteins, General Medicine, Biological Sciences, Medical and Health Sciences, Pedigree, Clinical Research, Mutation, Retinal Dystrophies, Genetics, Humans, 2.1 Biological and endogenous factors, Aetiology, Eye Proteins, Molecular Biology, Genetics (clinical)

الوصف: The purpose of this paper is to identify likely pathogenic non-coding variants in inherited retinal dystrophy (IRD) genes, using genome sequencing (GS). Patients with IRD were recruited to the study and underwent comprehensive ophthalmological evaluation and GS. The results of GS were investigated through virtual gene panel analysis, and plausible pathogenic variants and clinical phenotype evaluated by the multidisciplinary team (MDT) discussion. For unsolved patients in whom a specific gene was suspected to harbor a missed pathogenic variant, targeted re-analysis of non-coding regions was performed on GS data. Candidate variants were functionally tested by messenger RNA analysis, minigene or luciferase reporter assays. Previously unreported, likely pathogenic, non-coding variants in 7 genes (PRPF31, NDP, IFT140, CRB1, USH2A, BBS10 and GUCY2D), were identified in 11 patients. These were shown to lead to mis-splicing (PRPF31, IFT140, CRB1 and USH2A) or altered transcription levels (BBS10 and GUCY2D). MDT-led, phenotype-driven, non-coding variant re-analysis of GS is effective in identifying the missing causative alleles.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4eecf9b5f20e38556985a642ed4fc37bTest
https://escholarship.org/uc/item/4z14k3r2Test