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Smith CEL, Laugel-Haushalter V, Hany U, Best S, Taylor RL, Poulter JA, Wortmann SB, Feichtinger RG, Mayr JA, Al Bahlani S, Nikolopoulos G, Rigby A, Black GC, Watson CM, Mansour S, Inglehearn CF, Mighell AJ, Bloch-Zupan A. Biallelic variants in Plexin B2 ( PLXNB2) cause amelogenesis imperfecta, hearing loss and intellectual disability. J Med Genet 2024:jmg-2023-109728. [PMID: 38458752 DOI: 10.1136/jmg-2023-109728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/22/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Plexins are large transmembrane receptors for the semaphorin family of signalling proteins. Semaphorin-plexin signalling controls cellular interactions that are critical during development as well as in adult life stages. Nine plexin genes have been identified in humans, but despite the apparent importance of plexins in development, only biallelic PLXND1 and PLXNA1 variants have so far been associated with Mendelian genetic disease. METHODS Eight individuals from six families presented with a recessively inherited variable clinical condition, with core features of amelogenesis imperfecta (AI) and sensorineural hearing loss (SNHL), with variable intellectual disability. Probands were investigated by exome or genome sequencing. Common variants and those unlikely to affect function were excluded. Variants consistent with autosomal recessive inheritance were prioritised. Variant segregation analysis was performed by Sanger sequencing. RNA expression analysis was conducted in C57Bl6 mice. RESULTS Rare biallelic pathogenic variants in plexin B2 (PLXNB2), a large transmembrane semaphorin receptor protein, were found to segregate with disease in all six families. The variants identified include missense, nonsense, splicing changes and a multiexon deletion. Plxnb2 expression was detected in differentiating ameloblasts. CONCLUSION We identify rare biallelic pathogenic variants in PLXNB2 as a cause of a new autosomal recessive, phenotypically diverse syndrome with AI and SNHL as core features. Intellectual disability, ocular disease, ear developmental abnormalities and lymphoedema were also present in multiple cases. The variable syndromic human phenotype overlaps with that seen in Plxnb2 knockout mice, and, together with the rarity of human PLXNB2 variants, may explain why pathogenic variants in PLXNB2 have not been reported previously.
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Affiliation(s)
- Claire E L Smith
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Virginie Laugel-Haushalter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
| | - Ummey Hany
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Sunayna Best
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rachel L Taylor
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
- EMQN CIC, Manchester, UK
| | - James A Poulter
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Saskia B Wortmann
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
- Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands
| | - Rene G Feichtinger
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
| | - Johannes A Mayr
- Department of Paediatrics, University Children's Hospital, Salzburger Landesklinken (SALK) and Paracelsus Medical University, Salzburg, Austria
| | - Suhaila Al Bahlani
- Dental & OMFS Clinic, Al Nahdha Hospital, Government of Oman Ministry of Health, Muscat, Oman
| | | | - Alice Rigby
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- School of Dentistry, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Graeme C Black
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Division of Evolution and Genomic Sciences, Manchester Academic Health Science Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, University of Manchester, Manchester, UK
| | - Christopher M Watson
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Sahar Mansour
- Lymphovascular Research Unit, Molecular and Clinical Sciences Research Institute, St George's Hospital, University of London, London, UK
- SW Thames Regional Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Chris F Inglehearn
- Institute of Medical Research, St James's University Hospital, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Alan J Mighell
- School of Dentistry, University of Leeds Faculty of Medicine and Health, Leeds, UK
| | - Agnès Bloch-Zupan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France
- Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France
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Guidry CA, Chollet-Hinton L, Baker J, O'Dell JC, Beyene RT, Watson CM, Sawyer RG, Simpson SQ, Atchison L, Derickson M, Cooper LC, Pennington GP, VandenBerg S, Halimeh BN. Desirability of Outcome Ranking and Response Adjusted for Antibiotic Risk (DOOR/RADAR) Post Hoc Analysis Supports Equipoise for Antibiotic Initiation Strategies in Intensive Care Unit-Acquired Pneumonia. Surg Infect (Larchmt) 2024; 25:221-224. [PMID: 38466941 DOI: 10.1089/sur.2023.367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Abstract
Background: Pneumonia is the most common intensive care unit (ICU)-acquired infection and source of potential sepsis in ICU populations but can be difficult to diagnose in real-time. Despite limited data, rapid initiation of antibiotic agents is endorsed by society guidelines. We hypothesized that a post hoc analysis of a recent randomized pilot study would show no difference between two antibiotic initiation strategies. Patients and Methods: The recent Trial of Antibiotic Restraint in Presumed Pneumonia (TARPP) was a pragmatic cluster-randomized pilot of antibiotic initiation strategies for patients with suspected ICU-acquired pneumonia. Participating ICUs were cluster-randomized to either an immediate initiation protocol or a specimen-initiated protocol where a gram stain was required for initiation of antibiotics. Patients in the study were divided into one of seven mutually exclusive outcome rankings (desirability of outcome ranking; DOOR): (1) Survival, No Pneumonia, No adverse events; (2) Survival, Pneumonia, No adverse events; (3) Survival, No Pneumonia, ventilator-free-alive days ≤14; (4) Survival, Pneumonia, ventilator-free-alive days ≤14; (5) Survival, No Pneumonia, Subsequent episode of suspected pneumonia; (6) Survival, Pneumonia, Subsequent episode of suspected pneumonia; and (7) Death. These rankings were further refined using the duration of antibiotics prescribed for pneumonia (response adjusted for antibiotic risk; RADAR). Results: There were 186 patients enrolled in the study. After applying the DOOR analysis, a randomly selected patient was equally likely to have a better outcome in specimen-initiated arm as in the immediate initiation arm (DOOR probability: 50.8%; 95% confidence interval [CI], 42.7%-58.9%). Outcome probabilities were similar after applying the RADAR analysis (52.5%; 95% CI, 44.2%-60.6%; p = 0.31). Conclusions: We found that patients for whom antibiotic agents were withheld until there was objective evidence (specimen-initiated group) had similar outcome rankings to patients for whom antibiotic agents were started immediately. This supports the findings of the TARPP pilot trial and provides further evidence for equipoise between these two treatment strategies.
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Affiliation(s)
- Christopher A Guidry
- Department of Surgery, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Lynn Chollet-Hinton
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jordan Baker
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jacob C O'Dell
- Department of Surgery, University of Oklahoma Medical Center, Oklahoma City, Oklahoma, USA
| | - Robel T Beyene
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Robert G Sawyer
- Department of Surgery, Western Michigan Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Steven Q Simpson
- Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Leanne Atchison
- Department of Pharmaceutical Services, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael Derickson
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lindsey C Cooper
- Department of Pharmaceutical Services, Prisma Health Midlands, Columbia, South Carolina, USA
| | - G Patton Pennington
- Department of Surgery, Florida State University School of Medicine, Tallahassee Memorial Healthcare, Tallahassee, Florida, USA
| | - Sheri VandenBerg
- Department of Surgery, Division of Trauma Surgery, Bronson Methodist Hospital, Kalamazoo, Michigan, USA
| | - Bachar N Halimeh
- Department of Surgery, Boston University Medical Center, Boston, Massachusetts, USA
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Hany U, Watson CM, Liu L, Smith CEL, Harfoush A, Poulter JA, Nikolopoulos G, Balmer R, Brown CJ, Patel A, Simmonds J, Charlton R, Acosta de Camargo MG, Rodd HD, Jafri H, Antanaviciute A, Moffat M, Al-Jawad M, Inglehearn CF, Mighell AJ. Heterozygous COL17A1 variants are a frequent cause of amelogenesis imperfecta. J Med Genet 2024; 61:347-355. [PMID: 37979963 PMCID: PMC10982616 DOI: 10.1136/jmg-2023-109510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/17/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND Collagen XVII is most typically associated with human disease when biallelic COL17A1 variants (>230) cause junctional epidermolysis bullosa (JEB), a rare, genetically heterogeneous, mucocutaneous blistering disease with amelogenesis imperfecta (AI), a developmental enamel defect. Despite recognition that heterozygous carriers in JEB families can have AI, and that heterozygous COL17A1 variants also cause dominant corneal epithelial recurrent erosion dystrophy (ERED), the importance of heterozygous COL17A1 variants causing dominant non-syndromic AI is not widely recognised. METHODS Probands from an AI cohort were screened by single molecule molecular inversion probes or targeted hybridisation capture (both a custom panel and whole exome sequencing) for COL17A1 variants. Patient phenotypes were assessed by clinical examination and analyses of affected teeth. RESULTS Nineteen unrelated probands with isolated AI (no co-segregating features) had 17 heterozygous, potentially pathogenic COL17A1 variants, including missense, premature termination codons, frameshift and splice site variants in both the endo-domains and the ecto-domains of the protein. The AI phenotype was consistent with enamel of near normal thickness and variable focal hypoplasia with surface irregularities including pitting. CONCLUSION These results indicate that COL17A1 variants are a frequent cause of dominantly inherited non-syndromic AI. Comparison of variants implicated in AI and JEB identifies similarities in type and distribution, with five identified in both conditions, one of which may also cause ERED. Increased availability of genetic testing means that more individuals will receive reports of heterozygous COL17A1 variants. We propose that patients with isolated AI or ERED, due to COL17A1 variants, should be considered as potential carriers for JEB and counselled accordingly, reflecting the importance of multidisciplinary care.
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Affiliation(s)
- Ummey Hany
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Lu Liu
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
- School of Dentistry, Clarendon Way, University of Leeds, Leeds, UK
| | - Claire E L Smith
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Asmaa Harfoush
- School of Dentistry, Clarendon Way, University of Leeds, Leeds, UK
| | - James A Poulter
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Georgios Nikolopoulos
- Institute for Fundamental Biomedical Research, B.S.R.C. 'Alexander Fleming', Vari, Attica, Greece
| | - Richard Balmer
- School of Dentistry, Clarendon Way, University of Leeds, Leeds, UK
| | - Catriona J Brown
- Birmingham Dental Hospital, Mill Pool Way, Edgbaston, Birmingham, UK
| | - Anesha Patel
- LCRN West Midlands Core Team, NIHR Clinical Research Network (CRN), Birmingham Research Park (West Wing), Vincent Drive, Edgbaston, Birmingham, UK
| | - Jenny Simmonds
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Ruth Charlton
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | | | - Helen D Rodd
- Academic Unit of Oral Health Dentistry and Society, School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Hussain Jafri
- Fatima Jinnah Medical University, Punjab Thalassaemia and Other Genetic Disorders Prevention and Research Institute, Lahore, Pakistan
| | | | - Michelle Moffat
- Paediatric Dentistry, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Maisoon Al-Jawad
- School of Dentistry, Clarendon Way, University of Leeds, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Alan J Mighell
- School of Dentistry, Clarendon Way, University of Leeds, Leeds, UK
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Swilling AC, O'Dell JC, Beyene RT, Watson CM, Sawyer RG, Chollet-Hinton L, Simpson SQ, Atchison L, Derickson M, Cooper LC, Pennington GP, VandenBerg S, Halimeh BN, Hughes D, Guidry CA. Provider Perceptions of Antibiotic Initiation Strategies for Hospital-Acquired Pneumonia. Surg Infect (Larchmt) 2024; 25:109-115. [PMID: 38252553 DOI: 10.1089/sur.2023.310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Background: The practice of rapidly initiating antibiotic therapy for patients with suspected infection has recently been criticized yet remains commonplace. Provider comfort level has been an understudied aspect of this practice. Hypothesis: We hypothesized that there would be no significant differences in provider comfort level between the two treatment groups. Methods: We prospectively surveyed critical care intensivists who provided care for patients enrolled in the Trial of Antibiotic Restraint in Presumed Pneumonia (TARPP), which was a multicenter cluster-randomized crossover trial that evaluated an immediate antibiotic initiation protocol compared with a protocol of specimen-initiated antibiotic initiation in ventilated patients with suspected new-onset pneumonia. At the end of each enrollment arm, physicians at each center were surveyed regarding their overall comfort level with the recently completed treatment arm, and perception of adherence. Both a paired and unpaired analysis was performed. Results: We collected 51 survey responses from 31 unique participants. Providers perceived a higher rate of adherence to the immediate initiation arm than the specimen-initiated arm (Always Adherent: 37.5% vs. 11.1%; p = 0.045). Providers were less comfortable waiting for objective evidence of infection in the specimen-initiated arm than with starting antibiotic agents immediately (Very Comfortable: 83.3% vs. 40.7%; p = 0.004). For the smaller paired analysis, there was no longer a difference in comfort level. Conclusions: There may be differences in provider comfort levels and perceptions of adherence when considering two different antibiotic initiation strategies for suspected pneumonia in ventilated patients. These findings should be considered when planning future studies.
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Affiliation(s)
- Aubrey C Swilling
- Department of Surgery, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Jacob C O'Dell
- Department of Surgery, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Robel T Beyene
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Robert G Sawyer
- Department of Surgery, Western Michigan Homer Stryker M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Lynn Chollet-Hinton
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Steven Q Simpson
- Department of Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Leanne Atchison
- Department of Pharmaceutical Services, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Michael Derickson
- Department of Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lindsey C Cooper
- Department of Pharmaceutical Services, Prisma Health Midlands, Columbia, South Carolina, USA
| | - G Patton Pennington
- Department of Surgery, Florida State University School of Medicine, Tallahassee Memorial Healthcare, Tallahassee, Florida, USA
| | - Sheri VandenBerg
- Department of Surgery, Division of Trauma Surgery, Bronson Methodist Hospital, Kalamazoo, Michigan, USA
| | - Bachar N Halimeh
- Department of Surgery, Boston University Medical Center, Boston, Massachusetts, USA
| | - Dorothy Hughes
- Department of Population Health, University of Kansas School of Medicine, Salina, Kansas, USA
| | - Christopher A Guidry
- Department of Surgery, University of Kansas Medical Center, Kansas City, Kansas, USA
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Walker K, Mistry A, Watson CM, Nadat F, O'Callaghan E, Care M, Crinnion LA, Arumugakani G, Bonthron DT, Carter C, Doody GM, Savic S. Inherited CD19 Deficiency Does Not Impair Plasma Cell Formation or Response to CXCL12. J Clin Immunol 2023; 43:1543-1556. [PMID: 37246174 PMCID: PMC10499936 DOI: 10.1007/s10875-023-01511-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND The human CD19 antigen is expressed throughout B cell ontogeny with the exception of neoplastic plasma cells and a subset of normal plasma cells. CD19 plays a role in propagating signals from the B cell receptor and other receptors such as CXCR4 in mature B cells. Studies of CD19-deficient patients have confirmed its function during the initial stages of B cell activation and the production of memory B cells; however, its role in the later stages of B cell differentiation is unclear. OBJECTIVE Using B cells from a newly identified CD19-deficient individual, we investigated the role of CD19 in the generation and function of plasma cells using an in vitro differentiation model. METHODS Flow cytometry and long-read nanopore sequencing using locus-specific long-range amplification products were used to screen a patient with suspected primary immunodeficiency. Purified B cells from the patient and healthy controls were activated with CD40L, IL-21, IL-2, and anti-Ig, then transferred to different cytokine conditions to induce plasma cell differentiation. Subsequently, the cells were stimulated with CXCL12 to induce signalling through CXCR4. Phosphorylation of key downstream proteins including ERK and AKT was assessed by Western blotting. RNA-seq was also performed on in vitro differentiating cells. RESULTS Long-read nanopore sequencing identified the homozygous pathogenic mutation c.622del (p.Ser208Profs*19) which was corroborated by the lack of CD19 cell surface staining. CD19-deficient B cells that are predominantly naïve generate phenotypically normal plasma cells with expected patterns of differentiation-associated genes and normal levels of CXCR4. Differentiated CD19-deficient cells were capable of responding to CXCL12; however, plasma cells derived from naïve B cells, both CD19-deficient and sufficient, had relatively diminished signaling compared to those generated from total B cells. Additionally, CD19 ligation on normal plasma cells results in AKT phosphorylation. CONCLUSION CD19 is not required for generation of antibody-secreting cells or the responses of these populations to CXCL12, but may alter the response other ligands that require CD19 potentially affecting localization, proliferation, or survival. The observed hypogammaglobulinemia in CD19-deficient individuals is therefore likely attributable to the lack of memory B cells.
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Affiliation(s)
- Kieran Walker
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Anoop Mistry
- Department of Clinical Immunology and Allergy, St James's University Hospital, 5.18 Clinical Sciences Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Fatima Nadat
- Department of Clinical Immunology and Allergy, St James's University Hospital, 5.18 Clinical Sciences Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Eleanor O'Callaghan
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Matthew Care
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Gururaj Arumugakani
- Department of Clinical Immunology and Allergy, St James's University Hospital, 5.18 Clinical Sciences Building, Beckett Street, Leeds, LS9 7TF, UK
| | - David T Bonthron
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
- Department of Clinical Genetics, Chapel Allerton Hospital, Leeds, LS7 4SA, UK
| | - Clive Carter
- Department of Clinical Immunology and Allergy, St James's University Hospital, 5.18 Clinical Sciences Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Gina M Doody
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Sinisa Savic
- Department of Clinical Immunology and Allergy, St James's University Hospital, 5.18 Clinical Sciences Building, Beckett Street, Leeds, LS9 7TF, UK.
- National Institute for Health Research, Leeds Biomedical Research Centre and Leeds Institute of Rheumatic and Musculoskeletal Medicine (LIRMM), St James's University Hospital, Leeds, LS9 7TF, UK.
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Butterfield JH, Reparaz LB, Watson CM. Cryoablation versus rib plating: Is the real problem pain control or chest wall instability? Trauma Case Rep 2023; 46:100858. [PMID: 37347011 PMCID: PMC10279898 DOI: 10.1016/j.tcr.2023.100858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2023] [Indexed: 06/23/2023] Open
Affiliation(s)
- Jaron H. Butterfield
- Corresponding author at: 925 Native Rye Way, Columbia, SC 29073, United States of America.
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McClinton B, Watson CM, Crinnion LA, McKibbin M, Ali M, Inglehearn CF, Toomes C. Haplotyping Using Long-Range PCR and Nanopore Sequencing to Phase Variants: Lessons Learned From the ABCA4 Locus. J Transl Med 2023; 103:100160. [PMID: 37088464 DOI: 10.1016/j.labinv.2023.100160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/11/2023] [Accepted: 04/17/2023] [Indexed: 04/25/2023] Open
Abstract
Short-read next-generation sequencing has revolutionized our ability to identify variants underlying inherited diseases; however, it does not allow the phasing of variants to clarify their diagnostic interpretation. The advent of widespread, increasingly accurate long-read sequencing has opened up new applications not currently available through short-read next-generation sequencing. One such use is the ability to phase variants to clarify their diagnostic interpretation and to investigate the increasingly prevalent role of cis-acting variants in the pathogenesis of the inherited disease, so-called complex alleles. Complex alleles are becoming an increasingly prevalent part of the study of genes associated with inherited diseases, for example, in ABCA4-related diseases. We sought to establish a cost-effective method to phase contiguous segments of the 130-kb ABCA4 locus by long-read sequencing of overlapping amplification products. Using the comprehensively characterized CEPH sample, NA12878, we verified the accuracy and robustness of our assay. However, in-field assessment of its utility using clinical test cases was hampered by the paucity and distribution of identified variants and by PCR chimerism, particularly where the number of PCR cycles was high. Despite this, we were able to construct robust phase blocks of up to 94.9 kb, representing 73% of the ABCA4 locus. We conclude that, although haplotype analysis of variants located within discrete amplification products was robust and informative, the stitching together of larger phase blocks using overlapping single-molecule reads remained practically challenging.
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Affiliation(s)
- Benjamin McClinton
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK; Department of Ophthalmology, St. James's University Hospital, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, UK.
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8
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Yahya S, Watson CM, Carr I, McKibbin M, Crinnion LA, Taylor M, Bonin H, Fletcher T, El-Asrag ME, Ali M, Toomes C, Inglehearn CF. Long-Read Nanopore Sequencing of RPGR ORF15 is Enhanced Following DNase I Treatment of MinION Flow Cells. Mol Diagn Ther 2023; 27:525-535. [PMID: 37284979 PMCID: PMC10299921 DOI: 10.1007/s40291-023-00656-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
INTRODUCTION RPGR ORF15 is an exon present almost exclusively in the retinal transcript of RPGR. It is purine-rich, repetitive and notoriously hard to sequence, but is a hotspot for mutations causing X-linked retinitis pigmentosa. METHODS Long-read nanopore sequencing on MinION and Flongle flow cells was used to sequence RPGR ORF15 in genomic DNA from patients with inherited retinal dystrophy. A flow cell wash kit was used on a MinION flow cell to increase yield. Findings were confirmed by PacBio SMRT long-read sequencing. RESULTS We showed that long-read nanopore sequencing successfully reads through a 2 kb PCR-amplified fragment containing ORF15. We generated reads of sufficient quality and cumulative read-depth to detect pathogenic RP-causing variants. However, we observed that this G-rich, repetitive DNA segment rapidly blocks the available pores, resulting in sequence yields less than 5% of the expected output. This limited the extent to which samples could be pooled, increasing cost. We tested the utility of a MinION wash kit containing DNase I to digest DNA fragments remaining on the flow cell, regenerating the pores. Use of the DNase I treatment allowed repeated re-loading, increasing the sequence reads obtained. Our customised workflow was used to screen pooled amplification products from previously unsolved inherited retinal disease (IRD) in patients, identifying two new cases with pathogenic ORF15 variants. DISCUSSION We report the novel finding that long-read nanopore sequencing can read through RPGR-ORF15, a DNA sequence not captured by short-read next-generation sequencing (NGS), but with a more reduced yield. Use of a flow cell wash kit containing DNase I unblocks the pores, allowing reloading of further library aliquots over a 72-h period, increasing yield. The workflow we describe provides a novel solution to the need for a rapid, robust, scalable, cost-effective ORF15 screening protocol.
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Affiliation(s)
- Samar Yahya
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Medical Genetics, School of Medicine, King Abdulaziz University, Rabigh, Kingdom of Saudi Arabia
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
| | - Ian Carr
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Martin McKibbin
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Ophthalmology, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Morag Taylor
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Hope Bonin
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Tracy Fletcher
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Mohammed E El-Asrag
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
- Department of Zoology, Faculty of Science, Benha University, Banha, Egypt
- Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, St James's University Hospital, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, UK.
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9
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Erdinc D, Rodríguez-Luis A, Fassad MR, Mackenzie S, Watson CM, Valenzuela S, Xie X, Menger KE, Sergeant K, Craig K, Hopton S, Falkous G, Poulton J, Garcia-Moreno H, Giunti P, de Moura Aschoff CA, Morales Saute JA, Kirby AJ, Toro C, Wolfe L, Novacic D, Greenbaum L, Eliyahu A, Barel O, Anikster Y, McFarland R, Gorman GS, Schaefer AM, Gustafsson CM, Taylor RW, Falkenberg M, Nicholls TJ. Pathological variants in TOP3A cause distinct disorders of mitochondrial and nuclear genome stability. EMBO Mol Med 2023; 15:e16775. [PMID: 37013609 PMCID: PMC10165364 DOI: 10.15252/emmm.202216775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 03/10/2023] [Accepted: 03/14/2023] [Indexed: 04/05/2023] Open
Abstract
Topoisomerase 3α (TOP3A) is an enzyme that removes torsional strain and interlinks between DNA molecules. TOP3A localises to both the nucleus and mitochondria, with the two isoforms playing specialised roles in DNA recombination and replication respectively. Pathogenic variants in TOP3A can cause a disorder similar to Bloom syndrome, which results from bi-allelic pathogenic variants in BLM, encoding a nuclear-binding partner of TOP3A. In this work, we describe 11 individuals from 9 families with an adult-onset mitochondrial disease resulting from bi-allelic TOP3A gene variants. The majority of patients have a consistent clinical phenotype characterised by bilateral ptosis, ophthalmoplegia, myopathy and axonal sensory-motor neuropathy. We present a comprehensive characterisation of the effect of TOP3A variants, from individuals with mitochondrial disease and Bloom-like syndrome, upon mtDNA maintenance and different aspects of enzyme function. Based on these results, we suggest a model whereby the overall severity of the TOP3A catalytic defect determines the clinical outcome, with milder variants causing adult-onset mitochondrial disease and more severe variants causing a Bloom-like syndrome with mitochondrial dysfunction in childhood.
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Affiliation(s)
- Direnis Erdinc
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Alejandro Rodríguez-Luis
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Mahmoud R Fassad
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah Mackenzie
- The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Christopher M Watson
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, UK
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Sebastian Valenzuela
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Kate Sergeant
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kate Craig
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sila Hopton
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Joanna Poulton
- Nuffield Department of Women's & Reproductive Health, The Women's Centre, University of Oxford, Oxford, UK
| | - Hector Garcia-Moreno
- Department of Clinical and Movement Neurosciences, Ataxia Centre, UCL Queen Square Institute of Neurology, London, UK
| | - Paola Giunti
- Department of Clinical and Movement Neurosciences, Ataxia Centre, UCL Queen Square Institute of Neurology, London, UK
| | | | - Jonas A Morales Saute
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Amelia J Kirby
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lynne Wolfe
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Danica Novacic
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
- The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Aviva Eliyahu
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ortal Barel
- Genomics Unit, The Center for Cancer Research, Sheba Medical Center, Tel Hashomer, Israel
| | - Yair Anikster
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Gráinne S Gorman
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew M Schaefer
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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10
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McClinton B, Crinnion LA, McKibbin M, Mukherjee R, Poulter JA, Smith CEL, Ali M, Watson CM, Inglehearn CF, Toomes C. Targeted nanopore sequencing enables complete characterisation of structural deletions initially identified using exon-based short-read sequencing strategies. Mol Genet Genomic Med 2023:e2164. [PMID: 36934458 DOI: 10.1002/mgg3.2164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/23/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND The widespread adoption of exome sequencing has greatly increased the rate of genetic diagnosis for inherited conditions. However, the detection and validation of large deletions remains challenging. While numerous bioinformatics approaches have been developed to detect deletions from whole - exome sequencing and targeted panels, further work is typically required to define the physical breakpoints or integration sites. Accurate characterisation requires either expensive follow - up whole - genome sequencing or the time - consuming, laborious process of PCR walking, both of which are challenging when dealing with the repeat sequences which frequently intersect deletion breakpoints. The aim of this study was to develop a cost-effective, long-range sequencing method to characterise deletions. METHODS Genomic DNA was amplified with primers spanning the deletion using long-range PCR and the products purified. Sequencing was performed on MinION flongle flowcells. The resulting fast5 files were basecalled using Guppy, trimmed using Porechop and aligned using Minimap2. Filtering was performed using NanoFilt. Nanopore sequencing results were verified by Sanger sequencing. RESULTS Four cases with deletions detected following comparative read-depth analysis of targeted short-read sequencing were analysed. Nanopore sequencing defined breakpoints at the molecular level in all cases including homozygous breakpoints in EYS, CNGA1 and CNGB1 and a heterozygous deletion in PRPF31. All breakpoints were verified by Sanger sequencing. CONCLUSIONS In this study, a quick, accurate and cost - effective method is described to characterise deletions identified from exome, and similar data, using nanopore sequencing.
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Affiliation(s)
- Benjamin McClinton
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Martin McKibbin
- Department of Ophthalmology, St James's University Hospital, Leeds, UK
| | | | - James A Poulter
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Claire E L Smith
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
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11
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Garner SM, Reparaz L, Justice J, Foster AP, Litzenberger S, Bell N, Schaller SL, Spoor K, Cull J, Watson CM, Dunkelberger LC. Percutaneous Endoscopic Gastrostomy Placement in Trauma Patients: Early vs Delayed Initiation of Enteral Feeding. Am Surg 2023:31348231157880. [PMID: 36797814 DOI: 10.1177/00031348231157880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
In critically ill trauma patients, adequate nutrition is essential for the body's healing process. Currently, there is no clinical standard for initiating feeds after percutaneous endoscopic gastrostomy (PEG) tube placement. We aimed to demonstrate that early enteral nutrition (EN) is as safe as delayed EN in patients who have undergone PEG tube insertion. We conducted a multi-center, retrospective cohort study of 384 patients from the Prisma Health Trauma Registries who received PEGs. Feeding intolerance was defined as high gastric residuals, nausea, emesis, sustained diarrhea, or ileus. The probability that a patient would experience intolerance was 11.7% in those fed within 6 hours, 5.1% among patients fed between 6 and 12 hours, 6.0% among patients fed between 12 and 24 hours, and 7.6% among patients fed after 24 hours, for which no statistically significant difference was detected. These findings support that early EN after PEG placement is safe in critically ill, trauma patients.
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Affiliation(s)
- Sydney M Garner
- 12322University of South Carolina School of Medicine, Columbia, SC, USA
| | - Laura Reparaz
- Trauma Research Development, 2630Prisma Health Midlands, Columbia, SC, USA
| | | | | | | | - Nathaniel Bell
- College of Nursing, 2629University of South Carolina, Columbia, SC, USA
| | | | | | - John Cull
- 3626Prisma Health, Greenville, SC, USA
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12
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Mc Clinton B, Corradi Z, McKibbin M, Panneman DM, Roosing S, Boonen EGM, Ali M, Watson CM, Steel DH, Cremers FPM, Inglehearn CF, Hitti-Malin RJ, Toomes C. Effective smMIPs-Based Sequencing of Maculopathy-Associated Genes in Stargardt Disease Cases and Allied Maculopathies from the UK. Genes (Basel) 2023; 14:191. [PMID: 36672932 PMCID: PMC9859292 DOI: 10.3390/genes14010191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Macular dystrophies are a group of individually rare but collectively common inherited retinal dystrophies characterised by central vision loss and loss of visual acuity. Single molecule Molecular Inversion Probes (smMIPs) have proved effective in identifying genetic variants causing macular dystrophy. Here, a previously established smMIPs panel tailored for genes associated with macular diseases has been used to examine 57 UK macular dystrophy cases, achieving a high solve rate of 63.2% (36/57). Among 27 bi-allelic STGD1 cases, only three novel ABCA4 variants were identified, illustrating that the majority of ABCA4 variants in Caucasian STGD1 cases are currently known. We examined cases with ABCA4-associated disease in detail, comparing our results with a previously reported variant grading system, and found this model to be accurate and clinically useful. In this study, we showed that ABCA4-associated disease could be distinguished from other forms of macular dystrophy based on clinical evaluation in the majority of cases (34/36).
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Affiliation(s)
- Benjamin Mc Clinton
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- Department of Ophthalmology, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Christopher M. Watson
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - David H. Steel
- Sunderland Eye Infirmary, Sunderland SR2 9HP, UK
- The Bioscience Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chris F. Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
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13
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Petersen TL, King JC, Fussell JJ, Gans HA, Waggoner-Fountain LA, Castro D, Green ML, Hamilton MF, Marcdante K, Mink R, Nielsen KR, Turner DA, Watson CM, Zurca AD, Boyer DL. Benefits and Limitations of Virtual Recruitment: Perspectives From Subspeciality Directors. Pediatrics 2022; 150:189467. [PMID: 36082609 DOI: 10.1542/peds.2022-056735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Because of the coronavirus disease 2019 pandemic and recommendations from a range of leaders and organizations, the pediatrics subspecialty 2020 recruitment season was entirely virtual. Minimal data exist on the effect of this change to guide future strategies. The aim of this study was to understand the effects of virtual recruitment on pediatric subspecialty programs as perceived by program leaders. METHODS This concurrent, triangulation, mixed-methods study used a survey that was developed through an iterative (3 cycles), consensus-building, modified Delphi process and sent to all pediatric subspecialty program directors (PSPDs) between April and May 2021. Descriptive statistics and thematic analysis were used, and a conceptual framework was developed. RESULTS Forty-two percent (352 of 840) of PSPDs responded from 16 of the 17 pediatric (94%) subspecialties; 60% felt the virtual interview process was beneficial to their training program. A majority of respondents (72%) reported cost savings were a benefit; additional benefits included greater efficiency of time, more applicants per day, greater faculty involvement, and perceived less time away from residency for applicants. PSPDs reported a more diverse applicant pool. Without an in-person component, PSPDs worried about programs and applicants missing informative, in-person interactions and applicants missing hospital tours and visiting the city. A model based upon theory of change was developed to aid program considerations for future application cycles. CONCLUSIONS PSPDs identified several benefits to virtual recruitment, including ease of accommodating increased applicants with a diverse applicant pool and enhanced faculty involvement. Identified limitations included reduced interaction between the applicant and the larger institution/city.
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Affiliation(s)
- Tara L Petersen
- The Medical College of Wisconsin/Children's Wisconsin, Milwaukee, Wisconsin.,Contributed equally as co-first authors
| | - Jennifer C King
- The Monroe Carell Jr. Children's Hospital at Vanderbilt University, Nashville, Tennessee.,Contributed equally as co-first authors
| | - Jill J Fussell
- University of Arkansas for Medical Sciences/Arkansas Children's Hospital, Little Rock, Arkansas
| | - Hayley A Gans
- Stanford University Medical Center, Palo Alto, California
| | - Linda A Waggoner-Fountain
- University of Virginia School of Medicine and University of Virginia Children's Hospital, Charlottesville, Virginia
| | | | - Michael L Green
- University of Texas Southwestern Medical Center, Dallas, Texas
| | - Melinda F Hamilton
- UPMC Children's Hospital of Pittsburgh and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Karen Marcdante
- The Medical College of Wisconsin/Children's Wisconsin, Milwaukee, Wisconsin.,The Kern Institute for the Transformation of Medical Education, Milwaukee, Wisconsin
| | - Richard Mink
- The Lundquist Institute for Biomedical Innovation and Harbor-UCLA Medical Center, Los Angeles, California
| | - Katie R Nielsen
- Seattle Children's Hospital at the University of Washington, Seattle, Washington
| | - David A Turner
- American Board of Pediatrics, Chapel Hill, North Carolina
| | | | - Adrian D Zurca
- Penn State Children's Hospital at Penn State College of Medicine, Hershey, Pennsylvania
| | - Donald L Boyer
- Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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14
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Best S, Lord J, Roche M, Watson CM, Poulter JA, Bevers RPJ, Stuckey A, Szymanska K, Ellingford JM, Carmichael J, Brittain H, Toomes C, Inglehearn C, Johnson CA, Wheway G. Molecular diagnoses in the congenital malformations caused by ciliopathies cohort of the 100,000 Genomes Project. J Med Genet 2022; 59:737-747. [PMID: 34716235 PMCID: PMC9340050 DOI: 10.1136/jmedgenet-2021-108065] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/27/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Primary ciliopathies represent a group of inherited disorders due to defects in the primary cilium, the 'cell's antenna'. The 100,000 Genomes Project was launched in 2012 by Genomics England (GEL), recruiting National Health Service (NHS) patients with eligible rare diseases and cancer. Sequence data were linked to Human Phenotype Ontology (HPO) terms entered by recruiting clinicians. METHODS Eighty-three prescreened probands were recruited to the 100,000 Genomes Project suspected to have congenital malformations caused by ciliopathies in the following disease categories: Bardet-Biedl syndrome (n=45), Joubert syndrome (n=14) and 'Rare Multisystem Ciliopathy Disorders' (n=24). We implemented a bespoke variant filtering and analysis strategy to improve molecular diagnostic rates for these participants. RESULTS We determined a research molecular diagnosis for n=43/83 (51.8%) probands. This is 19.3% higher than previously reported by GEL (n=27/83 (32.5%)). A high proportion of diagnoses are due to variants in non-ciliopathy disease genes (n=19/43, 44.2%) which may reflect difficulties in clinical recognition of ciliopathies. n=11/83 probands (13.3%) had at least one causative variant outside the tiers 1 and 2 variant prioritisation categories (GEL's automated triaging procedure), which would not be reviewed in standard 100,000 Genomes Project diagnostic strategies. These include four structural variants and three predicted to cause non-canonical splicing defects. Two unrelated participants have biallelic likely pathogenic variants in LRRC45, a putative novel ciliopathy disease gene. CONCLUSION These data illustrate the power of linking large-scale genome sequence to phenotype information. They demonstrate the value of research collaborations in order to maximise interpretation of genomic data.
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Affiliation(s)
- Sunayna Best
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
- Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Jenny Lord
- Department of Human Development and Health, University of Southampton Faculty of Medicine, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Christopher M Watson
- Department of Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, West Yorkshire, UK
- School of Medicine, University of Leeds, Leeds, UK
| | - James A Poulter
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Roel P J Bevers
- Genomics England, Queen Mary University of London, London, UK
| | - Alex Stuckey
- Genomics England, Queen Mary University of London, London, UK
| | - Katarzyna Szymanska
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Jamie M Ellingford
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester, UK
| | - Jenny Carmichael
- East Anglian Medical Genetics Service, Addenbrooke's Hospital, Cambridge, UK
| | - Helen Brittain
- Genomics England, Queen Mary University of London, London, UK
| | - Carmel Toomes
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Chris Inglehearn
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Colin A Johnson
- Division of Molecular Medicine, University of Leeds Leeds Institute of Medical Research at St James's, Leeds, West Yorkshire, UK
| | - Gabrielle Wheway
- Department of Human Development and Health, University of Southampton Faculty of Medicine, Southampton, UK
- Southampton University Hospitals NHS Trust, Southampton, UK
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15
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Watson CM, Nadat F, Ahmed S, Crinnion LA, O'Riordan S, Carter C, Savic S. Identification of a novel MAGT1 mutation supports a diagnosis of XMEN disease. Genes Immun 2022; 23:66-72. [PMID: 35264785 PMCID: PMC9042700 DOI: 10.1038/s41435-022-00166-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/15/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Abstract
XMEN (X-linked immunodeficiency with magnesium defect) is caused by loss-of-function mutations in MAGT1 which is encoded on the X chromosome. The disorder is characterised by CD4 lymphopenia, severe chronic viral infections and defective T-lymphocyte activation. XMEN patients are susceptible to Epstein-Barr virus infections and persistently low levels of intracellular Mg2+. Here we describe a patient that presented with multiple recurrent infections and a subsequent diffuse B-cell lymphoma. Molecular genetic analysis by exome sequencing identified a novel hemizygous MAGT1 nonsense mutation c.1005T>A (NM_032121.5) p.(Cys335*), confirming a diagnosis of XMEN deficiency. Follow-up immunophenotyping was performed by antibody staining and flow cytometry; proliferation was determined by 3H-thymidine uptake after activation by PHA and anti-CD3. Cytotoxic natural killer cell activity was assessed with K562 target cells using the NKTESTTM assay. While lymphocyte populations were superficially intact, B cells were largely naive with a reduced memory cell compartment. Translated NKG2D was absent on both NK and T cells in the proband, and normally expressed in the carrier mother. In vitro NK cell activity was intact in both the proband and his mother. This report adds to the growing number of identified XMEN cases, raising awareness of a, still rare, X-linked immunodeficiency.
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Affiliation(s)
- Christopher M Watson
- North East and Yorkshire Genomic Laboratory Hub, The Leeds Teaching Hospitals NHS Trust, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK.,Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Fatima Nadat
- Department of Clinical Immunology and Allergy, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Sammiya Ahmed
- Department of Clinical Immunology and Allergy, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Laura A Crinnion
- North East and Yorkshire Genomic Laboratory Hub, The Leeds Teaching Hospitals NHS Trust, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK.,Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Sean O'Riordan
- Department of Paediatric Immunology, Leeds General Infirmary, Leeds, LS1 3EX, UK
| | - Clive Carter
- Department of Clinical Immunology and Allergy, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK
| | - Sinisa Savic
- Department of Clinical Immunology and Allergy, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK. .,National Institute for Health Research, Leeds Biomedical Research Centre and Leeds Institute of Rheumatic and Musculoskeletal Medicine (LIRMM), Wellcome Trust Brenner Building, St James's University Hospital, Beckett Street, Leeds, LS9 7TF, UK.
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16
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Best S, Inglehearn CF, Watson CM, Toomes C, Wheway G, Johnson CA. Unlocking the potential of the UK 100,000 Genomes Project-lessons learned from analysis of the "Congenital Malformations caused by Ciliopathies" cohort. Am J Med Genet C Semin Med Genet 2022; 190:5-8. [PMID: 35289502 PMCID: PMC9315030 DOI: 10.1002/ajmg.c.31965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/02/2022] [Accepted: 03/09/2022] [Indexed: 01/31/2023]
Affiliation(s)
- Sunayna Best
- Division of Molecular MedicineLeeds Institute of Medical Research at St. James's, University of Leeds, St. James's University HospitalLeedsUK,Yorkshire Regional Genetics ServiceLeedsUK
| | - Chris F. Inglehearn
- Division of Molecular MedicineLeeds Institute of Medical Research at St. James's, University of Leeds, St. James's University HospitalLeedsUK
| | - Christopher M. Watson
- North East and Yorkshire Genomic Laboratory Hub, Central LabSt. James's University HospitalLeedsUK
| | - Carmel Toomes
- Division of Molecular MedicineLeeds Institute of Medical Research at St. James's, University of Leeds, St. James's University HospitalLeedsUK
| | - Gabrielle Wheway
- University Hospital Southampton NHS Foundation TrustSouthamptonUK,Faculty of Medicine, Human Development and HealthUniversity of SouthamptonSouthamptonUK
| | - Colin A. Johnson
- Division of Molecular MedicineLeeds Institute of Medical Research at St. James's, University of Leeds, St. James's University HospitalLeedsUK
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17
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Watson CM, Holliday DL, Crinnion LA, Bonthron DT. Long‐read nanopore DNA sequencing can resolve complex intragenic duplication/deletion variants, providing information to enable preimplantation genetic diagnosis. Prenat Diagn 2022; 42:226-232. [PMID: 35014072 PMCID: PMC9305782 DOI: 10.1002/pd.6089] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/15/2021] [Accepted: 12/31/2021] [Indexed: 11/11/2022]
Abstract
Background Objective Methods Results Conclusion
What's already known about this topic?
Molecular diagnostic techniques that incompletely resolve pathogenic sequence variants can present a barrier for certain prenatal diagnostic approaches.
What does this study add?
This study demonstrates how nanopore‐based sequencing could be rapidly deployed for follow‐up analysis of previously identified, but incompletely‐defined structural variants, enabling onward referral to a national preimplantation genetic diagnosis service.
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Affiliation(s)
- Christopher M. Watson
- North East and Yorkshire Genomics Laboratory Hub Central Laboratory St. James's University Hospital Leeds UK
- Leeds Institute of Medical Research University of Leeds St. James's University Hospital Leeds UK
| | - Deborah L. Holliday
- Department of Clinical Genetics Leeds Teaching Hospitals NHS Trust Chapel Allerton Hospital Leeds West Yorkshire UK
| | - Laura A. Crinnion
- North East and Yorkshire Genomics Laboratory Hub Central Laboratory St. James's University Hospital Leeds UK
- Leeds Institute of Medical Research University of Leeds St. James's University Hospital Leeds UK
| | - David T. Bonthron
- Leeds Institute of Medical Research University of Leeds St. James's University Hospital Leeds UK
- Department of Clinical Genetics Leeds Teaching Hospitals NHS Trust Chapel Allerton Hospital Leeds West Yorkshire UK
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18
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Good RJ, Zurca AD, Turner DA, Bjorklund AR, Boyer DL, Krennerich EC, Petrillo T, Rozenfeld RA, Sasser WC, Schuette J, Tcharmtchi MH, Watson CM, Czaja AS. Transport Medical Control Education for Pediatric Critical Care Fellows: A National Needs Assessment Study. Pediatr Crit Care Med 2022; 23:e55-e59. [PMID: 34261945 DOI: 10.1097/pcc.0000000000002803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES Characterize transport medical control education in Pediatric Critical Care Medicine fellowship. DESIGN Cross-sectional survey study. SETTING Pediatric Critical Care Medicine fellowship programs in the United States. SUBJECTS Pediatric Critical Care Medicine fellowship program directors. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS We achieved a 74% (53/72) response rate. A majority of programs (85%) require fellows to serve as transport medical control, usually while carrying out other clinical responsibilities and sometimes without supervision. Fellows at most programs (80%) also accompany the transport team on patient retrievals. Most respondents (72%) reported formalized transport medical control teaching, primarily in a didactic format (76%). Few programs (25%) use a standardized assessment tool. Transport medical control was identified as requiring all six Accreditation Council for Graduate Medical Education competencies, with emphasis on professionalism and interpersonal and communication skills. CONCLUSIONS Transport medical control responsibilities are common for Pediatric Critical Care Medicine fellows, but training is inconsistent, assessment is not standardized, and supervision may be lacking. Fellow performance in transport medical control may help inform assessment in multiple domains of competencies. Further study is needed to identify effective methods for transport medical control education.
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Affiliation(s)
- Ryan J Good
- Section of Critical Care Medicine, Department of Pediatrics, University of Colorado at Denver, Anschutz Medical Campus, Denver, CO
| | - Adrian D Zurca
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Penn State Children's Hospital, Hershey, PA
| | - David A Turner
- Competency-Based Medical Education, American Board of Pediatrics, Chapel Hill, NC
- Division of Pediatric Critical Care, Department of Pediatrics, Duke University Hospital and Health System, Durham, NC
| | - Ashley R Bjorklund
- Division of Pediatric Critical Care, University of Minnesota, Minneapolis, MN
| | - Donald L Boyer
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Emily C Krennerich
- Section of Pediatric Critical Care, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Toni Petrillo
- Division of Critical Care Medicine, Department of Pediatrics, Emory School of Medicine, Atlanta, GA
| | - Ranna A Rozenfeld
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Hasbro Children's Hospital, Brown University, Providence, RI
| | - William C Sasser
- Division of Pediatric Critical Care Medicine, University of Alabama - Birmingham, Birmingham, AL
| | - Jennifer Schuette
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins Children's Center and Johns Hopkins School of Medicine, Baltimore, MD
| | - M Hossein Tcharmtchi
- Section of Pediatric Critical Care, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX
| | - Christopher M Watson
- Department of Pediatrics, Medical College of Georgia at Augusta University, Augusta, GA
| | - Angela S Czaja
- Section of Critical Care Medicine, Department of Pediatrics, University of Colorado at Denver, Anschutz Medical Campus, Denver, CO
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19
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Verdone K, Watson CM. Postextubation airway obstruction in children: Are steroids the key to prevention? Pediatr Pulmonol 2021; 56:2395-2396. [PMID: 34010510 DOI: 10.1002/ppul.25460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/09/2021] [Indexed: 11/06/2022]
Affiliation(s)
- Kaitlin Verdone
- Department of Pediatrics, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Christopher M Watson
- Department of Pediatrics, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
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20
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Ninmer EK, Stewart C, Sharron MP, Ashworth JN, Martinez-Schlurman N, Kavanagh RP, Signoff JK, McCrory MC, Eidman DB, Subbaswamy AV, Shea PL, Sheram ML, Watson CM, Spaeder MC. Taxonomy of Pathogen Codetection in Pediatric Case Fatalities with Adenoviral Respiratory Infection. J PEDIAT INF DIS-GER 2021. [DOI: 10.1055/s-0041-1731409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Abstract
Objective The aim of this study was to determine the prevalence and taxonomy of pathogen codetection in pediatric case fatalities associated with adenoviral respiratory infection.
Methods This retrospective case series included 107 pediatric case fatalities associated with adenoviral respiratory infection.
Results We observed a high rate of pathogen codetection with broad diversity from both respiratory and nonrespiratory sources. We noted differences in codetection characteristics based on immune status; most notably that immunocompromised cases were more likely to have bacteremia and adenoviremia.
Conclusions In pediatric case fatalities associated with adenoviral respiratory infection, we observed a high degree of pathogen codetection.
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Affiliation(s)
- Emily K. Ninmer
- Department of Pediatrics, Division of Pediatric Critical Care, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Claire Stewart
- Division of Critical Care Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States
| | - Matthew P. Sharron
- Division of Critical Care Medicine, Children's National Hospital, Washington, United States
| | - Julia Noether Ashworth
- Division of Pediatric Critical Care, Inova Children's Hospital, Falls Church, Virginia, United States
| | - Natalia Martinez-Schlurman
- Division of Pediatric Critical Care, University of Florida School of Medicine, Gainesville, Florida, United States
| | - Robert P. Kavanagh
- Division of Pediatric Critical Care, Penn State College of Medicine, Hershey, Pennsylvania, United States
| | - Jessica K. Signoff
- Division of Pediatric Critical Care, University of California at Davis School of Medicine, Sacramento, California, United States
| | - Michael C. McCrory
- Division of Pediatric Critical Care, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States
| | - Daniel B. Eidman
- Division of Pediatric Critical Care, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Anjali V. Subbaswamy
- Division of Pediatric Critical Care, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States
| | - Paul L. Shea
- Division of Pediatric Critical Care, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States
| | - Mary Lynn Sheram
- Department of Pediatrics, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Christopher M. Watson
- Department of Pediatrics, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
| | - Michael C. Spaeder
- Department of Pediatrics, Division of Pediatric Critical Care, University of Virginia School of Medicine, Charlottesville, Virginia, United States
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21
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Watson CM, Crinnion LA, Simmonds J, Camm N, Adlard J, Bonthron DT. Long-read nanopore sequencing enables accurate confirmation of a recurrent PMS2 insertion-deletion variant located in a region of complex genomic architecture. Cancer Genet 2021; 256-257:122-126. [PMID: 34116445 DOI: 10.1016/j.cancergen.2021.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/08/2021] [Accepted: 05/24/2021] [Indexed: 10/21/2022]
Abstract
Targeted next generation sequencing (NGS) is the predominant methodology for the molecular genetic diagnosis of inherited conditions. In many laboratories, NGS-identified variants are routinely validated using a different method, to minimize the risk of a false-positive diagnosis. This can be particularly important when pathogenic variants are located in complex genomic regions. In this situation, new long-read sequencing technologies have potential advantages over existing alternatives. However, practical examples of their utility for diagnostic purposes remain scant. Here, we report the use of nanopore sequencing to validate a PMS2 mutation refractory to conventional methods. In a patient who presented with colorectal cancer and loss of PMS2 immunostaining, short-read NGS of Lynch syndrome-associated genes identified the recurrent PMS2 insertion-deletion variant, c.736_741delinsTGTGTGTGAAG (p.Pro246Cysfs*3). Confirmation of this variant using bidirectional Sanger sequencing was impeded by an upstream intron 6 poly(T) tract. Using a locus-specific amplicon template, we undertook nanopore long-read sequencing in order to assess the diagnostic accuracy of this platform. Pairwise comparison between a curated benchmark allele (derived from short-read NGS and unidirectional Sanger sequencing) and the consensus nanopore dataset revealed 100% sequence identity. Our experience provides insight into the robustness and ease of deployment of "third-generation" sequencing for accurate characterisation of pathogenic variants.
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Affiliation(s)
- Christopher M Watson
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds LS9 7TF, United Kingdom; Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, United Kingdom.
| | - Laura A Crinnion
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds LS9 7TF, United Kingdom; Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Jennifer Simmonds
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Nick Camm
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Julian Adlard
- The Clinical Genetics Department, Chapel Allerton Hospital, Leeds LS7 4SA, United Kingdom
| | - David T Bonthron
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, United Kingdom; The Clinical Genetics Department, Chapel Allerton Hospital, Leeds LS7 4SA, United Kingdom
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22
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Watson CM, Crinnion LA, Lindsay H, Mitchell R, Camm N, Robinson R, Joyce C, Tanteles GA, Halloran DJO, Pena SDJ, Carr IM, Bonthron DT. Assessing the utility of long-read nanopore sequencing for rapid and efficient characterization of mobile element insertions. J Transl Med 2021; 101:442-449. [PMID: 32989232 DOI: 10.1038/s41374-020-00489-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/16/2022] Open
Abstract
Short-read next generation sequencing (NGS) has become the predominant first-line technique used to diagnose patients with rare genetic conditions. Inherent limitations of short-read technology, notably for the detection and characterization of complex insertion-containing variants, are offset by the ability to concurrently screen many disease genes. "Third-generation" long-read sequencers are increasingly being deployed as an orthogonal adjunct technology, but their full potential for molecular genetic diagnosis has yet to be exploited. Here, we describe three diagnostic cases in which pathogenic mobile element insertions were refractory to characterization by short-read sequencing. To validate the accuracy of the long-read technology, we first used Sanger sequencing to confirm the integration sites and derive curated benchmark sequences of the variant-containing alleles. Long-read nanopore sequencing was then performed on locus-specific amplicons. Pairwise comparison between these data and the previously determined benchmark alleles revealed 100% identity of the variant-containing sequences. We demonstrate a number of technical advantages over existing wet-laboratory approaches, including in silico size selection of a mixed pool of amplification products, and the relative ease with which an automated informatics workflow can be established. Our findings add to a growing body of literature describing the diagnostic utility of long-read sequencing.
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Affiliation(s)
- Christopher M Watson
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK.
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Laura A Crinnion
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Helen Lindsay
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Rowena Mitchell
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Nick Camm
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Rachel Robinson
- Yorkshire and North East Genomic Laboratory Hub, Central Lab, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - Caroline Joyce
- Department of Endocrinology, Cork University Hospital, Wilton, Cork, Ireland
| | - George A Tanteles
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, PO Box 23462, CY1683, Nicosia, Cyprus
| | | | | | - Ian M Carr
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK
| | - David T Bonthron
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK
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23
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Spaeder MC, Stewart C, Sharron MP, Noether JR, Martinez-Schlurman N, Kavanagh RP, Signoff JK, McCrory MC, Eidman DB, Subbaswamy AV, Shea PL, Harwayne-Gidansky I, Ninmer EK, Sheram ML, Watson CM. Adenoviral Respiratory Infection-Associated Mortality in Children: A Retrospective Case Series. J Pediatr Intensive Care 2020; 11:13-18. [DOI: 10.1055/s-0040-1718868] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/19/2020] [Indexed: 12/22/2022] Open
Abstract
AbstractViral respiratory infections are a leading cause of illness and hospitalization in young children worldwide. Case fatality rates in pediatric patients with adenoviral lower respiratory tract infection requiring intensive care unit (ICU) admission have been reported between 7 and 22%. We investigated the demographics and clinical characteristics in pediatric mortalities associated with adenoviral respiratory infection at 12 academic children's hospitals in the United States. There were 107 mortality cases included in our study, 73% of which had a chronic medical condition. The most common chronic medical condition was immunocompromised state in 37 cases (35%). The incidences of pediatric acute respiratory distress syndrome (78%) and multiple organ dysfunction syndrome (94%) were profound. Immunocompetent cases were more likely to receive mechanical ventilation within the first hour of ICU admission (60 vs. 14%, p < 0.001) and extracorporeal membrane oxygenation (27 vs. 5%, p = 0.009), and less likely to receive continuous renal replacement therapy (20 vs. 49%, p = 0.002) or have renal dysfunction (54 vs. 78%, p = 0.014) as compared with immunocompromised cases. Immunocompromised cases were more likely to have bacteremia (57 vs. 16%, p < 0.001) and adenoviremia (51 vs. 17%, p < 0.001) and be treated with antiviral medications (81 vs. 26%, p < 0.001). We observed a high burden of nonrespiratory organ system dysfunction in a cohort of pediatric case fatalities with adenoviral respiratory infection. The majority of cases had a chronic medical condition associated with an increased risk of complications from viral respiratory illness, most notably immunocompromised state. Important treatment differences were noted between immunocompromised and immunocompetent cases.
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Affiliation(s)
- Michael C. Spaeder
- Division of Pediatric Critical Care, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Claire Stewart
- Division of Critical Care Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States
| | - Matthew P. Sharron
- Division of Critical Care Medicine, Children's National Hospital, Washington, District of Columbia, United States
| | - Julia R. Noether
- Division of Pediatric Critical Care, Johns Hopkins All Children's Hospital, St. Petersburg, Florida, United States
| | - Natalia Martinez-Schlurman
- Division of Pediatric Critical Care, University of Florida School of Medicine, Gainesville, Florida, United States
| | - Robert P. Kavanagh
- Division of Pediatric Critical Care, Pennsylvania State University School of Medicine, Hershey, Pennsylvania, United States
| | - Jessica K. Signoff
- Division of Pediatric Critical Care, University of California at Davis School of Medicine, Sacramento, California, United States
| | - Michael C. McCrory
- Pediatric Critical Care, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States
| | - Daniel B. Eidman
- Pediatric Critical Care, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Anjali V. Subbaswamy
- Division of Pediatric Critical Care, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States
| | - Paul L. Shea
- Division of Pediatric Critical Care, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States
| | - Ilana Harwayne-Gidansky
- Division of Pediatric Critical Care, Renaissance School of Medicine at Stony Brook University, Stony Brook, New York, United States
| | - Emily K. Ninmer
- Division of Pediatric Critical Care, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Mary Lynn Sheram
- Department of Pediatrics, Medical College of Georgia at Augusta University, Augusta, Georgia, United States
| | - Christopher M. Watson
- Department of Pediatrics, Medical College of Georgia at Augusta University, Augusta, Georgia, United States
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24
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Prest PJ, Justice J, Bell N, McCarroll R, Watson CM. A Volume-Based Feeding Protocol Improves Nutrient Delivery and Glycemic Control in a Surgical Trauma Intensive Care Unit. JPEN J Parenter Enteral Nutr 2020; 44:880-888. [PMID: 31529520 DOI: 10.1002/jpen] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/11/2019] [Accepted: 08/29/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Inadequate delivery of nutrition in critically ill patients has been shown to have adverse outcomes. A surgical trauma intensive care unit provides unique challenges to enteral feeds. Although volume-based feeding protocols, like Enhanced Protein-Energy Provision via the Enteral Route Feeding Protocol (PEP uP), have been successfully used in medical intensive care patients, data are sparse on its safety and efficacy in a surgical intensive care unit population. METHODS A PEP uP protocol was recently initiated at our American College of Surgeons Level 1 verified trauma center. Medical records of 197 patients before this change (pre-PEP uP) were compared with 295 patients after this change (post-PEP uP). RESULTS The post-PEP uP group met/exceeded energy goals (defined as 80% of target) more often (57.0% compared with 26.9%, P-value < .001), with an adjusted odds ratio (OR) of 4.98 (95% CI 3.49-7.10), and more often met/exceeded protein goals (57.4% compared with 18.6%, P-value < .001), with an adjusted OR of 11.84 (95% CI 7.94-17.64). There was no significant difference in emesis during this time. Additionally, patients in the post-PEP uP arm had less episodes of hyperglycemia (9% compared with 14.4%, P-value < .001). CONCLUSIONS Volume-based feeding protocols like PEP uP are safe in critically ill trauma patients and are more effective at delivering energy and protein while limiting hyperglycemic episodes when compared with a traditional delivery method.
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Affiliation(s)
- Phillip J Prest
- Palmetto Health-University of South Carolina Medical Group, Columbia, South Carolina, USA
- The University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Jessica Justice
- Palmetto Health-University of South Carolina Medical Group, Columbia, South Carolina, USA
| | - Nathanial Bell
- The University of South Carolina College of Nursing, Columbia, South Carolina, USA
| | - Richard McCarroll
- Palmetto Health-University of South Carolina Medical Group, Columbia, South Carolina, USA
- The University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Christopher M Watson
- Palmetto Health-University of South Carolina Medical Group, Columbia, South Carolina, USA
- The University of South Carolina School of Medicine, Columbia, South Carolina, USA
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25
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Chapman LM, Spies N, Pai P, Lim CS, Carroll A, Narzisi G, Watson CM, Proukakis C, Clarke WE, Nariai N, Dawson E, Jones G, Blankenberg D, Brueffer C, Xiao C, Kolora SRR, Alexander N, Wolujewicz P, Ahmed AE, Smith G, Shehreen S, Wenger AM, Salit M, Zook JM. A crowdsourced set of curated structural variants for the human genome. PLoS Comput Biol 2020; 16:e1007933. [PMID: 32559231 PMCID: PMC7329145 DOI: 10.1371/journal.pcbi.1007933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 07/01/2020] [Accepted: 05/07/2020] [Indexed: 11/19/2022] Open
Abstract
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs) is more challenging. In this study, we manually curated 1235 SVs, which can ultimately be used to evaluate SV callers or train machine learning models. We developed a crowdsourcing app-SVCurator-to help GIAB curators manually review large indels and SVs within the human genome, and report their genotype and size accuracy. SVCurator displays images from short, long, and linked read sequencing data from the GIAB Ashkenazi Jewish Trio son [NIST RM 8391/HG002]. We asked curators to assign labels describing SV type (deletion or insertion), size accuracy, and genotype for 1235 putative insertions and deletions sampled from different size bins between 20 and 892,149 bp. 'Expert' curators were 93% concordant with each other, and 37 of the 61 curators had at least 78% concordance with a set of 'expert' curators. The curators were least concordant for complex SVs and SVs that had inaccurate breakpoints or size predictions. After filtering events with low concordance among curators, we produced high confidence labels for 935 events. The SVCurator crowdsourced labels were 94.5% concordant with the heuristic-based draft benchmark SV callset from GIAB. We found that curators can successfully evaluate putative SVs when given evidence from multiple sequencing technologies.
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Affiliation(s)
- Lesley M. Chapman
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Noah Spies
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
- The Joint Initiative for Metrology in Biology, Stanford University, Stanford, California, United States of America
- Departments of Genetics and Pathology, Stanford University, Stanford, California, United States of America
| | - Patrick Pai
- University of Maryland - College Park, College Park, Maryland, United States of America
| | - Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Andrew Carroll
- DNAnexus Inc, Mountain View, California, United States of America
| | - Giuseppe Narzisi
- New York Genome Center, New York, New York, United States of America
| | - Christopher M. Watson
- School of Medicine, University of Leeds, Saint James's University Hospital, Leeds, Leeds, United Kingdom
- Yorkshire Regional Genetics Service, The Leeds Teaching Hospitals NHS Trust, Saint James's University Hospital, Leeds, United Kingdom
| | - Christos Proukakis
- University College London, Institute of Neurology, London, United Kingdom
| | - Wayne E. Clarke
- New York Genome Center, New York, New York, United States of America
| | - Naoki Nariai
- Illumina, Inc. San Diego, California, United States of America
| | - Eric Dawson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland, United States of America
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Garan Jones
- University of Exeter Medical School, Epidemiology and Public Health Group, Barrack Road, Exeter, Devon, United Kingdom
| | - Daniel Blankenberg
- Genomic Medicine Institute Lerner Research Institute Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Christian Brueffer
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sree Rohit Raj Kolora
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Noah Alexander
- Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America
| | - Paul Wolujewicz
- Weill Cornell, Belfer Research Building, New York, New York, United States of America
| | - Azza E. Ahmed
- Center for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum and Department of Electrical and Electronic Engineering, Faculty of Engineering, University of Khartoum, Khartoum, Sudan
| | - Graeme Smith
- Guy's Hospital and St Thomas's NHS Foundation Trust Great Maze Pond, London, United Kingdom
| | - Saadlee Shehreen
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Bangladesh
| | - Aaron M. Wenger
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Marc Salit
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
- The Joint Initiative for Metrology in Biology, Stanford University, Stanford, California, United States of America
| | - Justin M. Zook
- Biosystems and Biomaterials Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
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26
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Fassad MR, Patel MP, Shoemark A, Cullup T, Hayward J, Dixon M, Rogers AV, Ollosson S, Jackson C, Goggin P, Hirst RA, Rutman A, Thompson J, Jenkins L, Aurora P, Moya E, Chetcuti P, O'Callaghan C, Morris-Rosendahl DJ, Watson CM, Wilson R, Carr S, Walker W, Pitno A, Lopes S, Morsy H, Shoman W, Pereira L, Constant C, Loebinger MR, Chung EMK, Kenia P, Rumman N, Fasseeh N, Lucas JS, Hogg C, Mitchison HM. Clinical utility of NGS diagnosis and disease stratification in a multiethnic primary ciliary dyskinesia cohort. J Med Genet 2019; 57:322-330. [PMID: 31879361 DOI: 10.1136/jmedgenet-2019-106501] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/23/2019] [Accepted: 11/01/2019] [Indexed: 01/21/2023]
Abstract
BACKGROUND Primary ciliary dyskinesia (PCD), a genetically heterogeneous condition enriched in some consanguineous populations, results from recessive mutations affecting cilia biogenesis and motility. Currently, diagnosis requires multiple expert tests. METHODS The diagnostic utility of multigene panel next-generation sequencing (NGS) was evaluated in 161 unrelated families from multiple population ancestries. RESULTS Most (82%) families had affected individuals with biallelic or hemizygous (75%) or single (7%) pathogenic causal alleles in known PCD genes. Loss-of-function alleles dominate (73% frameshift, stop-gain, splice site), most (58%) being homozygous, even in non-consanguineous families. Although 57% (88) of the total 155 diagnostic disease variants were novel, recurrent mutations and mutated genes were detected. These differed markedly between white European (52% of families carry DNAH5 or DNAH11 mutations), Arab (42% of families carry CCDC39 or CCDC40 mutations) and South Asian (single LRRC6 or CCDC103 mutations carried in 36% of families) patients, revealing a striking genetic stratification according to population of origin in PCD. Genetics facilitated successful diagnosis of 81% of families with normal or inconclusive ultrastructure and 67% missing prior ultrastructure results. CONCLUSIONS This study shows the added value of high-throughput targeted NGS in expediting PCD diagnosis. Therefore, there is potential significant patient benefit in wider and/or earlier implementation of genetic screening.
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Affiliation(s)
- Mahmoud R Fassad
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Mitali P Patel
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Amelia Shoemark
- PCD Diagnostic Team and Department of Pediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Thomas Cullup
- NE Thames Regional Molecular Genetics Laboratory, Great Ormond Street Hospital For Children NHS Foundation Trust, London, UK
| | - Jane Hayward
- NE Thames Regional Molecular Genetics Laboratory, Great Ormond Street Hospital For Children NHS Foundation Trust, London, UK
| | - Mellisa Dixon
- PCD Diagnostic Team and Department of Pediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Andrew V Rogers
- Host Defence Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Sarah Ollosson
- PCD Diagnostic Team and Department of Pediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Claire Jackson
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Patricia Goggin
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Andrew Rutman
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - James Thompson
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Lucy Jenkins
- NE Thames Regional Molecular Genetics Laboratory, Great Ormond Street Hospital For Children NHS Foundation Trust, London, UK
| | - Paul Aurora
- Department of Paediatric Respiratory Medicine, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.,Department of Respiratory, Critical Care and Anaesthesia Unit, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Eduardo Moya
- Children's Services (Paediatrics), Bradford Royal Infirmary, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Philip Chetcuti
- Department of Respiratory Paediatrics, Leeds General Infirmary, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Chris O'Callaghan
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK.,Department of Respiratory, Critical Care and Anaesthesia Unit, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Deborah J Morris-Rosendahl
- Clinical Genetics and Genomics Laboratory, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | | | - Robert Wilson
- Host Defence Unit, Royal Brompton and Harefield NHS Trust, London, UK
| | - Siobhan Carr
- PCD Diagnostic Team and Department of Pediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Woolf Walker
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Andreia Pitno
- PCD Diagnostic Team and Department of Pediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,Laboratório de Histologia e Patologia Comparada, Instituto de Medicina Molecular, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Susana Lopes
- CEDOC, Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Heba Morsy
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Walaa Shoman
- Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Alexandria, Egypt
| | - Luisa Pereira
- Paediatric Pulmonology Unit, Department of Pediatrics, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | - Carolina Constant
- Paediatric Pulmonology Unit, Department of Pediatrics, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
| | | | - Eddie M K Chung
- Population, Policy and Practice, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Priti Kenia
- Department of Respiratory Paediatrics, Birmingham Women's and Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Nisreen Rumman
- Pediatrics Department, Makassed Hospital, East Jerusalem, Israel
| | - Nader Fasseeh
- Department of Pediatrics, Faculty of Medicine, Alexandria University Children's Hospital, Alexandria, Egypt
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Claire Hogg
- PCD Diagnostic Team and Department of Pediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
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Watson CM, Dean P, Camm N, Bates J, Carr IM, Gardiner CA, Bonthron DT. Long-read nanopore sequencing resolves a TMEM231 gene conversion event causing Meckel-Gruber syndrome. Hum Mutat 2019; 41:525-531. [PMID: 31663672 DOI: 10.1002/humu.23940] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/12/2019] [Accepted: 10/28/2019] [Indexed: 12/30/2022]
Abstract
The diagnostic deployment of massively parallel short-read next-generation sequencing (NGS) has greatly improved genetic test availability, speed, and diagnostic yield, particularly for rare inherited disorders. Nonetheless, diagnostic approaches based on short-read sequencing have a poor ability to accurately detect gene conversion events. We report on the genetic analysis of a family in which 3 fetuses had clinical features consistent with the autosomal recessive disorder Meckel-Gruber syndrome (MKS). Targeted NGS of 29 known MKS-associated genes revealed a heterozygous TMEM231 splice donor variant c.929+1A>G. Comparative read-depth analysis, performed to identify a second pathogenic allele, revealed an apparent heterozygous deletion of TMEM231 exon 4. To verify this result we performed single-molecule long-read sequencing of a long-range polymerase chain reaction product spanning this locus. We identified four missense variants that were absent from the short-read dataset due to the preferential mapping of variant-containing reads to a downstream TMEM231 pseudogene. Consistent with the parental segregation analysis, we demonstrate that the single-molecule long reads could be used to show that the variants are arranged in trans. Our experience shows that robust validation of apparent dosage variants remains essential to avoid the pitfalls of short-read sequencing and that new third-generation long-read sequencing technologies can already aid routine clinical care.
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Affiliation(s)
- Christopher M Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK.,Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, UK
| | - Philip Dean
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK
| | - Nick Camm
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK
| | - Jennifer Bates
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK
| | - Ian M Carr
- Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, UK
| | - Carol A Gardiner
- West of Scotland Regional Genetics Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - David T Bonthron
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK.,Leeds Institute of Medical Research, St. James's University Hospital, University of Leeds, Leeds, UK
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28
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Prest PJ, Justice J, Bell N, McCarroll R, Watson CM. A Volume-Based Feeding Protocol Improves Nutrient Delivery and Glycemic Control in a Surgical Trauma Intensive Care Unit. JPEN J Parenter Enteral Nutr 2019; 44:880-888. [PMID: 31529520 DOI: 10.1002/jpen.1712] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/11/2019] [Accepted: 08/29/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Inadequate delivery of nutrition in critically ill patients has been shown to have adverse outcomes. A surgical trauma intensive care unit provides unique challenges to enteral feeds. Although volume-based feeding protocols, like Enhanced Protein-Energy Provision via the Enteral Route Feeding Protocol (PEP uP), have been successfully used in medical intensive care patients, data are sparse on its safety and efficacy in a surgical intensive care unit population. METHODS A PEP uP protocol was recently initiated at our American College of Surgeons Level 1 verified trauma center. Medical records of 197 patients before this change (pre-PEP uP) were compared with 295 patients after this change (post-PEP uP). RESULTS The post-PEP uP group met/exceeded energy goals (defined as 80% of target) more often (57.0% compared with 26.9%, P-value < .001), with an adjusted odds ratio (OR) of 4.98 (95% CI 3.49-7.10), and more often met/exceeded protein goals (57.4% compared with 18.6%, P-value < .001), with an adjusted OR of 11.84 (95% CI 7.94-17.64). There was no significant difference in emesis during this time. Additionally, patients in the post-PEP uP arm had less episodes of hyperglycemia (9% compared with 14.4%, P-value < .001). CONCLUSIONS Volume-based feeding protocols like PEP uP are safe in critically ill trauma patients and are more effective at delivering energy and protein while limiting hyperglycemic episodes when compared with a traditional delivery method.
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Affiliation(s)
- Phillip J Prest
- Palmetto Health-University of South Carolina Medical Group, Columbia, South Carolina, USA.,The University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Jessica Justice
- Palmetto Health-University of South Carolina Medical Group, Columbia, South Carolina, USA
| | - Nathanial Bell
- The University of South Carolina College of Nursing, Columbia, South Carolina, USA
| | - Richard McCarroll
- Palmetto Health-University of South Carolina Medical Group, Columbia, South Carolina, USA.,The University of South Carolina School of Medicine, Columbia, South Carolina, USA
| | - Christopher M Watson
- Palmetto Health-University of South Carolina Medical Group, Columbia, South Carolina, USA.,The University of South Carolina School of Medicine, Columbia, South Carolina, USA
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29
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Walker L, Watson CM, Hewitt S, Crinnion LA, Bonthron DT, Cohen KE. An alternative to array-based diagnostics: a prospectively recruited cohort, comparing arrayCGH to next-generation sequencing to evaluate foetal structural abnormalities. J OBSTET GYNAECOL 2019; 39:328-334. [PMID: 30714504 DOI: 10.1080/01443615.2018.1522529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Molecular diagnostic investigations, following the identification of foetal abnormalities, are routinely performed using array comparative genomic hybridisation (aCGH). Despite the utility of this technique, contemporary approaches for the detection of copy number variation are typically based on next-generation sequencing (NGS). We sought to compare an in-house NGS-based workflow (CNVseq) with aCGH, for invasively obtained foetal samples from pregnancies complicated by foetal structural abnormality. DNA from 40 foetuses was screened using both 8 × 60 K aCGH oligoarrays and low-coverage whole genome sequencing. Sequencer-compatible libraries were combined in a ten-sample multiplex and sequenced using an Illumina HiSeq2500. The mean resolution of CNVseq was 29 kb, compared to 60 kb for aCGH analyses. Four clinically significant, concordant, copy number imbalances were detected using both techniques, however, genomic breakpoints were more precisely defined by CNVseq. This data indicates CNVseq is a robust and sensitive alternative to aCGH, for the prenatal investigation of foetuses with structural abnormalities. Impact statement What is already known about this subject? Copy number variant analysis using next-generation sequencing has been successfully applied to investigations of tumour specimens and patients with developmental delays. The application of our approach, to a prospective prenatal diagnosis cohort, has not hitherto been assessed. What do the results of this study add? Next-generation sequencing has a comparable turnaround time and assay sensitivity to copy number variant analysis performed using array CGH. We demonstrate that having established a next-generation sequencing facility, high-throughput CNVseq sample processing and analysis can be undertaken within the framework of a regional diagnostic service. What are the implications of these findings for clinical practice and/or further research? Array CGH is a legacy technology which is likely to be superseded by low-coverage whole genome sequencing, for the detection of copy number variants, in the prenatal diagnosis of structural abnormalities.
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Affiliation(s)
- Lesley Walker
- a Department of Fetal Medicine , Leeds General Infirmary , Leeds , United Kingdom
| | - Christopher M Watson
- b Yorkshire Regional Genetics Service , St. James's University Hospital , Leeds , United Kingdom.,c School of Medicine , University of Leeds, St. James's University Hospital , Leeds , United Kingdom
| | - Sarah Hewitt
- b Yorkshire Regional Genetics Service , St. James's University Hospital , Leeds , United Kingdom
| | - Laura A Crinnion
- b Yorkshire Regional Genetics Service , St. James's University Hospital , Leeds , United Kingdom.,c School of Medicine , University of Leeds, St. James's University Hospital , Leeds , United Kingdom
| | - David T Bonthron
- b Yorkshire Regional Genetics Service , St. James's University Hospital , Leeds , United Kingdom.,c School of Medicine , University of Leeds, St. James's University Hospital , Leeds , United Kingdom
| | - Kelly E Cohen
- a Department of Fetal Medicine , Leeds General Infirmary , Leeds , United Kingdom
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30
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Hartill VL, van de Hoek G, Patel MP, Little R, Watson CM, Berry IR, Shoemark A, Abdelmottaleb D, Parkes E, Bacchelli C, Szymanska K, Knoers NV, Scambler PJ, Ueffing M, Boldt K, Yates R, Winyard PJ, Adler B, Moya E, Hattingh L, Shenoy A, Hogg C, Sheridan E, Roepman R, Norris D, Mitchison HM, Giles RH, Johnson CA. DNAAF1 links heart laterality with the AAA+ ATPase RUVBL1 and ciliary intraflagellar transport. Hum Mol Genet 2019; 27:529-545. [PMID: 29228333 PMCID: PMC5886296 DOI: 10.1093/hmg/ddx422] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/01/2017] [Indexed: 01/11/2023] Open
Abstract
DNAAF1 (LRRC50) is a cytoplasmic protein required for dynein heavy chain assembly and cilia motility, and DNAAF1 mutations cause primary ciliary dyskinesia (PCD; MIM 613193). We describe four families with DNAAF1 mutations and complex congenital heart disease (CHD). In three families, all affected individuals have typical PCD phenotypes. However, an additional family demonstrates isolated CHD (heterotaxy) in two affected siblings, but no clinical evidence of PCD. We identified a homozygous DNAAF1 missense mutation, p.Leu191Phe, as causative for heterotaxy in this family. Genetic complementation in dnaaf1-null zebrafish embryos demonstrated the rescue of normal heart looping with wild-type human DNAAF1, but not the p.Leu191Phe variant, supporting the conserved pathogenicity of this DNAAF1 missense mutation. This observation points to a phenotypic continuum between CHD and PCD, providing new insights into the pathogenesis of isolated CHD. In further investigations of the function of DNAAF1 in dynein arm assembly, we identified interactions with members of a putative dynein arm assembly complex. These include the ciliary intraflagellar transport protein IFT88 and the AAA+ (ATPases Associated with various cellular Activities) family proteins RUVBL1 (Pontin) and RUVBL2 (Reptin). Co-localization studies support these findings, with the loss of RUVBL1 perturbing the co-localization of DNAAF1 with IFT88. We show that RUVBL1 orthologues have an asymmetric left-sided distribution at both the mouse embryonic node and the Kupffer's vesicle in zebrafish embryos, with the latter asymmetry dependent on DNAAF1. These results suggest that DNAAF1-RUVBL1 biochemical and genetic interactions have a novel functional role in symmetry breaking and cardiac development.
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Affiliation(s)
- Verity L Hartill
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Glenn van de Hoek
- Department of Nephrology and Hypertension.,Department of Medical Genetics, University Medical Center, Utrecht, 3508 GA, The Netherlands
| | - Mitali P Patel
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Rosie Little
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Christopher M Watson
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - Ian R Berry
- Leeds Genetics Laboratory, Leeds Teaching Hospitals NHS Trust, Leeds LS9 7TF, UK
| | - Amelia Shoemark
- PCD Diagnostic Team and Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK.,School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Dina Abdelmottaleb
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK.,Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Emma Parkes
- Manchester Royal Infirmary, Manchester M13 9WL, UK
| | - Chiara Bacchelli
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Katarzyna Szymanska
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Nine V Knoers
- Department of Medical Genetics, University Medical Center, Utrecht, 3508 GA, The Netherlands
| | - Peter J Scambler
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK.,Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Marius Ueffing
- Department for Ophthalmology, Institute for Ophthalmic Research and Medical Bioanalytics Core, University of Tübingen, 72074 Tübingen, Germany
| | - Karsten Boldt
- Department for Ophthalmology, Institute for Ophthalmic Research and Medical Bioanalytics Core, University of Tübingen, 72074 Tübingen, Germany
| | - Robert Yates
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK.,Paediatric Cardiology Department, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Paul J Winyard
- Developmental Biology and Cancer Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Beryl Adler
- Department of Paediatrics, Luton and Dunstable Hospital NHS Trust, Luton LU4 0DZ, UK
| | - Eduardo Moya
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Louise Hattingh
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Anil Shenoy
- Department of Paediatrics, Bradford Teaching Hospitals NHS Trust, Bradford BD9 6RJ, UK
| | - Claire Hogg
- PCD Diagnostic Team and Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London SW3 6NP, UK
| | - Eamonn Sheridan
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, 6500HB Nijmegen, The Netherlands
| | - Dominic Norris
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Programme, UCL Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | | | - Colin A Johnson
- Leeds Institute of Biomedical and Clinical Sciences, Faculty of Medicine & Health, University of Leeds, Leeds LS9 7TF, UK
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Bonnefoy S, Watson CM, Kernohan KD, Lemos M, Hutchinson S, Poulter JA, Crinnion LA, Berry I, Simmonds J, Vasudevan P, O'Callaghan C, Hirst RA, Rutman A, Huang L, Hartley T, Grynspan D, Moya E, Li C, Carr IM, Bonthron DT, Leroux M, Boycott KM, Bastin P, Sheridan EG. Biallelic Mutations in LRRC56, Encoding a Protein Associated with Intraflagellar Transport, Cause Mucociliary Clearance and Laterality Defects. Am J Hum Genet 2018; 103:727-739. [PMID: 30388400 PMCID: PMC6218757 DOI: 10.1016/j.ajhg.2018.10.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023] Open
Abstract
Primary defects in motile cilia result in dysfunction of the apparatus responsible for generating fluid flows. Defects in these mechanisms underlie disorders characterized by poor mucus clearance, resulting in susceptibility to chronic recurrent respiratory infections, often associated with infertility; laterality defects occur in about 50% of such individuals. Here we report biallelic variants in LRRC56 (known as oda8 in Chlamydomonas) identified in three unrelated families. The phenotype comprises laterality defects and chronic pulmonary infections. High-speed video microscopy of cultured epithelial cells from an affected individual showed severely dyskinetic cilia but no obvious ultra-structural abnormalities on routine transmission electron microscopy (TEM). Further investigation revealed that LRRC56 interacts with the intraflagellar transport (IFT) protein IFT88. The link with IFT was interrogated in Trypanosoma brucei. In this protist, LRRC56 is recruited to the cilium during axoneme construction, where it co-localizes with IFT trains and is required for the addition of dynein arms to the distal end of the flagellum. In T. brucei carrying LRRC56-null mutations, or a variant resulting in the p.Leu259Pro substitution corresponding to the p.Leu140Pro variant seen in one of the affected families, we observed abnormal ciliary beat patterns and an absence of outer dynein arms restricted to the distal portion of the axoneme. Together, our findings confirm that deleterious variants in LRRC56 result in a human disease and suggest that this protein has a likely role in dynein transport during cilia assembly that is evolutionarily important for cilia motility.
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Affiliation(s)
- Serge Bonnefoy
- Trypanosome Cell Biology Unit & INSERM U1201, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France
| | - Christopher M Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Kristin D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Moara Lemos
- Trypanosome Cell Biology Unit & INSERM U1201, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France
| | - Sebastian Hutchinson
- Trypanosome Cell Biology Unit & INSERM U1201, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France
| | - James A Poulter
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Laura A Crinnion
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Ian Berry
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Jennifer Simmonds
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Pradeep Vasudevan
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester LE2 7LX, UK
| | - Chris O'Callaghan
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester LE2 7LX, UK; Respiratory, Critical Care & Anaesthesia, Institute of Child Health, University College London & Great Ormond Street Children's Hospital, 30 Guilford Street, London WC1N 1EH, UK
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester LE2 7LX, UK
| | - Andrew Rutman
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester LE2 7LX, UK
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - David Grynspan
- Department of Pathology, Children's Hospital of Eastern Ontario, 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | - Eduardo Moya
- Bradford Royal Infirmary, Bradford, West Yorkshire BD9 6R, UK
| | - Chunmei Li
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Ian M Carr
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - David T Bonthron
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK
| | - Michel Leroux
- Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON K1H 8L1, Canada
| | - Philippe Bastin
- Trypanosome Cell Biology Unit & INSERM U1201, Institut Pasteur, 25, rue du Docteur Roux, 75015 Paris, France.
| | - Eamonn G Sheridan
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds LS9 7TF, UK; School of Medicine, University of Leeds, St. James's University Hospital, Leeds LS9 7TF, UK.
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Phillips JB, Mohorn PL, Bookstaver RE, Ezekiel TO, Watson CM. Hemostatic Management of Trauma-Induced Coagulopathy. Crit Care Nurse 2018; 37:37-47. [PMID: 28765353 DOI: 10.4037/ccn2017476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Trauma-induced coagulopathy is a primary factor in many trauma-related fatalities. Management hinges upon rapid diagnosis of coagulation abnormalities and immediate administration of appropriate hemostatic agents. Use of crystalloids and packed red blood cells has traditionally been the core of trauma resuscitation, but current massive transfusion protocols include combination therapy with fresh frozen plasma and predefined ratios of platelets to packed red blood cells, limiting crystalloid administration. Hemostatic agents such as tranexamic acid, prothrombin complex concentrate, fibrinogen concentrate, and, in cases of refractory bleeding, recombinant activated factor VIIa may also be warranted. Goal-directed resuscitation using viscoelastic tools allows specific component-centered therapy based on individual clotting abnormalities that may limit blood product use and thromboembolic risks and may lead to reduced mortality. Because of the complex management of patients with trauma-induced coagulopathy, critical care nurses must be familiar with the pathophysiology, acute diagnostics, and pharmacotherapeutic options used to treat these patients.
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Affiliation(s)
- Janise B Phillips
- Janise B. Phillips is a critical care pharmacotherapy specialist, Department of Pharmacy Services, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Phillip L. Mohorn is a critical care clinical pharmacy specialist, Department of Pharmacy, Spartanburg Medical Center, Spartanburg Regional Healthcare System, Spartanburg, South Carolina.,Rebecca E. Bookstaver is a critical care clinical pharmacist, Department of Pharmacy, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina.,Tanya O. Ezekiel is a clinical informatics pharmacist, Department of Pharmaceutical Services and Clinical Nutrition, Palmetto Health Richland, Columbia, South Carolina.,Christopher M. Watson is chief of surgery, medical director of the surgical-trauma ICU and surgical step down unit, and program director of the surgical critical care fellowship, Division of Trauma, Acute Care Surgery, and Surgical Critical Care, Palmetto Health Richland and the University of South Carolina School of Medicine, Columbia, South Carolina
| | - Phillip L Mohorn
- Janise B. Phillips is a critical care pharmacotherapy specialist, Department of Pharmacy Services, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates. .,Phillip L. Mohorn is a critical care clinical pharmacy specialist, Department of Pharmacy, Spartanburg Medical Center, Spartanburg Regional Healthcare System, Spartanburg, South Carolina. .,Rebecca E. Bookstaver is a critical care clinical pharmacist, Department of Pharmacy, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina. .,Tanya O. Ezekiel is a clinical informatics pharmacist, Department of Pharmaceutical Services and Clinical Nutrition, Palmetto Health Richland, Columbia, South Carolina. .,Christopher M. Watson is chief of surgery, medical director of the surgical-trauma ICU and surgical step down unit, and program director of the surgical critical care fellowship, Division of Trauma, Acute Care Surgery, and Surgical Critical Care, Palmetto Health Richland and the University of South Carolina School of Medicine, Columbia, South Carolina.
| | - Rebecca E Bookstaver
- Janise B. Phillips is a critical care pharmacotherapy specialist, Department of Pharmacy Services, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Phillip L. Mohorn is a critical care clinical pharmacy specialist, Department of Pharmacy, Spartanburg Medical Center, Spartanburg Regional Healthcare System, Spartanburg, South Carolina.,Rebecca E. Bookstaver is a critical care clinical pharmacist, Department of Pharmacy, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina.,Tanya O. Ezekiel is a clinical informatics pharmacist, Department of Pharmaceutical Services and Clinical Nutrition, Palmetto Health Richland, Columbia, South Carolina.,Christopher M. Watson is chief of surgery, medical director of the surgical-trauma ICU and surgical step down unit, and program director of the surgical critical care fellowship, Division of Trauma, Acute Care Surgery, and Surgical Critical Care, Palmetto Health Richland and the University of South Carolina School of Medicine, Columbia, South Carolina
| | - Tanya O Ezekiel
- Janise B. Phillips is a critical care pharmacotherapy specialist, Department of Pharmacy Services, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Phillip L. Mohorn is a critical care clinical pharmacy specialist, Department of Pharmacy, Spartanburg Medical Center, Spartanburg Regional Healthcare System, Spartanburg, South Carolina.,Rebecca E. Bookstaver is a critical care clinical pharmacist, Department of Pharmacy, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina.,Tanya O. Ezekiel is a clinical informatics pharmacist, Department of Pharmaceutical Services and Clinical Nutrition, Palmetto Health Richland, Columbia, South Carolina.,Christopher M. Watson is chief of surgery, medical director of the surgical-trauma ICU and surgical step down unit, and program director of the surgical critical care fellowship, Division of Trauma, Acute Care Surgery, and Surgical Critical Care, Palmetto Health Richland and the University of South Carolina School of Medicine, Columbia, South Carolina
| | - Christopher M Watson
- Janise B. Phillips is a critical care pharmacotherapy specialist, Department of Pharmacy Services, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Phillip L. Mohorn is a critical care clinical pharmacy specialist, Department of Pharmacy, Spartanburg Medical Center, Spartanburg Regional Healthcare System, Spartanburg, South Carolina.,Rebecca E. Bookstaver is a critical care clinical pharmacist, Department of Pharmacy, Wake Forest Baptist Medical Center, Winston-Salem, North Carolina.,Tanya O. Ezekiel is a clinical informatics pharmacist, Department of Pharmaceutical Services and Clinical Nutrition, Palmetto Health Richland, Columbia, South Carolina.,Christopher M. Watson is chief of surgery, medical director of the surgical-trauma ICU and surgical step down unit, and program director of the surgical critical care fellowship, Division of Trauma, Acute Care Surgery, and Surgical Critical Care, Palmetto Health Richland and the University of South Carolina School of Medicine, Columbia, South Carolina
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33
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Elwood NR, Guidry CA, Duane TM, Cuschieri J, Cook CH, O'Neill PJ, Askari R, Napolitano LM, Namias N, Dellinger EP, Watson CM, Banton KL, Blake DP, Hassinger TE, Sawyer RG. Short-Course Antimicrobial Therapy Does Not Increase Treatment Failure Rate in Patients with Intra-Abdominal Infection Involving Fungal Organisms. Surg Infect (Larchmt) 2018; 19:376-381. [DOI: 10.1089/sur.2017.235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Nathan R. Elwood
- Department of Surgery, The University of Virginia Health System, Charlottesville, Virginia
| | | | - Therese M. Duane
- Department of Surgery, University of North Texas John Peter Smith Hospital, Fort Worth, Texas
| | - Joseph Cuschieri
- Department of Surgery, University of Washington, Seattle, Washington
| | - Charles H. Cook
- Department of Surgery, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | - Reza Askari
- Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Nicholas Namias
- Department of Surgery, University of Miami Miller School of Medicine, Miami, Florida
| | | | | | - Kaysie L. Banton
- Department of Surgery, Univeristy of Minnesota Medical School, Minneapolis, Minnesota
| | | | - Taryn E. Hassinger
- Department of Surgery, The University of Virginia Health System, Charlottesville, Virginia
| | - Robert G. Sawyer
- Department of Surgery, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, Michigan
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34
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Watson CM, Camm N, Crinnion LA, Clokie S, Robinson RL, Adlard J, Charlton R, Markham AF, Carr IM, Bonthron DT. Increased Sensitivity of Diagnostic Mutation Detection by Re-analysis Incorporating Local Reassembly of Sequence Reads. Mol Diagn Ther 2017; 21:685-692. [DOI: 10.1007/s40291-017-0304-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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35
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Battle SE, Augustine MR, Bookstaver PB, Watson CM, Owens W, Kohn J, Baddour LM, Al-Hasan MN. A Simplified Pitt Bacteremia Score (qPitt) to Predict Mortality in Patients with Gram-negative Bloodstream Infection. Open Forum Infect Dis 2017. [DOI: 10.1093/ofid/ofx163.1445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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36
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Antanaviciute A, Baquero-Perez B, Watson CM, Harrison SM, Lascelles C, Crinnion L, Markham AF, Bonthron DT, Whitehouse A, Carr IM. m6aViewer: software for the detection, analysis, and visualization of N6-methyladenosine peaks from m 6A-seq/ME-RIP sequencing data. RNA 2017; 23:1493-1501. [PMID: 28724534 PMCID: PMC5602108 DOI: 10.1261/rna.058206.116] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 07/07/2017] [Indexed: 05/29/2023]
Abstract
Recent methods for transcriptome-wide N6-methyladenosine (m6A) profiling have facilitated investigations into the RNA methylome and established m6A as a dynamic modification that has critical regulatory roles in gene expression and may play a role in human disease. However, bioinformatics resources available for the analysis of m6A sequencing data are still limited. Here, we describe m6aViewer-a cross-platform application for analysis and visualization of m6A peaks from sequencing data. m6aViewer implements a novel m6A peak-calling algorithm that identifies high-confidence methylated residues with more precision than previously described approaches. The application enables data analysis through a graphical user interface, and thus, in contrast to other currently available tools, does not require the user to be skilled in computer programming. m6aViewer and test data can be downloaded here: http://dna2.leeds.ac.uk/m6a.
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Affiliation(s)
- Agne Antanaviciute
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Belinda Baquero-Perez
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Christopher M Watson
- Yorkshire Regional Genetics Service, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Sally M Harrison
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Carolina Lascelles
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Laura Crinnion
- Yorkshire Regional Genetics Service, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Alexander F Markham
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - David T Bonthron
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James's University Hospital, Leeds LS9 7TF, United Kingdom
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ian M Carr
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds, St James's University Hospital, Leeds LS9 7TF, United Kingdom
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37
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Watson CM, Camm N, Crinnion LA, Antanaviciute A, Adlard J, Markham AF, Carr IM, Charlton R, Bonthron DT. Characterization and Genomic Localization of a SMAD4 Processed Pseudogene. J Mol Diagn 2017; 19:933-940. [PMID: 28867604 DOI: 10.1016/j.jmoldx.2017.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/16/2017] [Indexed: 12/30/2022] Open
Abstract
Like many clinical diagnostic laboratories, the Yorkshire Regional Genetics Service undertakes routine investigation of cancer-predisposed individuals by high-throughput sequencing of patient DNA that has been target-enriched for genes associated with hereditary cancer. Accurate diagnosis using such reagents requires alertness regarding rare nonpathogenic variants that may interfere with variant calling. In a cohort of 2042 such cases, we identified 5 that initially appeared to be carriers of a 95-bp deletion of SMAD4 intron 6. More detailed analysis indicated that these individuals all carried one copy of a SMAD4 processed gene. Because of its interference with diagnostic analysis, we characterized this processed gene in detail. Whole-genome sequencing and confirmatory Sanger sequencing of junction PCR products were used to show that in each of the 5 cases, the SMAD4 processed gene was integrated at the same position on chromosome 9, located within the last intron of the SCAI gene. This rare polymorphic processed gene therefore reflects the occurrence of a single ancestral retrotransposition event. Compared to the reference SMAD4 mRNA sequence NM_005359.5 (https://www.ncbi.nlm.nih.gov/nucleotide), the 5' and 3' untranslated regions of the processed gene are both truncated, but its open reading frame is unaltered. Our experience leads us to advocate the use of an RNA-seq aligner as part of diagnostic assay quality assurance, since this allows recognition of processed pseudogenes in a comparatively facile automated fashion.
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Affiliation(s)
- Christopher M Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom; MRC Medical Bioinformatics Centre, Leeds Institute for Data Analytics, St. James's University Hospital, Leeds, United Kingdom; MRC Single Cell Functional Genomics Centre, University of Leeds, St. James's University Hospital, Leeds, United Kingdom.
| | - Nick Camm
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Laura A Crinnion
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom; MRC Medical Bioinformatics Centre, Leeds Institute for Data Analytics, St. James's University Hospital, Leeds, United Kingdom; MRC Single Cell Functional Genomics Centre, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
| | - Agne Antanaviciute
- MRC Medical Bioinformatics Centre, Leeds Institute for Data Analytics, St. James's University Hospital, Leeds, United Kingdom
| | - Julian Adlard
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Alexander F Markham
- MRC Medical Bioinformatics Centre, Leeds Institute for Data Analytics, St. James's University Hospital, Leeds, United Kingdom
| | - Ian M Carr
- MRC Medical Bioinformatics Centre, Leeds Institute for Data Analytics, St. James's University Hospital, Leeds, United Kingdom; MRC Single Cell Functional Genomics Centre, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
| | - Ruth Charlton
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - David T Bonthron
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom; MRC Medical Bioinformatics Centre, Leeds Institute for Data Analytics, St. James's University Hospital, Leeds, United Kingdom; MRC Single Cell Functional Genomics Centre, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
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38
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Shoemark A, Moya E, Hirst RA, Patel MP, Robson EA, Hayward J, Scully J, Fassad MR, Lamb W, Schmidts M, Dixon M, Patel-King RS, Rogers AV, Rutman A, Jackson CL, Goggin P, Rubbo B, Ollosson S, Carr S, Walker W, Adler B, Loebinger MR, Wilson R, Bush A, Williams H, Boustred C, Jenkins L, Sheridan E, Chung EMK, Watson CM, Cullup T, Lucas JS, Kenia P, O'Callaghan C, King SM, Hogg C, Mitchison HM. High prevalence of CCDC103 p.His154Pro mutation causing primary ciliary dyskinesia disrupts protein oligomerisation and is associated with normal diagnostic investigations. Thorax 2017; 73:157-166. [PMID: 28790179 DOI: 10.1136/thoraxjnl-2017-209999] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 06/07/2017] [Accepted: 07/03/2017] [Indexed: 11/03/2022]
Abstract
RATIONALE Primary ciliary dyskinesia is a genetically heterogeneous inherited condition characterised by progressive lung disease arising from abnormal cilia function. Approximately half of patients have situs inversus. The estimated prevalence of primary ciliary dyskinesia in the UK South Asian population is 1:2265. Early, accurate diagnosis is key to implementing appropriate management but clinical diagnostic tests can be equivocal. OBJECTIVES To determine the importance of genetic screening for primary ciliary dyskinesia in a UK South Asian population with a typical clinical phenotype, where standard testing is inconclusive. METHODS Next-generation sequencing was used to screen 86 South Asian patients who had a clinical history consistent with primary ciliary dyskinesia. The effect of a CCDC103 p.His154Pro missense variant compared with other dynein arm-associated gene mutations on diagnostic/phenotypic variability was tested. CCDC103 p.His154Pro variant pathogenicity was assessed by oligomerisation assay. RESULTS Sixteen of 86 (19%) patients carried a homozygous CCDC103 p.His154Pro mutation which was found to disrupt protein oligomerisation. Variable diagnostic test results were obtained including normal nasal nitric oxide levels, normal ciliary beat pattern and frequency and a spectrum of partial and normal dynein arm retention. Fifteen (94%) patients or their sibling(s) had situs inversus suggesting CCDC103 p.His154Pro patients without situs inversus are missed. CONCLUSIONS The CCDC103 p.His154Pro mutation is more prevalent than previously thought in the South Asian community and causes primary ciliary dyskinesia that can be difficult to diagnose using pathology-based clinical tests. Genetic testing is critical when there is a strong clinical phenotype with inconclusive standard diagnostic tests.
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Affiliation(s)
- Amelia Shoemark
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, National Heart and Lung Institute, London, UK
| | - Eduardo Moya
- Division of Services for Women and Children, Women's and Newborn Unit Bradford Royal Infirmary, University of Bradford, Bradford, UK
| | - Robert A Hirst
- Department of Infection, Centre for PCD Diagnosis and Research, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Mitali P Patel
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Evelyn A Robson
- Division of Services for Women and Children, Women's and Newborn Unit Bradford Royal Infirmary, University of Bradford, Bradford, UK
| | - Jane Hayward
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, UK.,North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, London, UK
| | - Juliet Scully
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, UK.,Neuroscience and Mental Health Research Institute, School of Medicine and School of Bioscience, Cardiff University, London, UK
| | - Mahmoud R Fassad
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, UK.,Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - William Lamb
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Miriam Schmidts
- Genome Research Division, Human Genetics Department, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.,Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University of Freiburg Medical Center, Freiburg, Germany
| | - Mellisa Dixon
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, National Heart and Lung Institute, London, UK
| | - Ramila S Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Andrew V Rogers
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, National Heart and Lung Institute, London, UK.,Department of Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London, UK
| | - Andrew Rutman
- Department of Infection, Centre for PCD Diagnosis and Research, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Claire L Jackson
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Respiratory Biomedical Research Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Patricia Goggin
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Respiratory Biomedical Research Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Bruna Rubbo
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Respiratory Biomedical Research Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Sarah Ollosson
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, National Heart and Lung Institute, London, UK
| | - Siobhán Carr
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, National Heart and Lung Institute, London, UK
| | - Woolf Walker
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Respiratory Biomedical Research Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Beryl Adler
- Department of Paediatrics, Luton and Dunstable Hospital NHS Trust, Luton, UK
| | - Michael R Loebinger
- Department of Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London, UK
| | - Robert Wilson
- Department of Respiratory Medicine, Royal Brompton and Harefield NHS Trust, London, UK
| | - Andrew Bush
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, National Heart and Lung Institute, London, UK.,Department of Paediatric Respiratory Medicine, National Heart and Lung Institute, Imperial College, London, UK
| | - Hywel Williams
- Centre for Translational Omics-GOSgene, Genetics and Genomic Medicine, University College London, Institute of Child Health, London, UK
| | - Christopher Boustred
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, London, UK
| | - Lucy Jenkins
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, London, UK
| | - Eamonn Sheridan
- Yorkshire Regional Genetics Service and School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Eddie M K Chung
- Population, Policy and Practice Programme, University College London, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Christopher M Watson
- Yorkshire Regional Genetics Service and School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Thomas Cullup
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, London, UK
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, University Hospital Southampton NHS Foundation Trust and Clinical and Experimental Sciences Academic Unit, University of Southampton Faculty of Medicine, Southampton, UK.,NIHR Southampton Respiratory Biomedical Research Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Priti Kenia
- Department of Respiratory Paediatrics, Birmingham Children's Hospital NHS Foundation Trust, Birmingham, UK
| | - Christopher O'Callaghan
- Department of Infection, Centre for PCD Diagnosis and Research, Immunity and Inflammation, University of Leicester, Leicester, UK.,Infection, Immunity, Inflammation and Physiological Medicine, University College London, Institute of Child Health, London, UK
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Claire Hogg
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Trust, National Heart and Lung Institute, London, UK
| | - Hannah M Mitchison
- Genetics and Genomic Medicine, University College London, UCL Great Ormond Street Institute of Child Health, London, UK
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Parrish A, Caswell R, Jones G, Watson CM, Crinnion LA, Ellard S. An enhanced method for targeted next generation sequencing copy number variant detection using ExomeDepth. Wellcome Open Res 2017. [DOI: 10.12688/wellcomeopenres.11548.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Copy number variants (CNV) are a major cause of disease, with over 30,000 reported in the DECIPHER database. To use read depth data from targeted Next Generation Sequencing (NGS) panels to identify CNVs with the highest degree of sensitivity, it is necessary to account for biases inherent in the data. GC content and ambiguous mapping due to repetitive sequence elements and pseudogenes are the principal components of technical variability. In addition, the algorithms used favour the detection of multi-exon CNVs, and rely on suitably matched normal dosage samples for comparison. We developed a calling strategy that subdivides target intervals, and uses pools of historical control samples to overcome these limitations in a clinical diagnostic laboratory. We compared our enhanced strategy with an unmodified pipeline using the R software package ExomeDepth, using a cohort of 109 heterozygous CNVs (91 deletions, 18 duplications in 26 genes), including 25 single exon CNVs. The unmodified pipeline detected 104/109 CNVs, giving a sensitivity of 89.62% to 98.49% at the 95% confidence interval. The detection of all 109 CNVs by our enhanced method demonstrates 95% confidence the sensitivity is ≥96.67%, allowing NGS read depth analysis to be used for CNV detection in a clinical diagnostic setting.
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Diggle CP, Martinez-Garay I, Molnar Z, Brinkworth MH, White E, Fowler E, Hughes R, Hayward BE, Carr IM, Watson CM, Crinnion L, Asipu A, Woodman B, Coletta PL, Markham AF, Dear TN, Bonthron DT, Peckham M, Morrison EE, Sheridan E. A tubulin alpha 8 mouse knockout model indicates a likely role in spermatogenesis but not in brain development. PLoS One 2017; 12:e0174264. [PMID: 28388629 PMCID: PMC5384676 DOI: 10.1371/journal.pone.0174264] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 03/05/2017] [Indexed: 11/19/2022] Open
Abstract
Tubulin alpha 8 (Tuba8) is the most divergent member of the highly conserved alpha tubulin family, and uniquely lacks two key post-translational modification sites. It is abundantly expressed in testis and muscle, with lower levels in the brain. We previously identified homozygous hypomorphic TUBA8 mutations in human subjects with a polymicrogyria (PMG) syndrome, suggesting its involvement in development of the cerebral cortex. We have now generated and characterized a Tuba8 knockout mouse model. Homozygous mice were confirmed to lack Tuba8 protein in the testis, but did not display PMG and appeared to be neurologically normal. In response to this finding, we re-analyzed the human PMG subjects using whole exome sequencing. This resulted in identification of an additional homozygous loss-of-function mutation in SNAP29, suggesting that SNAP29 deficiency, rather than TUBA8 deficiency, may underlie most or all of the neurodevelopmental anomalies in these subjects. Nonetheless, in the mouse brain, Tuba8 specifically localised to the cerebellar Purkinje cells, suggesting that the human mutations may affect or modify motor control. In the testis, Tuba8 localisation was cell-type specific. It was restricted to spermiogenesis with a strong acrosomal localization that was gradually replaced by cytoplasmic distribution and was absent from spermatozoa. Although the knockout mice were fertile, the localisation pattern indicated that Tuba8 may have a role in spermatid development during spermatogenesis, rather than as a component of the mature microtubule-rich flagellum itself.
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Affiliation(s)
- Christine P. Diggle
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
- * E-mail:
| | - Isabel Martinez-Garay
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Zoltan Molnar
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Ed White
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Ewan Fowler
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Ruth Hughes
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Bruce E. Hayward
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Ian M. Carr
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Christopher M. Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Laura Crinnion
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom
| | - Aruna Asipu
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Ben Woodman
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - P. Louise Coletta
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Alexander F. Markham
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - T. Neil Dear
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - David T. Bonthron
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Ewan E. Morrison
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Eamonn Sheridan
- School of Medicine, St James's University Hospital, University of Leeds, Leeds, United Kingdom
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41
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Watson CM, Crinnion LA, Harrison SM, Lascelles C, Antanaviciute A, Carr IM, Bonthron DT, Sheridan E. A Chromosome 7 Pericentric Inversion Defined at Single-Nucleotide Resolution Using Diagnostic Whole Genome Sequencing in a Patient with Hand-Foot-Genital Syndrome. PLoS One 2016; 11:e0157075. [PMID: 27272187 PMCID: PMC4896502 DOI: 10.1371/journal.pone.0157075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 05/21/2016] [Indexed: 11/18/2022] Open
Abstract
Next generation sequencing methodologies are facilitating the rapid characterisation of novel structural variants at nucleotide resolution. These approaches are particularly applicable to variants initially identified using alternative molecular methods. We report a child born with bilateral postaxial syndactyly of the feet and bilateral fifth finger clinodactyly. This was presumed to be an autosomal recessive syndrome, due to the family history of consanguinity. Karyotype analysis revealed a homozygous pericentric inversion of chromosome 7 (46,XX,inv(7)(p15q21)x2) which was confirmed to be heterozygous in both unaffected parents. Since the resolution of the karyotype was insufficient to identify any putatively causative gene, we undertook medium-coverage whole genome sequencing using paired-end reads, in order to elucidate the molecular breakpoints. In a two-step analysis, we first narrowed down the region by identifying discordant read-pairs, and then determined the precise molecular breakpoint by analysing the mapping locations of “soft-clipped” breakpoint-spanning reads. PCR and Sanger sequencing confirmed the identified breakpoints, both of which were located in intergenic regions. Significantly, the 7p15 breakpoint was located 523 kb upstream of HOXA13, the locus for hand-foot-genital syndrome. By inference from studies of HOXA locus control in the mouse, we suggest that the inversion has delocalised a HOXA13 enhancer to produce the phenotype observed in our patient. This study demonstrates how modern genetic diagnostic approach can characterise structural variants at nucleotide resolution and provide potential insights into functional regulation.
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Affiliation(s)
- Christopher M. Watson
- Yorkshire Regional Genetics Service, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
- * E-mail:
| | - Laura A. Crinnion
- Yorkshire Regional Genetics Service, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
| | - Sally M. Harrison
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
| | - Carolina Lascelles
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
| | - Agne Antanaviciute
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
| | - Ian M. Carr
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
| | - David T. Bonthron
- Yorkshire Regional Genetics Service, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
| | - Eamonn Sheridan
- Yorkshire Regional Genetics Service, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
- School of Medicine, University of Leeds, St. James’s University Hospital, Leeds, LS9 7TF, United Kingdom
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Dietch ZC, Duane TM, Cook CH, O'Neill PJ, Askari R, Napolitano LM, Namias N, Watson CM, Dent DL, Edwards BL, Shah PM, Guidry CA, Davies SW, Willis RN, Sawyer RG. Obesity Is Not Associated with Antimicrobial Treatment Failure for Intra-Abdominal Infection. Surg Infect (Larchmt) 2016; 17:412-21. [PMID: 27027416 DOI: 10.1089/sur.2015.213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Obesity and commonly associated comorbidities are known risk factors for the development of infections. However, the intensity and duration of antimicrobial treatment are rarely conditioned on body mass index (BMI). In particular, the influence of obesity on failure of antimicrobial treatment for intra-abdominal infection (IAI) remains unknown. We hypothesized that obesity is associated with recurrent infectious complications in patients treated for IAI. METHODS Five hundred eighteen patients randomized to treatment in the Surgical Infection Society Study to Optimize Peritoneal Infection Therapy (STOP-IT) trial were evaluated. Patients were stratified by obese (BMI ≥30) versus non-obese (BMI≥30) status. Descriptive comparisons were performed using Chi-square test, Fisher exact test, or Wilcoxon rank-sum tests as appropriate. Multivariable logistic regression using a priori selected variables was performed to assess the independent association between obesity and treatment failure in patients with IAI. RESULTS Overall, 198 (38.3%) of patients were obese (BMI ≥30) versus 319 (61.7%) who were non-obese. Mean antibiotic d and total hospital d were similar between both groups. Unadjusted outcomes of surgical site infection (9.1% vs. 6.9%, p = 0.36), recurrent intra-abdominal infection (16.2% vs. 13.8, p = 0.46), death (1.0% vs. 0.9%, p = 1.0), and a composite of all complications (25.3% vs. 19.8%, p = 0.14) were also similar between both groups. After controlling for appropriate demographics, comorbidities, severity of illness, treatment group, and duration of antimicrobial therapy, obesity was not independently associated with treatment failure (c-statistic: 0.64). CONCLUSIONS Obesity is not associated with antimicrobial treatment failure among patients with IAI. These results suggest that obesity may not independently influence the need for longer duration of antimicrobial therapy in treatment of IAI versus non-obese patients.
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Affiliation(s)
- Zachary C Dietch
- 1 Department of Surgery, The University of Virginia Health System , Charlottesville, Virginia
| | - Therese M Duane
- 3 Department of Surgery, Virginia Commonwealth University , Richmond, Virginia
| | - Charles H Cook
- 4 Department of Surgery, Beth Israel Deaconess Medical Center , Boston, Massachusetts
| | - Patrick J O'Neill
- 5 Department of Surgery, Maricopa Integrated Health System , Phoenix, Arizona
| | - Reza Askari
- 6 Department of Surgery, Brigham and Women's Hospital , Boston, Massachusetts
| | - Lena M Napolitano
- 7 Department of Surgery, University of Michigan , Ann Arbor, Michigan
| | - Nicholas Namias
- 8 Department of Surgery, University of Miami Miller School of Medicine , Miami, Florida
| | - Christopher M Watson
- 9 Department of Surgery, University of South Carolina , Columbia, South Carolina
| | - Daniel L Dent
- 10 Department of Surgery, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Brandy L Edwards
- 1 Department of Surgery, The University of Virginia Health System , Charlottesville, Virginia
| | - Puja M Shah
- 1 Department of Surgery, The University of Virginia Health System , Charlottesville, Virginia
| | - Christopher A Guidry
- 1 Department of Surgery, The University of Virginia Health System , Charlottesville, Virginia
| | - Stephen W Davies
- 1 Department of Surgery, The University of Virginia Health System , Charlottesville, Virginia
| | - Rhett N Willis
- 1 Department of Surgery, The University of Virginia Health System , Charlottesville, Virginia
| | - Robert G Sawyer
- 1 Department of Surgery, The University of Virginia Health System , Charlottesville, Virginia.,2 Division of Patient Outcomes, Policy and Population Research, Department of Public Health Sciences, The University of Virginia Health System , Charlottesville, Virginia
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Watson CM, Crinnion LA, Murphy H, Newbould M, Harrison SM, Lascelles C, Antanaviciute A, Carr IM, Sheridan E, Bonthron DT, Smith A. Deficiency of the myogenic factor MyoD causes a perinatally lethal fetal akinesia. J Med Genet 2016; 53:264-9. [PMID: 26733463 PMCID: PMC4819622 DOI: 10.1136/jmedgenet-2015-103620] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/01/2015] [Indexed: 12/30/2022]
Abstract
Background Lethal fetal akinesia deformation sequence (FADS) describes a clinically and genetically heterogeneous phenotype that includes fetal akinesia, intrauterine growth retardation, arthrogryposis and developmental anomalies. Affected babies die as a result of pulmonary hypoplasia. We aimed to identify the underlying genetic cause of this disorder in a family in which there were three affected individuals from two sibships. Methods Autosomal-recessive inheritance was suggested by a family history of consanguinity and by recurrence of the phenotype between the two sibships. We performed exome sequencing of the affected individuals and their unaffected mother, followed by autozygosity mapping and variant filtering to identify the causative gene. Results Five autozygous regions were identified, spanning 31.7 Mb of genomic sequence and including 211 genes. Using standard variant filtering criteria, we excluded all variants as being the likely pathogenic cause, apart from a single novel nonsense mutation, c.188C>A p.(Ser63*) (NM_002478.4), in MYOD1. This gene encodes an extensively studied transcription factor involved in muscle development, which has nonetheless not hitherto been associated with a hereditary human disease phenotype. Conclusions We provide the first description of a human phenotype that appears to result from MYOD1 mutation. The presentation with FADS is consistent with a large body of data demonstrating that in the mouse, MyoD is a major controller of precursor cell commitment to the myogenic differentiation programme.
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Affiliation(s)
- Christopher M Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Laura A Crinnion
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Helen Murphy
- Genomic Medicine, Manchester Academic Health Science Centre, The University of Manchester, St Mary's Hospital, Manchester, UK
| | - Melanie Newbould
- Department of Paediatric Histopathology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Sally M Harrison
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Carolina Lascelles
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Agne Antanaviciute
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Ian M Carr
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Eamonn Sheridan
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - David T Bonthron
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK School of Medicine, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Audrey Smith
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, UK
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Watson CM, Crinnion LA, Berry IR, Harrison SM, Lascelles C, Antanaviciute A, Charlton RS, Dobbie A, Carr IM, Bonthron DT. Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping. BMC Med Genet 2016; 17:1. [PMID: 26729329 PMCID: PMC4700600 DOI: 10.1186/s12881-015-0265-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/16/2015] [Indexed: 12/16/2022]
Abstract
Background The widespread adoption of high-throughput sequencing technologies by genetic diagnostic laboratories has enabled significant expansion of their testing portfolios. Rare autosomal recessive conditions have been a particular focus of many new services. Here we report a cohort of 26 patients referred for genetic analysis of Joubert (JBTS) and Meckel-Gruber (MKS) syndromes, two clinically and genetically heterogeneous neurodevelopmental conditions that define a phenotypic spectrum, with MKS at the severe end. Methods Exome sequencing was performed for all cases, using Agilent SureSelect v5 reagents and Illumina paired-end sequencing. For two cases medium-coverage (9×) whole genome sequencing was subsequently undertaken. Results Using a standard analysis pipeline for the detection of single nucleotide and small insertion or deletion variants, molecular diagnoses were confirmed in 12 cases (4 %). Seeking to determine whether our cohort harboured pathogenic copy number variants (CNV), in JBTS- or MKS-associated genes, targeted comparative read-depth analysis was performed using FishingCNV. These analyses identified a putative intragenic AHI1 deletion that included three exons spanning at least 3.4 kb and an intergenic MPP4 to TMEM237 deletion that included exons spanning at least 21.5 kb. Whole genome sequencing enabled confirmation of the deletion-containing alleles and precise characterisation of the mutation breakpoints at nucleotide resolution. These data were validated following development of PCR-based assays that could be subsequently used for “cascade” screening and/or prenatal diagnosis. Conclusions Our investigations expand the AHI1 and TMEM237 mutation spectrum and highlight the importance of performing CNV screening of disease-associated genes. We demonstrate a robust increasingly cost-effective CNV detection workflow that is applicable to all MKS/JBTS referrals. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0265-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher M Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. .,School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Laura A Crinnion
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. .,School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Ian R Berry
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Sally M Harrison
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Carolina Lascelles
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Agne Antanaviciute
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Ruth S Charlton
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Angus Dobbie
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - Ian M Carr
- School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
| | - David T Bonthron
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, LS9 7TF, UK. .,School of Medicine, University of Leeds, St. James's University Hospital, Leeds, LS9 7TF, UK.
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Poulter JA, Smith CEL, Murrillo G, Silva S, Feather S, Howell M, Crinnion L, Bonthron DT, Carr IM, Watson CM, Inglehearn CF, Mighell AJ. A distinctive oral phenotype points to FAM20A mutations not identified by Sanger sequencing. Mol Genet Genomic Med 2015; 3:543-9. [PMID: 26740946 PMCID: PMC4694127 DOI: 10.1002/mgg3.164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/10/2015] [Accepted: 06/11/2015] [Indexed: 11/25/2022] Open
Abstract
Biallelic FAM20A mutations cause two conditions where Amelogenesis Imperfecta (AI) is the presenting feature: Amelogenesis Imperfecta and Gingival Fibromatosis Syndrome; and Enamel Renal Syndrome. A distinctive oral phenotype is shared in both conditions. On Sanger sequencing of FAM20A in cases with that phenotype, we identified two probands with single, likely pathogenic heterozygous mutations. Given the recessive inheritance pattern seen in all previous FAM20A mutation‐positive families and the potential for renal disease, further screening was carried out to look for a second pathogenic allele. Reverse transcriptase‐PCR on cDNA was used to determine transcript levels. CNVseq was used to screen for genomic insertions and deletions. In one family, FAM20A cDNA screening revealed only a single mutated FAM20A allele with the wild‐type allele not transcribed. In the second family, CNV detection by whole genome sequencing (CNVseq) revealed a heterozygous 54.7 kb duplication encompassing exons 1 to 4 of FAM20A. This study confirms the link between biallelic FAM20A mutations and the characteristic oral phenotype. It highlights for the first time examples of FAM20A mutations missed by the most commonly used mutation screening techniques. This information informed renal assessment and ongoing clinical care.
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Affiliation(s)
- James A Poulter
- Section of Ophthalmology and Neuroscience University of Leeds Leeds United Kingdom
| | - Claire E L Smith
- Section of Ophthalmology and Neuroscience University of Leeds Leeds United Kingdom
| | - Gina Murrillo
- School of Dentistry University of Costa Rica San Pedro Costa Rica
| | - Sandra Silva
- Biology Molecular Cellular Centre (CBCM) University of Costa Rica San Pedro Costa Rica
| | - Sally Feather
- Paediatric Nephrology Leeds Teaching Hospitals NHS Trust Leeds United Kingdom
| | - Marianella Howell
- Paediatric Nephrology National Children's Hospital San Jose Costa Rica
| | - Laura Crinnion
- Yorkshire Regional Genetics ServiceLeeds Teaching Hospitals NHS TrustLeedsUnited Kingdom; Section of GeneticsSchool of MedicineUniversity of LeedsLeedsUnited Kingdom
| | - David T Bonthron
- Yorkshire Regional Genetics ServiceLeeds Teaching Hospitals NHS TrustLeedsUnited Kingdom; Section of GeneticsSchool of MedicineUniversity of LeedsLeedsUnited Kingdom
| | - Ian M Carr
- Section of Genetics School of Medicine University of Leeds Leeds United Kingdom
| | - Christopher M Watson
- Yorkshire Regional Genetics ServiceLeeds Teaching Hospitals NHS TrustLeedsUnited Kingdom; Section of GeneticsSchool of MedicineUniversity of LeedsLeedsUnited Kingdom
| | - Chris F Inglehearn
- Section of Ophthalmology and Neuroscience University of Leeds Leeds United Kingdom
| | - Alan J Mighell
- Section of Ophthalmology and NeuroscienceUniversity of LeedsLeedsUnited Kingdom; Department of Oral MedicineSchool of DentistryUniversity of LeedsLeedsUnited Kingdom
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Antanaviciute A, Watson CM, Harrison SM, Lascelles C, Crinnion L, Markham AF, Bonthron DT, Carr IM. OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization. Bioinformatics 2015; 31:3822-9. [PMID: 26272982 PMCID: PMC4653395 DOI: 10.1093/bioinformatics/btv473] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 08/09/2015] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION Exome sequencing has become a de facto standard method for Mendelian disease gene discovery in recent years, yet identifying disease-causing mutations among thousands of candidate variants remains a non-trivial task. RESULTS Here we describe a new variant prioritization tool, OVA (ontology variant analysis), in which user-provided phenotypic information is exploited to infer deeper biological context. OVA combines a knowledge-based approach with a variant-filtering framework. It reduces the number of candidate variants by considering genotype and predicted effect on protein sequence, and scores the remainder on biological relevance to the query phenotype.We take advantage of several ontologies in order to bridge knowledge across multiple biomedical domains and facilitate computational analysis of annotations pertaining to genes, diseases, phenotypes, tissues and pathways. In this way, OVA combines information regarding molecular and physical phenotypes and integrates both human and model organism data to effectively prioritize variants. By assessing performance on both known and novel disease mutations, we show that OVA performs biologically meaningful candidate variant prioritization and can be more accurate than another recently published candidate variant prioritization tool. AVAILABILITY AND IMPLEMENTATION OVA is freely accessible at http://dna2.leeds.ac.uk:8080/OVA/index.jsp. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT umaan@leeds.ac.uk.
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Affiliation(s)
- Agne Antanaviciute
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and
| | - Christopher M Watson
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, UK
| | - Sally M Harrison
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and
| | - Carolina Lascelles
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and
| | - Laura Crinnion
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, UK
| | - Alexander F Markham
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and
| | - David T Bonthron
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and
| | - Ian M Carr
- Section of Genetics, Institute of Biomedical and Clinical Sciences, School of Medicine, University of Leeds and
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47
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Watson CM, Crinnion LA, Gurgel-Gianetti J, Harrison SM, Daly C, Antanavicuite A, Lascelles C, Markham AF, Pena SDJ, Bonthron DT, Carr IM. Rapid Detection of Rare Deleterious Variants by Next Generation Sequencing with Optional Microarray SNP Genotype Data. Hum Mutat 2015; 36:823-30. [PMID: 26037133 PMCID: PMC4744743 DOI: 10.1002/humu.22818] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/27/2015] [Indexed: 11/25/2022]
Abstract
Autozygosity mapping is a powerful technique for the identification of rare, autosomal recessive, disease‐causing genes. The ease with which this category of disease gene can be identified has greatly increased through the availability of genome‐wide SNP genotyping microarrays and subsequently of exome sequencing. Although these methods have simplified the generation of experimental data, its analysis, particularly when disparate data types must be integrated, remains time consuming. Moreover, the huge volume of sequence variant data generated from next generation sequencing experiments opens up the possibility of using these data instead of microarray genotype data to identify disease loci. To allow these two types of data to be used in an integrated fashion, we have developed AgileVCFMapper, a program that performs both the mapping of disease loci by SNP genotyping and the analysis of potentially deleterious variants using exome sequence variant data, in a single step. This method does not require microarray SNP genotype data, although analysis with a combination of microarray and exome genotype data enables more precise delineation of disease loci, due to superior marker density and distribution.
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Affiliation(s)
- Christopher M Watson
- School of Medicine, University of Leeds, Leeds, United Kingdom.,Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, United Kingdom
| | - Laura A Crinnion
- School of Medicine, University of Leeds, Leeds, United Kingdom.,Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, United Kingdom
| | - Juliana Gurgel-Gianetti
- Department of Pediatrics, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Catherine Daly
- School of Medicine, University of Leeds, Leeds, United Kingdom
| | | | | | | | - Sergio D J Pena
- Laboratory of Clinical Genomics, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,GENE-Nucleo de Genetica Medica de Minas Gerais, Belo Horizonte, Brazil
| | - David T Bonthron
- School of Medicine, University of Leeds, Leeds, United Kingdom.,Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, United Kingdom
| | - Ian M Carr
- School of Medicine, University of Leeds, Leeds, United Kingdom
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Onoufriadis A, Hjeij R, Watson CM, Slagle CE, Klena NT, Dougherty GW, Kurkowiak M, Loges NT, Diggle CP, Morante NF, Gabriel GC, Lemke KL, Li Y, Pennekamp P, Menchen T, Marthin JK, Mans D, Letteboer SJ, Werner C, Burgoyne T, Westermann C, Rutman A, Carr IM, O'Callaghan C, Moya E, Chung EMK, Sheridan E, Nielsen KG, Roepman R, Burdine RD, Lo CW, Omran H, Mitchison H. Gene discovery for motile cilia disorders: mutation spectrum in primary ciliary dyskinesia and discovery of mutations in CCDC151. Cilia 2015. [PMCID: PMC4518893 DOI: 10.1186/2046-2530-4-s1-p30] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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49
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Rosenberger LH, Guidry CA, Davis JP, Hranjec T, Johnston VK, Wages NA, Watson CM, Sawyer RG. Reducing Accidental Dislodgement of the Percutaneous Endoscopic Gastrostomy: A Prospective Trial of the "SafetyBreak" Device. Surg Innov 2015; 23:62-9. [PMID: 26002112 DOI: 10.1177/1553350615587408] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND The percutaneous endoscopic gastrostomy (PEG) is a ubiquitous feeding tube with high rates of accidental dislodgement, with significant morbidity and health care costs. We hypothesized use of a decoupling device is a safe and effective mechanism to reduce dislodgements. STUDY DESIGN We studied a prospective cohort of 100 patients from an academic center. Enrollment included patients requiring PEG tube placement with follow up extending through an individual's lifetime use of their PEG tube. The primary endpoint was accidental dislodgement of the principally placed PEG tube. The secondary endpoint was time to accidental dislodgement of the PEG tube. RESULTS All 100 patients received the SafetyBreak device and had complete follow-up. Half of the patients had at least a single episode of device decoupling, indicating prevention of dislodgement of the PEG. Eight patients ultimately had dislodgement, resulting in a significantly lower dislodgement rate when compared with a historical cohort (P = .036) and significantly longer survival of the PEG (log rank = 0.005). When compared with a concurrent cohort (without the device) there was also significantly lower dislodgement rate (P = .03) and a trend toward longer survival of the PEG (log rank = 0.08). CONCLUSIONS When compared with both a historical and concurrent cohort of patients, the SafetyBreak device reduces accidental dislodgement of PEG tubes. As an increasing number of PEGs are being placed, an increasing number of patients are at risk for dislodgement. The SafetyBreak device is an innovative, economical solution to the problem of accidental dislodgement of the PEG tube.
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Affiliation(s)
| | | | - John P Davis
- University of Virginia Health System, Charlottesville, VA, USA
| | - Tjasa Hranjec
- University of Virginia Health System, Charlottesville, VA, USA
| | | | - Nolan A Wages
- University of Virginia Health System, Charlottesville, VA, USA
| | | | - Robert G Sawyer
- University of Virginia Health System, Charlottesville, VA, USA
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50
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Sawyer RG, Claridge JA, Nathens AB, Rotstein OD, Duane TM, Evans HL, Cook CH, O'Neill PJ, Mazuski JE, Askari R, Wilson MA, Napolitano LM, Namias N, Miller PR, Dellinger EP, Watson CM, Coimbra R, Dent DL, Lowry SF, Cocanour CS, West MA, Banton KL, Cheadle WG, Lipsett PA, Guidry CA, Popovsky K. Trial of short-course antimicrobial therapy for intraabdominal infection. N Engl J Med 2015; 372:1996-2005. [PMID: 25992746 PMCID: PMC4469182 DOI: 10.1056/nejmoa1411162] [Citation(s) in RCA: 416] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The successful treatment of intraabdominal infection requires a combination of anatomical source control and antibiotics. The appropriate duration of antimicrobial therapy remains unclear. METHODS We randomly assigned 518 patients with complicated intraabdominal infection and adequate source control to receive antibiotics until 2 days after the resolution of fever, leukocytosis, and ileus, with a maximum of 10 days of therapy (control group), or to receive a fixed course of antibiotics (experimental group) for 4±1 calendar days. The primary outcome was a composite of surgical-site infection, recurrent intraabdominal infection, or death within 30 days after the index source-control procedure, according to treatment group. Secondary outcomes included the duration of therapy and rates of subsequent infections. RESULTS Surgical-site infection, recurrent intraabdominal infection, or death occurred in 56 of 257 patients in the experimental group (21.8%), as compared with 58 of 260 patients in the control group (22.3%) (absolute difference, -0.5 percentage point; 95% confidence interval [CI], -7.0 to 8.0; P=0.92). The median duration of antibiotic therapy was 4.0 days (interquartile range, 4.0 to 5.0) in the experimental group, as compared with 8.0 days (interquartile range, 5.0 to 10.0) in the control group (absolute difference, -4.0 days; 95% CI, -4.7 to -3.3; P<0.001). No significant between-group differences were found in the individual rates of the components of the primary outcome or in other secondary outcomes. CONCLUSIONS In patients with intraabdominal infections who had undergone an adequate source-control procedure, the outcomes after fixed-duration antibiotic therapy (approximately 4 days) were similar to those after a longer course of antibiotics (approximately 8 days) that extended until after the resolution of physiological abnormalities. (Funded by the National Institutes of Health; STOP-IT ClinicalTrials.gov number, NCT00657566.).
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Affiliation(s)
- Robert G Sawyer
- From the Department of Surgery, University of Virginia Health System, Charlottesville (R.G.S., C.A.G., K.P.); the Department of Surgery, Virginia Commonwealth University, Richmond (T.M.D.); the Department of Surgery, Case Western Reserve University, Cleveland (J.A.C.); the Department of Surgery, University of Toronto, Toronto (A.B.N., O.D.R.); the Department of Surgery, University of Washington, Seattle (H.L.E., E.P.D.); the Department of Surgery, Beth Israel Deaconess Medical Center (C.H.C.), and the Department of Surgery, Brigham and Women's Hospital (R.A.) - both in Boston; the Department of Surgery, Maricopa Integrated Health System, Phoenix, AZ (P.J.O.); the Department of Surgery, Washington University, St. Louis (J.E.M.); the Department of Surgery, VA Pittsburgh Healthcare System, Pittsburgh (M.A. Wilson); the Department of Surgery, University of Michigan, Ann Arbor (L.M.N.); the Department of Surgery, University of Miami Miller School of Medicine, Miami (N.N.); the Department of Surgery, Wake Forest School of Medicine, Winston-Salem, NC (P.R.M.); the Department of Surgery, University of South Carolina, Columbia (C.M.W.); University of California, San Diego, San Diego (R.C.), the Department of Surgery, UC Davis Medical Center, Sacramento (C.S.C.), and the Department of Surgery, University of California, San Francisco, San Francisco (M.A. West) - all in California; the Department of Surgery, University of Texas Health Science Center at San Antonio, San Antonio (D.L.D.); the Department of Surgery, University of Medicine and Dentistry of New Jersey, Newark (S.F.L.); the Department of Surgery, University of Minnesota Medical School, Minneapolis (K.L.B.); the Department of Surgery, University of Louisville School of Medicine, Louisville, KY (W.G.C.); and the Department of Surgery, Johns Hopkins University School of Medicine, Baltimore (P.A.L.)
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