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Mudau MM, Seymour H, Nevondwe P, Kerr R, Spencer C, Feben C, Lombard Z, Honey E, Krause A, Carstens N. A feasible molecular diagnostic strategy for rare genetic disorders within resource-constrained environments. J Community Genet 2024; 15:39-48. [PMID: 37815686 PMCID: PMC10858011 DOI: 10.1007/s12687-023-00674-8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Timely and accurate diagnosis of rare genetic disorders is critical, as it enables improved patient management and prognosis. In a resource-constrained environment such as the South African State healthcare system, the challenge is to design appropriate and cost-effective assays that will enable accurate genetic diagnostic services in patients of African ancestry across a broad disease spectrum. Next-generation sequencing (NGS) has transformed testing approaches for many Mendelian disorders, but this technology is still relatively new in our setting and requires cost-effective ways to implement. As a proof of concept, we describe a feasible diagnostic strategy for genetic disorders frequently seen in our genetics clinics (RASopathies, Cornelia de Lange syndrome, Treacher Collins syndrome, and CHARGE syndrome). The custom-designed targeted NGS gene panel enabled concurrent variant screening for these disorders. Samples were batched during sequencing and analyzed selectively based on the clinical phenotype. The strategy employed in the current study was cost-effective, with sequencing and analysis done at USD849.68 per sample and achieving an overall detection rate of 54.5%. The strategy employed is cost-effective as it allows batching of samples from patients with different diseases in a single run, an approach that can be utilized with rare and less frequently ordered molecular diagnostic tests. The subsequent selective analysis pipeline allowed for timeous reporting back of patients results. This is feasible with a reasonable yield and can be employed for the molecular diagnosis of a wide range of rare monogenic disorders in a resource-constrained environment.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Careni Spencer
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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Seymour H, Feben C, Nevondwe P, Kerr R, Spencer C, Mudau M, Honey E, Lombard Z, Krause A, Carstens N. Mutation profiling in South African patients with Cornelia de Lange syndrome phenotype. Mol Genet Genomic Med 2024; 12:e2342. [PMID: 38284454 PMCID: PMC10785556 DOI: 10.1002/mgg3.2342] [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] [Received: 09/07/2023] [Revised: 11/08/2023] [Accepted: 12/05/2023] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Cornelia de Lange Syndrome (CdLS) presents with a variable multi-systemic phenotype and pathogenic variants have been identified in five main genes. This condition has been understudied in African populations with little phenotypic and molecular information available. METHODS AND RESULTS We present a cohort of 14 patients with clinical features suggestive of CdLS. Clinical phenotyping was carried out and cases were classified according to the international consensus criteria. According to this criteria, nine patients had classical CdLS, one had non-classical CdLS and four presented with a phenotype that suggested molecular testing for CdLS. Each patient underwent mutation profiling using a targeted next generation sequencing panel of 18 genes comprising known and suspected CdLS causal genes. Of the 14 patients tested, pathogenic and likely pathogenic variants were identified in nine: eight variants in the NIPBL gene and one in the STAG1 gene. CONCLUSIONS We present the first molecular data for a cohort of South African patients with CdLS. Eight of the nine variants identified were in the NIPBL gene, the most commonly involved gene in cases of CdLS. This is also the first report of a patient of African ancestry presenting with STAG1-related CdLS.
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Affiliation(s)
- Heather Seymour
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Careni Spencer
- Division of Human Genetics, Department of MedicineUniversity of Cape Town and Groote Schuur HospitalCape TownSouth Africa
| | - Maria Mudau
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Engela Honey
- Department of Biochemistry, Genetics, Microbiology, Faculty of Natural and Agricultural ScienceUniversity of PretoriaPretoriaSouth Africa
| | - Zane Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Genomics Platform, South African Medical Research CouncilCape TownSouth Africa
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Taieb J, Sinicrope FA, Pederson L, Lonardi S, Alberts SR, George TJ, Yothers G, Van Cutsem E, Saltz L, Ogino S, Kerr R, Yoshino T, Goldberg RM, André T, Laurent-Puig P, Shi Q. Different prognostic values of KRAS exon 2 submutations and BRAF V600E mutation in microsatellite stable (MSS) and unstable (MSI) stage III colon cancer: an ACCENT/IDEA pooled analysis of seven trials. Ann Oncol 2023; 34:1025-1034. [PMID: 37619846 PMCID: PMC10938565 DOI: 10.1016/j.annonc.2023.08.006] [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: 06/27/2023] [Revised: 08/05/2023] [Accepted: 08/10/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND The prognostic value of KRAS and BRAFV600E mutations in stage III colon cancer (CC) remains controversial and has never been clearly analyzed in patients with microsatellite instability-high (MSI-H) tumors due to sample size limitations. Data are also lacking for KRAS submutations and prognosis. PATIENTS AND METHODS We examined clinicopathological variables and prognosis in patients with surgically resected stage III CC who participated in seven clinical trials from the ACCENT/IDEA databases. Associations between KRAS exon 2 and BRAFV600E mutations and time to recurrence (TTR), overall survival (OS), and survival after recurrence (SAR) were assessed using a Cox model. We also analyzed the prognostic value of KRAS exon 2 submutations. RESULTS Among 8460 patients, 11.4% had MSI-H status. In the MSI-H group, BRAFV600E, KRAS exon 2 mutants, and double-wild-type statuses were detected in 40.6%, 18.1%, and 41.3%, respectively, whereas and in the microsatellite stable (MSS) group, these were detected in 7.7%, 38.6%, and 53.8%, respectively. In the MSS group, 5-year TTR rates of 61.8%, 66.3%, and 72.9% were observed among patients with BRAFV600E, KRAS exon 2 mutants, and those who were DWT, respectively [adjusted hazard ratio (HR) = 1.58 and 1.31, both P < 0.001]. In the MSI-H group, 5-year TTR rates did not differ significantly among the mutated subgroups. Similar results were found for OS. However, survival after relapse was significantly shorter in the KRAS exon 2- and BRAFV600E-mutated patients in both MSS (adjusted HR = 2.06 and 1.15; both P < 0.05) and MSI-H (adjusted HR = 1.99 and 1.81; both P < 0.05) groups. In the MSS group, KRAS exon 2 mutations were associated with TTR, but only p.G12C, p.G12D, and p.G13D were associated with poor outcomes after disease recurrence. CONCLUSIONS Testing for both KRAS and BRAFV600E mutations in stage III patients should be considered as they can better define individual patient prognosis, and may also enable patient selection for (neo)adjuvant trials dedicated to specific molecular subtypes with poor prognosis.
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Affiliation(s)
- J Taieb
- Department of Gastroenterology and Digestive Oncology, Hôpital Européen Georges Pompidou, Université Paris Cité, AP-HP, SIRIC CARPEM, Paris, France; Department of Oncology, Mayo Clinic, Rochester, USA.
| | | | - L Pederson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, USA
| | - S Lonardi
- Department of Oncology, Veneto Institute of Oncology IRCCS, Padua, Italy
| | - S R Alberts
- Department of Oncology, Mayo Clinic, Rochester, USA
| | - T J George
- Department of Oncology, University of Florida and the University of Florida Health Cancer Center, Gainesville, USA
| | - G Yothers
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, USA
| | - E Van Cutsem
- Department of Digestive Oncology, University Hospitals Gasthuisberg Leuven and KU Leuven, Leuven, Belgium
| | - L Saltz
- Department of Oncology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - S Ogino
- Department of Pathology, Brigham & Women's Hospital, Boston, USA
| | - R Kerr
- Department of Oncology, Oxford University, Oxford, UK
| | - T Yoshino
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - R M Goldberg
- Department of Oncology, West Virginia University Cancer Institute, Morgantown, USA; Mary Babb Randolph Cancer Center, Morgantown, USA
| | - T André
- Sorbonne Université, Department of Medical Oncology, Hôpital Saint-Antoine, Paris, France
| | - P Laurent-Puig
- Institut du cancer Paris CARPEM, AP-HP, Université Paris Cité, Paris, France; Hôpital Européen Georges Pompidou, Department of Tumor and Cancer Genomic Medicine, Paris, France; Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris Cité, Team Personalized Medicine, Phamacogenomics and Therapeutic Optimization, Paris, France
| | - Q Shi
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, USA
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Saunders MP, Graham J, Cunningham D, Plummer R, Church D, Kerr R, Cook S, Zheng S, La Thangue N, Kerr D. CXD101 and nivolumab in patients with metastatic microsatellite-stable colorectal cancer (CAROSELL): a multicentre, open-label, single-arm, phase II trial. ESMO Open 2022; 7:100594. [PMID: 36327756 PMCID: PMC9808483 DOI: 10.1016/j.esmoop.2022.100594] [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: 02/01/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Patients with microsatellite stable (MSS) colorectal carcinoma (CRC) do not respond to immune checkpoint inhibitors. Preclinical models suggested synergistic anti-tumour activity combining CXD101 and anti-programmed cell death protein 1 treatment; therefore, we assessed the clinical combination of CXD101 and nivolumab in heavily pre-treated patients with MSS metastatic CRC (mCRC). PATIENTS AND METHODS This single-arm, open-label study enrolled patients aged 18 years or older with biopsy-confirmed MSS CRC; at least two lines of systemic anticancer therapies (including oxaliplatin and irinotecan); at least one measurable lesion; Eastern Cooperative Oncology Group performance status of 0, 1 or 2; predicted life expectancy above 3 months; and adequate organ and bone marrow function. Nine patients were enrolled in a safety run-in study to define a tolerable combination schedule of CXD101 and nivolumab, followed by 46 patients in the efficacy assessment phase. Patients in the efficacy assessment cohort were treated orally with 20 mg CXD101 twice daily for 5 consecutive days every 3 weeks, and intravenously with 240 mg nivolumab every 2 weeks. The primary endpoint was immune disease control rate (iDCR). RESULTS Between 2018 and 2020, 55 patients were treated with CXD101 and nivolumab. The combination therapy was well tolerated with the most frequent grade 3 or 4 adverse events being neutropenia (18%) and anaemia (7%). Immune-related adverse reactions commonly ascribed to checkpoint inhibitors were surprisingly rare although we did see single cases of pneumonitis, hypothyroidism and hypopituitarism. There were no treatment-related deaths. Of 46 patients assessable for efficacy, 4 (9%) achieved partial response and 18 (39%) achieved stable disease, translating to an immune disease control rate of 48%. The median overall survival (OS) was 7.0 months (95% confidence interval 5.13-10.22 months). CONCLUSIONS The primary endpoint was met in this phase II study, which showed that the combination of CXD101 and nivolumab, at full individual doses in the treatment of advanced or metastatic MSS CRC, was both well tolerated and efficacious.
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Affiliation(s)
- M P Saunders
- The Christie NHS Foundation Trust, Manchester, UK.
| | - J Graham
- The Beatson West of Scotland Cancer Centre, Glasgow, UK
| | - D Cunningham
- The Royal Marsden NHS Foundation Trust, London, UK
| | - R Plummer
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, UK
| | - D Church
- The Churchill Hospital Oxford University Hospitals NHS Trust, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - R Kerr
- The Churchill Hospital Oxford University Hospitals NHS Trust, Oxford, UK
| | - S Cook
- Celleron Therapeutics Limited, Oxford, UK
| | - S Zheng
- Celleron Therapeutics Limited, Oxford, UK
| | | | - D Kerr
- The Churchill Hospital Oxford University Hospitals NHS Trust, Oxford, UK; Celleron Therapeutics Limited, Oxford, UK
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Bateman KS, Stentiford GD, Kerr R, Hooper C, White P, Edwards M, Ross S, Hazelgrove R, Daumich C, Green MJ, Ivory D, Evans C, Bass D. Amoebic crab disease (ACD) in edible crab Cancer pagurus from the English Channel, UK. Dis Aquat Organ 2022; 150:1-16. [PMID: 35796507 DOI: 10.3354/dao03668] [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] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The genera Paramoeba and Neoparamoeba (Amoebozoa, Dactylopodida, Paramoebidae) include well-known opportunistic pathogens associated with fish (N. peruans; amoebic gill disease), lobsters, molluscs and sea urchins, but only rarely with crabs (grey crab disease of blue crabs). Following reports of elevated post-capture mortality in edible crabs Cancer pagurus captured from a site within the English Channel fishery in the UK, a novel disease (amoebic crab disease, ACD) was detected in significant proportions of the catch. We present histopathological, transmission electron microscopy and molecular phylogenetic data, showing that this disease is defined by colonization of haemolymph, connective tissues and fixed phagocytes by amoeboid cells, leading to tissue destruction and presumably death in severely diseased hosts. The pathology was strongly associated with a novel amoeba with a phylogenetic position on 18S rRNA gene trees robustly sister to Janickina pigmentifera (which groups within the current circumscription of Paramoeba/Neoparamoeba), herein described as Janickina feisti n. sp. We provide evidence that J. feisti is associated with ACD in 50% of C. pagurus sampled from the mortality event. A diversity of other paramoebid sequence types, clustering with known radiations of N. pemaquidensis and N. aestuarina and a novel N. aestuarina sequence type, was detected by PCR in most of the crabs investigated, but their detection was much less strongly associated with clinical signs of disease. The discovery of ACD in edible crabs from the UK is discussed relative to published historical health surveys for this species.
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Affiliation(s)
- K S Bateman
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth DT4 8UB, UK
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Nkera-Gutabara CK, Kerr R, Scholefield J, Hazelhurst S, Naidoo J. Microbiomics: The Next Pillar of Precision Medicine and Its Role in African Healthcare. Front Genet 2022; 13:869610. [PMID: 35480328 PMCID: PMC9037082 DOI: 10.3389/fgene.2022.869610] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/04/2022] [Indexed: 11/26/2022] Open
Abstract
Limited access to technologies that support early monitoring of disease risk and a poor understanding of the geographically unique biological and environmental factors underlying disease, represent significant barriers to improved health outcomes and precision medicine efforts in low to middle income countries. These challenges are further compounded by the rich genetic diversity harboured within Southern Africa thus necessitating alternative strategies for the prediction of disease risk and clinical outcomes in regions where accessibility to personalized healthcare remains limited. The human microbiome refers to the community of microorganisms (bacteria, archaea, fungi and viruses) that co-inhabit the human body. Perturbation of the natural balance of the gut microbiome has been associated with a number of human pathologies, and the microbiome has recently emerged as a critical determinant of drug pharmacokinetics and immunomodulation. The human microbiome should therefore not be omitted from any comprehensive effort towards stratified healthcare and would provide an invaluable and orthogonal approach to existing precision medicine strategies. Recent studies have highlighted the overarching effect of geography on gut microbial diversity as it relates to human health. Health insights from international microbiome datasets are however not yet verified in context of the vast geographical diversity that exists throughout the African continent. In this commentary we discuss microbiome research in Africa and its role in future precision medicine initiatives across the African continent.
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Affiliation(s)
- C K Nkera-Gutabara
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Bioengineering and Integrated Genomics Research Group, Council for Scientific and Industrial Research (CSIR), Pretoria, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R Kerr
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - J Scholefield
- Bioengineering and Integrated Genomics Research Group, Council for Scientific and Industrial Research (CSIR), Pretoria, South Africa
| | - S Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - J Naidoo
- Bioengineering and Integrated Genomics Research Group, Council for Scientific and Industrial Research (CSIR), Pretoria, South Africa
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Diggles BK, Bass D, Bateman KS, Chong R, Daumich C, Hawkins KA, Hazelgrove R, Kerr R, Moody NJG, Ross S, Stentiford GD. Haplosporidium acetes n. sp. infecting the hepatopancreas of jelly prawns Acetes sibogae australis from Moreton Bay, Australia. J Invertebr Pathol 2022; 190:107751. [DOI: 10.1016/j.jip.2022.107751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/22/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
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Kromberg JGR, Kerr R. Oculocutaneous albinism in southern Africa: Historical background, genetic, clinical and psychosocial issues. Afr J Disabil 2022; 11:877. [PMID: 36353393 PMCID: PMC9639357 DOI: 10.4102/ajod.v11i0.877] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 05/29/2022] [Indexed: 05/09/2023] Open
Abstract
Albinism is an inherited condition associated with significant depigmentation of the skin, hair and eyes. It occurs in every population with varying frequency, and narratives of people with albinism have been recorded since 200 BC. In southern Africa albinism is common, about 1 in 4000 people are affected, but it remains a poorly understood condition surrounded by myths and superstition. This article provides a historical background on oculocutaneous albinism (OCA) in southern Africa and presents relevant information from the literature regarding epidemiology, genetics and genetic counselling, health, psychosocial and cultural issues, and medical care. There are several recessively inherited types of OCA and a mutation, responsible for about 80% of South African variants, has been identified in OCA type 2. The physical characteristics associated with albinism, that is, sun-sensitive skin and low vision, can be managed. However, people with OCA in Africa also experience psychosocial issues, such as discrimination, because of the various superstitious beliefs and attitudes held in the community. Management should include medical care for health problems, appropriate adjustment of the schooling context and genetic counseling. In addition, widespread public awareness programmes are required to increase the knowledge of the genetic causes of OCA and of the nature of genetic counselling, to address the negative attitudes in the community, to reduce the marginalisation and stigmatization of people with albinism and to improve their quality of life.
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Affiliation(s)
- Jennifer G R Kromberg
- Department of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Robyn Kerr
- Department of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa
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Hayat M, Kerr R, Bentley AR, Rotimi CN, Raal FJ, Ramsay M. Correction: Genetic associations between serum low LDL-cholesterol levels and variants in LDLR, APOB, PCSK9 and LDLRAP1 in African populations. PLoS One 2021; 16:e0249478. [PMID: 33770136 PMCID: PMC7996995 DOI: 10.1371/journal.pone.0249478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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Olsson-Brown A, Hughes D, Purshouse K, Lee L, Cheng V, Lee A, Protheroe E, Smith A, Curley H, Arnold R, Cazier JB, D'Costa J, Palles C, Campton N, Varnai C, Sivakumar S, Kerr R, Middleton G. 1703P UK Coronavirus Cancer Monitoring Project (UKCCMP): A national reporting network for real time data of the COVID-19 pandemic. Ann Oncol 2020. [PMCID: PMC7506390 DOI: 10.1016/j.annonc.2020.08.1767] [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: 11/27/2022] Open
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Lee L, Starkey T, Cazier JB, Kerr R, Middleton G. 1677MO COVID-19 mortality in hospitalized cancer patients is not significantly affected by chemotherapy or other anti-cancer treatments. Ann Oncol 2020. [PMCID: PMC7506400 DOI: 10.1016/j.annonc.2020.08.1742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Taieb J, Shi Q, Pederson L, Alberts S, Wolmark N, Van Cutsem E, de Gramont A, Kerr R, Grothey A, Lonardi S, Yoshino T, Yothers G, Sinicrope FA, Zaanan A, André T. Prognosis of microsatellite instability and/or mismatch repair deficiency stage III colon cancer patients after disease recurrence following adjuvant treatment: results of an ACCENT pooled analysis of seven studies. Ann Oncol 2019; 30:1466-1471. [PMID: 31268130 PMCID: PMC7360150 DOI: 10.1093/annonc/mdz208] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [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] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Microsatellite instable/deficient mismatch repair (MSI/dMMR) metastatic colorectal cancers have been reported to have a poor prognosis. Frequent co-occurrence of MSI/dMMR and BRAFV600E complicates the association. PATIENTS AND METHODS Patients with resected stage III colon cancer (CC) from seven adjuvant studies with available data for disease recurrence and MMR and BRAFV600E status were analyzed. The primary end point was survival after recurrence (SAR). Associations of markers with SAR were analyzed using Cox proportional hazards models adjusted for age, gender, performance status, T stage, N stage, primary tumor location, grade, KRAS status, and timing of recurrence. RESULTS Among 2630 patients with cancer recurrence (1491 men [56.7%], mean age, 58.5 [19-85] years), multivariable analysis revealed that patients with MSI/dMMR tumors had significantly longer SAR than did patients with microsatellite stable/proficient MMR tumors (MSS/pMMR) (adjusted hazard ratio [aHR], 0.82; 95% CI [confidence interval], 0.69-0.98; P = 0.029). This finding remained when looking at patients treated with standard oxaliplatin-based adjuvant chemotherapy regimens only (aHR, 0.76; 95% CI, 0.58-1.00; P = 0.048). Same trends for SAR were observed when analyzing MSI/dMMR versus MSS/pMMR tumor subgroups lacking BRAFV600E (aHR, 0.84; P = 0.10) or those harboring BRAFV600E (aHR, 0.88; P = 0.43), without reaching statistical significance. Furthermore, SAR was significantly shorter in tumors with BRAFV600E versus those lacking this mutation (aHR, 2.06; 95% CI, 1.73-2.46; P < 0.0001), even in the subgroup of MSI/dMMR tumors (aHR, 2.65; 95% CI, 1.67-4.21; P < 0.0001). Other factors associated with a shorter SAR were as follows: older age, male gender, T4/N2, proximal primary tumor location, poorly differentiated adenocarcinoma, and early recurrence. CONCLUSIONS In stage III CC patients recurring after adjuvant chemotherapy, and before the era of immunotherapy, the MSI/dMMR phenotype was associated with a better SAR compared with MSS/pMMR. BRAFV600E mutation was a poor prognostic factor for both MSI/dMMR and MSS/pMMR patients. TRIAL IDENTIFICATION NUMBERS NCT00079274, NCT00265811, NCT00004931, NCT00004931, NCT00026273, NCT00096278, NCT00112918.
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Affiliation(s)
- J Taieb
- Department of Gastroenterology and GI oncology, Sorbonne Paris Cité, Université Paris Descartes, Hopital Européen Georges Pompidou, Paris, France.
| | - Q Shi
- Department of Health Science Research, Mayo Clinic, Rochester
| | - L Pederson
- Department of Health Science Research, Mayo Clinic, Rochester
| | - S Alberts
- Division of Medical Oncology, Mayo Clinic, Rochester
| | - N Wolmark
- National Surgical Adjuvant Breast and Bowel Project, Pittsburgh, USA
| | - E Van Cutsem
- Department of Medical Oncology, University Hospitals Gasthuisberg Leuven and KU Leuven, Leuven, Belgium
| | - A de Gramont
- Department of Medical Oncology, Franco British Institute, Levallois Perret, France
| | - R Kerr
- MRC Clinical Trials Unit at UCL, London, UK
| | - A Grothey
- Department of GI Oncology, West Cancer Center, The University of Tennessee, Memphis, USA
| | - S Lonardi
- Department of Medical Oncology Unit 1, Veneto Oncology Institute-IRCCS, Padua, Italy
| | - T Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - G Yothers
- Department of Biostatistics, University of Pittsburgh, Pittsburgh
| | - F A Sinicrope
- Department of Oncology, Mayo Clinic Comprehensive Cancer Center, Rochester, USA
| | - A Zaanan
- Department of Gastroenterology and GI oncology, Sorbonne Paris Cité, Université Paris Descartes, Hopital Européen Georges Pompidou, Paris, France
| | - T André
- Department of Medical Oncology, Sorbonne Universités and Hôpital Saint-Antoine, Assistance Publique - Hôpitaux de Paris and Groupe Coopérateur Multidisciplinaire en Oncologie (GERCOR), Paris, France
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Lee L, Starkey T, Sivakumar S, Fotheringham S, Mozolowski G, Shearwood V, Palles C, Camilleri P, Kerr R, Kerr D. ToxNav germline genetic testing and PROMinet digital mobile application toxicity monitoring: results of a prospective single centre clinical utility study (PRECISE STUDY). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz155.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Jandu H, Church D, Paul J, Tomlinson I, Iveson T, Kerr R, Kerr D, Palles C. Hand-foot syndrome is a biomarker of improved survival following treatment with capecitabine. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz156.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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15
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Chen WC, Bye H, Matejcic M, Amar A, Govender D, Khew YW, Beynon V, Kerr R, Singh E, Prescott NJ, Lewis CM, Babb de Villiers C, Parker MI, Mathew CG. Association of genetic variants in CHEK2 with oesophageal squamous cell carcinoma in the South African Black population. Carcinogenesis 2019; 40:513-520. [PMID: 30753320 PMCID: PMC6556703 DOI: 10.1093/carcin/bgz026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 08/24/2018] [Revised: 12/18/2018] [Accepted: 02/07/2019] [Indexed: 12/15/2022] Open
Abstract
Oesophageal squamous cell carcinoma (OSCC) has a high incidence in southern Africa and a poor prognosis. Limited information is available on the contribution of genetic variants in susceptibility to OSCC in this region. However, recent genome-wide association studies have identified multiple susceptibility loci in Asian and European populations. In this study, we investigated genetic variants from seven OSCC risk loci identified in non-African populations for association with OSCC in the South African Black population. We performed association studies in a total of 1471 cases and 1791 controls from two study sample groups, which included 591 cases and 852 controls from the Western Cape and 880 cases and 939 controls from the Johannesburg region in the Gauteng province. Thereafter, we performed a meta-analysis for 11 variants which had been genotyped in both studies. A single nucleotide polymorphism in the CHEK2 gene, rs1033667, was significantly associated with OSCC [P = 0.002; odds ratio (OR) = 1.176; 95% confidence interval (CI): 1.06-1.30]. However, single nucleotide polymorphisms in the CASP8/ALS2CR12, TMEM173, PLCE1, ALDH2, ATP1B2/TP53 and RUNX1 loci were not associated with the disease (P > 0.05). The lack of association of six of these loci with OSCC in South African populations may reflect different genetic risk factors in non-African and African populations or differences in the genetic architecture of African genomes. The association at CHEK2, a gene with key roles in cell cycle regulation and DNA repair, in an African population provides further support for the contribution of common genetic variants at this locus to the risk of oesophageal cancer.
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Affiliation(s)
- Wenlong C Chen
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, School of Pathology, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - Hannah Bye
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Marco Matejcic
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ariella Amar
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Dhiren Govender
- Division of Anatomical Pathology, University of Cape Town, Cape Town, South Africa
| | - Yee Wen Khew
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Victoria Beynon
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Robyn Kerr
- Division of Human Genetics, School of Pathology, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - Elvira Singh
- National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Natalie J Prescott
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Cathryn M Lewis
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King’s College London, London, United Kingdom
| | - Chantal Babb de Villiers
- Division of Human Genetics, School of Pathology, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
| | - M Iqbal Parker
- Division of Medical Biochemistry and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Christopher G Mathew
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, School of Pathology, National Health Laboratory Service and University of the Witwatersrand, Johannesburg, South Africa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
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16
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Kerr R, Thomson WM, Smith DJ. Mathematical modelling of the vitamin C clock reaction. R Soc Open Sci 2019; 6:181367. [PMID: 31183115 PMCID: PMC6502385 DOI: 10.1098/rsos.181367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
Chemical clock reactions are characterized by a relatively long induction period followed by a rapid 'switchover' during which the concentration of a clock chemical rises rapidly. In addition to their interest in chemistry education, these reactions are relevant to industrial and biochemical applications. A substrate-depletive, non-autocatalytic clock reaction involving household chemicals (vitamin C, iodine, hydrogen peroxide and starch) is modelled mathematically via a system of nonlinear ordinary differential equations. Following dimensional analysis, the model is analysed in the phase plane and via matched asymptotic expansions. Asymptotic approximations are found to agree closely with numerical solutions in the appropriate time regions. Asymptotic analysis also yields an approximate formula for the dependence of switchover time on initial concentrations and the rate of the slow reaction. This formula is tested via 'kitchen sink chemistry' experiments, and is found to enable a good fit to experimental series varying in initial concentrations of both iodine and vitamin C. The vitamin C clock reaction provides an accessible model system for mathematical chemistry.
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Affiliation(s)
| | | | - D. J. Smith
- Author for correspondence: D. J. Smith e-mail:
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17
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Wolff A, Joshi RK, Ekström J, Aframian D, Pedersen AML, Proctor G, Narayana N, Villa A, Sia YW, Aliko A, McGowan R, Kerr R, Jensen SB, Vissink A, Dawes C. [Medicaments and oral healthcare. Systematic review of the -literature assessing the effect of drugs on the salivary glands]. Ned Tijdschr Tandheelkd 2018; 125:593-601. [PMID: 30457580 DOI: 10.5177/ntvt.2018.11.18203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Evidence-based reviews of drugs causing medication-induced salivary gland dysfunction, such as xerostomia (sensation of oral dryness) and subjective sialorrhea are lacking. To compile a list of medicaments that influence salivary gland function, electronic databases were searched for relevant articles published up to June 2013. A total of 269 papers out of 3,867 records located satisfied the inclusion criteria (relevance, quality of methodology, strength of evidence). A total of 56 active substances with a higher level of evidence and 50 active substances with a moderate level of evidence of causing salivary gland dysfunction are described in this article. While xerostomia was a commonly reported outcome, the objective effect on salivary secretion was rarely measured. Xerostomia was, moreover, mostly reported as a negative side effect instead of the intended effect of that drug. A comprehensive list of medications having documented effects on salivary gland function or symptoms was compiled, which may assist practitioners in assessing patients who complain of dry mouth while taking medications.
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18
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Danielsen HE, Hveem TS, Domingo E, Pradhan M, Kleppe A, Syvertsen RA, Kostolomov I, Nesheim JA, Askautrud HA, Nesbakken A, Lothe RA, Svindland A, Shepherd N, Novelli M, Johnstone E, Tomlinson I, Kerr R, Kerr DJ. Prognostic markers for colorectal cancer: estimating ploidy and stroma. Ann Oncol 2018; 29:616-623. [PMID: 29293881 PMCID: PMC5889021 DOI: 10.1093/annonc/mdx794] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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] [Indexed: 02/07/2023] Open
Abstract
Background We report here the prognostic value of ploidy and digital tumour-stromal morphometric analyses using material from 2624 patients with early stage colorectal cancer (CRC). Patients and methods DNA content (ploidy) and stroma-tumour fraction were estimated using automated digital imaging systems and DNA was extracted from sections of formalin-fixed paraffin-embedded (FFPE) tissue for analysis of microsatellite instability. Samples were available from 1092 patients recruited to the QUASAR 2 trial and two large observational series (Gloucester, n = 954; Oslo University Hospital, n = 578). Resultant biomarkers were analysed for prognostic impact using 5-year cancer-specific survival (CSS) as the clinical end point. Results Ploidy and stroma-tumour fraction were significantly prognostic in a multivariate model adjusted for age, adjuvant treatment, and pathological T-stage in stage II patients, and the combination of ploidy and stroma-tumour fraction was found to stratify these patients into three clinically useful groups; 5-year CSS 90% versus 83% versus 73% [hazard ratio (HR) = 1.77 (95% confidence interval (95% CI): 1.13-2.77) and HR = 2.95 (95% CI: 1.73-5.03), P < 0.001]. Conclusion A novel biomarker, combining estimates of ploidy and stroma-tumour fraction, sampled from FFPE tissue, identifies stage II CRC patients with low, intermediate or high risk of CRC disease specific death, and can reliably stratify clinically relevant patient sub-populations with differential risks of tumour recurrence and may support choice of adjuvant therapy for these individuals.
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Affiliation(s)
- H E Danielsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway; Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, UK; Department of Informatics, University of Oslo, Oslo, Norway
| | - T S Hveem
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway; Department of Informatics, University of Oslo, Oslo, Norway
| | - E Domingo
- Department of Oncology, University of Oxford, Oxford, UK; Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK; Oxford NIHR Comprehensive Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M Pradhan
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - A Kleppe
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway; Department of Informatics, University of Oslo, Oslo, Norway
| | - R A Syvertsen
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - I Kostolomov
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
| | - J A Nesheim
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - H A Askautrud
- Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway; Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - A Nesbakken
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo; Department of Gastrointestinal Surgery, Oslo University Hospital, Oslo; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo
| | - R A Lothe
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway; K.G. Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo; Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital - Norwegian Radium Hospital, Oslo; Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo
| | - A Svindland
- Institute of Clinical Medicine, University of Oslo, Oslo; Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - N Shepherd
- Gloucestershire Cellular Pathology Laboratory, Cheltenham General Hospital, Cheltenham
| | - M Novelli
- Research Department of Pathology, University College London Medical School, London, UK
| | - E Johnstone
- Department of Oncology, University of Oxford, Oxford, UK
| | - I Tomlinson
- Molecular and Population Genetics Laboratory, University of Oxford, Oxford, UK
| | - R Kerr
- Department of Oncology, University of Oxford, Oxford, UK
| | - D J Kerr
- Nuffield Division of Clinical Laboratory Sciences, University of Oxford, Oxford, UK.
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Chen WC, Kerr R, May A, Ndlovu B, Sobalisa A, Duze ST, Joseph L, Mathew CG, Babb de Villiers C. The Integrity and Yield of Genomic DNA Isolated from Whole Blood Following Long-Term Storage at -30°C. Biopreserv Biobank 2018; 16:106-113. [PMID: 29298092 DOI: 10.1089/bio.2017.0050] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 11/12/2022] Open
Abstract
Long-term storage of whole blood can affect the integrity of DNA if it is not done under optimal conditions. The aim of this study was to determine whether long-term storage (2-19 years) of whole blood samples at -30°C had a negative effect on the quality or quantity of genomic DNA that could be recovered at extraction. Genomic DNA was isolated from 2758 whole blood samples collected in 4 mL EDTA vacutainers from 1997 to 2012. DNA was extracted using the Qiagen® FlexiGene® DNA kit. The average storage duration at -30°C was 12 years. The quality and quantity of the isolated DNA were assessed using spectrophotometry (NanoDrop™), a fluorometric assay for double-stranded DNA (Qubit™), and agarose gel electrophoresis. The mean DNA yield per sample was found to be 114 μg from whole blood volumes that ranged from 0.5 to 4 mL. The mean A260/280 ratio and median A260/280 ratios were both 1.8. No correlation was found between the duration of storage and the total yield or the quality of DNA extracted. These data suggest that high-quality DNA can be extracted from whole blood samples that are stored at -30°C for up to 19 years.
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Affiliation(s)
- Wenlong Carl Chen
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa .,2 Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , Johannesburg, South Africa .,3 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa
| | - Robyn Kerr
- 3 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa .,4 Division of Human Genetics, National Health Laboratory Service , Johannesburg, South Africa
| | - Andrew May
- 3 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa .,4 Division of Human Genetics, National Health Laboratory Service , Johannesburg, South Africa
| | - Babongile Ndlovu
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa
| | - Anelisa Sobalisa
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa .,4 Division of Human Genetics, National Health Laboratory Service , Johannesburg, South Africa
| | - Sanelisiwe T Duze
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa .,5 Centre for Enteric Diseases, National Institute for Communicable Diseases , Johannesburg, South Africa
| | - Lavania Joseph
- 1 National Cancer Registry, National Health Laboratory Service , Johannesburg, South Africa
| | - Christopher G Mathew
- 2 Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand , Johannesburg, South Africa .,6 Division of Medical Biochemistry, University of Cape Town , Cape Town, South Africa
| | - Chantal Babb de Villiers
- 3 Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand , Johannesburg, South Africa .,7 Primary Care Unit, Department of Public Health and Primary Care, University of Cambridge , Cambridge, United Kingdom
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Chen WC, Bye H, Matejcic M, Kerr R, Singh E, Prescott NJ, Lewis CM, Villers CBD, Parker I, Mathew CG. Abstract A34: The genetic etiology of esophageal cancer in South African Black populations. Cancer Res 2017. [DOI: 10.1158/1538-7445.newfront17-a34] [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: 11/16/2022]
Abstract
Abstract
Esophageal squamous cell carcinoma (ESCC) is common in Black populations of the sub-Saharan Africa, with high incidence regions in East and South Africa. Clinical presentation in Africa is late, and treatment is mainly palliative with a very poor prognosis. Various environmental risk factors have been identified, but the possible contribution of genetics to disease risk is an important question, which is unresolved. The aim of this project is to test the hypothesis that genetic variation in the South African Black population contributes significantly to the risk of ESCC. We have begun by testing genetic risk factors for ESCC which were identified by genome-wide association scans in other populations for association with ESCC in the South African Black population. Cases with a histologically confirmed diagnosis of ESCC and population controls were recruited, with informed consent and institutional ethical approval. All individuals were from the Black population of the Western Cape, with 98.2% being from the Xhosa ethnic group. A total of 513 ESCC cases and 820 controls were genotyped for 15 single nucleotide polymorphisms (SNPs) by validated TaqMan assays on a 7900HT (Applied Biosystems). SNPs were tested for association using an allelic chi-square test; odds ratios (OR) and 95% confidence intervals (CI) used the common allele as reference. A significance threshold of p=0.0033 was applied, from a Bonferroni multiple testing correction for 15 SNPs. No significant evidence of association was observed for the index SNPs at the previously reported loci ATP1B2, CASP8, c20orf54, HEATR3, PDE4D, PLCE1, PTPN2, RUNX1, SMG6, ST6GAL1, TMEM173 and UNC5L loci. However, the SNP rs2239815 at XBP1 on chromosome 22q12 was associated with ESCC (OR =1.41, P = 0.00087), as were 2 SNPs in CHEK2, rs4822983 (OR = 1.31, P = 0.0013) and rs1033667 (OR = 1.29, P = 0.0025). These 3 SNPs are within 70kb of each other and are in partial linkage disequilibrium in African populations. Fine-mapping of this locus will be required to determine the causal gene and variant/s driving this association. The lack of association with ESCC in the Black South African population at most of the loci previously associated in Asian GWAS suggests that at least some of these may not contribute to susceptibility to ESCC in the South African population. However, expansion of samples sizes and thus statistical power is required for more definitive exclusions, and the lower level of linkage disequilibrium (LD) across African genomes may produce a negative result if the SNP which is tagging the causal variant in Asian or European populations is in weak LD with the causal SNP in African populations. In order to address these issues we are now expanding the power and density of this study by genotyping 36 SNPs from loci of interest in 1000 South African ESCC cases and 940 controls from the Johannesburg Cancer Study by mass spectrometry using the MassArray genotyping system (Agena Bioscience).
Citation Format: Wenlong Carl Chen, Hannah Bye, Marco Matejcic, Robyn Kerr, Elvira Singh, Natalie J. Prescott, Cathryn M. Lewis, Chantal Babb de Villers, Iqbal Parker, Christopher G. Mathew. The genetic etiology of esophageal cancer in South African Black populations [abstract]. In: Proceedings of the AACR International Conference: New Frontiers in Cancer Research; 2017 Jan 18-22; Cape Town, South Africa. Philadelphia (PA): AACR; Cancer Res 2017;77(22 Suppl):Abstract nr A34.
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Affiliation(s)
- Wenlong Carl Chen
- 1Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa,
| | - Hannah Bye
- 2Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom,
| | - Marco Matejcic
- 3International Centre for Genetics Engineering and Molecular Biology, University of Cape Town, Cape Town, South Africa,
| | - Robyn Kerr
- 4Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa,
| | - Elvira Singh
- 5National Cancer Registry, National Health Laboratory Service, Johannesburg, South Africa
| | - Natalie J. Prescott
- 2Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom,
| | - Cathryn M. Lewis
- 2Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom,
| | | | - Iqbal Parker
- 3International Centre for Genetics Engineering and Molecular Biology, University of Cape Town, Cape Town, South Africa,
| | - Christopher G. Mathew
- 1Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa,
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21
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Iveson T, Kerr R, Saunders M, Hollander N, Tabernero J, Haydon A, Glimelius B, Harkin A, Scudder C, Boyd K, Waterston A, Medley L, Wilson C, Ellis R, Essapen S, Dhadda A, Harrison M, Falk S, Abdel-Raouf S, Paul J. Updated results of the SCOT study: An international phase III randomised (1:1) non-inferiority trial comparing 3 versus 6 months of oxaliplatin based adjuvant chemotherapy for colorectal cancer. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx440.015] [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: 11/14/2022] Open
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22
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Grothey A, Sobrero A, Meyerhardt J, Yoshino T, Paul J, Taieb J, Souglakos I, Kerr R, Labianca R, Shields A, Bonnetain F, Yamanaka T, Boukovinas I, Shi Q, Meyers J, Niedzwiecki D, Torri V, Sargent D, André T, Iveson T. Prospective pooled analysis of six phase III trials investigating duration of adjuvant (adjuv) oxaliplatin-based therapy (3 vs 6 months) for patients (pts) with stage III colon cancer (CC): Updated results of IDEA (International Duration Evaluation of Adjuvant chemotherapy). Ann Oncol 2017. [DOI: 10.1093/annonc/mdx440.014] [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: 11/13/2022] Open
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Abstract
BACKGROUND Work Positive is Ireland's national policy initiative to control work-related stress. Since the introduction of the UK Health and Safety Executive's Management Standards (MS) in 2004, a number of studies have been undertaken to assess the potential adaptation of the MS framework within Ireland. AIMS To investigate the dimensionality, reliability and validity of the Irish version of the MS Indicator Tool (ROI-MSIT). METHODS Between February 2011 and June 2014, we collected data from a wide range of public and private sector organizations that used the ROI-MSIT. In addition to the ROI-MSIT, respondents completed the WHO-Five Well-being Index (WHO-5). Exploratory factor analysis (EFA) was used to determine whether the ROI-MSIT maintained the structure of the UK instrument. The internal consistency of the ROI-MSIT was also assessed to determine its reliability, while its criterion-related validity was explored through correlation analysis with the WHO-5. RESULTS Data were collected from 7377 participants. The factor structure of the ROI-MSIT consisted of six factors; the Demands, Control, Peer Support, Relationships and Role factors were equivalent to the original UK factors. Like the Italian version, a principal factor emerged that combined the Manager Support and Change domains. Cronbach's alpha scores ranged from 0.75 to 0.91. Finally, the ROI-MSIT's subscales and WHO-5 were positively correlated (r = 0.42-0.59, P < 0.001). CONCLUSIONS The ROI-MSIT is reliable and valid, with a factor structure similar to the original UK instrument and the Italian MSIT. Further psychometric evaluation of the ROI-MSIT is recommended.
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Affiliation(s)
- S Boyd
- Council for the Homeless Northern Ireland (CHNI), 4th Floor, Andras House, 60 Great Victoria Street, Belfast BT2 7BB, UK,
| | - R Kerr
- Department of Management and Leadership, University of Ulster, Ulster Business School, Jordanstown, County Antrim BT37 0QB, Northern Ireland
| | - P Murray
- Health and Safety Authority, Dublin D01 K0Y8, Ireland
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Naidu SB, Kerr R, Kecman M, Klaber R. P149 Designing a management plan: a mixed methods approach to exploring patient journeys in children with severe and recurrent wheeze. Thorax 2016. [DOI: 10.1136/thoraxjnl-2016-209333.292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Glaire M, Domingo E, Vermeulen L, van Wezel T, Liefers GJ, Lothe R, Nesbakkend A, Danielsen S, Zlobec I, Koelzer V, Berger M, Castellví-Bel S, de Bruyn M, Novelli M, Tejpar S, Delorenzi M, Kerr R, Kerr D, Tomlinson I, Church D. POLE proofreading domain mutation defines a subset of immunogenic colorectal cancers with excellent prognosis. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw370.09] [Citation(s) in RCA: 5] [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: 11/13/2022] Open
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Fotheringham S, Danielsen H, Hveem T, Domingo E, Pradhan M, Syvertsen R, Kostolomov I, Nesheim J, Johnstone E, Novelli M, Tomlinson I, Kerr R, Kerr D. O-016 A prognostic marker for colorectal cancer: combining analyses of ploidy and stroma. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw198.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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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Sanfilippo N, Vasconcelos R, Moya J, Malamud D, Barber C, Smith B, DeLacure M, Kerr R, Schmidt B, Myssiorek D, Corby P. The Effect of an Oral Care Intervention in Decreasing the Expression of Proinflammatory Cytokines in Patients Receiving Chemoradiation for Oral Cancer: A Randomized Clinical Trial. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2015.12.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Bundy M, Rogerson N, Dalal A, Kerr R, Finch G, Read K, Kilvington C, McLennan A. Lingual frenectomy in infants and its effect on breastfeeding. Br J Oral Maxillofac Surg 2015. [DOI: 10.1016/j.bjoms.2015.08.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Francies FZ, Wainstein T, De Leeneer K, Cairns A, Murdoch M, Nietz S, Cubasch H, Poppe B, Van Maerken T, Crombez B, Coene I, Kerr R, Slabbert JP, Vral A, Krause A, Baeyens A, Claes KBM. BRCA1, BRCA2 and PALB2 mutations and CHEK2 c.1100delC in different South African ethnic groups diagnosed with premenopausal and/or triple negative breast cancer. BMC Cancer 2015; 15:912. [PMID: 26577449 PMCID: PMC4647511 DOI: 10.1186/s12885-015-1913-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 11/05/2015] [Indexed: 12/20/2022] Open
Abstract
Background Current knowledge of the aetiology of hereditary breast cancer in the four main South African population groups (black, coloured, Indian and white) is limited. Risk assessments in the black, coloured and Indian population groups are challenging because of restricted information regarding the underlying genetic contributions to inherited breast cancer in these populations. We focused this study on premenopausal patients (diagnosed with breast cancer before the age of 50; n = 78) and triple negative breast cancer (TNBC) patients (n = 30) from the four South African ethnic groups. The aim of this study was to determine the frequency and spectrum of germline mutations in BRCA1, BRCA2 and PALB2 and to evaluate the presence of the CHEK2 c.1100delC allele in these patients. Methods In total, 108 South African breast cancer patients underwent mutation screening using a Next-Generation Sequencing (NGS) approach in combination with Multiplex Ligation-dependent Probe Amplification (MLPA) to detect large rearrangements in BRCA1 and BRCA2. Results In 13 (12 %) patients a deleterious mutation in BRCA1/2 was detected, three of which were novel mutations in black patients. None of the study participants was found to have an unequivocal pathogenic mutation in PALB2. Two (white) patients tested positive for the CHEK2 c.1100delC mutation, however, one of these also carried a deleterious BRCA2 mutation. Additionally, six variants of unknown clinical significance were identified (4 in BRCA2, 2 in PALB2), all in black patients. Within the group of TNBC patients, a higher mutation frequency was obtained (23.3 %; 7/30) than in the group of patients diagnosed before the age of 50 (7.7 %; 6/78). Conclusion This study highlights the importance of evaluating germline mutations in major breast cancer genes in all of the South African population groups. This NGS study shows that mutation analysis is warranted in South African patients with triple negative and/or in premenopausal breast cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1913-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- F Z Francies
- iThemba LABS-National Research Foundation, Somerset West, South Africa. .,Department of Radiation Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - T Wainstein
- Division of Human Genetics, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
| | - K De Leeneer
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - A Cairns
- Department of Surgery, Charlotte Maxeke Johannesburg Academic Hospital and Donald Gordon Medical Centre, Johannesburg, South Africa.
| | - M Murdoch
- Department of Surgery, Charlotte Maxeke Johannesburg Academic Hospital and Donald Gordon Medical Centre, Johannesburg, South Africa.
| | - S Nietz
- Department of Surgery, Charlotte Maxeke Johannesburg Academic Hospital and Donald Gordon Medical Centre, Johannesburg, South Africa.
| | - H Cubasch
- Batho Pele Breast Unit, Chris Hani Baragwanath Academic Hospital, Johannesburg, South Africa.
| | - B Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - T Van Maerken
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - B Crombez
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - I Coene
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - R Kerr
- Division of Human Genetics, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa.
| | - J P Slabbert
- iThemba LABS-National Research Foundation, Somerset West, South Africa.
| | - A Vral
- Department of Basic Medical Sciences, Ghent University, Ghent, Belgium.
| | - A Krause
- Division of Human Genetics, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa. .,Division of Human Genetics, National Health Laboratory Services, Johannesburg, South Africa.
| | - A Baeyens
- iThemba LABS-National Research Foundation, Somerset West, South Africa. .,Department of Radiation Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Department of Basic Medical Sciences, Ghent University, Ghent, Belgium.
| | - K B M Claes
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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Stentiford GD, Ross SH, Kerr R, Bass D, Bateman KS. Paradoxium irvingi n.gen. n.sp. (Microsporidia) infecting the musculature of European pink shrimp Pandalus montagui. J Invertebr Pathol 2015; 130:1-8. [PMID: 26146229 DOI: 10.1016/j.jip.2015.06.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [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: 03/12/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 11/28/2022]
Abstract
This paper utilises histological, ultrastructure and molecular phylogenetic data to describe a novel genus and species (Paradoxium irvingi n.gen., n.sp.) within clade 5 of the phylum Microsporidia. The parasite infects the musculature of the pink shrimp Pandalus montagui captured from United Kingdom waters. The novel microsporidium is morphologically and phylogenetically dissimilar to its nearest phylogenetic branch relative Thelohania butleri infecting the sister shrimp taxon Pandalus jordani. Furthermore, it is morphologically distinct from the type species of the genus Thelohania, Thelohania giardi infecting European brown shrimp Crangon crangon. Since phylogenetic data pertaining to type T. giardi is not currently available, our discovery places some doubt on the likelihood that T. butleri represents the proposed surrogate for the type taxon. Further it demonstrates potential for significant morphological plasticity in this clade of muscle-infecting microsporidians of crustaceans which contains the genera Myospora, Cucumispora, Thelohania, and now Paradoxium. Since it cannot be stated with certainty that T. butleri (or other taxa within the clade) represent true close relatives of T. giardi, clarity on this issue will only occur with re-discovery and genotyping of type T. giardi infecting C. crangon from European waters.
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Affiliation(s)
- G D Stentiford
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom.
| | - S H Ross
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
| | - R Kerr
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
| | - D Bass
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
| | - K S Bateman
- European Union Reference Laboratory for Crustacean Diseases, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom
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Houdmont J, Clemes S, Munir F, Wilson K, Kerr R, Addley K. Psychosocial work environment and leisure-time physical activity: the Stormont Study. Occup Med (Lond) 2015; 65:215-9. [DOI: 10.1093/occmed/kqu208] [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: 11/14/2022] Open
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Finch G, Read K, Kilvington C, Dalal A, McClennan A, Kerr R, Rogerson N. Impact of tongue tie surgery on infant feeding behaviour. Appetite 2014. [DOI: 10.1016/j.appet.2014.06.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Gustafson MP, Matsumoto K, Janikowski J, Kerr R, MacFarlane DR, Winther-Jensen B. Novel polymerisation of conducting thienothiophenes via vapour phase polymerisation: a comparative study. RSC Adv 2014. [DOI: 10.1039/c4ra10200b] [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: 11/21/2022] Open
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Addley K, Boyd S, Kerr R, McQuillan P, Houdmont J, McCrory M. The impact of two workplace-based health risk appraisal interventions on employee lifestyle parameters, mental health and work ability: results of a randomized controlled trial. Health Educ Res 2014; 29:247-258. [PMID: 24399261 DOI: 10.1093/her/cyt113] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Health risk appraisals (HRA) are a common type of workplace health promotion programme offered by American employers. In the United Kingdom, evidence of their effectiveness for promoting health behaviour change remains inconclusive. This randomized controlled trial examined the effects of two HRA interventions on lifestyle parameters, mental health and work ability in a UK context. A total of 180 employees were randomized into one of three groups: Group A (HRA augmented with health promotion and education activities), Group B (HRA only) and Group C (control, no intervention). After 12 months, changes in mean scoring in 10 lifestyle, mental health and work ability indices were compared, Groups A and B demonstrated non-significant improvements in 70% and 80%, respectively, compared with controls (40%). Odds ratios revealed that, compared with the control group, Group A was 29.2 (95% CI: 9.22-92.27) times more likely to report a perceived change in lifestyle behaviour; Group B 4.4 times (95% CI: 1.65-11.44). In conclusion, participation in the HRA was associated with a higher likelihood of perceived lifestyle behaviour change which was further increased in the augmented HRA group, thereby providing preliminary evidence that HRA and augmented HRA in particular may help UK employees make positive healthy lifestyle changes.
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Affiliation(s)
- K Addley
- NICS Occupational Health Service, Lincoln Building, 27-45 Great Victoria Street, Belfast BT2 7SH, Northern Ireland, Ulster Business School, University of Ulster, Newtownabbey BT37 0QB, Northern Ireland and Institute of Work, Health & Organisations, University of Nottingham, Jubilee Campus, Wollaton Road, Nottingham NG8 1BB, UK
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Abstract
The effect of an underwater environment on the human motor capacity, as measured by Fitts' Law, was determined. Five Ss performed a reciprocal tapping task both on land and underwater. The results showed that movement time (MT) was significantly slower (p < 01) underwater than on land. Underwater the amplitude of the movement was found to have a greater influence on MT than the required precision of the movement. On land the reverse was found to be true with movement precision having a greater influence on MT.
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Affiliation(s)
- R Kerr
- a Department of Physical Education , Memorial University of Newfoundland
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Khan MM, Tait RC, Kerr R, Ludlam CA, Lowe GDO, Murray W, Watson HG. Hepatitis C infection and outcomes in the Scottish haemophilia population. Haemophilia 2013; 19:870-5. [DOI: 10.1111/hae.12218] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2013] [Indexed: 12/11/2022]
Affiliation(s)
- M. M. Khan
- Department of Haematology; Aberdeen Royal Infirmary; Aberdeen UK
| | - R. C. Tait
- Haemophilia Centre; Glasgow Royal Infirmary; Glasgow UK
| | - R. Kerr
- Department of Haematology; Ninewells Hospital; Dundee UK
| | - C. A. Ludlam
- Haemophilia and Thrombosis Centre; New Royal Infirmary of Edinburgh; Edinburgh UK
| | - G. D. O. Lowe
- Haemophilia Centre; Glasgow Royal Infirmary; Glasgow UK
| | - W. Murray
- Department of Haematology; Raigmore Hospital; Inverness UK
| | - H. G. Watson
- Department of Haematology; Aberdeen Royal Infirmary; Aberdeen UK
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Fahey S, Kerr R, Hamlin M. Secular trends in body mass and physical activity of New Zealand adults. Obes Res Clin Pract 2012. [DOI: 10.1016/j.orcp.2012.08.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Holladay SD, Kerr R, Holladay JP, Meldrum B, Williams SM, Gogal RM. Persistent increase of blood lead level and suppression of δ-ALAD activity in northern bobwhite quail orally dosed with even a single 2-mm spent lead shot. Arch Environ Contam Toxicol 2012; 63:421-428. [PMID: 22562752 DOI: 10.1007/s00244-012-9772-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Accepted: 04/23/2012] [Indexed: 05/31/2023]
Abstract
Birds that display grit ingestion behavior are potentially at risk of lead (Pb) poisoning from mistaken ingestion of spent Pb shot pellets. The majority of available studies designed to assess such risk have used unspent shot pellets rather than field-obtained spent shot, which is oxidized and otherwise changed by weathering. Available studies also often administered more or heavier shot pellets to a bird than it might be expected to ingest. The current study dosed northern bobwhite quail (Colinus virginianus) weighing 194.6 ± 23.1 g (female birds) and 199.3 ± 12.2 g (male birds) with one to three spent no. 9 Pb shot collected from a skeet range, with particular interest in the toxicity that may occur from ingestion of a single 2-mm, 50 mg shot. An 8 week post-dosing clinical observation period was employed, over which feed consumption, body weight, blood Pb levels, and a battery of blood physiological parameters were made. Weight loss occurred in the birds, including male birds dosed with one Pb pellet. Erythrocyte delta aminolevulinic acid dehydratase (δ-ALAD) levels were decreased for the duration of the study across exposures and to levels associated with injury in wild bird populations. Decreased ALAD was particularly severe in female birds dosed with one Pb pellet and was still 92 % decreased at 8 weeks after dosing. Together, these results suggest that inadvertent ingestion of a single no. 9 Pb shot pellet can adversely affect the health of northern bobwhite quail.
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Affiliation(s)
- S D Holladay
- Department of Biosciences and Diagnostic Imaging, College of Veterinary Medicine, University of Georgia, H343, 501 DW Brooks Dr, Athens, GA 30602-7382, USA
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Kromberg JGR, Bothwell J, Kidson SH, Manga P, Kerr R, Jenkins T. TYPES OF ALBINISM IN THE BLACK SOUTHERN AFRICA POPULATION. East Afr Med J 2012; 89:20-27. [PMID: 26845807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND Oculocutaneous albinism (OCA) is the most common inherited disorder in Southern African blacks and several types have been described. Molecular techniques, where available, can be used to confirm a clinical diagnosis and the type of OCA, if necessary, and for prenatal diagnosis. OBJECTIVES To investigate and classify the different types of albinism commonly found and to determine the clinical implications for each type. DESIGN A descriptive survey. SETTING Gauteng province, South Africa, and Lesotho. SUBJECTS Three groups of subjects with OCA (96 from a genetics clinic, 62 from a dermatology clinic, and 31 from community surveys) from the black African population participated. MAIN OUTCOME MEASURES Subjects underwent clinical and/or dermatological examinations and were then classified according to type of OCA. RESULTS Four forms of OCA were identified: most (82%) subjects had OCA2 (a tyrosinase- positive type) with three sub-types: those without large freckles (ephelides) on exposed areas (named OCA 2a in this study), those with such freckles (named OCA 2b), and those with brown albinism (BOCA); the remainder had red/rufous albinism, ROCA (OCA 3). The four forms could be distinguished from each other clinically without using molecular genetic testing. CONCLUSION The most common types of albinism found in the black population of Southern Africa are OCA2 and OCA3. Given the high prevalence of the disorder, together with the high risk of skin cancer, and the recent persecution of affected individuals in certain East African countries, these findings and their clinical implications have significance in terms of both education and awareness for health professionals and lay people caring for those with albinism.
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Gogal RM, Kerr R, Kingsley DH, Granata LA, LeRoith T, Holliman SD, Dancho BA, Flick GJ. High hydrostatic pressure processing of murine norovirus 1-contaminated oysters inhibits oral infection in STAT-1(-/-)-deficient female mice. J Food Prot 2011; 74:209-14. [PMID: 21333139 DOI: 10.4315/0362-028x.jfp-10-235] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have previously demonstrated that high pressure processing (HPP) is effective in preventing in vitro replication of murine norovirus strain 1 (MNV-1), a human norovirus surrogate, in a monocyte cell line following extraction from MNV-1-contaminated oysters. In the present study, the efficacy of HPP to prevent in vivo replication within mice fed HPP-treated MNV-1-seeded oyster extracts was evaluated. Oyster homogenate extracts seeded with MNV-1 were given 5-min, 400-MPa (58,016-psi) treatments and orally gavaged into immunodeficient (STAT-1(-/-)) female mice. Mice orally gavaged with HPP-treated MNV-1 showed significant (P ≤ 0.05) weight loss leading to enhanced morbidity, whereas those given 100 and 200 PFU of HPP-treated MNV-1 were comparable to uninfected controls. MNV-1 was detected, via real-time PCR, within the liver, spleen, and brain of all mice fed non-HPP-treated homogenate but was not detected in the tissues of mice fed HPP-treated homogenates or in uninfected control mice. Hepatocellular necrosis and lymphoid depletion in the spleen were observed in non-HPP-treated MNV-1 mice only. These results clearly show that HPP prevents MNV-1 infection in vivo and validates that viral inactivation by HPP in vitro is essentially equivalent to that in vivo. Further, the data suggest that HPP may be an effective food processing intervention for norovirus-contaminated shellfish and thus may decrease risk to both immunocompromised and immunocompetent individuals who consume shellfish.
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Affiliation(s)
- R M Gogal
- Center for Molecular Medicine and Infectious Disease, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic and State University, Blacksburg, Virginia 24061, USA.
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Shinn A, Collins C, García-Vásquez A, Snow M, Matějusová I, Paladini G, Longshaw M, Lindenstrøm T, Stone D, Turnbull J, Picon-Camacho S, Rivera CV, Duguid R, Mo T, Hansen H, Olstad K, Cable J, Harris P, Kerr R, Graham D, Monaghan S, Yoon G, Buchmann K, Taylor N, Bakke T, Raynard R, Irving S, Bron J. Multi-centre testing and validation of current protocols for the identification of Gyrodactylus salaris (Monogenea). Int J Parasitol 2010; 40:1455-67. [DOI: 10.1016/j.ijpara.2010.04.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2010] [Revised: 04/29/2010] [Accepted: 04/30/2010] [Indexed: 10/19/2022]
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Evans DGR, Baser ME, O'Reilly B, Rowe J, Gleeson M, Saeed S, King A, Huson SM, Kerr R, Thomas N, Irving R, MacFarlane R, Ferner R, McLeod R, Moffat D, Ramsden R. Management of the patient and family with neurofibromatosis 2: a consensus conference statement. Br J Neurosurg 2009; 19:5-12. [PMID: 16147576 DOI: 10.1080/02688690500081206] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
A consensus conference on neurofibromatosis 2 (NF2) was held in 2002 at the request of the United Kingdom (UK) Neurofibromatosis Association, with particular emphasis on vestibular schwannoma (VS) surgery. NF2 patients should be managed at specialty treatment centres, whose staff has extensive experience with the disease. All NF2 patients and their families should have access to genetic testing because presymptomatic diagnosis improves the clinical management of the disease. Some clinical manifestations of NF2, such as ocular abnormalities, can be detected in infancy; therefore, clinical screening for at-risk members of NF2 families can start at birth, with the first magnetic resonance (MRI) scan at 10-12 years of age. Minimal interference, maintenance of quality of life, and conservation of function or auditory rehabilitation are the cornerstones of NF2 management, and the decision points to achieve these goals for patients with different clinical presentations are discussed.
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Affiliation(s)
- D G R Evans
- Department of Medical Genetics, St Mary's Hospital, Manchester, UK.
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Mustafa A, Holladay SD, Goff M, Witonsky SG, Kerr R, Reilly CM, Sponenberg DP, Gogal RM. An enhanced postnatal autoimmune profile in 24 week-old C57BL/6 mice developmentally exposed to TCDD. Toxicol Appl Pharmacol 2008; 232:51-9. [PMID: 18534654 DOI: 10.1016/j.taap.2008.04.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Revised: 04/12/2008] [Accepted: 04/15/2008] [Indexed: 11/27/2022]
Abstract
Developmental exposure of mice to the environmental contaminant and AhR agonist, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), causes persistent postnatal suppression of T cell-mediated immune responses. The extent to which prenatal TCDD may induce or exacerbate postnatal autoimmune disease remains unknown. In the present study, time-pregnant high affinity AhR C57BL/6 mice received a single oral administration of 0, 2.5, or 5 microg/kg TCDD on gestation day (gd) 12. Offspring of these mice (n=5/gender/treatment) were evaluated at 24 weeks-of-age and showed considerable immune dysregulation that was often gender-specific. Decreased thymic weight and percentages of CD4(+)CD8(+) thymocytes, and increased CD4(+)CD8(-) thymocytes, were present in the female but not male offspring. Males but not females showed decreased CD4(-)CD8(+) T cells, and increased Vbeta3(+) and Vbeta17a(+) T cells, in the spleen. Males but not females also showed increased percentages of bone marrow CD24(-)B220(+) B cell progenitors. Antibody titers to dsDNA, ssDNA and cardiolipin displayed increasing trends in both male and female mice, reaching significance for anti-dsDNA in both genders and for ssDNA in males at 5 microg/kg TCDD. Immunofluorescent staining of IgG and C3 deposition in kidney glomeruli increased in both genders of prenatal TCDD-exposed mice, suggestive of early stages of autoimmune glomerulonephritis. Collectively, these results show that exposure to TCDD during immune system development causes persistent humoral immune dysregulation as well as altered cell-mediated responses, and induces an adult profile of changes suggestive of increased risk for autoimmune disease.
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Affiliation(s)
- A Mustafa
- Center for Molecular Medicine and Infectious Diseases, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0342, USA
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Seidman A, Conlin A, Moynahan M, Bach A, Troso-Sandoval T, Sugarman S, Forero A, Kerr R, Wright G, Hudis C. Nanoparticle albumin-bound paclitaxel in 3 dosing schedules with bevacizumab as first line therapy for HER2-negative metastatic breast cancer: an interim safety analysis. EJC Suppl 2008. [DOI: 10.1016/s1359-6349(08)70889-9] [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: 11/26/2022] Open
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Abstract
Osteosarcoma uncommonly arises in craniofacial bones and has only rarely been reported to arise in the ethmoid sinus. Most primary osteosarcomas arising in paranasal sinuses are high-grade malignancies. A low-grade osteosarcoma arising in the ethmoid sinus has not previously been described. We report the clinical, radiological and histological findings of a case of low-grade (parosteal osteosarcoma-like) osteosarcoma which arose in the ethmoid sinus.
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Affiliation(s)
- M Vlychou
- Department of Musculoskeletal Radiology, Nuffield Orthopaedic Centre, Windmill Road, Oxford, OX3 7LD, UK
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