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Guilhamon P, Butcher LM, Presneau N, Wilson GA, Feber A, Paul DS, Schütte M, Haybaeck J, Keilholz U, Hoffman J, Ross MT, Flanagan AM, Beck S. Assessment of patient-derived tumour xenografts (PDXs) as a discovery tool for cancer epigenomics. Genome Med 2014; 6:116. [PMID: 25587359 PMCID: PMC4292812 DOI: 10.1186/s13073-014-0116-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/25/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The use of tumour xenografts is a well-established research tool in cancer genomics but has not yet been comprehensively evaluated for cancer epigenomics. METHODS In this study, we assessed the suitability of patient-derived tumour xenografts (PDXs) for methylome analysis using Infinium 450 K Beadchips and MeDIP-seq. RESULTS Controlled for confounding host (mouse) sequences, comparison of primary PDXs and matching patient tumours in a rare (osteosarcoma) and common (colon) cancer revealed that an average 2.7% of the assayed CpG sites undergo major (Δβ ≥ 0.51) methylation changes in a cancer-specific manner as a result of the xenografting procedure. No significant subsequent methylation changes were observed after a second round of xenografting between primary and secondary PDXs. Based on computational simulation using publically available methylation data, we additionally show that future studies comparing two groups of PDXs should use 15 or more samples in each group to minimise the impact of xenografting-associated changes in methylation on comparison results. CONCLUSIONS Our results from rare and common cancers indicate that PDXs are a suitable discovery tool for cancer epigenomics and we provide guidance on how to overcome the observed limitations.
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Affiliation(s)
- Paul Guilhamon
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
| | - Lee M Butcher
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
| | - Nadege Presneau
- Genetics and Cell Biology of Sarcoma, UCL Cancer Institute, University College London, London, WC1E 6DD UK ; Department of Biomedical Sciences, University of Westminster, London, W1W 6UW UK
| | - Gareth A Wilson
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK ; Translational Cancer Therapeutics Laboratory, CR-UK London Research Institute, London, WC2A 3LY UK
| | - Andrew Feber
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
| | - Dirk S Paul
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
| | | | - Johannes Haybaeck
- Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Ulrich Keilholz
- Department of Hematology and Medical Oncology, Charité Comprehensive Cancer Center, D-10117 Berlin, Germany
| | | | - Mark T Ross
- Illumina Cambridge Ltd, Chesterford Research Park, Little Chesterford, CB10 1XL UK
| | - Adrienne M Flanagan
- Genetics and Cell Biology of Sarcoma, UCL Cancer Institute, University College London, London, WC1E 6DD UK ; Department of Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, London, HA7 4LP UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6DD UK
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Liede A, Bach BA, Stryker S, Hernandez RK, Sobocki P, Bennett B, Wong SS. Regional variation and challenges in estimating the incidence of giant cell tumor of bone. J Bone Joint Surg Am 2014; 96:1999-2007. [PMID: 25471915 DOI: 10.2106/jbjs.n.00367] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Estimating the incidence of giant cell tumor of bone is challenging because few population-based cancer registries record benign bone tumors. We compared two approaches, the indirect (relative index) estimation approach used in The Burden of Musculoskeletal Diseases in the United States (BMUS) and a direct incidence rate approach (from registries that record giant cell tumor), to estimate giant cell tumor incidence in France, Germany, Italy, Spain, the U.K., Sweden, Australia, Canada, Japan, and the U.S. METHODS Giant cell tumor of bone incidence was calculated with use of the BMUS relative index of giant cell tumor to osteosarcoma in three scenarios (low, base case, and high) from case series. We compared the BMUS approach with the latest data from tumor registries in Australia (1972 to 1996), Japan (2006 to 2008), and Sweden (1993 to 2011) that record giant cell tumors. United Nations population estimates were used to project results to 2013. RESULTS The low scenario in the BMUS approach reflects data from Unni and Inwards; the incidence of giant cell tumor of bone is 0.34 relative to osteosarcoma. As the incidence of osteosarcoma is 31.4% of the total incidence of bone and joint cancers, the incidence of giant cell tumor is 0.11 times that of all bone and joint cancers. The base scenario reflects the series by Mirra et al., with a giant cell tumor incidence of 0.47 relative to osteosarcoma (0.15 to all bone and joint cancers). The high scenario reflects the series by Ward, with an incidence of 0.84 relative to osteosarcoma (0.26 to all bone and joint cancers). Differences among the three series reflect referral to a national center of excellence compared with referral to a local oncology practice. Registry data indicated a giant cell tumor incidence rate per million per year of 1.33 in Australia, 1.03 in Japan, and 1.11 in Sweden in 2013. The estimated incidence rate per million in the ten countries in 2013 ranged from 1.03 (Japan) to 1.17 (Canada) with use of the registry-based approach and from 0.73 (Japan) for the low scenario) to 2.20 (Germany) for the base case with use of the BMUS approach. CONCLUSIONS Giant cell tumor of bone affects approximately one person per million per year in the ten countries studied. Estimates derived with use of age-specific incidences from tumor registries were typically within the range of the low and base case BMUS scenarios. We recommend the registry-derived method for estimating the incidence of giant cell tumor.
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Affiliation(s)
- Alexander Liede
- Center for Observational Research, Amgen, 1120 Veterans Boulevard, ASF5, South San Francisco, CA 94080. E-mail address for A. Liede:
| | - Bruce Allen Bach
- Global Development (Oncology), Amgen Inc., One Amgen Center Drive, MS 38-2-B, Thousand Oaks, CA 91320
| | - Scott Stryker
- Center for Observational Research, Amgen, 1120 Veterans Boulevard, ASF5, South San Francisco, CA 94080. E-mail address for A. Liede:
| | - Rohini K Hernandez
- Center for Observational Research, Amgen Inc., One Amgen Center Drive, MS 24-2-A, Thousand Oaks, CA 91320-1799
| | - Patrik Sobocki
- Real-World Evidence Solutions & HEOR, IMS Health (Pygargus), Sveavägen 155, SE-113 46 Stockholm, Sweden
| | - Brian Bennett
- Plan A Inc., 759 Villa Street, Suite A, Mountain View, CA 94041
| | - Steven S Wong
- Plan A Inc., 759 Villa Street, Suite A, Mountain View, CA 94041
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Blakey K, Feltbower RG, Parslow RC, James PW, Gómez Pozo B, Stiller C, Vincent TJ, Norman P, McKinney PA, Murphy MF, Craft AW, McNally RJQ. Is fluoride a risk factor for bone cancer? Small area analysis of osteosarcoma and Ewing sarcoma diagnosed among 0-49-year-olds in Great Britain, 1980-2005. Int J Epidemiol 2014; 43:224-34. [PMID: 24425828 PMCID: PMC3937980 DOI: 10.1093/ije/dyt259] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2013] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Artificial fluoridation of drinking water to improve dental health has long been a topic of controversy. Opponents of this public health measure have cited the possibility of bone cancer induction. The study objective was to examine whether increased risk of primary bone cancer was associated with living in areas with higher concentrations of fluoride in drinking water. METHODS Case data on osteosarcoma and Ewing sarcoma, diagnosed at ages 0-49 years in Great Britain (GB) (defined here as England, Scotland and Wales) during the period 1980-2005, were obtained from population-based cancer registries. Data on fluoride levels in drinking water in England and Wales were accessed through regional water companies and the Drinking Water Inspectorate. Scottish Water provided data for Scotland. Negative binomial regression was used to examine the relationship between incidence rates and level of fluoride in drinking water at small area level. RESULTS The study analysed 2566 osteosarcoma and 1650 Ewing sarcoma cases. There was no evidence of an association between osteosarcoma risk and fluoride in drinking water [relative risk (RR) per one part per million increase in the level of fluoride = 1·001; 90% confidence interval (CI) 0·871, 1·151] and similarly there was no association for Ewing sarcoma (RR = 0·929; 90% CI 0·773, 1·115). CONCLUSIONS The findings from this study provide no evidence that higher levels of fluoride (whether natural or artificial) in drinking water in GB lead to greater risk of either osteosarcoma or Ewing sarcoma.
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Affiliation(s)
- Karen Blakey
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Richard G Feltbower
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Roger C Parslow
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Peter W James
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Basilio Gómez Pozo
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Charles Stiller
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Tim J Vincent
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Norman
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Patricia A McKinney
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Michael F Murphy
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Alan W Craft
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Richard JQ McNally
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK, Paediatric Epidemiology Group, University of Leeds, Leeds, UK, Clinical Management Unit of Preventive Medicine, Surveillance and Health Promotion, Granada-Metropolitan Primary Health Care District, Andalusian Health Service, Granada, Spain, Childhood Cancer Research Group, Department of Paediatrics, University of Oxford, Oxford, UK, School of Geography, University of Leeds, Leeds, UK and Northern Institute of Cancer Research, Newcastle University, Newcastle upon Tyne, UK
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