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Ralli S, Vira T, Robles-Espinoza CD, Adams DJ, Brooks-Wilson AR. Variant ranking pipeline for complex familial disorders. Sci Rep 2024; 14:13599. [PMID: 38866901 PMCID: PMC11169219 DOI: 10.1038/s41598-024-64169-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
Identifying genetic susceptibility factors for complex disorders remains a challenging task. To analyze collections of small and large pedigrees where genetic heterogeneity is likely, but biological commonalities are plausible, we have developed a weights-based pipeline to prioritize variants and genes. The Weights-based vAriant Ranking in Pedigrees (WARP) pipeline prioritizes variants using 5 weights: disease incidence rate, number of cases in a family, genome fraction shared amongst cases in a family, allele frequency and variant deleteriousness. Weights, except for the population allele frequency weight, are normalized between 0 and 1. Weights are combined multiplicatively to produce family-specific-variant weights that are then averaged across all families in which the variant is observed to generate a multifamily weight. Sorting multifamily weights in descending order creates a ranked list of variants and genes for further investigation. WARP was validated using familial melanoma sequence data from the European Genome-phenome Archive. The pipeline identified variation in known germline melanoma genes POT1, MITF and BAP1 in 4 out of 13 families (31%). Analysis of the other 9 families identified several interesting genes, some of which might have a role in melanoma. WARP provides an approach to identify disease predisposing genes in studies with small and large pedigrees.
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Affiliation(s)
- Sneha Ralli
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Tariq Vira
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada
| | | | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Angela R Brooks-Wilson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, V5Z 1L3, Canada.
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada.
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Kaiser I, Pfahlberg AB, Mathes S, Uter W, Diehl K, Steeb T, Heppt MV, Gefeller O. Inter-Rater Agreement in Assessing Risk of Bias in Melanoma Prediction Studies Using the Prediction Model Risk of Bias Assessment Tool (PROBAST): Results from a Controlled Experiment on the Effect of Specific Rater Training. J Clin Med 2023; 12:jcm12051976. [PMID: 36902763 PMCID: PMC10003882 DOI: 10.3390/jcm12051976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Assessing the risk of bias (ROB) of studies is an important part of the conduct of systematic reviews and meta-analyses in clinical medicine. Among the many existing ROB tools, the Prediction Model Risk of Bias Assessment Tool (PROBAST) is a rather new instrument specifically designed to assess the ROB of prediction studies. In our study we analyzed the inter-rater reliability (IRR) of PROBAST and the effect of specialized training on the IRR. Six raters independently assessed the risk of bias (ROB) of all melanoma risk prediction studies published until 2021 (n = 42) using the PROBAST instrument. The raters evaluated the ROB of the first 20 studies without any guidance other than the published PROBAST literature. The remaining 22 studies were assessed after receiving customized training and guidance. Gwet's AC1 was used as the primary measure to quantify the pairwise and multi-rater IRR. Depending on the PROBAST domain, results before training showed a slight to moderate IRR (multi-rater AC1 ranging from 0.071 to 0.535). After training, the multi-rater AC1 ranged from 0.294 to 0.780 with a significant improvement for the overall ROB rating and two of the four domains. The largest net gain was achieved in the overall ROB rating (difference in multi-rater AC1: 0.405, 95%-CI 0.149-0.630). In conclusion, without targeted guidance, the IRR of PROBAST is low, questioning its use as an appropriate ROB instrument for prediction studies. Intensive training and guidance manuals with context-specific decision rules are needed to correctly apply and interpret the PROBAST instrument and to ensure consistency of ROB ratings.
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Affiliation(s)
- Isabelle Kaiser
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany
- Correspondence:
| | - Annette B. Pfahlberg
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Sonja Mathes
- Department of Dermatology and Allergy Biederstein, Faculty of Medicine, Technical University of Munich, 80802 Munich, Germany
| | - Wolfgang Uter
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Katharina Diehl
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Theresa Steeb
- Department of Dermatology, University Hospital Erlangen, 91054 Erlangen, Germany
| | - Markus V. Heppt
- Department of Dermatology, University Hospital Erlangen, 91054 Erlangen, Germany
- Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), 91054 Erlangen, Germany
| | - Olaf Gefeller
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany
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Using the Prediction Model Risk of Bias Assessment Tool (PROBAST) to Evaluate Melanoma Prediction Studies. Cancers (Basel) 2022; 14:cancers14123033. [PMID: 35740698 PMCID: PMC9221327 DOI: 10.3390/cancers14123033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Simple Summary The rising incidence of cutaneous melanoma over recent decades, combined with a general interest in cancer risk prediction, has led to a high number of published melanoma risk prediction models. The aim of our work was to assess the validity of these models in order to discuss the current state of knowledge about how to predict incident cutaneous melanoma. To assess the risk of bias, we used a standardized procedure based on PROBAST (Prediction model Risk Of Bias ASsessment Tool). Only one of the 42 studies identified was rated as having a low risk of bias. However, it was encouraging to observe a recent reduction of problematic statistical methods used in the analyses. Nevertheless, the evidence base of high-quality studies that can be used to draw conclusions on the prediction of incident cutaneous melanoma is currently much weaker than the high number of studies on this topic would suggest. Abstract Rising incidences of cutaneous melanoma have fueled the development of statistical models that predict individual melanoma risk. Our aim was to assess the validity of published prediction models for incident cutaneous melanoma using a standardized procedure based on PROBAST (Prediction model Risk Of Bias ASsessment Tool). We included studies that were identified by a recent systematic review and updated the literature search to ensure that our PROBAST rating included all relevant studies. Six reviewers assessed the risk of bias (ROB) for each study using the published “PROBAST Assessment Form” that consists of four domains and an overall ROB rating. We further examined a temporal effect regarding changes in overall and domain-specific ROB rating distributions. Altogether, 42 studies were assessed, of which the vast majority (n = 34; 81%) was rated as having high ROB. Only one study was judged as having low ROB. The main reasons for high ROB ratings were the use of hospital controls in case-control studies and the omission of any validation of prediction models. However, our temporal analysis results showed a significant reduction in the number of studies with high ROB for the domain “analysis”. Nevertheless, the evidence base of high-quality studies that can be used to draw conclusions on the prediction of incident cutaneous melanoma is currently much weaker than the high number of studies on this topic would suggest.
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Reporting Quality of Studies Developing and Validating Melanoma Prediction Models: An Assessment Based on the TRIPOD Statement. Healthcare (Basel) 2022; 10:healthcare10020238. [PMID: 35206853 PMCID: PMC8871554 DOI: 10.3390/healthcare10020238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022] Open
Abstract
Transparent and accurate reporting is essential to evaluate the validity and applicability of risk prediction models. Our aim was to evaluate the reporting quality of studies developing and validating risk prediction models for melanoma according to the TRIPOD (Transparent Reporting of a multivariate prediction model for Individual Prognosis Or Diagnosis) checklist. We included studies that were identified by a recent systematic review and updated the literature search to ensure that our TRIPOD rating included all relevant studies. Six reviewers assessed compliance with all 37 TRIPOD components for each study using the published “TRIPOD Adherence Assessment Form”. We further examined a potential temporal effect of the reporting quality. Altogether 42 studies were assessed including 35 studies reporting the development of a prediction model and seven studies reporting both development and validation. The median adherence to TRIPOD was 57% (range 29% to 78%). Study components that were least likely to be fully reported were related to model specification, title and abstract. Although the reporting quality has slightly increased over the past 35 years, there is still much room for improvement. Adherence to reporting guidelines such as TRIPOD in the publication of study results must be adopted as a matter of course to achieve a sufficient level of reporting quality necessary to foster the use of the prediction models in applications.
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Reis LB, Bakos RM, Vianna FSL, Macedo GS, Jacovas VC, Ribeiro-Dos-Santos AM, Santos S, Bakos L, Ashton-Prolla P. Skin pigmentation polymorphisms associated with increased risk of melanoma in a case-control sample from southern Brazil. BMC Cancer 2020; 20:1069. [PMID: 33167923 PMCID: PMC7650158 DOI: 10.1186/s12885-020-07485-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 10/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Melanoma is the most aggressive type of skin cancer and is associated with environmental and genetic risk factors. It originates in melanocytes, the pigment-producing cells. Single nucleotide polymorphisms (SNPs) in pigmentation genes have been described in melanoma risk modulation, but knowledge in the field is still limited. METHODS In a case-control approach (107 cases and 119 controls), we investigated the effect of four pigmentation gene SNPs (TYR rs1126809, HERC2 rs1129038, SLC24A5 rs1426654, and SLC45A2 rs16891982) on melanoma risk in individuals from southern Brazil using a multivariate logistic regression model and multifactor dimensionality reduction (MDR) analysis. RESULTS Two SNPs were associated with an increased risk of melanoma in a dominant model: rs1129038AA and rs1426654AA [OR = 2.094 (95% CI: 1.106-3.966), P = 2.3 10- 2 and OR = 7.126 (95% CI: 1.873-27.110), P = 4.0 10- 3, respectively]. SNP rs16891982CC was associated with a lower risk to melanoma development in a log-additive model when the allele C was inherited [OR = 0.081 (95% CI: 0.008-0.782), P = 3 10- 2]. In addition, MDR analysis showed that the combination of the rs1426654AA and rs16891982GG genotypes was associated with a higher risk for melanoma (P = 3 10- 3), with a redundant effect. CONCLUSIONS These results contribute to the current knowledge and indicate that epistatic interaction of these SNPs, with an additive or correlational effect, may be involved in modulating the risk of melanoma in individuals from a geographic region with a high incidence of the disease.
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Affiliation(s)
- Larissa B Reis
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Renato M Bakos
- Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fernanda S L Vianna
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Gabriel S Macedo
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil
| | - Vanessa C Jacovas
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Sidney Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará (UFPA), Belém, Pará, Brazil
| | - Lúcio Bakos
- Serviço de Dermatologia, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Patricia Ashton-Prolla
- Serviço de Pesquisa Experimental, Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, Porto Alegre, Rio Grande do Sul, 2350, Brazil. .,Programa de Pós-Graduação em Medicina: Ciências Médicas, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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Kaiser I, Pfahlberg AB, Uter W, Heppt MV, Veierød MB, Gefeller O. Risk Prediction Models for Melanoma: A Systematic Review on the Heterogeneity in Model Development and Validation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17217919. [PMID: 33126677 PMCID: PMC7662952 DOI: 10.3390/ijerph17217919] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/15/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022]
Abstract
The rising incidence of cutaneous melanoma over the past few decades has prompted substantial efforts to develop risk prediction models identifying people at high risk of developing melanoma to facilitate targeted screening programs. We review these models, regarding study characteristics, differences in risk factor selection and assessment, evaluation, and validation methods. Our systematic literature search revealed 40 studies comprising 46 different risk prediction models eligible for the review. Altogether, 35 different risk factors were part of the models with nevi being the most common one (n = 35, 78%); little consistency in other risk factors was observed. Results of an internal validation were reported for less than half of the studies (n = 18, 45%), and only 6 performed external validation. In terms of model performance, 29 studies assessed the discriminative ability of their models; other performance measures, e.g., regarding calibration or clinical usefulness, were rarely reported. Due to the substantial heterogeneity in risk factor selection and assessment as well as methodologic aspects of model development, direct comparisons between models are hardly possible. Uniform methodologic standards for the development and validation of risk prediction models for melanoma and reporting standards for the accompanying publications are necessary and need to be obligatory for that reason.
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Affiliation(s)
- Isabelle Kaiser
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany; (I.K.); (A.B.P.); (W.U.)
| | - Annette B. Pfahlberg
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany; (I.K.); (A.B.P.); (W.U.)
| | - Wolfgang Uter
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany; (I.K.); (A.B.P.); (W.U.)
| | - Markus V. Heppt
- Department of Dermatology, University Hospital Erlangen, 91054 Erlangen, Germany;
| | - Marit B. Veierød
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway;
| | - Olaf Gefeller
- Department of Medical Informatics, Biometry and Epidemiology, Friedrich Alexander University of Erlangen-Nuremberg, 91054 Erlangen, Germany; (I.K.); (A.B.P.); (W.U.)
- Correspondence:
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7
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Systematic analysis of genes and diseases using PheWAS-Associated networks. Comput Biol Med 2019; 109:311-321. [DOI: 10.1016/j.compbiomed.2019.04.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/28/2019] [Accepted: 04/28/2019] [Indexed: 02/08/2023]
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Fesenko DO, Abramov IS, Shershov VE, Kuznetsova VE, Surzhikov SA, Grechishnikova IV, Barsky VE, Chudinov AV, Nasedkina TV. Multiplex Assay to Evaluate the Genetic Risk of Developing Human Melanoma. Mol Biol 2018. [DOI: 10.1134/s0026893318060079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Gu F, Chen TH, Pfeiffer RM, Fargnoli MC, Calista D, Ghiorzo P, Peris K, Puig S, Menin C, De Nicolo A, Rodolfo M, Pellegrini C, Pastorino L, Evangelou E, Zhang T, Hua X, DellaValle CT, Timothy Bishop D, MacGregor S, Iles MI, Law MH, Cust A, Brown KM, Stratigos AJ, Nagore E, Chanock S, Shi J, Consortium MMA, Consortium M, Landi MT. Combining common genetic variants and non-genetic risk factors to predict risk of cutaneous melanoma. Hum Mol Genet 2018; 27:4145-4156. [PMID: 30060076 PMCID: PMC6240742 DOI: 10.1093/hmg/ddy282] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/14/2018] [Accepted: 07/24/2018] [Indexed: 02/04/2023] Open
Abstract
Melanoma heritability is among the highest for cancer and single nucleotide polymorphisms (SNPs) contribute to it. To date, only SNPs that reached statistical significance in genome-wide association studies or few candidate SNPs have been included in melanoma risk prediction models. We compared four approaches for building polygenic risk scores (PRS) using 12 874 melanoma cases and 23 203 controls from Melanoma Meta-Analysis Consortium as a training set, and newly genotyped 3102 cases and 2301 controls from the MelaNostrum consortium for validation. We estimated adjusted odds ratios (ORs) for melanoma risk using traditional melanoma risk factors and the PRS with the largest area under the receiver operator characteristics curve (AUC). We estimated absolute risks combining the PRS and other risk factors, with age- and sex-specific melanoma incidence and competing mortality rates from Italy as an example. The best PRS, including 204 SNPs (AUC = 64.4%; 95% confidence interval (CI) = 63-65.8%), developed using winner's curse estimate corrections, had a per-quintile OR = 1.35 (95% CI = 1.30-1.41), corresponding to a 3.33-fold increase comparing the 5th to the 1st PRS quintile. The AUC improvement by adding the PRS was up to 7%, depending on adjusted factors and country. The 20-year absolute risk estimates based on the PRS, nevus count and pigmentation characteristics for a 60-year-old Italian man ranged from 0.5 to 11.8% (relative risk = 26.34), indicating good separation.
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Affiliation(s)
- Fangyi Gu
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ting-Huei Chen
- Department of Mathematics and Statistics, Laval University, Quebec, Canada
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Donato Calista
- Department of Dermatology, Maurizio Bufalini Hospital, Cesena, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa and Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
| | - Ketty Peris
- Institute of Dermatology, Catholic University, Rome, Italy
| | - Susana Puig
- Dermatology Department, Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona, Barcelona, Spain and Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Valencia, Spain
| | - Chiara Menin
- Department of Immunology and Molecular Oncology, Veneto Institute of Oncology IOV–IRCCS, Padua, Italy
| | - Arcangela De Nicolo
- Cancer Genomics Program, Veneto Institute of Oncology IOV–IRCCS, Padua, Italy
| | - Monica Rodolfo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties, University of Genoa and Genetics of Rare Cancers, Ospedale Policlinico San Martino, Genoa, Italy
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xing Hua
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Curt T DellaValle
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, UK
| | - Stuart MacGregor
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mark I Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, UK
| | - Matthew H Law
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Anne Cust
- Sydney School of Public Health, and Melanoma Institute Australia, The University of Sydney, Sydney, Australia
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alexander J Stratigos
- 1 Department of Dermatology–Venereology, National and Kapodistrian University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, València, Spain
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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10
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Cust AE, Drummond M, Kanetsky PA, Goldstein AM, Barrett JH, MacGregor S, Law MH, Iles MM, Bui M, Hopper JL, Brossard M, Demenais F, Taylor JC, Hoggart C, Brown KM, Landi MT, Newton-Bishop JA, Mann GJ, Bishop DT. Assessing the Incremental Contribution of Common Genomic Variants to Melanoma Risk Prediction in Two Population-Based Studies. J Invest Dermatol 2018; 138:2617-2624. [PMID: 29890168 PMCID: PMC6249137 DOI: 10.1016/j.jid.2018.05.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 01/02/2023]
Abstract
It is unclear to what degree genomic and traditional (phenotypic and environmental) risk factors overlap in their prediction of melanoma risk. We evaluated the incremental contribution of common genomic variants (in pigmentation, nevus, and other pathways) and their overlap with traditional risk factors, using data from two population-based case-control studies from Australia (n = 1,035) and the United Kingdom (n = 1,460) that used the same questionnaires. Polygenic risk scores were derived from 21 gene regions associated with melanoma and odds ratios from published meta-analyses. Logistic regression models were adjusted for age, sex, center, and ancestry. Adding the polygenic risk score to a model with traditional risk factors increased the area under the receiver operating characteristic curve (AUC) by 2.3% (P = 0.003) for Australia and by 2.8% (P = 0.002) for Leeds. Gene variants in the pigmentation pathway, particularly MC1R, were responsible for most of the incremental improvement. In a cross-tabulation of polygenic by traditional tertile risk scores, 59% (Australia) and 49% (Leeds) of participants were categorized in the same (concordant) tertile. Of participants with low traditional risk, 9% (Australia) and 21% (Leeds) had high polygenic risk. Testing of genomic variants can identify people who are susceptible to melanoma despite not having a traditional phenotypic risk profile.
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Affiliation(s)
- Anne E Cust
- Cancer Epidemiology and Prevention Research, Sydney School of Public Health, The University of Sydney, Sydney, Australia; Melanoma Institute Australia, The University of Sydney, Sydney, Australia.
| | - Martin Drummond
- Cancer Epidemiology and Prevention Research, Sydney School of Public Health, The University of Sydney, Sydney, Australia; Melanoma Institute Australia, The University of Sydney, Sydney, Australia
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Alisa M Goldstein
- Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jennifer H Barrett
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Stuart MacGregor
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Matthew H Law
- Statistical Genetics Lab, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Mark M Iles
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Minh Bui
- Centre for Epidemiology and Biostatistics, Melbourne School of Population Health, University of Melbourne, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population Health, University of Melbourne, Australia
| | - Myriam Brossard
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France; Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Florence Demenais
- INSERM, UMR 946, Genetic Variation and Human Diseases Unit, Paris, France; Institut Universitaire d'Hématologie, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - John C Taylor
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Clive Hoggart
- Section of Paediatrics, Division of Infectious Diseases, Department of Medicine, Imperial College London, London, UK
| | - Kevin M Brown
- Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Maria Teresa Landi
- Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Julia A Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, Australia; Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Sydney, Australia
| | - D Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
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Kocarnik JM, Richard M, Graff M, Haessler J, Bien S, Carlson C, Carty CL, Reiner AP, Avery CL, Ballantyne CM, LaCroix AZ, Assimes TL, Barbalic M, Pankratz N, Tang W, Tao R, Chen D, Talavera GA, Daviglus ML, Chirinos-Medina DA, Pereira R, Nishimura K, Bůžková P, Best LG, Ambite JL, Cheng I, Crawford DC, Hindorff LA, Fornage M, Heiss G, North KE, Haiman CA, Peters U, Le Marchand L, Kooperberg C. Discovery, fine-mapping, and conditional analyses of genetic variants associated with C-reactive protein in multiethnic populations using the Metabochip in the Population Architecture using Genomics and Epidemiology (PAGE) study. Hum Mol Genet 2018; 27:2940-2953. [PMID: 29878111 PMCID: PMC6077792 DOI: 10.1093/hmg/ddy211] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/02/2018] [Accepted: 05/28/2018] [Indexed: 12/11/2022] Open
Abstract
C-reactive protein (CRP) is a circulating biomarker indicative of systemic inflammation. We aimed to evaluate genetic associations with CRP levels among non-European-ancestry populations through discovery, fine-mapping and conditional analyses. A total of 30 503 non-European-ancestry participants from 6 studies participating in the Population Architecture using Genomics and Epidemiology study had serum high-sensitivity CRP measurements and ∼200 000 single nucleotide polymorphisms (SNPs) genotyped on the Metabochip. We evaluated the association between each SNP and log-transformed CRP levels using multivariate linear regression, with additive genetic models adjusted for age, sex, the first four principal components of genetic ancestry, and study-specific factors. Differential linkage disequilibrium patterns between race/ethnicity groups were used to fine-map regions associated with CRP levels. Conditional analyses evaluated for multiple independent signals within genetic regions. One hundred and sixty-three unique variants in 12 loci in overall or race/ethnicity-stratified Metabochip-wide scans reached a Bonferroni-corrected P-value <2.5E-7. Three loci have no (HACL1, OLFML2B) or only limited (PLA2G6) previous associations with CRP levels. Six loci had different top hits in race/ethnicity-specific versus overall analyses. Fine-mapping refined the signal in six loci, particularly in HNF1A. Conditional analyses provided evidence for secondary signals in LEPR, IL1RN and HNF1A, and for multiple independent signals in CRP and APOE. We identified novel variants and loci associated with CRP levels, generalized known CRP associations to a multiethnic study population, refined association signals at several loci and found evidence for multiple independent signals at several well-known loci. This study demonstrates the benefit of conducting inclusive genetic association studies in large multiethnic populations.
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Affiliation(s)
- Jonathan M Kocarnik
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Institute of Translational Health Sciences, University of Washington, Seattle, WA, USA
| | - Melissa Richard
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Misa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey Haessler
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stephanie Bien
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chris Carlson
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Alexander P Reiner
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christie M Ballantyne
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Z LaCroix
- Department of Epidemiology, University of San Diego, San Diego, CA, USA
| | | | - Maja Barbalic
- Division of Epidemiology, Human Genetics & Environmental Sciences, The University of Texas, Houston, TX, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Weihong Tang
- Division of Epidemiology & Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dongquan Chen
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Gregory A Talavera
- Division of Health Promotion and Behavioral Science, San Diego State University, San Diego, CA, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois College of Medicine, Chicago, IL, USA
| | - Diana A Chirinos-Medina
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Rocio Pereira
- Division of Endocrinology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katie Nishimura
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Petra Bůžková
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Lyle G Best
- Missouri Breaks Industries Research, Inc., Eagle Butte, SD, USA
| | - José Luis Ambite
- Information Sciences Institute, University of Southern California, Marina del Rey, CA, USA
| | - Iona Cheng
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Dana C Crawford
- Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA
| | | | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX, USA
| | - Gerardo Heiss
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ulrike Peters
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Charles Kooperberg
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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12
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Guen VJ, Gamble C, Lees JA, Colas P. The awakening of the CDK10/Cyclin M protein kinase. Oncotarget 2018; 8:50174-50186. [PMID: 28178678 PMCID: PMC5564841 DOI: 10.18632/oncotarget.15024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/09/2017] [Indexed: 12/22/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) play important roles in the control of fundamental cellular processes. Some of the most characterized CDKs are considered to be pertinent therapeutic targets for cancers and other diseases, and first clinical successes have recently been obtained with CDK inhibitors. Although discovered in the pre-genomic era, CDK10 attracted little attention until it was identified as a major determinant of resistance to endocrine therapy for breast cancer. In some studies, CDK10 has been shown to promote cell proliferation whereas other studies have revealed a tumor suppressor function. The recent discovery of Cyclin M as a CDK10 activating partner has allowed the unveiling of a protein kinase activity against the ETS2 oncoprotein, whose degradation is activated by CDK10/Cyclin M-mediated phosphorylation. CDK10/Cyclin M has also been shown to repress ciliogenesis and to maintain actin network architecture, through the phoshorylation of the PKN2 protein kinase and the control of RhoA stability. These findings shed light on the molecular mechanisms underlying STAR syndrome, a severe human developmental genetic disorder caused by mutations in the Cyclin M coding gene. They also pave the way to a better understanding of the role of CDK10/Cyclin M in cancer.
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Affiliation(s)
- Vincent J Guen
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States of America
| | - Carly Gamble
- P2I2 Group, Protein Phosphorylation and Human Disease Laboratory, Station Biologique de Roscoff, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Roscoff, France
| | - Jacqueline A Lees
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States of America
| | - Pierre Colas
- P2I2 Group, Protein Phosphorylation and Human Disease Laboratory, Station Biologique de Roscoff, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie, Roscoff, France
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Tagliabue E, Gandini S, Bellocco R, Maisonneuve P, Newton-Bishop J, Polsky D, Lazovich D, Kanetsky PA, Ghiorzo P, Gruis NA, Landi MT, Menin C, Fargnoli MC, García-Borrón JC, Han J, Little J, Sera F, Raimondi S. MC1R variants as melanoma risk factors independent of at-risk phenotypic characteristics: a pooled analysis from the M-SKIP project. Cancer Manag Res 2018; 10:1143-1154. [PMID: 29795986 PMCID: PMC5958947 DOI: 10.2147/cmar.s155283] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Melanoma represents an important public health problem, due to its high case-fatality rate. Identification of individuals at high risk would be of major interest to improve early diagnosis and ultimately survival. The aim of this study was to evaluate whether MC1R variants predicted melanoma risk independently of at-risk phenotypic characteristics. MATERIALS AND METHODS Data were collected within an international collaboration - the M-SKIP project. The present pooled analysis included data on 3,830 single, primary, sporadic, cutaneous melanoma cases and 2,619 controls from seven previously published case-control studies. All the studies had information on MC1R gene variants by sequencing analysis and on hair color, skin phototype, and freckles, ie, the phenotypic characteristics used to define the red hair phenotype. RESULTS The presence of any MC1R variant was associated with melanoma risk independently of phenotypic characteristics (OR 1.60; 95% CI 1.36-1.88). Inclusion of MC1R variants in a risk prediction model increased melanoma predictive accuracy (area under the receiver-operating characteristic curve) by 0.7% over a base clinical model (P=0.002), and 24% of participants were better assessed (net reclassification index 95% CI 20%-30%). Subgroup analysis suggested a possibly stronger role of MC1R in melanoma prediction for participants without the red hair phenotype (net reclassification index: 28%) compared to paler skinned participants (15%). CONCLUSION The authors suggest that measuring the MC1R genotype might result in a benefit for melanoma prediction. The results could be a valid starting point to guide the development of scientific protocols assessing melanoma risk prediction tools incorporating the MC1R genotype.
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Affiliation(s)
- Elena Tagliabue
- Clinical Trial Center, Scientific Directorate, Fondazione IRCCS Istituto Nazionale dei Tumori
| | - Sara Gandini
- Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy
| | - Rino Bellocco
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Statistics and Quantitative Methods, University of Milano-Bicocca, Milan, Italy
| | - Patrick Maisonneuve
- Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - David Polsky
- Ronald O. Perelman Department of Dermatology, New York University School of Medicine, NYU Langone Medical Center, New York, NY
| | - DeAnn Lazovich
- Division of Epidemiology and Community Health, University of Minnesota, MN
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties, University of Genoa
- IRCCS AOU San Martino-IST, Genoa, Italy
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology, IOV-IRCCS, Padua
| | | | - Jose Carlos García-Borrón
- Department of Biochemistry, Molecular Biology, and Immunology, University of Murcia
- IMIB-Arrixaca, Murcia, Spain
| | - Jiali Han
- Department of Epidemiology, Richard M Fairbanks School of Public Health, Melvin and Bren Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON, Canada
| | - Francesco Sera
- Department of Social and Environmental Health Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Sara Raimondi
- Division of Epidemiology and Biostatistics, European Institute of Oncology, Milan, Italy
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14
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Jiao X, Liu W, Mahdessian H, Bryant P, Ringdahl J, Timofeeva M, Farrington SM, Dunlop M, Lindblom A. Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population. PLoS One 2018; 13:e0193547. [PMID: 29547645 PMCID: PMC5856271 DOI: 10.1371/journal.pone.0193547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/13/2018] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified dozens of common genetic variants associated with risk of colorectal cancer (CRC). However, the majority of CRC heritability remains unclear. In order to discover low-frequency, high-risk CRC susceptibility variants in Swedish population, we genotyped 1 515 CRC patients enriched for familial cases, and 12 108 controls. Case/control association analysis suggested eight novel variants associated with CRC risk (OR 2.0-17.6, p-value < 2.0E-07), comprised of seven coding variants in genes RAB11FIP5, POTEA, COL27A1, MUC5B, PSMA8, MYH7B, and PABPC1L as well as one variant downstream of NEU1 gene. We also confirmed 27 out of 30 risk variants previously reported from GWAS in CRC with a mixed European population background. This study identified rare, coding sequence variants associated with CRC risk through analysis in a relatively homogeneous population. The segregation data suggest a complex mode of inheritance in seemingly dominant pedigrees.
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Affiliation(s)
- Xiang Jiao
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Wen Liu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Hovsep Mahdessian
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Patrick Bryant
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Ringdahl
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Susan M. Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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15
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Zhi L, Liu D, Wu SG, Li T, Zhao G, Zhao B, Li M. Association of common variants in MTAP with susceptibility and overall survival of osteosarcoma: a two-stage population-based study in Han Chinese. J Cancer 2016; 7:2179-2186. [PMID: 27994653 PMCID: PMC5166526 DOI: 10.7150/jca.16609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/04/2016] [Indexed: 12/19/2022] Open
Abstract
Osteosarcoma (OS) is a common malignant tumor, which exists widely in the bone of children and adolescents, and genetic factors may influence its susceptibility. Recently, the gene MTAP has been reported to be associated with OS in a Caucasian population. To investigate the association of common variants in MTAP with OS risk in Han Chinese individuals, we designed a two-stage case-control study with 392 OS patients and 1,578 unrelated healthy controls of Han Chinese individuals. A total of 17 tagging single nucleotide polymorphisms (SNPs) were firstly genotyped in the discovery stage, and single-SNP association and haplotypic association analyses have been performed. The SNP rs7023329 was found to be strongly associated with the OS risk (adjusted P = 0.002908), and the results of odds ratios (ORs) and 95% confidence intervals (CI) revealed increased risks from A allele of the SNP on OS (OR=1.33, 95% CI=1.13-1.62). The results were confirmed with a similar pattern in the validation stage (adjusted P = 0.006737, OR=1.49, 95% CI=1.11-2.00). Moreover, haplotypic analyses indicated that one haplotype block containing rs7023329 was significantly associated with OS risk in both stages (both global P<0.0001). The statistically significant association between the rs7023329 genotype and poor survival in OS patients was also observed. To sum up, our results prove that MTAP plays an important role in the etiology of OS, suggesting this gene as a potential genetic modifier for OS development.
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Affiliation(s)
- Liqiang Zhi
- Department of Orthopedic, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Dan Liu
- Department of Rheumatology and Immunology, the Fifth Hospital of Xi'an, Xi'an, China
| | - Stephen G Wu
- Department of Energy, Environment and Chemical Engineering, Washington University, Saint Louis, MO, USA
| | - Tianqing Li
- Department of Orthopedic, Xijing Orthopedic Hospital, the Fourth Military Medical University, Xi'an, China
| | - Guanghui Zhao
- Department of Orthopedic, Hong-hui Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, China
| | - Bo Zhao
- Department of Orthopedic, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Meng Li
- Department of Orthopedic, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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16
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Evangelou E, Stratigos AJ. Lessons from genome-wide studies of melanoma: towards precision medicine. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2016. [DOI: 10.1080/23808993.2016.1240586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Fesenko DO, Chudinov AV, Surzhikov SA, Zasedatelev AS. Biochip-Based Genotyping Assay for Detection of Polymorphisms in Pigmentation Genes Associated with Cutaneous Melanoma. Genet Test Mol Biomarkers 2016; 20:208-12. [PMID: 26848990 DOI: 10.1089/gtmb.2015.0272] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AIMS The purpose of the study was to develop a new assay for genotyping nine single nucleotide polymorphisms (SNPs) that are known to be associated with melanoma. METHODS Two-stage single tube polymerase chain reaction (PCR) followed by hybridization on a biochip was developed and applied in the study. RESULTS A total of nine SNPs were selected from five genes: MC1R (rs1805006, rs1805007, rs1805009, rs11547464), HERC2 (rs12913832), OCA2 (rs1800407), SLC45A2 (rs16891982), TYR (rs1393350), and a SNP from the intergenic locus rs12896399 were used for the synthesis of ssDNAs via a single-stage PCR process. The assays were performed on a biochip-based platform that is capable of SNP genotyping via a single reaction-tube PCR, followed by on chip hybridization. We tested 69 DNAs obtained from healthy persons and demonstrated the assays' ability to discriminate all three genotypes for almost all of the SNPs. CONCLUSIONS The developed approach proved robust, suggesting that it might be useful for the personalized genotyping of large cohorts of patients.
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Affiliation(s)
- Denis O Fesenko
- 1 Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia
- 2 N.N. Blokhin Russian Cancer Research Center , Russian Academy of Sciences, Moscow, Russia
| | - Alexander V Chudinov
- 1 Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia
| | - Sergey A Surzhikov
- 1 Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Zasedatelev
- 1 Engelhardt Institute of Molecular Biology , Russian Academy of Sciences, Moscow, Russia
- 2 N.N. Blokhin Russian Cancer Research Center , Russian Academy of Sciences, Moscow, Russia
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18
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Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds. Genetics 2016; 203:433-50. [PMID: 27017625 DOI: 10.1534/genetics.115.181594] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 03/03/2016] [Indexed: 01/25/2023] Open
Abstract
Detecting the molecular basis of adaptation is one of the major questions in population genetics. With the advance in sequencing technologies, nearly complete interrogation of genome-wide polymorphisms in multiple populations is becoming feasible in some species, with the expectation that it will extend quickly to new ones. Here, we investigate the advantages of sequencing for the detection of adaptive loci in multiple populations, exploiting a recently published data set in cattle (Bos taurus). We used two different approaches to detect statistically significant signals of positive selection: a within-population approach aimed at identifying hard selective sweeps and a population-differentiation approach that can capture other selection events such as soft or incomplete sweeps. We show that the two methods are complementary in that they indeed capture different kinds of selection signatures. Our study confirmed some of the well-known adaptive loci in cattle (e.g., MC1R, KIT, GHR, PLAG1, NCAPG/LCORL) and detected some new ones (e.g., ARL15, PRLR, CYP19A1, PPM1L). Compared to genome scans based on medium- or high-density SNP data, we found that sequencing offered an increased detection power and a higher resolution in the localization of selection signatures. In several cases, we could even pinpoint the underlying causal adaptive mutation or at least a very small number of possible candidates (e.g., MC1R, PLAG1). Our results on these candidates suggest that a vast majority of adaptive mutations are likely to be regulatory rather than protein-coding variants.
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19
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Asgari MM, Wang W, Ioannidis NM, Itnyre J, Hoffmann T, Jorgenson E, Whittemore AS. Identification of Susceptibility Loci for Cutaneous Squamous Cell Carcinoma. J Invest Dermatol 2016; 136:930-937. [PMID: 26829030 DOI: 10.1016/j.jid.2016.01.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/04/2016] [Accepted: 01/06/2016] [Indexed: 12/20/2022]
Abstract
We report a genome-wide association study of cutaneous squamous cell carcinoma conducted among non-Hispanic white members of the Kaiser Permanente Northern California health care system. The study includes a genome-wide screen of 61,457 members (6,891 cases and 54,566 controls) genotyped on the Affymetrix Axiom European array and a replication phase involving an independent set of 6,410 additional members (810 cases and 5,600 controls). Combined analysis of screening and replication phases identified 10 loci containing single-nucleotide polymorphisms (SNPs) with P-values < 5 × 10(-8). Six loci contain genes in the pigmentation pathway; SNPs at these loci appear to modulate squamous cell carcinoma risk independently of the pigmentation phenotypes. Another locus contains HLA class II genes studied in relation to elevated squamous cell carcinoma risk following immunosuppression. SNPs at the remaining three loci include an intronic SNP in FOXP1 at locus 3p13, an intergenic SNP at 3q28 near TP63, and an intergenic SNP at 9p22 near BNC2. These findings provide insights into the genetic factors accounting for inherited squamous cell carcinoma susceptibility.
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Affiliation(s)
- Maryam M Asgari
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA; Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Wei Wang
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Nilah M Ioannidis
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA; Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Jacqueline Itnyre
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas Hoffmann
- Department of Epidemiology and Biostatistics and Institute for Human Genetics, University of California, San Francisco, California, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Alice S Whittemore
- Department of Health Research and Policy, Stanford University School of Medicine, Stanford, California, USA.
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20
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Sitek A, Rosset I, Żądzińska E, Kasielska-Trojan A, Neskoromna-Jędrzejczak A, Antoszewski B. Skin color parameters and Fitzpatrick phototypes in estimating the risk of skin cancer: A case-control study in the Polish population. J Am Acad Dermatol 2016; 74:716-23. [PMID: 26777103 DOI: 10.1016/j.jaad.2015.10.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/11/2015] [Accepted: 10/12/2015] [Indexed: 01/14/2023]
Abstract
BACKGROUND Light skin pigmentation is a known risk factor for skin cancer. OBJECTIVE Skin color parameters and Fitzpatrick phototypes were evaluated in terms of their usefulness in predicting the risk of skin cancer. METHODS A case-control study involved 133 individuals with skin cancer (100 with basal cell carcinoma, 21 with squamous cell carcinoma, 12 with melanoma) and 156 healthy individuals. All of them had skin phototype determined and spectrophotometric skin color measurements were done on the inner surfaces of their arms and on the buttock. Using those data, prediction models were built and subjected to 17-fold stratified cross-validation. RESULTS A model, based on skin phototypes, was characterized by area under the receiver operating characteristic curve = 0.576 and exhibited a lower predictive power than the models, which were mostly based on spectrophotometric variables describing pigmentation levels. The best predictors of skin cancer were R coordinate of RGB color space (area under the receiver operating characteristic curve 0.687) and melanin index (area under the receiver operating characteristic curve 0.683) for skin on the buttock. LIMITATIONS A small number of patients were studied. Models were not externally validated. CONCLUSIONS Skin color parameters are more accurate predictors of skin cancer occurrence than skin phototypes. Spectrophotometry is a quick, easy, and affordable method offering relatively good predictive power.
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Affiliation(s)
- Aneta Sitek
- Department of Anthropology, University of Lodz, Lodz, Poland
| | - Iwona Rosset
- Department of Anthropology, University of Lodz, Lodz, Poland
| | - Elżbieta Żądzińska
- Department of Anthropology, University of Lodz, Lodz, Poland; Biological Anthropology and Comparative Anatomy Research Unit, School of Medicine, The University of Adelaide, Australia
| | - Anna Kasielska-Trojan
- Department of Plastic, Reconstructive, and Aesthetic Surgery, University Hospital No. 1, Lodz, Poland
| | | | - Bogusław Antoszewski
- Plastic, Reconstructive and Aesthetic Surgery Clinic, Medical University of Lodz, Lodz, Poland.
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21
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Prediction of Melanoma Risk in a Southern European Population Based on a Weighted Genetic Risk Score. J Invest Dermatol 2015; 136:690-695. [PMID: 27015455 DOI: 10.1016/j.jid.2015.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 11/06/2015] [Accepted: 11/13/2015] [Indexed: 12/23/2022]
Abstract
Many single nucleotide polymorphisms (SNPs) have been described as putative risk factors for melanoma. The aim of our study was to validate the most prominent genetic risk loci in an independent Greek melanoma case-control dataset and to assess their cumulative effect solely or combined with established phenotypic risk factors on individualized risk prediction. We genotyped 59 SNPs in 800 patients and 800 controls and tested their association with melanoma using logistic regression analyses. We constructed a weighted genetic risk score (GRSGWS) based on SNPs that showed genome-wide significant (GWS) association with melanoma in previous studies and assessed their impact on risk prediction. Fifteen independent SNPs from 12 loci were significantly associated with melanoma (P < 0.05). Risk score analysis yielded an odds ratio of 1.36 per standard deviation increase of the GRSGWS (P = 1.1 × 10(-7)). Individuals in the highest 20% of the GRSGWS had a 1.88-fold increase in melanoma risk compared with those in the middle quintile. By adding the GRSGWS to a phenotypic risk model, the C-statistic increased from 0.764 to 0.775 (P = 0.007). In summary, the GRSGWS is associated with melanoma risk and achieves a modest improvement in risk prediction when added to a phenotypic risk model.
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Mitochondrial DNA copy number in peripheral blood and melanoma risk. PLoS One 2015; 10:e0131649. [PMID: 26110424 PMCID: PMC4482392 DOI: 10.1371/journal.pone.0131649] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 06/05/2015] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) copy number in peripheral blood has been suggested as risk modifier in various types of cancer. However, its influence on melanoma risk is unclear. We evaluated the association between mtDNA copy number in peripheral blood and melanoma risk in 500 melanoma cases and 500 healthy controls from an ongoing melanoma study. The mtDNA copy number was measured using real-time polymerase chain reaction. Overall, mean mtDNA copy number was significantly higher in cases than in controls (1.15 vs 0.99, P<0.001). Increased mtDNA copy number was associated with a 1.45-fold increased risk of melanoma (95% confidence interval: 1.12-1.97). Significant joint effects between mtDNA copy number and variables related to pigmentation and history of sunlight exposure were observed. This study supports an association between increased mtDNA copy number and melanoma risk that is independent on the known melanoma risk factors (pigmentation and history of sunlight exposure).
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Molinaro AM, Ferrucci LM, Cartmel B, Loftfield E, Leffell DJ, Bale AE, Mayne ST. Indoor tanning and the MC1R genotype: risk prediction for basal cell carcinoma risk in young people. Am J Epidemiol 2015; 181:908-16. [PMID: 25858289 PMCID: PMC4445390 DOI: 10.1093/aje/kwu356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/01/2014] [Indexed: 12/25/2022] Open
Abstract
Basal cell carcinoma (BCC) incidence is increasing, particularly in young people, and can be associated with significant morbidity and treatment costs. To identify young individuals at risk of BCC, we assessed existing melanoma or overall skin cancer risk prediction models and built a novel risk prediction model, with a focus on indoor tanning and the melanocortin 1 receptor gene, MC1R. We evaluated logistic regression models among 759 non-Hispanic whites from a case-control study of patients seen between 2006 and 2010 in New Haven, Connecticut. In our data, the adjusted area under the receiver operating characteristic curve (AUC) for a model by Han et al. (Int J Cancer. 2006;119(8):1976-1984) with 7 MC1R variants was 0.72 (95% confidence interval (CI): 0.66, 0.78), while that by Smith et al. (J Clin Oncol. 2012;30(15 suppl):8574) with MC1R and indoor tanning had an AUC of 0.69 (95% CI: 0.63, 0.75). Our base model had greater predictive ability than existing models and was significantly improved when we added ever-indoor tanning, burns from indoor tanning, and MC1R (AUC = 0.77, 95% CI: 0.74, 0.81). Our early-onset BCC risk prediction model incorporating MC1R and indoor tanning extends the work of other skin cancer risk prediction models, emphasizes the value of both genotype and indoor tanning in skin cancer risk prediction in young people, and should be validated with an independent cohort.
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Affiliation(s)
- Annette M. Molinaro
- Correspondence to Dr. Annette M. Molinaro, Department of Neurosurgery, University of California, San Francisco, 400 Parnassus Avenue, Room A 808, San Francisco, CA 94143-0372 (e-mail: )
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Papakostas D, Stefanaki I, Stratigos A. Genetic epidemiology of malignant melanoma susceptibility. Melanoma Manag 2015; 2:165-169. [PMID: 30190845 DOI: 10.2217/mmt.15.7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Germline CDKN2A mutations were the first to be associated with familial melanoma. MC1R polymorphisms are associated, in conformity with epidemiological observations, with fair skin phenotype and a moderately increased risk for melanoma. The wider implementation of genome-wide association studies along with improved whole exome sequencing techniques made possible the identification of novel high-penetrant mutations (TERT, MITF, POT1, BAP1) beyond the established pathways of pigmentation and nevus count suggesting an additional role for pathways involved in cell cycle control and DNA repair. A multitude of common polymorphisms in the general population have been associated through candidate gene studies with a low risk for melanoma, supporting the hypothesis of a complex disease.
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Affiliation(s)
- Dimitrios Papakostas
- Department of Dermatology, Dermatooncology Unit, A. Syggros Hospital, University of Athens, Greece
| | - Irene Stefanaki
- Department of Dermatology, Dermatooncology Unit, A. Syggros Hospital, University of Athens, Greece
| | - Alexander Stratigos
- Department of Dermatology, Dermatooncology Unit, A. Syggros Hospital, University of Athens, Greece
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Antonopoulou K, Stefanaki I, Lill CM, Chatzinasiou F, Kypreou KP, Karagianni F, Athanasiadis E, Spyrou GM, Ioannidis JPA, Bertram L, Evangelou E, Stratigos AJ. Updated field synopsis and systematic meta-analyses of genetic association studies in cutaneous melanoma: the MelGene database. J Invest Dermatol 2015; 135:1074-1079. [PMID: 25407435 DOI: 10.1038/jid.2014.491] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 10/09/2014] [Accepted: 10/31/2014] [Indexed: 12/26/2022]
Abstract
We updated a field synopsis of genetic associations of cutaneous melanoma (CM) by systematically retrieving and combining data from all studies in the field published as of August 31, 2013. Data were available from 197 studies, which included 83,343 CM cases and 187,809 controls and reported on 1,126 polymorphisms in 289 different genes. Random-effects meta-analyses of 81 eligible polymorphisms evaluated in >4 data sets confirmed 20 single-nucleotide polymorphisms across 10 loci (TYR, AFG3L1P, CDK10, MYH7B, SLC45A2, MTAP, ATM, CLPTM1L, FTO, and CASP8) that have previously been published with genome-wide significant evidence for association (P<5 × 10(-8)) with CM risk, with certain variants possibly functioning as proxies of already tagged genes. Four other loci (MITF, CCND1, MX2, and PLA2G6) were also significantly associated with 5 × 10(-8)
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Affiliation(s)
- Kyriaki Antonopoulou
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Irene Stefanaki
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Christina M Lill
- Neuropsychiatric Genetics Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Neurology, Focus Program Translational Neuroscience, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Foteini Chatzinasiou
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Katerina P Kypreou
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Fani Karagianni
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece
| | - Emmanouil Athanasiadis
- Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - George M Spyrou
- Center of Systems Biology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - John P A Ioannidis
- Department of Medicine, Stanford Prevention Research Center, Stanford University School of Medicine, Stanford, California, USA
| | - Lars Bertram
- Neuropsychiatric Genetics Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany; Department of Medicine, School of Public Health, Imperial College London, London, UK
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, Clinical and Molecular Epidemiology Unit, School of Medicine, University of Ioannina, Ioannina, Greece; Department of Epidemiology and Biostatistics, Imperial College London, St Mary's Campus, London, UK
| | - Alexander J Stratigos
- Department of Dermatology, University of Athens School of Medicine, Andreas Sygros Hospital, Athens, Greece.
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Sobota RS, Shriner D, Kodaman N, Goodloe R, Zheng W, Gao YT, Edwards TL, Amos CI, Williams SM. Addressing population-specific multiple testing burdens in genetic association studies. Ann Hum Genet 2015; 79:136-47. [PMID: 25644736 DOI: 10.1111/ahg.12095] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/06/2014] [Indexed: 01/06/2023]
Abstract
The number of effectively independent tests performed in genome-wide association studies (GWAS) varies by population, making a universal P-value threshold inappropriate. We estimated the number of independent SNPs in Phase 3 HapMap samples by: (1) the LD-pruning function in PLINK, and (2) an autocorrelation-based approach. Autocorrelation was also used to estimate the number of independent SNPs in whole genome sequences from 1000 Genomes. Both approaches yielded consistent estimates of numbers of independent SNPs, which were used to calculate new population-specific thresholds for genome-wide significance. African populations had the most stringent thresholds (1.49 × 10(-7) for YRI at r(2) = 0.3), East Asian populations the least (3.75 × 10(-7) for JPT at r(2) = 0.3). We also assessed how using population-specific significance thresholds compared to using a single multiple testing threshold at the conventional 5 × 10(-8) cutoff. Applied to a previously published GWAS of melanoma in Caucasians, our approach identified two additional genes, both previously associated with the phenotype. In a Chinese breast cancer GWAS, our approach identified 48 additional genes, 19 of which were in or near genes previously associated with the phenotype. We conclude that the conventional genome-wide significance threshold generates an excess of Type 2 errors, particularly in GWAS performed on more recently founded populations.
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Affiliation(s)
- Rafal S Sobota
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee; Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
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Olsen CM, Neale RE, Green AC, Webb PM, The QSkin Study, The Epigene Study, Whiteman DC. Independent validation of six melanoma risk prediction models. J Invest Dermatol 2014; 135:1377-1384. [PMID: 25548858 DOI: 10.1038/jid.2014.533] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 11/18/2014] [Accepted: 12/09/2014] [Indexed: 11/10/2022]
Abstract
Identifying people at high risk of melanoma is important for targeted prevention activities and surveillance. Several tools have been developed to classify melanoma risk, but few have been independently validated. We assessed the discriminatory performance of six melanoma prediction tools by applying them to individuals from two independent data sets, one comprising 762 melanoma cases and the second a population-based sample of 42,116 people without melanoma. We compared the model predictions with actual melanoma status to measure sensitivity and specificity. The performance of the models was variable with sensitivity ranging from 97.7 to 10.5% and specificity from 99.6 to 1.3%. The ability of all the models to discriminate between cases and controls, however, was generally high. The model developed by MacKie et al. (1989) had higher sensitivity and specificity for men (0.89 and 0.88) than women (0.79 and 0.72). The tool developed by Cho et al. (2005) was highly specific (men, 0.92; women, 0.99) but considerably less sensitive (men, 0.64; women, 0.37). Other models were either highly specific but lacked sensitivity or had low to very low specificity and higher sensitivity. Poor performance was partly attributable to the use of non-standardized assessment items and various differing interpretations of what constitutes "high risk".
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Affiliation(s)
- Catherine M Olsen
- Cancer Control Group, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rachel E Neale
- Cancer Control Group, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Adèle C Green
- Cancer Control Group, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; Cancer Research UK Manchester Institute and Institute of Inflammation and Repair, University of Manchester, Manchester, UK
| | - Penelope M Webb
- Cancer Control Group, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - The QSkin Study
- Cancer Control Group, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - The Epigene Study
- Cancer Control Group, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David C Whiteman
- Cancer Control Group, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
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Abstract
The incidence of melanoma continues to rise in most fair-skinned populations. Strategies to curb the toll from melanoma include targeting the patients who are at highest risk with the aim of either preventing the onset of cancer or intervening early in order to improve survival. The challenge has been to synthesize the available information on risk factors into prediction tools with clinical utility, such that 'high-risk' patients can be identified with accuracy. While a number of risk prediction tools for melanoma have been developed, few have undergone rigorous evaluation of their performance in order to assess calibration or discrimination, and even fewer have been validated in independent populations. Future research should assess the validity of existing tools and seek to integrate the increasing volumes of data being generated by genomic studies.
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Affiliation(s)
- David Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, PO Royal Brisbane & Women's Hospital, Brisbane, Queensland, Australia
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Development of a melanoma risk prediction model incorporating MC1R genotype and indoor tanning exposure: impact of mole phenotype on model performance. PLoS One 2014; 9:e101507. [PMID: 25003831 PMCID: PMC4086828 DOI: 10.1371/journal.pone.0101507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 06/08/2014] [Indexed: 12/21/2022] Open
Abstract
Background Identifying individuals at increased risk for melanoma could potentially improve public health through targeted surveillance and early detection. Studies have separately demonstrated significant associations between melanoma risk, melanocortin receptor (MC1R) polymorphisms, and indoor ultraviolet light (UV) exposure. Existing melanoma risk prediction models do not include these factors; therefore, we investigated their potential to improve the performance of a risk model. Methods Using 875 melanoma cases and 765 controls from the population-based Minnesota Skin Health Study we compared the predictive ability of a clinical melanoma risk model (Model A) to an enhanced model (Model F) using receiver operating characteristic (ROC) curves. Model A used self-reported conventional risk factors including mole phenotype categorized as “none”, “few”, “some” or “many” moles. Model F added MC1R genotype and measures of indoor and outdoor UV exposure to Model A. We also assessed the predictive ability of these models in subgroups stratified by mole phenotype (e.g. nevus-resistant (“none” and “few” moles) and nevus-prone (“some” and “many” moles)). Results Model A (the reference model) yielded an area under the ROC curve (AUC) of 0.72 (95% CI = 0.69, 0.74). Model F was improved with an AUC = 0.74 (95% CI = 0.71–0.76, p<0.01). We also observed substantial variations in the AUCs of Models A & F when examined in the nevus-prone and nevus-resistant subgroups. Conclusions These results demonstrate that adding genotypic information and environmental exposure data can increase the predictive ability of a clinical melanoma risk model, especially among nevus-prone individuals.
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García-Borrón JC, Abdel-Malek Z, Jiménez-Cervantes C. MC1R, the cAMP pathway, and the response to solar UV: extending the horizon beyond pigmentation. Pigment Cell Melanoma Res 2014; 27:699-720. [PMID: 24807163 DOI: 10.1111/pcmr.12257] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 05/01/2014] [Indexed: 12/20/2022]
Abstract
The melanocortin 1 receptor (MC1R) is a G protein-coupled receptor crucial for the regulation of melanocyte proliferation and function. Upon binding melanocortins, MC1R activates several signaling cascades, notably the cAMP pathway leading to synthesis of photoprotective eumelanin. Polymorphisms in the MC1R gene are a major source of normal variation of human hair color and skin pigmentation, response to ultraviolet radiation (UVR), and skin cancer susceptibility. The identification of a surprisingly high number of MC1R natural variants strongly associated with pigmentary phenotypes and increased skin cancer risk has prompted research on the functional properties of the wild-type receptor and frequent mutant alleles. We summarize current knowledge on MC1R structural and functional properties, as well as on its intracellular trafficking and signaling. We also review the current knowledge about the function of MC1R as a skin cancer, particularly melanoma, susceptibility gene and how it modulates the response of melanocytes to UVR.
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Affiliation(s)
- Jose C García-Borrón
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Murcia, Murcia, Spain; Instituto Murciano de Investigación Biomédica (IMIB), El Palmar, Murcia, Spain
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Konitsiotis S, Bostantjopoulou S, Chondrogiorgi M, Katsarou Z, Tagaris G, Mavromatis I, Ntzani EE, Mentenopoulos G. Clinical characteristics of Parkinson's disease patients in Greece: a multicenter, nation-wide, cross-sectional study. J Neurol Sci 2014; 343:36-40. [PMID: 24950902 DOI: 10.1016/j.jns.2014.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/19/2014] [Accepted: 05/02/2014] [Indexed: 11/25/2022]
Abstract
Parkinson's disease is a neurodegenerative disease, with a constantly increasing prevalence and a high global financial impact arising from direct and indirect costs. Large-scale, observational studies provide data that support the better comprehension of disease aspects, constitute a baseline reference for future studies and assist comparisons among different patient populations, allowing the recognition of distinctive characteristics and special needs. The present study is the first to depict the clinical characteristics and their interplay in a large sample of Parkinson's disease (PD) patients in Greece. Nine hundred eighty six consecutive PD outpatients were recruited from 17 centers around Greece in the time period from 8/2007 to 7/2009 and were examined and interviewed by movement disorders experts. Multiple clinical characteristics were recorded including age at diagnosis, disease severity, patients' self classification of PD symptoms and their relevance to physician's global clinical impression, smoking, alcohol consumption, presence of family history for PD, dementia, depression, hypertension, cancer and other comorbidities. Associations of high clinical significance were found between certain clinical characteristics.
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Affiliation(s)
- Spiridon Konitsiotis
- Department of Neurology, Medical School, University of Ioannina, Stavrou Niarchou Av., University Campus, P.C. 45110 Ioannina, Greece.
| | - Sevasti Bostantjopoulou
- 3rd Department of Neurology, Medical School, Aristotle University of Thessaloniki, P.C. 54124 Thessaloniki, Greece
| | - Maria Chondrogiorgi
- Department of Neurology, Medical School, University of Ioannina, Stavrou Niarchou Av., University Campus, P.C. 45110 Ioannina, Greece
| | - Zoe Katsarou
- Department of Neurology, Hipporkation Hospital, Konstantinoupoleos 49, P.C. 54642 Thessaloniki Greece
| | - Georgios Tagaris
- Department of Neurology, Gennimatas General Hospital, Mesogion Av 154, P.C. 11527 Athens, Greece
| | - Ioannis Mavromatis
- 2nd Department of Neurology, Medical School, Aristotle University of Thessaloniki, P.C. 54124 Thessaloniki, Greece
| | - Evangelia E Ntzani
- Department of Hygiene and Epidemiology, Medical School, University of Ioannina, Stavrou Niarchou Av., University Campus, P.C. 45110 Ioannina, Greece
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Talaganis JA, Biello K, Plaka M, Polydorou D, Papadopoulos O, Trakatelli M, Sotiriadis D, Tsoutsos D, Kechagias G, Gogas H, Antoniou C, Swetter SM, Geller AC, Stratigos AJ. Demographic, behavioural and physician-related determinants of early melanoma detection in a low-incidence population. Br J Dermatol 2014; 171:832-8. [PMID: 24749902 DOI: 10.1111/bjd.13068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND Knowledge of the factors that influence early detection of melanoma is important in developing strategies to reduce associated mortality. OBJECTIVES To identify sociodemographic, behavioural and medical care-related factors associated with melanoma thickness in a low-incidence population but with a high case fatality. PATIENTS AND METHODS In a multicentre, retrospective, survey-based study of 202 patients with a recent diagnosis of invasive melanoma (< 1 year), we collected data on demographic and behavioural factors, attitudes towards prevention, access to medical care, frequency of skin self-examination (SSE) and physician skin examination (PSE) in relation to melanoma thickness. RESULTS Thinner tumours (≤ 1 mm, 80 melanomas) were associated with female sex (P ≤ 0.049), nonnodular (superficial spreading melanoma, lentigo maligna melanoma, acral lentiginous melanoma) histological subtypes (P < 0.001), absence of ulceration (P ≤ 0.001), and location other than lower extremity or trunk location (P ≤ 0.004). Patients married at the time of diagnosis or who performed SSE during the year prior to diagnosis were more likely to have thinner tumours than those who did not [odds ratio (OR) 3.45, 95% confidence interval (CI) 1.48-8.04 and OR 2.43, 95% CI 1.10-5.34, respectively]. Full-body skin examination by a physician was not significantly associated with thinner melanoma (OR 1.99, 95% CI 0.66-6.07). CONCLUSIONS SSE was shown to be an important factor in the detection of thin melanoma, in contrast to partial or full-body PSE, which did not show any statistically significant effect on tumour thickness.
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Affiliation(s)
- J A Talaganis
- Department of Dermatology, University of Athens Medical School, Andreas Sygros Hospital, Dragoumi 5, 161 21, Athens, Greece
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Cust AE, Goumas C, Vuong K, Davies JR, Barrett JH, Holland EA, Schmid H, Agha-Hamilton C, Armstrong BK, Kefford RF, Aitken JF, Giles GG, Bishop D, Newton-Bishop JA, Hopper JL, Mann GJ, Jenkins MA. MC1R genotype as a predictor of early-onset melanoma, compared with self-reported and physician-measured traditional risk factors: an Australian case-control-family study. BMC Cancer 2013; 13:406. [PMID: 24134749 PMCID: PMC3766240 DOI: 10.1186/1471-2407-13-406] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Accepted: 08/29/2013] [Indexed: 11/10/2022] Open
Abstract
Background Melanocortin-1 receptor (MC1R) gene variants are very common and are associated with melanoma risk, but their contribution to melanoma risk prediction compared with traditional risk factors is unknown. We aimed to 1) evaluate the separate and incremental contribution of MC1R genotype to prediction of early-onset melanoma, and compare this with the contributions of physician-measured and self-reported traditional risk factors, and 2) develop risk prediction models that include MC1R, and externally validate these models using an independent dataset from a genetically similar melanoma population. Methods Using data from an Australian population-based, case-control-family study, we included 413 case and 263 control participants with sequenced MC1R genotype, clinical skin examination and detailed questionnaire. We used unconditional logistic regression to estimate predicted probabilities of melanoma. Results were externally validated using data from a similar study in England. Results When added to a base multivariate model containing only demographic factors, MC1R genotype improved the area under the receiver operating characteristic curve (AUC) by 6% (from 0.67 to 0.73; P < 0.001) and improved the quartile classification by a net 26% of participants. In a more extensive multivariate model, the factors that contributed significantly to the AUC were MC1R genotype, number of nevi and previous non-melanoma skin cancer; the AUC was 0.78 (95% CI 0.75-0.82) for the model with self-reported nevi and 0.83 (95% CI 0.80-0.86) for the model with physician-counted nevi. Factors that did not further contribute were sun and sunbed exposure and pigmentation characteristics. Adding MC1R to a model containing pigmentation characteristics and other self-reported risk factors increased the AUC by 2.1% (P = 0.01) and improved the quartile classification by a net 10% (95% CI 1-18%, P = 0.03). Conclusions Although MC1R genotype is strongly associated with skin and hair phenotype, it was a better predictor of early-onset melanoma than was pigmentation characteristics. Physician-measured nevi and previous non-melanoma skin cancer were also strong predictors. There might be modest benefit to measuring MC1R genotype for risk prediction even if information about traditional self-reported or clinically measured pigmentation characteristics and nevi is already available.
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