Prediction of non-muscle invasive bladder cancer outcomes assessed by innovative multimarker prognostic models

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Background:
We adapted Bayesian statistical learning strategies to the prognosis field to investigate if genome-wide common SNP improve the prediction ability of clinico-pathological prognosticators and applied it to non-muscle invasive bladder cancer (NMIBC) patients.

Methods:
Adapted Bayesian sequential threshold models in combination with LASSO were applied to consider the time-to-event and the censoring nature of data. We studied 822 NMIBC patients followed-up >10 years. The study outcomes were time-to-first-recurrence and time-to-progression. The predictive ability of the models including up to 171,304 SNP and/or 6 clinico-pathological prognosticators was evaluated using AUC-ROC and determination coefficient.

Results:
Clinico-pathological prognosticators explained a larger proportion of the time-to-first-recurrence (3.1 %) and time-to-progression (5.4 %) phenotypic variances than SNPs (1 and 0.01 %, respectively). Adding SNPs to the clinico-pathological-parameters model slightly improved the prediction of time-to-first-recurrence (up to 4 %). The prediction of time-to-progression using both clinico-pathological prognosticators and SNP did not improve. Heritability (ĥ ²) of both outcomes was <1 % in NMIBC.

Conclusions:
We adapted a Bayesian statistical learning method to deal with a large number of parameters in prognostic studies. Common SNPs showed a limited role in predicting NMIBC outcomes yielding a very low heritability for both outcomes. We report for the first time a heritability estimate for a disease outcome. Our method can be extended to other disease models.

Keywords:
Multimarker models Bayesian statistical learning method Bayesian regression Bayesian LASSO AUC-ROC Determination coefficient heritability Bladder cancer outcome Prognosis Recurrence Progression Genome-wide common SNP Illumina Infinium HumanHap 1 M array Predictive ability

Autoři: E. López De Maturana ¹; A. Picornell ¹; A. Masson-Lecomte ¹; M. Kogevinas ^2,10; M. Márquez ¹; A. Carrato ³; A. Tardón ^4,10; J. Lloreta ⁵; M. García-Closas ⁶; D. Silverman ⁷; N. Rothman ⁷; S. Chanock ⁷; F. X. Real ⁸; M. E. Goddard ⁹; N. Malats ^1*; And On Behalf Of The Sbc/epicuro Study Investigators
Působiště autorů: Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández, Almagro , 80 , Madrid, Spain ¹; Centre for Research in Environmental Epidemiology (CREAL), Parc de Salut Mar, Barcelona, Spain ²; Servicio de Oncología, Hospital Universitario Ramon y Cajal, Madrid, and Servicio de Oncología, Hospital Universitario de Elche, Elche, Spain ³; Department of Preventive Medicine Universidad de Oviedo, Oviedo, Spain ⁴; Parc de Salut Mar and Departament of Pathology, Hospital del Mar - IMAS, Barcelona, Spain ⁵; Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK ⁶; Division of Cancer Epidemiology and Genetics, National Cancer Institute, Department of Health and Human Services, Bethesda, Maryland, USA ⁷; Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), Madrid, and Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain ⁸; Biosciences Research Division, Department of Environment and Primary Industries, Agribio, and Department of Food and Agricultural Systems, University of Melbourne, Melbourne, Australia ⁹; CIBERESP, Madrid, Spain. ¹⁰
Vyšlo v časopise: BMC Cancer 2016, 351:16
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1186/s12885-016-2361-7

© 2016 de Maturana et al.

Open access
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
The electronic version of this article is the complete one and can be found online at: http://bmccancer.biomedcentral.com/articles/10.1186/s12885-016-2361-7

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