Benchmarking machine learning models for late-onset alzheimer's disease prediction from genomic data

被引：48

作者：

De Velasco Oriol, Javier ^{[1
]}

Vallejo, Edgar E. ^{[1
]}

Estrada, Karol ^{[2
]}

Tamez Pena, Jose Gerardo ^{[1
]}

机构：

[1] Tecnol Monterrey, Escuela Med & Ciencias Salud, Dept Bioinformat, Monterrey 64710, Mexico

[2] Brandeis Univ, Grad Profess Studies, Waltham, MA 02453 USA

来源：

BMC BIOINFORMATICS | 2019年 / 20卷 / 01期

关键词：

Alzheimer's disease; Machine learning; Benchmarking; Genome-wide association studies; GENETICS; BIOMARKERS; PHENOTYPES; PROGRESS; LOCI;

D O I：

10.1186/s12859-019-3158-x

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Background: Late-Onset Alzheimer's Disease (LOAD) is a leading form of dementia. There is no effective cure for LOAD, leaving the treatment efforts to depend on preventive cognitive therapies, which stand to benefit from the timely estimation of the risk of developing the disease. Fortunately, a growing number of Machine Learning methods that are well positioned to address this challenge are becoming available. Results: We conducted systematic comparisons of representative Machine Learning models for predicting LOAD from genetic variation data provided by the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. Our experimental results demonstrate that the classification performance of the best models tested yielded similar to 72% of area under the ROC curve. Conclusions: Machine learning models are promising alternatives for estimating the genetic risk of LOAD. Systematic machine learning model selection also provides the opportunity to identify new genetic markers potentially associated with the disease.

引用

页数：17

共 32 条

[1] A Bayesian Model for the Prediction and Early Diagnosis of Alzheimer's Disease [J].

Alexiou, Athanasios ;

Mantzavinos, Vasileios D. ;

Greig, Nigel H. ;

Kamal, Mohammad A. .

FRONTIERS IN AGING NEUROSCIENCE, 2017, 9

[2] ANALYSIS OF GENETICS AND RISK FACTORS OF ALZHEIMER'S DISEASE [J].

Ates, M. Panpalli ;

Karaman, Y. ;

Guntekin, S. ;

Ergun, M. A. .

NEUROSCIENCE, 2016, 325 :124-131

[3] Alzheimer's disease [J].

Ballard, Clive ;

Gauthier, Serge ;

Corbett, Anne ;

Brayne, Carol ;

Aarsland, Dag ;

Jones, Emma .

LANCET, 2011, 377 (9770) :1019-1031

[4] An Expanded View of Complex Traits: From Polygenic to Omnigenic [J].

Boyle, Evan A. ;

Li, Yang I. ;

Pritchard, Jonathan K. .

CELL, 2017, 169 (07) :1177-1186

[5] Prediction to prevention in Alzheimer's disease and dementia [J].

Dufouil, Carole ;

Glymour, M. Maria .

LANCET NEUROLOGY, 2018, 17 (05) :388-389

[6] Exploring Genetic Associations of Alzheimer's Disease Loci With Mild Cognitive Impairment Neurocognitive Endophenotypes [J].

Espinosa, Ana ;

Hernandez-Olasagarre, Begona ;

Moreno-Grau, Sonia ;

Kleineidam, Luca ;

Heilmann-Heimbach, Stefanie ;

Hernandez, Isabel ;

Wolfsgruber, Steffen ;

Wagner, Holger ;

Rosende-Roca, Maitee ;

Mauleon, Ana ;

Vargas, Liliana ;

Lafuente, Asuncion ;

Rodriguez-Gomez, Octavio ;

Abdelnour, Carla ;

Gil, Silvia ;

Marquie, Marta ;

Santos-Santos, Miguel A. ;

Sanabria, Angela ;

Ortega, Gemma ;

Monte-Rubio, Gemma ;

Perez, Alba ;

Ibarria, Marta ;

Ruiz, Susana ;

Kornhuber, Johannes ;

Peters, Oliver ;

Froelich, Lutz ;

Huell, Michael ;

Wiltfang, Jens ;

Luck, Tobias ;

Riedel-Heller, Steffi ;

Montrreal, Laura ;

Canabate, Pilar ;

Moreno, Mariola ;

Preckler, Silvia ;

Aguilera, Nuria ;

de Rojas, Itziar ;

Orellana, Adelina ;

Alegret, Montserrat ;

Valero, Sergi ;

Noethen, Markus M. ;

Wagner, Michael ;

Jessen, Frank ;

Tarraga, Lluis ;

Boada, Merce ;

Ramirez, Alfredo ;

Ruiz, Agustin .

FRONTIERS IN AGING NEUROSCIENCE, 2018, 10

[7] Machine Learning SNP Based Prediction for Precision Medicine [J].

Ho, Daniel Sik Wai ;

Schierding, William ;

Wake, Melissa ;

Saffery, Richard ;

O'Sullivan, Justin .

FRONTIERS IN GENETICS, 2019, 10

[8] Genome-wide significant risk factors for Alzheimer's disease: role in progression to dementia due to Alzheimer's disease among subjects with mild cognitive impairment [J].

Lacour, A. ;

Espinosa, A. ;

Louwersheimer, E. ;

Heilmann, S. ;

Hernandez, I. ;

Wolfsgruber, S. ;

Fernandez, V. ;

Wagner, H. ;

Rosende-Roca, M. ;

Mauleon, A. ;

Moreno-Grau, S. ;

Vargas, L. ;

Pijnenburg, Y. A. L. ;

Koene, T. ;

Rodriguez-Gomez, O. ;

Ortega, G. ;

Ruiz, S. ;

Holstege, H. ;

Sotolongo-Grau, O. ;

Kornhuber, J. ;

Peters, O. ;

Froelich, L. ;

Huell, M. ;

Ruether, E. ;

Wiltfang, J. ;

Scherer, M. ;

Riedel-Heller, S. ;

Alegret, M. ;

Noethen, M. M. ;

Scheltens, P. ;

Wagner, M. ;

Tarraga, L. ;

Jessen, F. ;

Boada, M. ;

Maier, W. ;

van der Flier, W. M. ;

Becker, T. ;

Ramirez, A. ;

Ruiz, A. .

MOLECULAR PSYCHIATRY, 2017, 22 (01) :153-160

[9] Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease [J].

Lambert, Jean-Charles ;

Ibrahim-Verbaas, Carla A. ;

Harold, Denise ;

Naj, Adam C. ;

Sims, Rebecca ;

Bellenguez, Celine ;

Jun, Gyungah ;

DeStefano, Anita L. ;

Bis, Joshua C. ;

Beecham, Gary W. ;

Grenier-Boley, Benjamin ;

Russo, Giancarlo ;

Thornton-Wells, Tricia A. ;

Jones, Nicola ;

Smith, Albert V. ;

Chouraki, Vincent ;

Thomas, Charlene ;

Ikram, M. Arfan ;

Zelenika, Diana ;

Vardarajan, Badri N. ;

Kamatani, Yoichiro ;

Lin, Chiao-Feng ;

Gerrish, Amy ;

Schmidt, Helena ;

Kunkle, Brian ;

Dunstan, Melanie L. ;

Ruiz, Agustin ;

Bihoreau, Marie-Therese ;

Choi, Seung-Hoan ;

Reitz, Christiane ;

Pasquier, Florence ;

Hollingworth, Paul ;

Ramirez, Alfredo ;

Hanon, Olivier ;

Fitzpatrick, Annette L. ;

Buxbaum, Joseph D. ;

Campion, Dominique ;

Crane, Paul K. ;

Baldwin, Clinton ;

Becker, Tim ;

Gudnason, Vilmundur ;

Cruchaga, Carlos ;

Craig, David ;

Amin, Najaf ;

Berr, Claudine ;

Lopez, Oscar L. ;

De Jager, Philip L. ;

Deramecourt, Vincent ;

Johnston, Janet A. ;

Evans, Denis .

NATURE GENETICS, 2013, 45 (12) :1452-U206

[10] APP, PSEN1, and PSEN2 mutations in early-onset Alzheimer disease: A genetic screening study of familial and sporadic cases [J].

Lanoiselee, Helene-Marie ;

Nicolas, Gael ;

Wallon, David ;

Rovelet-Lecrux, Anne ;

Lacour, Morgane ;

Rousseau, Stephane ;

Richard, Anne -Claire ;

Pasquier, Florence ;

Rollin-Sillaire, Adeline ;

Martinaudl, Olivier ;

Quillard-Muraine, Muriel ;

de la Sayette, Vincent ;

Boutoleau-Bretonniere, Claire ;

Etcharry-Bouyx, Frederique ;

Chauvire, Valerie ;

Sarazin, Marie ;

le Berl, Isabelle ;

Epelbaum, Stephane ;

Jonveaux, Therese ;

Rouaud, Olivier ;

Ceccaldi, Mathieu ;

Felician, Olivier ;

Godefroy, Olivier ;

Formaglio, Maite ;

Croisile, Bernard ;

Auriacombe, Sophie ;

Chamard, Ludivine ;

Vincent, Jean-Louis ;

Sauvee, Mathilde ;

Marelli-Tosi, Cecilia ;

Gabelle, Audrey ;

Ozsancak, Canan ;

Pariente, Jeremie ;

Paquet, Claire ;

Hannequin, Didier ;

Campion, Dominique .

PLOS MEDICINE, 2017, 14 (03)

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