Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data
Creators: name: Romagnoni, Alberto
name: Jégou, Simon
name: Van Steen, Kristel
name: Wainrib, Gilles
name: Hugot, Jean-Pierre
name: Peyrin-Biroulet, Laurent
name: Chamaillard, Mathias
name: Colombel, Jean-Frederick
name: Cottone, Mario
name: D’Amato, Mauro
name: D’Incà, Renata
name: Halfvarson, Jonas
name: Henderson, Paul
name: Karban, Amir
name: Kennedy, Nicholas A.
name: Khan, Mohammed Azam
name: Lémann, Marc
name: Levine, Arie
name: Massey, Dunecan
name: Milla, Monica
name: Ng, Sok Meng Evelyn
name: Oikonomou, Ioannis
name: Peeters, Harald
name: Proctor, Deborah D.
name: Rahier, Jean-Francois
name: Rutgeerts, Paul
name: Seibold, Frank
name: Stronati, Laura
name: Taylor, Kirstin M.
name: Törkvist, Leif
name: Ublick, Kullak
name: Van Limbergen, Johan
name: Van Gossum, Andre
name: Vatn, Morten H.
name: Zhang, Hu
name: Zhang, Wei
name: Andrews, Jane M.
name: Bampton, Peter A.
name: Barclay, Murray
name: Florin, Timothy H.
name: Gearry, Richard
name: Krishnaprasad, Krupa
name: Lawrance, Ian C.
name: Mahy, Gillian
name: Montgomery, Grant W.
name: Radford-Smith, Graham
name: Roberts, Rebecca L.
name: Simms, Lisa A.
name: Hanigan, Katherine
name: Croft, Anthony
name: Amininijad, Leila
name: Cleynen, Isabelle
name: Dewit, Olivier
name: Franchimont, Denis
name: Georges, Michel
name: Laukens, Debby
name: Theatre, Emilie
name: Van Gossum, André
name: Vermeire, Severine
name: Aumais, Guy
name: Baidoo, Leonard
name: Barrie, Arthur M.
name: Beck, Karen
name: Bernard, Edmond-Jean
name: Binion, David G.
name: Bitton, Alain
name: Brant, Steve R.
name: Cho, Judy H.
name: Cohen, Albert
name: Croitoru, Kenneth
name: Daly, Mark J.
name: Datta, Lisa W.
name: Deslandres, Colette
name: Duerr, Richard H.
name: Dutridge, Debra
name: Ferguson, John
name: Fultz, Joann
name: Goyette, Philippe
name: Greenberg, Gordon R.
name: Haritunians, Talin
name: Jobin, Gilles
name: Katz, Seymour
name: Lahaie, Raymond G.
name: McGovern, Dermot P.
name: Nelson, Linda
name: Ng, Sok Meng
name: Ning, Kaida
name: Paré, Pierre
name: Regueiro, Miguel D.
name: Rioux, John D.
name: Ruggiero, Elizabeth
name: Schumm, L. Philip
name: Schwartz, Marc
name: Scott, Regan
name: Sharma, Yashoda
name: Silverberg, Mark S.
name: Spears, Denise
name: Steinhart, A. Hillary
name: Stempak, Joanne M.
name: Swoger, Jason M.
name: Tsagarelis, Constantina
name: Zhang, Clarence
name: Zhao, Hongyu
name: Aerts, Jan
name: Ahmad, Tariq
name: Arbury, Hazel
name: Attwood, Anthony
name: Auton, Adam
name: Ball, Stephen G.
name: Balmforth, Anthony J.
name: Barnes, Chris
name: Barrett, Jeffrey C.
name: Barroso, Inês
name: Barton, Anne
name: Bennett, Amanda J.
name: Bhaskar, Sanjeev
name: Blaszczyk, Katarzyna
name: Bowes, John
name: Brand, Oliver J.
name: Braund, Peter S.
name: Bredin, Francesca
name: Breen, Gerome
name: Brown, Morris J.
name: Bruce, Ian N.
name: Bull, Jaswinder
name: Burren, Oliver S.
name: Burton, John
name: Byrnes, Jake
name: Caesar, Sian
name: Cardin, Niall
name: Clee, Chris M.
name: Coffey, Alison J.
name: MC Connell, John
name: Conrad, Donald F.
name: Cooper, Jason D.
name: Dominiczak, Anna F.
name: Downes, Kate
name: Drummond, Hazel E.
name: Dudakia, Darshna
name: Dunham, Andrew
name: Ebbs, Bernadette
name: Eccles, Diana
name: Edkins, Sarah
name: Edwards, Cathryn
name: Elliot, Anna
name: Emery, Paul
name: Evans, David M.
name: Evans, Gareth
name: Eyre, Steve
name: Farmer, Anne
name: Ferrier, I. Nicol
name: Flynn, Edward
name: Forbes, Alistair
name: Forty, Liz
name: Franklyn, Jayne A.
name: Frayling, Timothy M.
name: Freathy, Rachel M.
name: Giannoulatou, Eleni
name: Gibbs, Polly
name: Gilbert, Paul
name: Gordon-Smith, Katherine
name: Gray, Emma
name: Green, Elaine
name: Groves, Chris J.
name: Grozeva, Detelina
name: Gwilliam, Rhian
name: Hall, Anita
name: Hammond, Naomi
name: Hardy, Matt
name: Harrison, Pile
name: Hassanali, Neelam
name: Hebaishi, Husam
name: Hines, Sarah
name: Hinks, Anne
name: Hitman, Graham A.
name: Hocking, Lynne
name: Holmes, Chris
name: Howard, Eleanor
name: Howard, Philip
name: Howson, Joanna M. M.
name: Hughes, Debbie
name: Hunt, Sarah
name: Isaacs, John D.
name: Jain, Mahim
name: Jewell, Derek P.
name: Johnson, Toby
name: Jolley, Jennifer D.
name: Jones, Ian R.
name: Jones, Lisa A.
name: Kirov, George
name: Langford, Cordelia F.
name: Lango-Allen, Hana
name: Lathrop, G. Mark
name: Lee, James
name: Lee, Kate L.
name: Lees, Charlie
name: Lewis, Kevin
name: Lindgren, Cecilia M.
name: Maisuria-Armer, Meeta
name: Maller, Julian
name: Mansfield, John
name: Marchini, Jonathan L.
name: Martin, Paul
name: Massey, Dunecan CO
name: McArdle, Wendy L.
name: McGuffin, Peter
name: McLay, Kirsten E.
name: McVean, Gil
name: Mentzer, Alex
name: Mimmack, Michael L.
name: Morgan, Ann E.
name: Morris, Andrew P.
name: Mowat, Craig
name: Munroe, Patricia B.
name: Myers, Simon
name: Newman, William
name: Nimmo, Elaine R.
name: O’Donovan, Michael C.
name: Onipinla, Abiodun
name: Ovington, Nigel R.
name: Owen, Michael J.
name: Palin, Kimmo
name: Palotie, Aarno
name: Parnell, Kirstie
name: Pearson, Richard
name: Pernet, David
name: Perry, John RB
name: Phillips, Anne
name: Plagnol, Vincent
name: Prescott, Natalie J.
name: Prokopenko, Inga
name: Quail, Michael A.
name: Rafelt, Suzanne
name: Rayner, Nigel W.
name: Reid, David M.
name: Renwick, Anthony
name: Ring, Susan M.
name: Robertson, Neil
name: Robson, Samuel
name: Russell, Ellie
name: Clair, David St
name: Sambrook, Jennifer G.
name: Sanderson, Jeremy D.
name: Sawcer, Stephen J.
name: Schuilenburg, Helen
name: Scott, Carol E.
name: Scott, Richard
name: Seal, Sheila
name: Shaw-Hawkins, Sue
name: Shields, Beverley M.
name: Simmonds, Matthew J.
name: Smyth, Debbie J.
name: Somaskantharajah, Elilan
name: Spanova, Katarina
name: Steer, Sophia
name: Stephens, Jonathan
name: Stevens, Helen E.
name: Stirrups, Kathy
name: Stone, Millicent A.
name: Strachan, David P.
name: Su, Zhan
name: Symmons, Deborah P. M.
name: Thompson, John R.
name: Thomson, Wendy
name: Tobin, Martin D.
name: Travers, Mary E.
name: Turnbull, Clare
name: Vukcevic, Damjan
name: Wain, Louise V.
name: Walker, Mark
name: Walker, Neil M.
name: Wallace, Chris
name: Warren-Perry, Margaret
name: Watkins, Nicholas A.
name: Webster, John
name: Weedon, Michael N.
name: Wilson, Anthony G.
name: Woodburn, Matthew
name: Wordsworth, B. Paul
name: Yau, Chris
name: Young, Allan H.
name: Zeggini, Eleftheria
name: Brown, Matthew A.
name: Burton, Paul R.
name: Caulfield, Mark J.
name: Compston, Alastair
name: Farrall, Martin
name: Gough, Stephen C. L.
name: Hall, Alistair S.
name: Hattersley, Andrew T.
name: Hill, Adrian V. S.
name: Mathew, Christopher G.
name: Pembrey, Marcus
name: Satsangi, Jack
name: Stratton, Michael R.
name: Worthington, Jane
name: Hurles, Matthew E.
name: Duncanson, Audrey
name: Ouwehand, Willem H.
name: Parkes, Miles
name: Rahman, Nazneen
name: Todd, John A.
name: Samani, Nilesh J.
name: Kwiatkowski, Dominic P.
name: McCarthy, Mark I.
name: Craddock, Nick
name: Deloukas, Panos
name: Donnelly, Peter
name: Blackwell, Jenefer M.
name: Bramon, Elvira
name: Casas, Juan P.
name: Corvin, Aiden
name: Jankowski, Janusz
name: Markus, Hugh S.
name: Palmer, Colin NA
name: Plomin, Robert
name: Rautanen, Anna
name: Trembath, Richard C.
name: Viswanathan, Ananth C.
name: Wood, Nicholas W.
name: Spencer, Chris C. A.
name: Band, Gavin
name: Bellenguez, Céline
name: Freeman, Colin
name: Hellenthal, Garrett
name: Pirinen, Matti
name: Strange, Amy
name: Blackburn, Hannah
name: Bumpstead, Suzannah J.
name: Dronov, Serge
name: Gillman, Matthew
name: Jayakumar, Alagurevathi
name: McCann, Owen T.
name: Liddle, Jennifer
name: Potter, Simon C.
name: Ravindrarajah, Radhi
name: Ricketts, Michelle
name: Waller, Matthew
name: Weston, Paul
name: Widaa, Sara
name: Whittaker, Pamela
Publisher: name: Apollo - University of Cambridge Repository
Year: 2019
Subjects: Article
/692/4020/1503/257/1402
/692/308/2056
/45
/45/43
/129
article

description: Abstract: Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machine learning (ML) approaches incited us to apply them to classify healthy and diseased people according to their genomic information. The Immunochip dataset containing 18,227 CD patients and 34,050 healthy controls enrolled and genotyped by the international Inflammatory Bowel Disease genetic consortium (IIBDGC) has been re-analyzed using a set of ML methods: penalized logistic regression (LR), gradient boosted trees (GBT) and artificial neural networks (NN). The main score used to compare the methods was the Area Under the ROC Curve (AUC) statistics. The impact of quality control (QC), imputing and coding methods on LR results showed that QC methods and imputation of missing genotypes may artificially increase the scores. At the opposite, neither the patient/control ratio nor marker preselection or coding strategies significantly affected the results. LR methods, including Lasso, Ridge and ElasticNet provided similar results with a maximum AUC of 0.80. GBT methods like XGBoost, LightGBM and CatBoost, together with dense NN with one or more hidden layers, provided similar AUC values, suggesting limited epistatic effects in the genetic architecture of the trait. ML methods detected near all the genetic variants previously identified by GWAS among the best predictors plus additional predictors with lower effects. The robustness and complementarity of the different methods are also studied. Compared to LR, non-linear models such as GBT or NN may provide robust complementary approaches to identify and classify genetic markers.