Literature DB >> 25362243

Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression.

Robert Küffner1, Neta Zach2, Raquel Norel3, Johann Hawe4, David Schoenfeld5, Liuxia Wang6, Guang Li6, Lilly Fang7, Lester Mackey8, Orla Hardiman9, Merit Cudkowicz10, Alexander Sherman10, Gokhan Ertaylan11, Moritz Grosse-Wentrup12, Torsten Hothorn13, Jules van Ligtenberg14, Jakob H Macke15, Timm Meyer12, Bernhard Schölkopf12, Linh Tran16, Rubio Vaughan14, Gustavo Stolovitzky3, Melanie L Leitner17.   

Abstract

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with substantial heterogeneity in its clinical presentation. This makes diagnosis and effective treatment difficult, so better tools for estimating disease progression are needed. Here, we report results from the DREAM-Phil Bowen ALS Prediction Prize4Life challenge. In this crowdsourcing competition, competitors developed algorithms for the prediction of disease progression of 1,822 ALS patients from standardized, anonymized phase 2/3 clinical trials. The two best algorithms outperformed a method designed by the challenge organizers as well as predictions by ALS clinicians. We estimate that using both winning algorithms in future trial designs could reduce the required number of patients by at least 20%. The DREAM-Phil Bowen ALS Prediction Prize4Life challenge also identified several potential nonstandard predictors of disease progression including uric acid, creatinine and surprisingly, blood pressure, shedding light on ALS pathobiology. This analysis reveals the potential of a crowdsourcing competition that uses clinical trial data for accelerating ALS research and development.

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Year:  2014        PMID: 25362243     DOI: 10.1038/nbt.3051

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


  47 in total

1.  Factors associated with survival in the National Registry of Veterans with ALS.

Authors:  Daniel M Pastula; Cynthia J Coffman; Kelli D Allen; Eugene Z Oddone; Edward J Kasarskis; Jennifer H Lindquist; Joel C Morgenlander; Barbara B Norman; Marvin P Rozear; Laura A Sams; Arman Sabet; Richard S Bedlack
Journal:  Amyotroph Lateral Scler       Date:  2009 Oct-Dec

2.  RandomForest4Life: a Random Forest for predicting ALS disease progression.

Authors:  Torsten Hothorn; Hans H Jung
Journal:  Amyotroph Lateral Scler Frontotemporal Degener       Date:  2014-09       Impact factor: 4.092

3.  A predictive model for progression of chronic kidney disease to kidney failure.

Authors:  Navdeep Tangri; Lesley A Stevens; John Griffith; Hocine Tighiouart; Ognjenka Djurdjev; David Naimark; Adeera Levin; Andrew S Levey
Journal:  JAMA       Date:  2011-04-11       Impact factor: 56.272

4.  Serum uric acid levels and the risk of Parkinson disease.

Authors:  Lonneke M L de Lau; Peter J Koudstaal; Albert Hofman; Monique M B Breteler
Journal:  Ann Neurol       Date:  2005-11       Impact factor: 10.422

5.  Amyotrophic lateral sclerosis disease progression model.

Authors:  Roberto Gomeni; Maurizio Fava
Journal:  Amyotroph Lateral Scler Frontotemporal Degener       Date:  2013-09-26       Impact factor: 4.092

6.  Uric acid levels predict survival in men with amyotrophic lateral sclerosis.

Authors:  Sabrina Paganoni; May Zhang; Alejandro Quiroz Zárate; Matthew Jaffa; Hong Yu; Merit E Cudkowicz; Anne-Marie Wills
Journal:  J Neurol       Date:  2012-02-10       Impact factor: 4.849

7.  Pattern of spread and prognosis in lower limb-onset ALS.

Authors:  Martin R Turner; Alice Brockington; Jakub Scaber; Hannah Hollinger; Rachael Marsden; Pamela J Shaw; Kevin Talbot
Journal:  Amyotroph Lateral Scler       Date:  2010-08

8.  Alzheimer's disease: diagnostics, prognostics and the road to prevention.

Authors:  Iris Grossman; Michael W Lutz; Donna G Crenshaw; Ann M Saunders; Daniel K Burns; Allen D Roses
Journal:  EPMA J       Date:  2010-06-29       Impact factor: 6.543

9.  Urate as a predictor of the rate of clinical decline in Parkinson disease.

Authors:  Alberto Ascherio; Peter A LeWitt; Kui Xu; Shirley Eberly; Arthur Watts; Wayne R Matson; Connie Marras; Karl Kieburtz; Alice Rudolph; Mikhail B Bogdanov; Steven R Schwid; Marsha Tennis; Caroline M Tanner; M Flint Beal; Anthony E Lang; David Oakes; Stanley Fahn; Ira Shoulson; Michael A Schwarzschild
Journal:  Arch Neurol       Date:  2009-12

10.  Wisdom of crowds for robust gene network inference.

Authors:  Daniel Marbach; James C Costello; Robert Küffner; Nicole M Vega; Robert J Prill; Diogo M Camacho; Kyle R Allison; Manolis Kellis; James J Collins; Gustavo Stolovitzky
Journal:  Nat Methods       Date:  2012-07-15       Impact factor: 28.547

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  70 in total

1.  Industry-academia collaborations for biomarkers.

Authors:  Khusru Asadullah; Andreas Busch; Matthias Gottwald; Petra Reinke; Lilla Landeck
Journal:  Nat Rev Drug Discov       Date:  2015-10-30       Impact factor: 84.694

2.  Transplantation of spinal cord-derived neural stem cells for ALS: Analysis of phase 1 and 2 trials.

Authors:  Jonathan D Glass; Vicki S Hertzberg; Nicholas M Boulis; Jonathan Riley; Thais Federici; Meraida Polak; Jane Bordeau; Christina Fournier; Karl Johe; Tom Hazel; Merit Cudkowicz; Nazem Atassi; Lawrence F Borges; Seward B Rutkove; Jayna Duell; Parag G Patil; Stephen A Goutman; Eva L Feldman
Journal:  Neurology       Date:  2016-06-29       Impact factor: 9.910

Review 3.  Defining Glomerular Disease in Mechanistic Terms: Implementing an Integrative Biology Approach in Nephrology.

Authors:  Laura H Mariani; William F Pendergraft; Matthias Kretzler
Journal:  Clin J Am Soc Nephrol       Date:  2016-09-14       Impact factor: 8.237

4.  DREAMing of benchmarks.

Authors:  Irene Jarchum; Susan Jones
Journal:  Nat Biotechnol       Date:  2015-01       Impact factor: 54.908

5.  Modeling the course of amyotrophic lateral sclerosis.

Authors:  Christina Fournier; Jonathan D Glass
Journal:  Nat Biotechnol       Date:  2015-01       Impact factor: 54.908

6.  Prognostic models for amyotrophic lateral sclerosis: a systematic review.

Authors:  Lu Xu; Bingjie He; Yunjing Zhang; Lu Chen; Dongsheng Fan; Siyan Zhan; Shengfeng Wang
Journal:  J Neurol       Date:  2021-03-10       Impact factor: 4.849

7.  Model-Based and Model-Free Techniques for Amyotrophic Lateral Sclerosis Diagnostic Prediction and Patient Clustering.

Authors:  Ming Tang; Chao Gao; Stephen A Goutman; Alexandr Kalinin; Bhramar Mukherjee; Yuanfang Guan; Ivo D Dinov
Journal:  Neuroinformatics       Date:  2019-07

8.  Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach.

Authors:  Robert Kueffner; Neta Zach; Maya Bronfeld; Raquel Norel; Nazem Atassi; Venkat Balagurusamy; Barbara Di Camillo; Adriano Chio; Merit Cudkowicz; Donna Dillenberger; Javier Garcia-Garcia; Orla Hardiman; Bruce Hoff; Joshua Knight; Melanie L Leitner; Guang Li; Lara Mangravite; Thea Norman; Liuxia Wang; Jinfeng Xiao; Wen-Chieh Fang; Jian Peng; Chen Yang; Huan-Jui Chang; Gustavo Stolovitzky
Journal:  Sci Rep       Date:  2019-01-24       Impact factor: 4.379

Review 9.  Crowdsourcing biomedical research: leveraging communities as innovation engines.

Authors:  Julio Saez-Rodriguez; James C Costello; Stephen H Friend; Michael R Kellen; Lara Mangravite; Pablo Meyer; Thea Norman; Gustavo Stolovitzky
Journal:  Nat Rev Genet       Date:  2016-07-15       Impact factor: 53.242

10.  Urate levels predict survival in amyotrophic lateral sclerosis: Analysis of the expanded Pooled Resource Open-Access ALS clinical trials database.

Authors:  Sabrina Paganoni; Katharine Nicholson; James Chan; Amy Shui; David Schoenfeld; Alexander Sherman; James Berry; Merit Cudkowicz; Nazem Atassi
Journal:  Muscle Nerve       Date:  2017-09-21       Impact factor: 3.217

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