Predicting amyotrophic lateral sclerosis (ALS) progression with machine learning

References

• Bensimon G, Lacomblez L, Meininger V. A controlled trial of riluzole in amyotrophic lateral sclerosis. ALS/Riluzole Study Group. N Engl J Med. 1994;330:585–91.
   PubMed Web of Science ®Google Scholar
• Lacomblez L, Bensimon G, Leigh PN, Guillet P, Meininger V. Dose-ranging study of riluzole in amyotrophic lateral sclerosis. Amyotrophic Lateral Sclerosis/Riluzole Study Group II. Lancet. 1996;347:1425–31.
   PubMed Web of Science ®Google Scholar
• EDARAVONE (MCI-186) ALS 16 STUDY GROUP. A post-hoc subgroup analysis of outcomes in the first phase III clinical study of edaravone (MCI-186) in amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener. 2017;18:11–9.
   PubMed Web of Science ®Google Scholar
• Paganoni S, Macklin EA, Hendrix S, Berry JD, Elliott MA, Maiser S, et al. Trial of sodium phenylbutyrate-taurursodiol for amyotrophic lateral sclerosis. N Engl J Med. 2020;383:919–30.
   PubMed Web of Science ®Google Scholar
• Miller TM, Cudkowicz ME, Genge A, Shaw PJ, Sobue G, Bucelli RC, et al. Trial of antisense oligonucleotide tofersen for SOD1 ALS. N Engl J Med. 2022;387:1099–110.
   PubMed Web of Science ®Google Scholar
• Küffner R, Zach N, Norel R, Hawe J, Schoenfeld D, Wang L, et al. Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression. Nat Biotechnol. 2015;33:51–7.
   PubMed Web of Science ®Google Scholar
• Hothorn T, Jung HH. RandomForest4Life: a Random Forest for predicting ALS disease progression. Amyotroph Lateral Scler Frontotemporal Degener. 2014;15:444–52.
   PubMed Web of Science ®Google Scholar
• Tang M, Gao C, Goutman SA, Kalinin A, Mukherjee B, Guan Y, et al. Model-based and model-free techniques for amyotrophic lateral sclerosis diagnostic prediction and patient clustering. Neuroinform 2019;17:407–21.
   PubMed Web of Science ®Google Scholar
• Pancotti C, Birolo G, Rollo C, Sanavia T, Di Camillo B, Manera U, et al. Deep learning methods to predict amyotrophic lateral sclerosis disease progression. Sci Rep. 2022;12:13738.
   PubMed Web of Science ®Google Scholar
• Gomeni R, Fava M. Amyotrophic lateral sclerosis disease progression model. Amyotroph Lateral Scler Frontotemporal Degener. 2014;15:119–29.
   PubMed Web of Science ®Google Scholar
• Ong ML, Tan PF, Holbrook JD. Predicting functional decline and survival in amyotrophic lateral sclerosis. PLoS One. 2017;12:e0174925.
   PubMed Web of Science ®Google Scholar
• Hadad B, Lerner B. Domain adaptation from clinical trials data to the tertiary care clinic – Application to ALS. In: 2020 19th IEEE International Conference on Machine Learning and Applications (ICMLA). 2020:539–44.
   Google Scholar
• Taylor AA, Fournier C, Polak M, Wang L, Zach N, Keymer M, et al. Predicting disease progression in amyotrophic lateral sclerosis. Ann Clin Transl Neurol. 2016;3:866–75.
   PubMed Web of Science ®Google Scholar
• Gordon J, Lerner B. Insights into amyotrophic lateral sclerosis from a machine learning perspective. J Clin Med 2019;8:1578.
   PubMed Web of Science ®Google Scholar
• Halbersberg D, Lerner B. Temporal modeling of deterioration patterns and clustering for disease prediction of ALS patients. In: 2019 18th IEEE International Conference on Machine Learning And Applications (ICMLA). 2019:62–8.
   Google Scholar
• Cedarbaum JM, Stambler N, Malta E, Fuller C, Hilt D, Thurmond B, et al. The ALSFRS-R: a revised ALS functional rating scale that incorporates assessments of respiratory function. J Neurol Sci. 1999;169:13–21.
   PubMed Web of Science ®Google Scholar
• Zhou N, Manser P. Does including machine learning predictions in ALS clinical trial analysis improve statistical power? Ann Clin Transl Neurol. 2020;7:1756–65.
   PubMed Web of Science ®Google Scholar
• Fournier CN, James V, Glass JD. Clinically meaningful change: evaluation of the Rasch-built Overall Amyotrophic Lateral Sclerosis Disability Scale (ROADS) and the ALSFRS-R. Amyotroph Lateral Scler Frontotemporal Degener. 2023;24:311–6.
   PubMed Web of Science ®Google Scholar
• Atassi N, Berry J, Shui A, Zach N, Sherman A, Sinani E, et al. The PRO-ACT database: design, initial analyses, and predictive features. Neurology 2014;83:1719–25.
   PubMed Web of Science ®Google Scholar
• Statland JM, Moore D, Wang Y, Walsh M, Mozaffar T, Elman L, et al. Rasagiline for amyotrophic lateral sclerosis: a randomized, controlled trial. Muscle Nerve. 2019;59:201–7.
   PubMed Web of Science ®Google Scholar
• Writing Group, Edaravone (MCI-186) ALS 19 Study Group Safety and efficacy of edaravone in well defined patients with amyotrophic lateral sclerosis: a randomised, double-blind, placebo-controlled trial. Lancet Neurol 2017;16:505–12.
   PubMed Web of Science ®Google Scholar
• Luo L, Song Z, Li X, Huiwang n, Zeng Y, Qinwang n, et al. Efficacy and safety of edaravone in treatment of amyotrophic lateral sclerosis-a systematic review and meta-analysis. Neurol Sci. 2019;40:235–41.
   PubMed Web of Science ®Google Scholar
• Shefner JM, Andrews JA, Genge A, Jackson C, Lechtzin N, Miller TM, et al. A phase 2, double-blind, randomized, dose-ranging trial of reldesemtiv in patients with ALS. Amyotroph Lateral Scler Frontotemporal Degener. 2021;22:287–99.
   PubMed Web of Science ®Google Scholar
• Mario Negri Institute for Pharmacological Research. The effect of RNS60 on ALS biomarkers [Internet]. clinicaltrials.gov; 2023 Apr [cited 2023 Aug 16]. Report No.: NCT03456882. Available at: https://clinicaltrials.gov/study/NCT03456882
   Google Scholar
• Cudkowicz ME. HEALEY ALS platform trial - regimen B verdiperstat [Internet]. clinicaltrials.gov; 2023 May [cited 2023 Aug 16]. Report No.: NCT04436510. Available at: https://clinicaltrials.gov/study/NCT04436510
   Google Scholar
• Cudkowicz ME. HEALEY ALS Platform Trial - Regimen A Zilucoplan [Internet]. clinicaltrials.gov; 2023 Jun [cited 2023 Aug 16]. Report No.: NCT04436497. Available at: https://clinicaltrials.gov/study/NCT04436497
   Google Scholar
• WRITING GROUP ON BEHALF OF THE EDARAVONE (MCI-186) ALS 18 STUDY GROUP. Exploratory double-blind, parallel-group, placebo-controlled study of edaravone (MCI-186) in amyotrophic lateral sclerosis (Japan ALS severity classification: grade 3, requiring assistance for eating, excretion or ambulation). Amyotroph Lateral Scler Frontotemporal Degener 2017;18:40–8.
   PubMed Web of Science ®Google Scholar
• Mallinckrodt. A. Acthar® Gel in the Treatment of Subjects With Amyotrophic Lateral Sclerosis [Internet]. clinicaltrials.gov; 2020 Sep [cited 2023 Aug 16]. Report No.: NCT03068754. Available at: https://clinicaltrials.gov/study/NCT03068754
   Google Scholar
• Alexion. A Phase 3, Double-Blind, Randomized, Placebo-Controlled, Parallel Group, Multicenter Study With an Open-Label Extension to Evaluate the Efficacy and Safety of Ravulizumab in Patients With Amyotrophic Lateral Sclerosis (ALS) [Internet]. clinicaltrials.gov; 2022 Dec [cited 2023 Aug 16]. Report No.: NCT04248465. Available at: https://clinicaltrials.gov/study/NCT04248465
   Google Scholar
• Meininger V, Genge A, van den Berg LH, Robberecht W, Ludolph A, Chio A, et al. Safety and efficacy of ozanezumab in patients with amyotrophic lateral sclerosis: a randomised, double-blind, placebo-controlled, phase 2 trial. Lancet Neurol. 2017;16:208–16.
   PubMed Web of Science ®Google Scholar
• Weiss MD. Effect of mexiletine on cortical hyperexcitability in sporadic amyotrophic lateral sclerosis (SALS) [Internet]. clinicaltrials.gov; 2019 Nov [cited 2023 Aug 16]. Report No.: NCT02781454. Available at: https://clinicaltrials.gov/study/NCT02781454
   Google Scholar
• Cytokinetics. A phase 2, multi-center, double-blind, randomized, dose-ranging, placebo-controlled study to evaluate the efficacy, safety and tolerability of CK-2127107 in patients with amyotrophic lateral sclerosis (ALS) [Internet]. clinicaltrials.gov; 2020 Aug [cited 2023 Aug 16]. Report No.: NCT03160898. Available at: https://clinicaltrials.gov/study/NCT03160898
   Google Scholar
• Chen PC, Hsieh YC, Huang CC, Hu CJ. Tamoxifen for amyotrophic lateral sclerosis: a randomized double-blind clinical trial. Medicine (Baltimore). 2020;99:e20423.
   PubMed Web of Science ®Google Scholar
• Abe K, Itoyama Y, Sobue G, Tsuji S, Aoki M, Doyu M, et al. Confirmatory double-blind, parallel-group, placebo-controlled study of efficacy and safety of edaravone (MCI-186) in amyotrophic lateral sclerosis patients. Amyotroph Lateral Scler Frontotemporal Degener. 2014;15:610–7.
   PubMed Web of Science ®Google Scholar
• Dorst J, Kühnlein P, Hendrich C, Kassubek J, Sperfeld AD, Ludolph AC. Patients with elevated triglyceride and cholesterol serum levels have a prolonged survival in amyotrophic lateral sclerosis. J Neurol. 2011;258:613–7.
   PubMed Web of Science ®Google Scholar
• Wei QQ, Chen Y, Cao B, Ou RW, Zhang L, Hou Y, et al. Blood hemoglobin A1c levels and amyotrophic lateral sclerosis survival. Mol Neurodegener. 2017;12:69.
   PubMed Web of Science ®Google Scholar
• Guo Y, Liu Z, Krishnswamy P, Ramasamy S. Bayesian recurrent framework for missing data imputation and prediction with clinical time series [Internet]. arXiv; 2020 [cited 2022 Nov 10]. Available at: http://arxiv.org/abs/1911.07572
   Google Scholar
• Indurkhya N, Weiss SM. Solving regression problems with rule-based ensemble classifiers. In: Proceedings of the seventh ACM SIGKDD international conference on Knowledge discovery and data mining [Internet]. New York: Association for Computing Machinery; 2001:287–92. (KDD ’01).
   Google Scholar
• Westeneng HJ, Debray TPA, Visser AE, van Eijk RPA, Rooney JPK, Calvo A, et al. Prognosis for patients with amyotrophic lateral sclerosis: development and validation of a personalised prediction model. Lancet Neurol. 2018;17:423–33.
   PubMed Web of Science ®Google Scholar
• Cudkowicz ME, Shefner JM, Schoenfeld DA, Zhang H, Andreasson KI, Rothstein JD, et al. Trial of celecoxib in amyotrophic lateral sclerosis. Ann Neurol. 2006;60:22–31.
   PubMed Web of Science ®Google Scholar
• Wolff RF, Moons KGM, Riley RD, Whiting PF, Westwood M, Collins GS, et al. PROBAST: a tool to assess the risk of bias and applicability of prediction model studies. Ann Intern Med. 2019;170:51–8.
   PubMed Web of Science ®Google Scholar
• Lerman J. Study design in clinical research: sample size estimation and power analysis. Can J Anaesth. 1996;43:184–91.
   PubMed Web of Science ®Google Scholar
• Din Abdul Jabbar MA, Guo L, Guo Y, Simmons Z, Pioro EP, Ramasamy S, et al. Describing and characterising variability in ALS disease progression. Amyotroph Lateral Scler Frontotemporal Degener. 2023:1–12. doi: 10.1080/21678421.2023.2260838.
   PubMed Web of Science ®Google Scholar
• Bedlack RS, Vaughan T, Wicks P, Heywood J, Sinani E, Selsov R, et al. How common are ALS plateaus and reversals? Neurology 2016;86:808–12.
   PubMed Web of Science ®Google Scholar
• Hu N, Shen D, Yang X, Cui L, Liu M. Plateaus and reversals evaluated by different methods in patients with limb-onset amyotrophic lateral sclerosis. J Clin Neurosci. 2022;97:93–8.
   PubMed Web of Science ®Google Scholar
• Goyal NA, Berry JD, Windebank A, Staff NP, Maragakis NJ, van den Berg LH, et al. Addressing heterogeneity in amyotrophic lateral sclerosis CLINICAL TRIALS. Muscle Nerve. 2020;62:156–66.
   PubMed Web of Science ®Google Scholar
• Huber RG, Pandey S, Chhangani D, Rincon-Limas DE, Staff NP, Yeo CJJ. Identification of potential pathways and biomarkers linked to progression in ALS. Ann Clin Transl Neurol. 2023;10:150–65. Available at: https://onlinelibrary.wiley.com/doi/abs/10<?sch-permit JATS-0034-007?>.1002/acn3.51697
   PubMed Web of Science ®Google Scholar
• Gordon PH, Cheng B, Salachas F, Pradat PF, Bruneteau G, Corcia P, et al. Progression in ALS is not linear but is curvilinear. J Neurol. 2010;257:1713–7.
   PubMed Web of Science ®Google Scholar
• Jahandideh S, Taylor AA, Beaulieu D, Keymer M, Meng L, Bian A, et al. Longitudinal modeling to predict vital capacity in amyotrophic lateral sclerosis. Amyotroph Lateral Scler Frontotemporal Degener. 2018;19:294–302.
   PubMed Web of Science ®Google Scholar
• Seibold H, Zeileis A, Hothorn T. Individual treatment effect prediction for amyotrophic lateral sclerosis patients. Stat Methods Med Res. 2018;27:3104–25.
   PubMed Web of Science ®Google Scholar
• Czaplinski A, Yen AA, Appel SH. Forced vital capacity (FVC) as an indicator of survival and disease progression in an ALS clinic population. J Neurol Neurosurg Psychiatry. 2006;77:390–2.
   PubMed Web of Science ®Google Scholar
• Chio A, Logroscino G, Hardiman O, Swingler R, Mitchell D, Beghi E, et al. Prognostic factors in ALS: a critical review. Amyotroph Lateral Scler. 2009;10:310–23.
   PubMed Web of Science ®Google Scholar
• Lee I, Kazamel M, McPherson T, McAdam J, Bamman M, Amara A, et al. Fat mass loss correlates with faster disease progression in amyotrophic lateral sclerosis patients: exploring the utility of dual-energy x-ray absorptiometry in a prospective study. PLoS One. 2021;16:e0251087.
   PubMed Web of Science ®Google Scholar
• Ngo ST, Steyn FJ, McCombe PA. Body mass index and dietary intervention: implications for prognosis of amyotrophic lateral sclerosis. J Neurol Sci. 2014;340:5–12.
   PubMed Web of Science ®Google Scholar
• Stambler N, Charatan M, Cedarbaum JM. Prognostic indicators of survival in ALS. ALS CNTF Treatment Study Group. Neurology. 1998;50:66–72.
   PubMed Web of Science ®Google Scholar
• Tsai PH, Yang HC, Lin C, Sung CC, Chu P, Hsu YJ. Association of serum phosphate with low handgrip strength in patients with advanced chronic kidney disease. Nutrients 2021;13:3605.
   PubMed Web of Science ®Google Scholar
• Li C, Yang W, Wei Q, Shang H. Causal association of leukocytes count and amyotrophic lateral sclerosis: a Mendelian randomization study. Mol Neurobiol. 2020;57:4622–7.
   PubMed Web of Science ®Google Scholar
• Forgrave LM, Ma M, Best JR, DeMarco ML. The diagnostic performance of neurofilament light chain in CSF and blood for Alzheimer’s disease, frontotemporal dementia, and amyotrophic lateral sclerosis: a systematic review and meta-analysis. Alzheimers Dement (Amst). 2019;11:730–43.
   PubMedGoogle Scholar