Cited by 50Dementia and Cognitive Impairment ResearchAlzheimer's disease research and treatmentsArtificial Intelligence in Healthcare

Machine learning based multimodal neuroimaging genomics dementia score for predicting future conversion to alzheimer’s disease

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Mirabnahrazam, Ghazal, the Alzheimer’s Disease Neuroimaging Initiative, Ma, Da, Lee, Sieun, Popuri, Karteek, Lee, Hyunwoo, Cao, Jiguo, Wang, Lei +2 more·2022·Journal of Alzheimer's Disease

Abstract

Background: The increasing availability of databases containing both magnetic resonance imaging (MRI) and genetic data allows researchers to utilize multimodal data to better understand the characteristics of dementia of Alzheimer’s type (DAT). Objective: The goal of this study was to develop and analyze novel biomarkers that can help predict the development and progression of DAT. Methods: We used feature selection and ensemble learning classifier to develop an image/genotype-based DAT score that represents a subject’s likelihood of developing DAT in the future. Three feature types were used: MRI only, genetic only, and combined multimodal data. We used a novel data stratification method to better represent different stages of DAT. Using a pre-defined 0.5 threshold on DAT scores, we predicted whether a subject would develop DAT in the future. Results: Our results on Alzheimer’s Disease Neuroimaging Initiative (ADNI) database showed that dementia scores using genetic data could better predict future DAT progression for currently normal control subjects (Accuracy = 0.857) compared to MRI (Accuracy = 0.143), while MRI can better characterize subjects with stable mild cognitive impairment (Accuracy = 0.614) compared to genetics (Accuracy = 0.356). Combining MRI and genetic data showed improved classification performance in the remaining stratified groups. Conclusion: MRI and genetic data can contribute to DAT prediction in different ways. MRI data reflects anatomical changes in the brain, while genetic data can detect the risk of DAT progression prior to the symptomatic onset. Combining information from multimodal data appropriately can improve prediction performance.

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  1. [2]He Y, Wang L, Zang Y, Tian L, Zhang X, Li K, Jiang T (2007) Regional coherence changes in the early stages of Alzheimer’s disease: A combined structural and resting-state functional MRI study. Neuroimage 35, 488– 500. 17254803
  2. [3]Hua X, Leow AD, Parikshak N, Lee S, Chiang MC, Toga AW, Jack CR, Weiner MW, Thompson PM (2008) Tensor-based morphometry as a neuroimaging biomarker for Alzheimer’s disease: An MRI study of 676 AD, MCI, and normal subjects. Neuroimage 43, 458– 469. 18691658 PMC3197851
  3. [4]Popuri K, Ma D, Wang L, Beg MF (2020) Using machine learning to quantify structural MRI neurodegeneration patterns of Alzheimer’s disease into dementia score: Independent validation on 8,834 images from ADNI, AIBL, OASIS, and MIRIAD databases. Hum Brain Mapp 41, 4127– 4147. 32614505 PMC7469784
  4. [5]Scheltens P, Leys D, Barkhof F, Huglo D, Weinstein HC, Vermersch P, Kuiper M, Steinling M, Wolters EC, Valk J (1992) Atrophy of medial temporal lobes on MRI in" probable" Alzheimer’s disease and normal ageing: diagnostic value and neuropsychological correlates. J Neurol Neurosurg Psychiatry 55, 967– 972. 1431963 PMC1015202
  5. [6]Vemuri P, Jack CR (2010) Role of structural MRI in Alzheimer’s disease. Alzheimers Res Ther 2, 1– 10. 20807454 PMC2949589
  6. [7]Lambert J-C, Ibrahim-Verbaas CA, Harold D, Naj AC, Sims R, Bellenguez C, Jun G, DeStefano AL, Bis JC, Beecham GW, others (2013) Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer’s disease. Nat Genet 45, 1452– 1458. 24162737 PMC3896259
  7. [8]Bertram L, McQueen MB, Mullin K, Blacker D, Tanzi RE (2007) Systematic meta-analyses of Alzheimer disease genetic association studies: The AlzGene database. Nat Genet 39, 17– 23. 17192785
  8. [9]Jansen IE, Savage JE, Watanabe K, Bryois J, Williams DM, Steinberg S, others (2019) Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer’s disease risk. Nat Genet 51, 404– 413. 30617256 PMC6836675
  9. [10]Karch CM, Goate AM (2015) Alzheimer’s disease risk genes and mechanisms of disease pathogenesis. Biol Psychiatry 77, 43– 51. 24951455 PMC4234692
  10. [11]Kunkle BW, Grenier-Boley B, Sims R, Bis JC, Damotte V, Naj AC, Boland A, Vronskaya M, Van Der Lee SJ, Amlie-Wolf A, others (2019) Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. Nat Genet 51, 414– 430. 30820047 PMC6463297
  11. [12]Schwartzentruber J, Cooper S, Liu JZ, Barrio-Hernandez I, Bello E, Kumasaka N, Young AMH, Franklin RJM, Johnson T, Estrada K, others (2021) Genome-wide meta-analysis, fine-mapping and integrative prioritization implicate new Alzheimer’s disease risk genes. Nat Genet 1– 11. 33589840 PMC7610386
  12. [13]Sumirtanurdin R, Thalib AY, Cantona K, Abdulah R (2019) Effect of genetic polymorphisms on alzheimer’s disease treatment outcomes: An update. Clin Interv Aging 14, 631– 642. 30992661 PMC6445219
  13. [14]An L, Adeli E, Liu M, Zhang J, Lee SW, Shen D (2017) A Hierarchical Feature and Sample Selection Framework and Its Application for Alzheimer’s Disease Diagnosis. Sci Rep 7, 1– 11. 28358032 PMC5372170
  14. [16]Ning K, Chen B, Sun F, Hobel Z, Zhao L, Matloff W, Toga AW (2018) Classifying Alzheimer’s disease with brain imaging and genetic data using a neural network framework. Neurobiol Aging 68, 151– 158. 29784544 PMC5993633
  15. [17]Peng J, An L, Zhu X, Jin Y, Shen D (2016) Structured sparse kernel learning for imaging genetics based Alzheimer’s disease diagnosis. In International Conference on Medical Image Computing and Computer-Assisted Intervention, pp. 70– 78. PMC5451201 28580458
  16. [19]Wang H, Nie F, Huang H, Risacher SL, Saykin AJ, Shen L (2012) Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning. Bioinformatics 28, i127– i136. 22689752 PMC3371860
  17. [20]Zhang Z, Huang H, Shen D (2014) Integrative analysis of multi-dimensional imaging genomics data for alzheimer’s disease prediction. Front Aging Neurosci 6, 260. 25368574 PMC4201101
  18. [21]Zhou T, Thung KH, Zhu X, Shen D (2019) Effective feature learning and fusion of multimodality data using stage-wise deep neural network for dementia diagnosis. Hum Brain Mapp 40, 1001– 1016. 30381863 PMC6865441
  19. [22]Zhou T, Liu M, Thung KH, Shen D (2019) Latent Representation Learning for Alzheimer’s Disease Diagnosis with Incomplete Multi-Modality Neuroimaging and Genetic Data. IEEE Trans Med Imaging 38, 2411– 2422. 31021792 PMC8034601
  20. [23]Mueller SG, Weiner MW, Thal LJ, Petersen RC, Jack CR, Jagust W, Trojanowski JQ, Toga AW, Beckett L (2005) Ways toward an early diagnosis in Alzheimer’s disease: the Alzheimer’s Disease Neuroimaging Initiative (ADNI). Alzheimer’s Dement 1, 55– 66. 17476317 PMC1864941
  21. [24]Popuri K, Balachandar R, Alpert K, Lu D, Bhalla M, Mackenzie IR, Hsiung RGY, Wang L, Beg MF (2018) Development and validation of a novel dementia of Alzheimer’s type (DAT) score based on metabolism FDG-PET imaging. NeuroImage Clin 18, 802– 813. 29876266 PMC5988459
  22. [25]Chang CC, Chow CC, Tellier LCAM, Vattikuti S, Purcell SM, Lee JJ (2015) Second-generation PLINK: Rising to the challenge of larger and richer datasets. Gigascience 4. PMC4342193 25722852
  23. [26]Saykin AJ, Shen L, Foroud TM, Potkin SG, Swaminathan S, Kim S, Risacher SL, Nho K, Huentelman MJ, Craig DW, others (2010) Alzheimer’s Disease Neuroimaging Initiative biomarkers as quantitative phenotypes: Genetics core aims, progress, and plans. Alzheimer’s Dement 6, 265– 273. 20451875 PMC2868595
  24. [27]Dale AM, Fischl B, Sereno MI (1999) Cortical surface-based analysis: I. Segmentation and surface reconstruction. Neuroimage 9, 179– 194. 9931268
  25. [28]Desikan RS, Ségonne F, Fischl B, Quinn BT, Dickerson BC, Blacker D, Buckner RL, Dale AM, Maguire RP, Hyman BT, Albert MS, Killiany RJ (2006) An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage 31, 968– 980. 16530430
  26. [29]Fischl B, Salat DH, Busa E, Albert M, Dieterich M, Haselgrove C, Van Der Kouwe A, Killiany R, Kennedy D, Klaveness S, others (2002) Whole brain segmentation: automated labeling of neuroanatomical structures in the human brain. Neuron 33, 341– 355. 11832223
  27. [30]Ma D, Popuri K, Bhalla M, Sangha O, Lu D, Cao J, Jacova C, Wang L, Beg MF (2019) Quantitative assessment of field strength, total intracranial volume, sex, and age effects on the goodness of harmonization for volumetric analysis on the ADNI database. Hum Brain Mapp 40, 1507– 1527. 30431208 PMC6449147
  28. [31]Dietterich TG (2000) Ensemble methods in machine learning. In International workshop on multiple classifier systems, pp. 1– 15.
  29. [32]Akritas MG, Politis DN (2003) Recent Advances and Trends in Nonparametric Statistics, Elsevier.
  30. [35]Raamana PR, Weiner MW, Wang L, Beg MF (2015) Thickness network features for prognostic applications in dementia. Neurobiol Aging 36, S91– S102. 25444603 PMC5849081
  31. [38]Welch BL (1947) The generalization of student’s’ problem when several different population variances are involved. Biometrika 34, 28– 35. 20287819
  32. [39]Sullivan GM, Feinn R (2012) Using Effect Size—or Why the P Value Is Not Enough. J Grad Med Educ 4, 279– 282. 23997866 PMC3444174
  33. [41]Damoulas T, Girolami MA (2008) Probabilistic multi-class multi-kernel learning: On protein fold recognition and remote homology detection. Bioinformatics 24, 1264– 1270. 18378524
  34. [42]Cristianini N, Shawe-Taylor J (2004) Kernel methods for pattern analysis, Cambridge University Press Cambridge.
  35. [43]Devyatkin VA, Redina OE, Kolosova NG, Muraleva NA (2020) Single-Nucleotide Polymorphisms Associated with the Senescence-Accelerated Phenotype of OXYS Rats: A Focus on Alzheimer’s Disease-Like and Age-Related-Macular-Degeneration-Like Pathologies. J Alzheimers Dis 73, 1167– 1183. 31929160
  36. [44]Golanska E, Hulas-Bigoszewska K, Sieruta M, Zawlik I, Witusik M, Gresner SM, Sobow T, Styczynska M, Peplonska B, Barcikowska M, Liberski PP, Corder EH (2009) Earlier onset of alzheimer’s disease: Risk polymorphisms within PRNP, PRND, CYP46, and APOE genes. J Alzheimer’s Dis 17, 359– 368. 19363267
  37. [45]Mochida GH, Mahajnah M, Hill AD, Basel-Vanagaite L, Gleason D, Hill RS, Bodell A, Crosier M, Straussberg R, Walsh CA (2009) A Truncating Mutation of TRAPPC9 Is Associated with Autosomal-Recessive Intellectual Disability and Postnatal Microcephaly. Am J Hum Genet 85, 897– 902. 20004763 PMC2790576
  38. [46]Potts RC, Zhang P, Wurster AL, Precht P, Mughal MR, Wood WH, Zhang Y, Becker KG, Mattson MP, Pazin MJ (2011) CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes, regulates expression of neuronal genes. PLoS One 6, e24515. 21931736 PMC3172237
  39. [48]Yu L, Liu H (2003) Efficiently handling feature redundancy in high-dimensional data. In Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 685– 690.
  40. [49]Meda SA, Narayanan B, Liu J, Perrone-Bizzozero NI, Stevens MC, Calhoun VD, Glahn DC, Shen L, Risacher SL, Saykin AJ, Pearlson GD (2012) A large scale multivariate parallel ICA method reveals novel imaging-genetic relationships for Alzheimer’s disease in the ADNI cohort. Neuroimage 60, 1608– 1621. 22245343 PMC3312985
  41. [50]Vounou M, Janousova E, Wolz R, Stein JL, Thompson PM, Rueckert D, Montana G (2012) Sparse reduced-rank regression detects genetic associations with voxel-wise longitudinal phenotypes in Alzheimer’s disease. Neuroimage 60, 700– 716. 22209813 PMC3551466
  42. [51]Humphries CE, Kohli MA, Nathanson L, Whitehead P, Beecham G, Martin E, Mash DC, Pericak-Vance MA, Gilbert J (2015) Integrated whole transcriptome and DNA methylation analysis identifies gene networks specific to late-onset Alzheimer’s disease. J Alzheimer’s Dis 44, 977– 987. 25380588
  43. [52]Gal J, Chen J, Katsumata Y, Fardo DW, Wang WX, Artiushin S, Price D, Anderson S, Patel E, Zhu H, Nelson PT (2018) Detergent insoluble proteins and inclusion body-like structures immunoreactive for PRKDC/DNA-PK/DNA-PKcs, FTL, NNT, and AIFM1 in the amygdala of cognitively impaired elderly persons. J Neuropathol Exp Neurol 77, 21– 39. 29186589 PMC6251632
  44. [53]Young FB, Butland SL, Sanders SS, Sutton LM, Hayden MR (2012) Putting proteins in their place: palmitoylation in Huntington disease and other neuropsychiatric diseases. Prog Neurobiol 97, 220– 238. 22155432
  45. [55]Ma D, Yee E, Stocks JK, Jenkins LM, Popuri K, Chausse G, Wang L, Probst S, Beg MF (2021) Blinded Clinical Evaluation for Dementia of Alzheimer’s Type Classification Using FDG-PET: A Comparison Between Feature-Engineered and Non-Feature-Engineered Machine Learning Methods. J Alzheimer’s Dis 80, 715– 726. 33579858 PMC8978589

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Authors
Mirabnahrazam, G., Initiative, T. A. D. N., Ma, D., Lee, S., Popuri, K., Lee, H., Cao, J., Wang, L., Galvin, J. E., & Beg, M. F.
Affiliations
  • Simon Fraser University (CA)
  • University of Nottingham (GB)
  • University of British Columbia (CA)
  • The Ohio State University Wexner Medical Center (US)
  • University of Miami (US)
Corresponding author
Beg, Mirza Faisal
Venue
Journal of Alzheimer's Disease
Published
2022-05-31
Volume
87
Issue
3
Pages
1345-1365
ISSN
  • 1387-2877 (ISSN-L)
  • 1875-8908
OpenAlex
W4221154077
Cited by
50
References
4
Citations by year
2026: 19 · 2025: 12 · 2024: 9 · 2023: 9 · 2022: 1
FWCI
5.05
Type
journal article
Language
en
Open access
Locations
  • Journal of Alzheimer s Disease (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • arXiv (Cornell University)
Funders
  • National Institutes of Health (UL1TR001420, 5u01ag024904-10)
  • National Institute on Aging (U01-AG-024904, R01AG069765, R01AG055121, K24AG045333, P01AG019724, R01AG071514)
  • National Institute of Neurological Disorders and Stroke (R01NS101483)
  • National Center for Advancing Translational Sciences
Topics
  • Health Sciences › Medicine › Psychiatry and Mental health › Dementia and Cognitive Impairment Research
  • Health Sciences › Medicine › Physiology › Alzheimer's disease research and treatments
  • Health Sciences › Health Professions › Health Information Management › Artificial Intelligence in Healthcare
Keywords
Alzheimer's disease
MeSH terms
Machine Learning, Alzheimer Disease, Brain, Humans, Magnetic Resonance Imaging, Disease Progression, Genomics, Neuroimaging, Cognitive Dysfunction

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