Machine Learning Analyses Reveal Circadian Features Predictive of Risk for Sleep Disturbance

References

• Fang H, Tu S, Sheng J, Shao A. Depression in sleep disturbance: a review on a bidirectional relationship, mechanisms and treatment. J Cell Mol Med. 2019;23(4):2324–2332. doi:10.1111/jcmm.14170
   PubMed Web of Science ®Google Scholar
• Utge SJ, Soronen P, Loukola A, et al. Systematic analysis of circadian genes in a population-based sample reveals association of TIMELESS with depression and sleep disturbance. PLoS One. 2010;5(2):e9259. doi:10.1371/journal.pone.0009259
   PubMed Web of Science ®Google Scholar
• Borbély AA, Daan S, Wirz-Justice A, Deboer T. The two-process model of sleep regulation: a reappraisal. J Sleep Res. 2016;25(2):131–143. doi:10.1111/jsr.12371
   PubMed Web of Science ®Google Scholar
• Dijk DJ, Archer SN. PERIOD3, circadian phenotypes, and sleep homeostasis. Sleep Med Rev. 2010;14(3):151–160. doi:10.1016/j.smrv.2009.07.002
   PubMed Web of Science ®Google Scholar
• Evans JA, Pan H, Liu AC, Welsh DK. Cry1-/- circadian rhythmicity depends on SCN intercellular coupling. J Biol Rhythms. 2012;27(6):443–452. doi:10.1177/0748730412461246
   PubMed Web of Science ®Google Scholar
• Walker WH, Walton JC, DeVries AC, Nelson RJ. Circadian rhythm disruption and mental health. Transl Psychiatry. 2020;10(1). doi:10.1038/S41398-020-0694-0
   PubMed Web of Science ®Google Scholar
• Jagannath A, Taylor L, Wakaf Z, Vasudevan SR, Foster RG. The genetics of circadian rhythms, sleep and health. Hum Mol Genet. 2017;26(R2):R128–R138. doi:10.1093/hmg/ddx240
   PubMed Web of Science ®Google Scholar
• Reppert SM, Weaver DR. Coordination of circadian timing in mammals. Nature. 2002;418(6901):935–941. doi:10.1038/nature00965
   PubMed Web of Science ®Google Scholar
• Patke A, Murphy PJ, Onat OE, et al. Mutation of the Human Circadian Clock Gene CRY1 in Familial Delayed Sleep Phase Disorder. Cell. 2017;169(2):203–215.e13. doi:10.1016/j.cell.2017.03.027
   PubMed Web of Science ®Google Scholar
• Archer SN, Schmidt C, Vandewalle G, Dijk DJ. Phenotyping of PER3 variants reveals widespread effects on circadian preference, sleep regulation, and health. Sleep Med Rev. 2018;40:109–126. doi:10.1016/j.smrv.2017.10.008
   PubMed Web of Science ®Google Scholar
• Weiss C, Woods K, Filipowicz A, Ingram KK. Sleep Quality, Sleep Structure, and PER3 Genotype Mediate Chronotype Effects on Depressive Symptoms in Young Adults. Front Psychol. 2020;11(August):1–11. doi:10.3389/fpsyg.2020.02028
   PubMed Web of Science ®Google Scholar
• Duffy JF, Abbott SM, Burgess HJ, et al. Circadian rhythm sleep-wake disorders: gaps and opportunities. Sleep. 2021;44(5):1–15. doi:10.1093/sleep/zsaa281
   Web of Science ®Google Scholar
• Chellappa SL. Individual differences in light sensitivity affect sleep and circadian rhythms. Sleep. 2021;44(2):1–10. doi:10.1093/sleep/zsaa214
   Web of Science ®Google Scholar
• Challet E, Caldelas I, Graff C, Pévet P. Regulation of Molecular Oscillations in Extra- SCN Brain and Peripheral Oscillators. Acta Physiol. 2003;384:711–719. doi:10.1515/BC.2003.079
   Web of Science ®Google Scholar
• Mistlberger RE, Landry GJ, Marchant EG. Sleep deprivation can attenuate light-induced phase shifts of circadian rhythms in hamsters. Neurosci Lett. 1997;238(1–2):5–8. doi:10.1016/s0304-3940(97)
   PubMed Web of Science ®Google Scholar
• van Diepen HC, Lucassen EA, Yasenkov R, et al. Caffeine increases light responsiveness of the mouse circadian pacemaker. Eur J Neurosci. 2014;40(10):3504–3511. doi:10.1111/ejn.12715
   PubMed Web of Science ®Google Scholar
• Bottaro LB. Partial sleep deprivation reduces phase advances to light in humans. J Biol Rhythms. 2010;25(6):460–468. doi:10.1177/0748730410385544.Partial
   PubMed Web of Science ®Google Scholar
• Russo PM, Biasi V, Cipolli C, Mallia L, Caponera E. Sleep habits, circadian preference, and school performance in early adolescents. Sleep Med. 2017;29:20–22. doi:10.1016/j.sleep.2016.09.019
   PubMed Web of Science ®Google Scholar
• Albrecht U. Molecular mechanisms in mood regulation involving the circadian clock. Front Neurol. 2017;8(FEB). doi:10.3389/fneur.2017.00030
   Web of Science ®Google Scholar
• Yu L, Buysse DJ, Germain A, et al. Development of Short Forms From the PROMISTM Sleep Disturbance and Sleep-Related Impairment Item Banks. Behav Sleep Med. 2012;10(1):6–24. doi:10.1080/15402002.2012.636266
   Web of Science ®Google Scholar
• Horne JA, Ostberg O. A self-assessment questionnaire to determine morningness-eveningness in human circadian rhythms. Int J Chronobiol. 1976;4(2):97–110.
   PubMedGoogle Scholar
• Ebisawa T, Uchiyama M, Kajimura N, et al. Association of structural polymorphisms in the human period3 gene with delayed sleep phase syndrome. EMBO Rep. 2001;2(4):342–346. doi:10.1093/embo-reports/kve070
   PubMed Web of Science ®Google Scholar
• Nguyen C, Murray G, Anderson S, Filipowicz A, Ingram KK. In vivo molecular chronotyping, circadian misalignment, and high rates of depression in young adults. J Affect Disord. 2019;250:425–431. doi:10.1016/j.jad.2019.03.050
   PubMed Web of Science ®Google Scholar
• Liberman AR, Kwon SB, Vu HT, Filipowicz A, Ay A, Ingram KK. Circadian Clock Model Supports Molecular Link between PER3 and Human Anxiety. Sci Rep. 2017;7(1):1–10. doi:10.1038/s41598-017-07957-4
   PubMed Web of Science ®Google Scholar
• Quinlan JR, Quinlan JR. Induction of decision trees. Mach Learn. 1986;1:81–106. doi:10.1007/BF00116251
   Google Scholar
• Robnik-Sikonja M, Kononenko I An Adaptation of Relief for Attribute Estimation in Regression. In: Proceedings of the Fourteenth International Conference on Machine Learning. ICML ’97. Morgan Kaufmann Publishers Inc; 1997:296–304.
   Google Scholar
• Ding C, Peng H Minimum redundancy feature selection from microarray gene expression data. In: Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003; 2003: 523–528. doi:10.1109/CSB.2003.1227396.
   Google Scholar
• Yang HH, Moody JE Feature Selection Based on Joint Mutual Information. 1999.
   Google Scholar
• Boser BE, Guyon I, Vapnik VN A training algorithm for optimal margin classifiers. In: COLT ’92; 1992.
   Google Scholar
• Chen T, Guestrin C XGBoost: a Scalable Tree Boosting System. In: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. KDD ’16. Association for Computing Machinery; 2016:785–794. doi:10.1145/2939672.2939785.
   Google Scholar
• Statistics LB, Breiman L. Random Forests. Mach Learn. 2001;1;5–32.
   Google Scholar
• Fukunaga K. The Optimal Distance Measure for Nearest Neighbor Classification. IEEE Trans Inf Theory. 1981;27(5):622–627. doi:10.1109/TIT.1981.1056403
   Web of Science ®Google Scholar
• Chawla N, Bowyer KW, Hall LO, Kegelmeyer WP. SMOTE: synthetic Minority over-Sampling Technique. J Artif Int Res. 2002;16(1):321–357.
   Web of Science ®Google Scholar
• R Core Team. R: a Language and Environment for Statistical Computing; 2020. Available from: https://www.r-project.org/. Accessed October 13, 2022.
   Google Scholar
• Bozdogan H. Model selection and Akaike’s Information Criterion (AIC): the general theory and its analytical extensions. Psychometrika. 1987;52(3):345–370. doi:10.1007/BF02294361
   Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Royal Statistical Soc. 1995;57(1):289–300. doi:10.1111/J.2517-6161.1995.TB02031.X
   Google Scholar
• Imai K, Keele L, Tingley D, Yamamoto T. Causal Mediation Analysis Using R. In: Vinod HD, editor. Advances in Social Science Research Using R. Springer-Verlag; 2010.
   Google Scholar
• Fox J, Weisberg S An {R} Companion to Applied Regression. Sage; 2019. Available from: https://socialsciences.mcmaster.ca/jfox/Books/Companion/. Accessed October 13, 2022.
   Google Scholar
• Hahsler M, Chelluboina S, Hornik K, Buchta C. The arules R-Package Ecosystem: analyzing Interesting Patterns from Large Transaction Datasets. J Mach Learn Res. 2011;12:1977–1981.
   Web of Science ®Google Scholar
• Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal. 2006;1;1695.
   Google Scholar
• Margolin AA, Nemenman I, Basso K, et al. ARACNE: an Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context. BMC Bioinform. 2006;7(1):1–15. doi:10.1186/1471-2105-7-S1-S7
   PubMed Web of Science ®Google Scholar
• Meyer PE, Lafitte F, Bontempi G. MINET: an open source R/Bioconductor Package for Mutual Information based Network Inference. BMC Bioinform. 2008;9. doi:10.1186/1471-2105-9-9
   PubMed Web of Science ®Google Scholar
• Archer SN, Robilliard DL, Skene DJ, et al. A length polymorphism in the circadian clock gene Per3 is linked to delayed sleep phase syndrome and extreme diurnal preference. Sleep. 2003;26(4):413–415. doi:10.1093/sleep/26.4.413
   PubMed Web of Science ®Google Scholar
• Partonen T, Treutlein J, Alpman A, et al. Three circadian clock genes Per2, Arntl, and Npas2 contribute to winter depression. Ann Med. 2007;39(3):229–238. doi:10.1080/07853890701278795
   PubMed Web of Science ®Google Scholar
• Zhang L, Hirano A, Hsu PK, et al. A PERIOD3 variant causes a circadian phenotype and is associated with a seasonal mood trait. Proc Natl Acad Sci U S A. 2016;113(11):E1536–E1544. doi:10.1073/pnas.1600039113
   PubMed Web of Science ®Google Scholar
• Hida A, Kitamura S, Katayose Y, et al. Screening of clock gene polymorphisms demonstrates association of a PER3 polymorphism with morningness-eveningness preference and circadian rhythm sleep disorder. Sci Rep. 2014;4:6309. doi:10.1038/srep06309
   PubMed Web of Science ®Google Scholar
• Liberman AR, Halitjaha L, Ay A, Ingram KK. Modeling Strengthens Molecular Link between Circadian Polymorphisms and Major Mood Disorders. J Biol Rhythms. 2018;33(3):318–336. doi:10.1177/0748730418764540
   PubMed Web of Science ®Google Scholar
• Turco M, Biscontin A, Corrias M, et al. Diurnal preference, mood and the response to morning light in relation to polymorphisms in the human clock gene PER3. Sci Rep. 2017;7(1):1–10. doi:10.1038/s41598-017-06769-w
   PubMed Web of Science ®Google Scholar
• Archer SN, Oster H. How sleep and wakefulness influence circadian rhythmicity: effects of insufficient and mistimed sleep on the animal and human transcriptome. J Sleep Res. 2015;24(5):476–493. doi:10.1111/jsr.12307
   PubMed Web of Science ®Google Scholar
• Fares S, Hermens DF, Naismith SL, White D, Hickie IB, Robillard R. Clinical correlates of chronotypes in young persons with mental disorders. Chronobiol Int. 2015;32(9):1183–1191. doi:10.3109/07420528.2015.1078346
   PubMed Web of Science ®Google Scholar
• Levandovski R, Dantas G, Fernandes LC, et al. Depression scores associate with chronotype and social jetlag in a rural population. Chronobiol Int. 2011;28(9):771–778. doi:10.3109/07420528.2011.602445
   PubMed Web of Science ®Google Scholar
• Lázár AS, Slak A, Lo JCY, et al. Sleep, diurnal preference, health, and psychological well-being: a prospective single-allelic-variation study. Chronobiol Int. 2012;29(2):131–146. doi:10.3109/07420528.2011.641193
   PubMed Web of Science ®Google Scholar
• Vieira J, Jones AR, Danon A, et al. Human Cryptochrome-1 Confers Light Independent Biological Activity in Transgenic Drosophila Correlated with Flavin Radical Stability. PLoS One. 2012;7(3):e31867. doi:10.1371/journal.pone.0031867
   PubMed Web of Science ®Google Scholar
• Dardente H, Fortier EE, Martineau V, Cermakian N. Cryptochromes impair phosphorylation of transcriptional activators in the clock: a general mechanism for circadian repression. Biochem J. 2007;402:525–536. doi:10.1042/BJ20060827
   PubMed Web of Science ®Google Scholar
• Hua P, Liu W, Chen D, et al. Cry1 and Tef gene polymorphisms are associated with major depressive disorder in the Chinese population. J Affect Disord. 2014;157:100–103. doi:10.1016/j.jad.2013.11.019
   PubMed Web of Science ®Google Scholar
• Buoli M, Serati M, Grassi S, et al. The role of clock genes in the etiology of Major Depressive Disorder: special Section on “Translational and Neuroscience Studies in Affective Disorders”. Section Editor, Maria Nobile MD, PhD. This Section of JAD focuses on the relevance of translational a. J Affect Disord. 2018;234:351–357. doi:10.1016/j.jad.2017.11.015
   PubMed Web of Science ®Google Scholar
• Soria V, Martínez-Amorós È, Escaramís G, et al. Differential association of circadian genes with mood disorders: CRY1 and NPAS2 are associated with unipolar major depression and clock and VIP with bipolar disorder. Neuropsychopharmacology. 2010;35(6):1279–1289. doi:10.1038/npp.2009.230
   PubMed Web of Science ®Google Scholar
• Wisor JP, O’Hara BF, Terao A, et al. A role for cryptochromes in sleep regulation. BMC Neurosci. 2002;3:20. doi:10.1186/1471-2202-3-20
   PubMed Web of Science ®Google Scholar
• Partonen T. Clock gene variants in mood and anxiety disorders. J Neural Transm. 2012;119(10):1133–1145. doi:10.1007/s00702-012-0810-2
   PubMed Web of Science ®Google Scholar
• Lavebratt C, Sjöholm LK. CRY2 is associated with depression. PLoS One. 2010;5(2):e9407. doi:10.1371/journal.pone.0009407
   PubMed Web of Science ®Google Scholar
• Kovanen L, Kaunisto M, Donner K, Saarikoski ST, Partonen T. CRY2 genetic variants associate with dysthymia. PLoS One. 2013;8(8):e71450. doi:10.1371/journal.pone.0071450
   PubMed Web of Science ®Google Scholar
• Zhang L, Hirano A, Hsu PK, et al. A PERIOD3 variant causes a circadian phenotype and is associated with a seasonal mood trait. Proc Natl Acad Sci U S A. 2016;113(11):E1536. doi:10.1073/pnas.1600039113
   PubMed Web of Science ®Google Scholar
• Shi SQ, White MJ, Borsetti HM, et al. Molecular analyses of circadian gene variants reveal sex-dependent links between depression and clocks. Transl Psychiatry. 2016;6(December):2015. doi:10.1038/tp.2016.9
   Web of Science ®Google Scholar
• Quinlan JR, Quinlan JR. Induction of Decision Trees. Mach Learn. 1986;2(1):81–106.
   Google Scholar