DIYgenomics Sleep SNPs

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Genetic research findings linking SNPs to sleep quality and conditions

SNPs to include in sleep studies:

rs762551, rs2472297, rs4410790, rs73598374, rs57875989, rs73598374, rs5751876, rs6265, rs4680, rs1799990, rs95215856, rs5797225, rs7137588, rs4964059, rs1801260, rs95215860, rs2304669, rs228697, rs10462021, rs4238989, rs687577, rs1154155, rs2305795, rs4804122, rs738499, rs6311, rs6313, rs2770304, rs4941573, rs11706236, rs12895096, rs158856, rs16905439, rs1791933, rs2065779, rs2103117, rs2388082, rs6575353, rs7628219

Description:

Caffeine-related SNPs: CYP1A2 (rs762551) related to caffeine metabolism (23andMe,[1] Pathway Genomics[2]^,[3]), habitual caffeine consumption reviewed by 23andMe CYP1A1-CYP1A2 (rs2472297)[4] and AHR (rs4410790),[5] and ADA G22A (rs73598374).[6] Research has related other SNPs to insomnia and caffeine consumption, neural membrane regulator PRIMA1 rs6573232 and rs12895096, melatonin receptor-related MTNR1B rs10830964, ion channel regulation and hypertension-related NEDD4L rs158856, cellular calcium intake controller P2RY2 rs1791933, and RP11 rs7628219, rs2065779, and rs11706236, RP1 rs2103117, MTUS2 rs2388082, and AC105008 rs16905439.[7]

Healthy sleep SNPs: linked to healthy sleeping profiles with PER3 (rs57875989), ADA (rs73598374), ADORA2A (rs5751876),[8]^,[9] BDNF (rs6265), COMT VAL158MET (rs4680), PRNP (rs1799990),[10] genetic determination of sleep EEG profiles in healthy humans with ARNTL (rs95215856), ARNTL2 (rs5797225, rs7137588, rs4964059), CLOCK (rs1801260, rs95215860), PER2 (rs2304669), PER3 (rs228697, AB047536 5-repeat, rs10462021), AANAT (rs4238989) [available in 23andMe data: rs10462021, rs1801260, rs228697, rs2304669, rs4964059],[11] and in women, a link between depression and sleep quantity: GRIA3 (rs687577).[12] Repeating sequences in the circadian gene PERIOD3 (PER3) have been associated with sleep quality, but repeat data is not available from 23andMe.[13]^,[14]

Sleep malady SNPs: TCRA (rs1154155) related to essential hypersomnia,[15] P2RY11 (rs2305795, rs4804122) linked to narcolepsy,[16] TEF (rs738499) related to sleep disturbance in Parkinson’s disease,[17] Serotonin gene 5-HT2A -1438G/A polymorphism (rs6311) related to apnea and impulsive behavior,[18]^,[19] TNFA (rs1800629) associated with obstructive sleep apnea but is not in 23andMe data,[20] and HTR2A (rs6313, rs2770304, and rs4941573) related to sleep bruxism (a sleep-related movement disorder).[21]

Potential citizen ethicist review: (see Ethical Review Q&A)

Alexander Gerlyand, Biotechnology professional

Amanda Kahn-Kirby, Biotechnology professional

References:

[1] Cornelis MC, El-Sohemy A, Kabagambe EK, Campos H. Coffee, CYP1A2 genotype, and risk of myocardial infarction. JAMA. 2006 Mar 8;295(10):1135-41.

[2] Sachse C, Brockmöller J, Bauer S, Roots I. Functional significance of a C-->A polymorphism in intron 1 of the cytochrome P450 CYP1A2 gene tested with caffeine. Br J Clin Pharmacol. 1999 Apr;47(4):445-9.

[3] Cornelis MC, El-Sohemy A. Coffee, caffeine, and coronary heart disease. Curr Opin Clin Nutr Metab Care. 2007 Nov;10(6):745-51.

[4] Sulem P, Gudbjartsson DF, Geller F, Prokopenko I, Feenstra B, Aben KK, Franke B, den Heijer M, Kovacs P, Stumvoll M, Mägi R, Yanek LR, Becker LC, Boyd HA, Stacey SN, Walters GB, Jonasdottir A, Thorleifsson G, Holm H, Gudjonsson SA, Rafnar T, Björnsdottir G, Becker DM, Melbye M, Kong A, Tönjes A, Thorgeirsson T, Thorsteinsdottir U, Kiemeney LA, Stefansson K. Sequence variants at CYP1A1-CYP1A2 and AHR associate with coffee consumption. Hum Mol Genet. 2011 May 15;20(10):2071-7.

[5] Cornelis MC, Monda KL, Yu K, Paynter N, Azzato EM, Bennett SN, Berndt SI, Boerwinkle E, Chanock S, Chatterjee N, Couper D, Curhan G, Heiss G, Hu FB, Hunter DJ, Jacobs K, Jensen MK, Kraft P, Landi MT, Nettleton JA, Purdue MP, Rajaraman P, Rimm EB, Rose LM, Rothman N, Silverman D, Stolzenberg-Solomon R, Subar A, Yeager M, Chasman DI, van Dam RM, Caporaso NE. Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption. PLoS Genet. 2011 Apr;7(4):e1002033.

[6] Mazzotti DR, Guindalini C, Pellegrino R, Barrueco KF, Santos-Silva R, Bittencourt LR, Tufik S. Effects of the adenosine deaminase polymorphism and caffeine intake on sleep parameters in a large population sample. Sleep. 2011 Mar 1;34(3):399-402.

[7] Byrne EM, Johnson J, McRae AF, Nyholt DR, Medland SE, Gehrman PR, Heath AC, Madden PA, Montgomery GW, Chenevix-Trench G, Martin NG. A genome-wide association study of caffeine-related sleep disturbance: confirmation of a role for a common variant in the adenosine receptor. Sleep. 2012 Jul 1;35(7):967-75.

[8] Bodenmann S, Hohoff C, Freitag C, Deckert J, Rétey JV, Bachmann V, Landolt HP. Polymorphisms of ADORA2A modulate psychomotor vigilance and the effects of caffeine on neurobehavioural performance and sleep EEG after sleep deprivation. Br J Pharmacol. 2012 Mar;165(6):1904-13.

[9] Nova P, Hernandez B, Ptolemy AS, Zeitzer JM. Modeling caffeine concentrations with the Stanford Caffeine Questionnaire: preliminary evidence for an interaction of chronotype with the effects of caffeine on sleep. Sleep Med. 2012 Apr;13(4):362-7.

[10] Landolt HP. Genetic determination of sleep EEG profiles in healthy humans. Prog Brain Res. 2011;193:51-61.

[11] Ciarleglio CM, Ryckman KK, Servick SV, Hida A, Robbins S, Wells N, Hicks J, Larson SA, Wiedermann JP, Carver K, Hamilton N, Kidd KK, Kidd JR, Smith JR, Friedlaender J, McMahon DG, Williams SM, Summar ML, Johnson CH. Genetic differences in human circadian clock genes among worldwide populations. J Biol Rhythms. 2008 Aug;23(4):330-40.

[12] Utge S, Kronholm E, Partonen T, Soronen P, Ollila HM, Loukola A, Perola M, Salomaa V, Porkka-Heiskanen T, Paunio T. Shared genetic background for regulation of mood and sleep: association of GRIA3 with sleep duration in healthy Finnish women. Sleep. 2011 Oct 1;34(10):1309-16.

[13] Goel N, Banks S, Mignot E, Dinges DF. PER3 polymorphism predicts cumulative sleep homeostatic but not neurobehavioral changes to chronic partial sleep deprivation. PLoS One. 2009 Jun 11;4(6):e5874.

[14] Viola AU, Archer SN, James LM, Groeger JA, Lo JC, Skene DJ, von Schantz M, Dijk DJ. PER3 polymorphism predicts sleep structure and waking performance. Curr Biol. 2007 Apr 3;17(7):613-8.

[15] Miyagawa T, Honda M, Kawashima M, Shimada M, Tanaka S, Honda Y, Tokunaga K. Polymorphism located in TCRA locus confers susceptibility to essential hypersomnia with HLA-DRB1*1501-DQB1*0602 haplotype. J Hum Genet. 2010 Jan;55(1):63-5.

[16] Kornum BR, Kawashima M, Faraco J, Lin L, Rico TJ, Hesselson S, Axtell RC, Kuipers H, Weiner K, Hamacher A, Kassack MU, Han F, Knudsen S, Li J, Dong X, Winkelmann J, Plazzi G, Nevsimalova S, Hong SC, Honda Y, Honda M, Högl B, Ton TG, Montplaisir J, Bourgin P, Kemlink D, Huang YS, Warby S, Einen M, Eshragh JL, Miyagawa T, Desautels A, Ruppert E, Hesla PE, Poli F, Pizza F, Frauscher B, Jeong JH, Lee SP, Strohl KP, Longstreth WT Jr, Kvale M, Dobrovolna M, Ohayon MM, Nepom GT, Wichmann HE, Rouleau GA, Gieger C, Levinson DF, Gejman PV, Meitinger T, Peppard P, Young T, Jennum P, Steinman L, Tokunaga K,

Kwok PY, Risch N, Hallmayer J, Mignot E. Common variants in P2RY11 are associated with narcolepsy. Nat Genet. 2011 Jan;43(1):66-71.

[17] Viola AU, Archer SN, James LM, Groeger JA, Lo JC, Skene DJ, von Schantz M, Dijk DJ. PER3 polymorphism predicts sleep structure and waking performance. Curr Biol. 2007 Apr 3;17(7):613-8.

[18] Yin G, Ye J, Han D, Zhang Y, Zeng W, Liang C. Association of the 5-HT2A receptor gene polymorphisms with obstructive sleep apnea hypopnea syndrome in Chinese Han population. Acta Otolaryngol. 2012 Feb;132(2):203-9.

[19] Nomura M, Kusumi I, Kaneko M, Masui T, Daiguji M, Ueno T, Koyama T, Nomura Y. Involvement of a polymorphism in the 5-HT2A receptor gene in impulsive behavior. Psychopharmacology (Berl). 2006 Jul;187(1):30-5.

[20] Varvarigou V, Dahabreh IJ, Malhotra A, Kales SN. A review of genetic association studies of obstructive sleep apnea: field synopsis and meta-analysis. Sleep. 2011 Nov 1;34(11):1461-8.

[21] Abe Y, Suganuma T, Ishii M, Yamamoto G, Gunji T, Clark GT, Tachikawa T, Kiuchi Y, Igarashi Y, Baba K. Association of genetic, psychological and behavioral factors with sleep bruxism in a Japanese population. J Sleep Res. 2012 Jun;21(3):289-96.