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Gene Expression

J. L. Del-Aguila, Li, Z., Dube, U., Mihindukulasuriya, K. A., Budde, J. P., Fernández, M. Victoria, Ibañez, L., Bradley, J., Wang, F., Bergmann, K., Davenport, R., Morris, J. C., Holtzman, D. M., Perrin, R. J., Benitez, B. A., Dougherty, J., Cruchaga, C., and Harari, O., “A single-nuclei RNA sequencing study of Mendelian and sporadic AD in the human brain.”, Alzheimers Res Ther, vol. 11, no. 1, p. 71, 2019.

M. Malik, Chiles, J., Xi, H. S., Medway, C., Simpson, J., Potluri, S., Howard, D., Liang, Y., Paumi, C. M., Mukherjee, S., Crane, P., Younkin, S., Fardo, D. W., and Estus, S., “Genetics of CD33 in Alzheimer's disease and acute myeloid leukemia.”, Hum Mol Genet, vol. 24, no. 12, pp. 3557-70, 2015.

Y. - C. Hwang, Zheng, Q., Gregory, B. D., and San Wang, L. -, “High-throughput identification of long-range regulatory elements and their target promoters in the human genome.”, Nucleic Acids Res, vol. 41, no. 9, pp. 4835-46, 2013.

Y. Hu, Li, M., Lu, Q., Weng, H., Wang, J., Zekavat, S. M., Yu, Z., Li, B., Gu, J., Muchnik, S., Shi, Y., Kunkle, B. W., Mukherjee, S., Natarajan, P., Naj, A., Kuzma, A., Zhao, Y., Crane, P. K., Lu, H., and Zhao, H., “A statistical framework for cross-tissue transcriptome-wide association analysis.”, Nat Genet, vol. 51, no. 3, pp. 568-576, 2019.

P. - T. Xu, Li, Y. - J., Qin, X. - J., Scherzer, C. R., Xu, H., Schmechel, D. E., Hulette, C. M., Ervin, J., Gullans, S. R., Haines, J., Pericak-Vance, M. A., and Gilbert, J. R., “Differences in apolipoprotein E3/3 and E4/4 allele-specific gene expression in hippocampus in Alzheimer disease.”, Neurobiol Dis, vol. 21, no. 2, pp. 256-75, 2006.

V. Busby, Goossens, S., Nowotny, P., Hamilton, G., Smemo, S., Harold, D., Turic, D., Jehu, L., Myers, A., Womick, M., Woo, D., Compton, D., Doil, L. M., Tacey, K. M., Lau, K. F., Al-Saraj, S., Killick, R., Pickering-Brown, S., Moore, P., Hollingworth, P., Archer, N., Foy, C., Walter, S., Lendon, C., Iwatsubo, T., Morris, J. C., Norton, J., Mann, D., Janssens, B., Hardy, J., O'Donovan, M., Jones, L., Williams, J., Holmans, P., Owen, M. J., Grupe, A., Powell, J., van Hengel, J., Goate, A., Van Roy, F., and Lovestone, S., “Alpha-T-catenin is expressed in human brain and interacts with the Wnt signaling pathway but is not responsible for linkage to chromosome 10 in Alzheimer's disease.”, Neuromolecular Med, vol. 5, no. 2, pp. 133-46, 2004.

Gene Expression Profiling

J. H. Lee, Barral, S., and Reitz, C., “The neuronal sortilin-related receptor gene SORL1 and late-onset Alzheimer's disease.”, Curr Neurol Neurosci Rep, vol. 8, no. 5, pp. 384-91, 2008.

J. A. Webster, J Gibbs, R., Clarke, J., Ray, M., Zhang, W., Holmans, P., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., McCorquodale, D. S., Cuello, C., Leung, D., Bryden, L., Nath, P., Zismann, V. L., Joshipura, K., Huentelman, M. J., Hu-Lince, D., Coon, K. D., Craig, D. W., Pearson, J. V., Heward, C. B., Reiman, E. M., Stephan, D., Hardy, J., and Myers, A. J., “Genetic control of human brain transcript expression in Alzheimer disease.”, Am J Hum Genet, vol. 84, no. 4, pp. 445-58, 2009.

A. J. Myers, J Gibbs, R., Webster, J. A., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., Leung, D., Bryden, L., Nath, P., Zismann, V. L., Joshipura, K., Huentelman, M. J., Hu-Lince, D., Coon, K. D., Craig, D. W., Pearson, J. V., Holmans, P., Heward, C. B., Reiman, E. M., Stephan, D., and Hardy, J., “A survey of genetic human cortical gene expression.”, Nat Genet, vol. 39, no. 12, pp. 1494-9, 2007.

A. Amlie-Wolf, Ryvkin, P., Tong, R., Dragomir, I., Suh, E. R., Xu, Y., Van Deerlin, V. M., Gregory, B. D., Kwong, L. K., Trojanowski, J. Q., Lee, V. M. - Y., San Wang, L. -, and Lee, E. B., “Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin.”, PLoS One, vol. 10, no. 10, p. e0141836, 2015.

R. Sims, van der Lee, S. J., Naj, A. C., Bellenguez, C., Badarinarayan, N., Jakobsdottir, J., Kunkle, B. W., Boland, A., Raybould, R., Bis, J. C., Martin, E. R., Grenier-Boley, B., Heilmann-Heimbach, S., Chouraki, V., Kuzma, A. B., Sleegers, K., Vronskaya, M., Ruiz, A., Graham, R. R., Olaso, R., Hoffmann, P., Grove, M. L., Vardarajan, B. N., Hiltunen, M., Nöthen, M. M., White, C. C., Hamilton-Nelson, K. L., Epelbaum, J., Maier, W., Choi, S. - H., Beecham, G. W., Dulary, C., Herms, S., Smith, A. V., Funk, C. C., Derbois, C., Forstner, A. J., Ahmad, S., Li, H., Bacq, D., Harold, D., Satizabal, C. L., Valladares, O., Squassina, A., Thomas, R., Brody, J. A., Qu, L., Sánchez-Juan, P., Morgan, T., Wolters, F. J., Zhao, Y., Garcia, F. Sanchez, Denning, N., Fornage, M., Malamon, J., Naranjo, M. Candida De, Majounie, E., Mosley, T. H., Dombroski, B., Wallon, D., Lupton, M. K., Dupuis, J., Whitehead, P., Fratiglioni, L., Medway, C., Jian, X., Mukherjee, S., Keller, L., Brown, K., Lin, H., Cantwell, L. B., Panza, F., McGuinness, B., Moreno-Grau, S., Burgess, J. D., Solfrizzi, V., Proitsi, P., Adams, H. H., Allen, M., Seripa, D., Pastor, P., L Cupples, A., Price, N. D., Hannequin, D., Frank-Garcia, A., Levy, D., Chakrabarty, P., Caffarra, P., Giegling, I., Beiser, A. S., Giedraitis, V., Hampel, H., Garcia, M. E., Wang, X., Lannfelt, L., Mecocci, P., Eiriksdottir, G., Crane, P. K., Pasquier, F., Boccardi, V., Henández, I., Barber, R. C., Scherer, M., Tarraga, L., Adams, P. M., Leber, M., Chen, Y., Albert, M. S., Riedel-Heller, S., Emilsson, V., Beekly, D., Braae, A., Schmidt, R., Blacker, D., Masullo, C., Schmidt, H., Doody, R. S., Spalletta, G., Longstreth, W. T., Fairchild, T. J., Bossù, P., Lopez, O. L., Frosch, M. P., Sacchinelli, E., Ghetti, B., Yang, Q., Huebinger, R. M., Jessen, F., Li, S., M Kamboh, I., Morris, J., Sotolongo-Grau, O., Katz, M. J., Corcoran, C., Dunstan, M., Braddel, A., Thomas, C., Meggy, A., Marshall, R., Gerrish, A., Chapman, J., Aguilar, M., Taylor, S., Hill, M., Fairén, M. Díez, Hodges, A., Vellas, B., Soininen, H., Kloszewska, I., Daniilidou, M., Uphill, J., Patel, Y., Hughes, J. T., Lord, J., Turton, J., Hartmann, A. M., Cecchetti, R., Fenoglio, C., Serpente, M., Arcaro, M., Caltagirone, C., Orfei, M. Donata, Ciaramella, A., Pichler, S., Mayhaus, M., Gu, W., Lleó, A., Fortea, J., Blesa, R., Barber, I. S., Brookes, K., Cupidi, C., Maletta, R. Giovanni, Carrell, D., Sorbi, S., Moebus, S., Urbano, M., Pilotto, A., Kornhuber, J., Bosco, P., Todd, S., Craig, D., Johnston, J., Gill, M., Lawlor, B., Lynch, A., Fox, N. C., Hardy, J., Albin, R. L., Apostolova, L. G., Arnold, S. E., Asthana, S., Atwood, C. S., Baldwin, C. T., Barnes, L. L., Barral, S., Beach, T. G., Becker, J. T., Bigio, E. H., Bird, T. D., Boeve, B. F., Bowen, J. D., Boxer, A., Burke, J. R., Burns, J. M., Buxbaum, J. D., Cairns, N. J., Cao, C., Carlson, C. S., Carlsson, C. M., Carney, R. M., Carrasquillo, M. M., Carroll, S. L., Diaz, C. Ceballos, Chui, H. C., Clark, D. G., Cribbs, D. H., Crocco, E. A., DeCarli, C., Dick, M., Duara, R., Evans, D. A., Faber, K. M., Fallon, K. B., Fardo, D. W., Farlow, M. R., Ferris, S., Foroud, T. M., Galasko, D. R., Gearing, M., Geschwind, D. H., Gilbert, J. R., Graff-Radford, N. R., Green, R. C., Growdon, J. H., Hamilton, R. L., Harrell, L. E., Honig, L. S., Huentelman, M. J., Hulette, C. M., Hyman, B. T., Jarvik, G. P., Abner, E., Jin, L. - W., Jun, G., Karydas, A., Kaye, J. A., Kim, R., Kowall, N. W., Kramer, J. H., LaFerla, F. M., Lah, J. J., Leverenz, J. B., Levey, A. I., Li, G., Lieberman, A. P., Lunetta, K. L., Lyketsos, C. G., Marson, D. C., Martiniuk, F., Mash, D. C., Masliah, E., McCormick, W. C., McCurry, S. M., McDavid, A. N., McKee, A. C., Mesulam, M., Miller, B. L., Miller, C. A., Miller, J. W., Morris, J. C., Murrell, J. R., Myers, A. J., O'Bryant, S., Olichney, J. M., Pankratz, V. S., Parisi, J. E., Paulson, H. L., Perry, W., Peskind, E., Pierce, A., Poon, W. W., Potter, H., Quinn, J. F., Raj, A., Raskind, M., Reisberg, B., Reitz, C., Ringman, J. M., Roberson, E. D., Rogaeva, E., Rosen, H. J., Rosenberg, R. N., Sager, M. A., Saykin, A. J., Schneider, J. A., Schneider, L. S., Seeley, W. W., Smith, A. G., Sonnen, J. A., Spina, S., Stern, R. A., Swerdlow, R. H., Tanzi, R. E., Thornton-Wells, T. A., Trojanowski, J. Q., Troncoso, J. C., Van Deerlin, V. M., Van Eldik, L. J., Vinters, H. V., Vonsattel, J. Paul, Weintraub, S., Welsh-Bohmer, K. A., Wilhelmsen, K. C., Williamson, J., Wingo, T. S., Woltjer, R. L., Wright, C. B., Yu, C. - E., Yu, L., Garzia, F., Golamaully, F., Septier, G., Engelborghs, S., Vandenberghe, R., De Deyn, P. P., Fernadez, C. Muñoz, Benito, Y. Aladro, Thonberg, H., Forsell, C., Lilius, L., Kinhult-Stählbom, A., Kilander, L., Brundin, R. M., Concari, L., Helisalmi, S., Koivisto, A. Maria, Haapasalo, A., Dermecourt, V., Fievet, N., Hanon, O., Dufouil, C., Brice, A., Ritchie, K., Dubois, B., Himali, J. J., C Keene, D., Tschanz, J. A., Fitzpatrick, A. L., Kukull, W. A., Norton, M., Aspelund, T., Larson, E. B., Munger, R., Rotter, J. I., Lipton, R. B., Bullido, M. J., Hofman, A., Montine, T. J., Coto, E., Boerwinkle, E., Petersen, R. C., Alvarez, V., Rivadeneira, F., Reiman, E. M., Gallo, M., O'Donnell, C. J., Reisch, J. S., Bruni, A. Cecilia, Royall, D. R., Dichgans, M., Sano, M., Galimberti, D., St George-Hyslop, P., Scarpini, E., Tsuang, D. W., Mancuso, M., Bonuccelli, U., Winslow, A. R., Daniele, A., Wu, C. - K., Peters, O., Nacmias, B., Riemenschneider, M., Heun, R., Brayne, C., Rubinsztein, D. C., Brás, J., Guerreiro, R., Al-Chalabi, A., Shaw, C. E., Collinge, J., Mann, D., Tsolaki, M., Clarimón, J., Sussams, R., Lovestone, S., O'Donovan, M. C., Owen, M. J., Behrens, T. W., Mead, S., Goate, A. M., Uitterlinden, A. G., Holmes, C., Cruchaga, C., Ingelsson, M., Bennett, D. A., Powell, J., Golde, T. E., Graff, C., De Jager, P. L., Morgan, K., Ertekin-Taner, N., Combarros, O., Psaty, B. M., Passmore, P., Younkin, S. G., Berr, C., Gudnason, V., Rujescu, D., Dickson, D. W., Dartigues, J. - F., DeStefano, A. L., Ortega-Cubero, S., Hakonarson, H., Campion, D., Boada, M., Kauwe, J. Keoni, Farrer, L. A., Van Broeckhoven, C., M Ikram, A., Jones, L., Haines, J. L., Tzourio, C., Launer, L. J., Escott-Price, V., Mayeux, R., Deleuze, J. - F., Amin, N., Holmans, P. A., Pericak-Vance, M. A., Amouyel, P., van Duijn, C. M., Ramirez, A., San Wang, L. -, Lambert, J. - C., Seshadri, S., Williams, J., and Schellenberg, G. D., “Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease.”, Nat Genet, vol. 49, no. 9, pp. 1373-1384, 2017.

Gene Expression Regulation

C. M. Karch, Ezerskiy, L. A., Bertelsen, S., and Goate, A. M., “Alzheimer's Disease Risk Polymorphisms Regulate Gene Expression in the ZCWPW1 and the CELF1 Loci.”, PLoS One, vol. 11, no. 2, p. e0148717, 2016.

E. M. Reiman, Webster, J. A., Myers, A. J., Hardy, J., Dunckley, T., Zismann, V. L., Joshipura, K. D., Pearson, J. V., Hu-Lince, D., Huentelman, M. J., Craig, D. W., Coon, K. D., Liang, W. S., Herbert, R. L. H., Beach, T., Rohrer, K. C., Zhao, A. S., Leung, D., Bryden, L., Marlowe, L., Kaleem, M., Mastroeni, D., Grover, A., Heward, C. B., Ravid, R., Rogers, J., Hutton, M. L., Melquist, S., Petersen, R. C., Alexander, G. E., Caselli, R. J., Kukull, W., Papassotiropoulos, A., and Stephan, D. A., “GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriers.”, Neuron, vol. 54, no. 5, pp. 713-20, 2007.

F. Zou, Chai, H. Seng, Younkin, C. S., Allen, M., Crook, J., V Pankratz, S., Carrasquillo, M. M., Rowley, C. N., Nair, A. A., Middha, S., Maharjan, S., Nguyen, T., Ma, L., Malphrus, K. G., Palusak, R., Lincoln, S., Bisceglio, G., Georgescu, C., Kouri, N., Kolbert, C. P., Jen, J., Haines, J. L., Mayeux, R., Pericak-Vance, M. A., Farrer, L. A., Schellenberg, G. D., Petersen, R. C., Graff-Radford, N. R., Dickson, D. W., Younkin, S. G., and Ertekin-Taner, N., “Brain expression genome-wide association study (eGWAS) identifies human disease-associated variants.”, PLoS Genet, vol. 8, no. 6, p. e1002707, 2012.

Gene Frequency

M. Saleh, Vaillancourt, J. P., Graham, R. K., Huyck, M., Srinivasula, S. M., Alnemri, E. S., Steinberg, M. H., Nolan, V., Baldwin, C. T., Hotchkiss, R. S., Buchman, T. G., Zehnbauer, B. A., Hayden, M. R., Farrer, L. A., Roy, S., and Nicholson, D. W., “Differential modulation of endotoxin responsiveness by human caspase-12 polymorphisms.”, Nature, vol. 429, no. 6987, pp. 75-9, 2004.

J. J. Corneveaux, Myers, A. J., Allen, A. N., Pruzin, J. J., Ramirez, M., Engel, A., Nalls, M. A., Chen, K., Lee, W., Chewning, K., Villa, S. E., Meechoovet, H. B., Gerber, J. D., Frost, D., Benson, H. L., O'Reilly, S., Chibnik, L. B., Shulman, J. M., Singleton, A. B., Craig, D. W., Van Keuren-Jensen, K. R., Dunckley, T., Bennett, D. A., De Jager, P. L., Heward, C., Hardy, J., Reiman, E. M., and Huentelman, M. J., “Association of CR1, CLU and PICALM with Alzheimer's disease in a cohort of clinically characterized and neuropathologically verified individuals.”, Hum Mol Genet, vol. 19, no. 16, pp. 3295-301, 2010.

M. M. Carrasquillo, Zou, F., V Pankratz, S., Wilcox, S. L., Ma, L., Walker, L. P., Younkin, S. G., Younkin, C. S., Younkin, L. H., Bisceglio, G. D., Ertekin-Taner, N., Crook, J. E., Dickson, D. W., Petersen, R. C., Graff-Radford, N. R., and Younkin, S. G., “Genetic variation in PCDH11X is associated with susceptibility to late-onset Alzheimer's disease.”, Nat Genet, vol. 41, no. 2, pp. 192-8, 2009.

P. M. Erlich, Lunetta, K. L., L Cupples, A., Huyck, M., Green, R. C., Baldwin, C. T., and Farrer, L. A., “Polymorphisms in the PON gene cluster are associated with Alzheimer disease.”, Hum Mol Genet, vol. 15, no. 1, pp. 77-85, 2006.

R. K. Gopalraj, Zhu, H., Kelly, J. F., Mendiondo, M., Pulliam, J. F., Bennett, D. A., and Estus, S., “Genetic association of low density lipoprotein receptor and Alzheimer's disease.”, Neurobiol Aging, vol. 26, no. 1, pp. 1-7, 2005.

A. Patel, Rees, S. D., M Kelly, A., Bain, S. C., Barnett, A. H., Prasher, A., Arshad, H., and Prasher, V. P., “Genetic variants conferring susceptibility to Alzheimer's disease in the general population; do they also predispose to dementia in Down's syndrome.”, BMC Res Notes, vol. 7, p. 42, 2014.

P. Nowotny, Hinrichs, A. L., Smemo, S., Kauwe, J. S. K., Maxwell, T., Holmans, P., Hamshere, M., Turic, D., Jehu, L., Hollingworth, P., Moore, P., Bryden, L., Myers, A., Doil, L. M., Tacey, K. M., Gibson, A. M., McKeith, I. G., Perry, R. H., Morris, C. M., Thal, L., Morris, J. C., O'Donovan, M. C., Lovestone, S., Grupe, A., Hardy, J., Owen, M. J., Williams, J., and Goate, A., “Association studies between risk for late-onset Alzheimer's disease and variants in insulin degrading enzyme.”, Am J Med Genet B Neuropsychiatr Genet, vol. 136B, no. 1, pp. 62-8, 2005.

R. A. Nafikov, Nato, A. Q., Sohi, H., Wang, B., Brown, L., Horimoto, A. R., Vardarajan, B. N., Barral, S. M., Tosto, G., Mayeux, R. P., Thornton, T. A., Blue, E., and Wijsman, E. M., “Analysis of pedigree data in populations with multiple ancestries: Strategies for dealing with admixture in Caribbean Hispanic families from the ADSP.”, Genet Epidemiol, vol. 42, no. 6, pp. 500-515, 2018.

F. W. Lohoff, Sander, T., Ferraro, T. N., Dahl, J. P., Gallinat, J., and Berrettini, W. H., “Confirmation of association between the Val66Met polymorphism in the brain-derived neurotrophic factor (BDNF) gene and bipolar I disorder.”, Am J Med Genet B Neuropsychiatr Genet, vol. 139B, no. 1, pp. 51-3, 2005.