Rare coding mutations identified by sequencing of Alzheimer disease genome-wide association studies loci

Annals of Neurology

Volumn 78, Issue 3, 2015, Pages 487-498

  Vardarajan, Badri N ^a,b,c,d   Ghani, Mahdi ^e   Kahn, Amanda ^a   Sheikh, Stephanie ^a,c   Sato, Christine ^e   Barral, Sandra ^a,b,c   Lee, Joseph H ^a,b,f   Cheng, Rong ^a,b   Reitz, Christiane ^a,b,c   Lantigua, Rafael ^a,c   Reyes Dumeyer, Dolly ^a,b   Medrano, Martin ^g   Jimenez Velazquez, Ivonne Z ^h   Rogaeva, Ekaterina ^e   St George Hyslop, Peter ^e,i   Mayeux, Richard ^a,b,c,f  

^a NewYork Presbyterian Hospital   (United States)

^b Taub Institute for Research on Alzheimer's Disease and the Aging Brain and the Gertrude H Sergievsky Center   (United States)

^c University of Toronto ^*  (United States)

^d Och Spine at New York Presbyterian Hospitals   (United States)

^e UNIVERSITY OF TORONTO   (Canada)

^f University of Cambridge ^*  (United States)

^g UNIVERSITY OF CHILE   (Chile)

^h UNIVERSITY OF PUERTO RICO SCHOOL OF MEDICINE   (Puerto Rico)

ⁱ UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ATP BINDING CASSETTE TRANSPORTER A7; BIN1 PROTEIN; CD2 ASSOCIATED PROTEIN; CLU PROTEIN; CR1 PROTEIN; EPHRIN RECEPTOR A1; MS4A6A PROTEIN; PICALM PROTEIN; PROTEIN; UNCLASSIFIED DRUG;

AGED; ALZHEIMER DISEASE; ARTICLE; CARIBBEAN (PERSON); CAUCASIAN; CLINICAL DEMENTIA RATING; CONTROLLED STUDY; DISEASE COURSE; EXOME; FAMILY STUDY; FEMALE; FOLLOW UP; GENE FREQUENCY; GENE IDENTIFICATION; GENE LOCUS; GENE MUTATION; GENE SEQUENCE; GENE TARGETING; GENETIC ASSOCIATION; GENETIC CODE; GENETIC VARIABILITY; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HISPANIC; HUMAN; LOSS OF FUNCTION MUTATION; MAJOR CLINICAL STUDY; MALE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MISSENSE MUTATION; MULTIPLEX POLYMERASE CHAIN REACTION; MUTATION RATE; ONSET AGE; PATHOGENESIS; PRIORITY JOURNAL; COHORT ANALYSIS; GENETIC PREDISPOSITION; GENETICS; MUTATION; OPEN READING FRAME; PEDIGREE; PROCEDURES; VERY ELDERLY;

AGED; AGED, 80 AND OVER; ALZHEIMER DISEASE; COHORT STUDIES; FEMALE; FOLLOW-UP STUDIES; GENETIC LOCI; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; MUTATION; OPEN READING FRAMES; PEDIGREE;

EID: 84939654955     PISSN: 03645134     EISSN: 15318249     Source Type: Journal    
DOI: 10.1002/ana.24466     Document Type: Article

References (41)

1. Harold D, Abraham R, Hollingworth P, et al., Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nat Genet 2009; 41: 1088-1093.
2. Lambert JC, Heath S, Even G, et al., Genome-wide association study identifies variants at CLU and CR1 associated with Alzheimer's disease. Nat Genet 2009; 41: 1094-1099.
3. Seshadri S, Fitzpatrick AL, Ikram MA, et al., Genome-wide analysis of genetic loci associated with Alzheimer disease. JAMA 2010; 303: 1832-1840.
4. Jun G, Naj AC, Beecham GW, et al., Meta-analysis confirms CR1, CLU, and PICALM as Alzheimer disease risk loci and reveals interactions with APOE genotypes. Arch Neurol 2010; 67: 1473-1484.
5. Wijsman EM, Pankratz ND, Choi Y, et al., Genome-wide association of familial late-onset Alzheimer's disease replicates BIN1 and CLU and nominates CUGBP2 in interaction with APOE. PLoS Genet 2011; 7: e1001308.
6. Farrer LA, Cupples LA, Haines JL, et al., Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium. JAMA 1997; 278: 1349-1356.
7. Naj AC, Jun G, Beecham GW, et al., Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer's disease. Nat Genet 2011; 43: 436-441.
8. Hollingworth P, Harold D, Sims R, et al., Common variants at ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and CD2AP are associated with Alzheimer's disease. Nat Genet 2011; 43: 429-435.
9. Pottier C, Hannequin D, Coutant S, et al., High frequency of potentially pathogenic SORL1 mutations in autosomal dominant early-onset Alzheimer disease. Mol Psychiatry 2012; 17: 875-879.
10. Vardarajan BN, Zhang Y, Lee JH, et al., Coding mutations in SORL1 and Alzheimer's disease. Ann Neurol 2015; 77: 215-227.
11. Lee JH, Kahn A, Cheng R, et al., Disease-related mutations among Caribbean Hispanics with familial dementia. Mol Genet Genomic Med 2014; 2: 430-437.
12. Guerreiro R, Wojtas A, Bras J, et al., TREM2 variants in Alzheimer's disease. N Engl J Med 2013; 368: 117-127.
13. Kim M, Suh J, Romano D, et al., Potential late-onset Alzheimer's disease-associated mutations in the ADAM10 gene attenuate {alpha}-secretase activity. Hum Mol Genet 2009; 18: 3987-3996.
14. Jonsson T, Stefansson H, Steinberg S, et al., Variant of TREM2 associated with the risk of Alzheimer's disease. N Engl J Med 2013; 368: 107-116.
15. Cruchaga C, Karch CM, Jin SC, et al., Rare coding variants in the phospholipase D3 gene confer risk for Alzheimer's disease. Nature 2014; 505: 550-554.
16. Seshadri S, Fitzpatrick AL, Ikram MA, et al., Genome-wide analysis of genetic loci associated with Alzheimer disease. JAMA 2010; 303: 1832-1840.
17. Harold D, Abraham R, Hollingworth P, et al., Genome-wide association study identifies variants at CLU and PICALM associated with Alzheimer's disease. Nat Genet 2009; 41: 1088-1093.
18. Lambert JC, Ibrahim-Verbaas CA, Harold D, et al., Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat Genet 2013; 45: 1452-1458.
19. Lee JH, Cheng R, Barral S, et al., Identification of novel loci for Alzheimer disease and replication of CLU, PICALM, and BIN1 in Caribbean Hispanic individuals. Arch Neurol 2011; 68: 320-328.
20. Li H, Durbin R,. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25: 1754-1760.
21. McKenna A, Hanna M, Banks E, et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: 1297-1303.
22. Wang K, Li M, Hakonarson H,. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010; 38: e164.
23. Adzhubei I, Jordan DM, Sunyaev SR,. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet 2013;Chapter 7:Unit 7.20.
24. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A,. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 2010; 20: 110-121.
25. Neale BM, Rivas MA, Voight BF, et al., Testing for an unusual distribution of rare variants. PLoS Genet 2011; 7: e1001322.
26. Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB,. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet 2013; 9: e1003709.
27. Myers AJ, Gibbs JR, Webster JA, et al., A survey of genetic human cortical gene expression. Nat Genet 2007; 39: 1494-1499.
28. Karch CM, Jeng AT, Nowotny P, Cady J, Cruchaga C, Goate AM,. Expression of novel Alzheimer's disease risk genes in control and Alzheimer's disease brains. PLoS One 2012; 7: e50976.
29. Kim WS, Li H, Ruberu K, et al., Deletion of Abca7 increases cerebral amyloid-beta accumulation in the J20 mouse model of Alzheimer's disease. The Journal of neuroscience: the official journal of the Society for Neuroscience 2013; 33: 4387-4394.
30. Satoh K, Abe-Dohmae S, Yokoyama S, St.George-Hyslop P, Fraser P,. ATP-binding cassette transporter A7 (ABCA7) effects on amyloid processing and relevance to Alzheimer's disease. Alzheimer's & Dementia: The Journal of the Alzheimer's Association 8: P473.
31. Tanaka N, Abe-Dohmae S, Iwamoto N, Yokoyama S,. Roles of ATP-binding cassette transporter A7 in cholesterol homeostasis and host defense system. J Atheroscler Thromb 2011; 18: 274-281.
32. Chan SL, Kim WS, Kwok JB, et al., ATP-binding cassette transporter A7 regulates processing of amyloid precursor protein in vitro. J Neurochem 2008; 106: 793-804.
33. Reitz C, Jun G, Naj A, et al., Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E 4,and the risk of late-onset Alzheimer disease in African Americans. JAMA 2013; 309: 1483-1492.
34. Steinberg S, Stefansson H, Jonsson T, et al., Loss-of-function variants in ABCA7 confer risk of Alzheimer's disease. Nat Genet 2015; 47: 445-447.
35. Lambert JC, Ibrahim-Verbaas CA, Harold D, et al., Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat Genet 2013; 45: 1452-1458.
36. Chapuis J, Hansmannel F, Gistelinck M, et al., Increased expression of BIN1 mediates Alzheimer genetic risk by modulating tau pathology. Mol Psychiatry 2013; 18: 1225-1234.
37. Tan MS, Yu JT, Jiang T, Zhu XC, Guan HS, Tan L,. Genetic variation in BIN1 gene and Alzheimer's disease risk in Han Chinese individuals. Neurobiol Aging 2014; 35: 1781.e1-1781.e8.
38. Omenn GS, Guan Y, Menon R,. A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. J Proteomics 2014; 107: 103-112.
39. Wyatt A, Yerbury J, Poon S, Dabbs R, Wilson M,. Chapter 6: The chaperone action of Clusterin and its putative role in quality control of extracellular protein folding. Adv Cancer Res 2009; 104: 89-114.
40. Narayan P, Orte A, Clarke RW, et al., The extracellular chaperone clusterin sequesters oligomeric forms of the amyloid-beta(1-40) peptide. Nat Struct Mol Biol 2012; 19: 79-83.
41. Bettens K, Brouwers N, Engelborghs S, et al., Both common variations and rare non-synonymous substitutions and small insertion/deletions in CLU are associated with increased Alzheimer risk. Mol neurodegener 2012; 7: 3.