Lack of independent associations of apolipoprotein E promoter and intron 1 polymorphisms with Alzheimer's disease G. William Rebeck * , Bonnie S. Cheung, Whit®eld B. Growdon, Amy Deng, Praveen Akuthota, Joseph Locascio, Steven M. Greenberg, Bradley T. Hyman Alzheimer Research Unit, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129, USA Received 10 June 1999; accepted 7 July 1999 Abstract Several studies have demonstrated genetic associations between Alzheimer's disease (AD) and polymorphisms in the promoter/enhancer regions of the apolipoprotein E (APOE) gene. These studies raise the possibility that APOE transcrip- tion control may be involved in altered risks for AD. We evaluated polymorphic sites in the intron-1 enhancer element (IE- 1G/C) and in the APOE promoter (2219G/T). For the IE-1 polymorphism, we analyzed 433 individuals (183 AD and 250 controls), and found a strong linkage between the IE-1G allele and APOE-14. When we controlled for this linkage using log-linear model analysis, we found no independent association between the IE-1 polymorphism and AD. For the 2219 polymorphism, we analyzed 475 individuals (168 AD cases, 234 controls, and 73 cases of cerebral amyloid angiopathy (CAA)). We found strong linkages between the 2219G allele and APOE-12 and between the 2219 T allele and APOE-14. Controlling for these linkages, we found no independent association between the 2219 polymorphism and AD or CAA. Thus, our studies do not support independent associations between AD and either the IE-1 or the 2219 polymorphisms. q 1999 Elsevier Science Ireland Ltd. All rights reserved. Keywords: Apolipoprotein E; Allelic imbalance; Th1/E47; Genetic linkage Genetic studies have consistently demonstrated a strong association between the 14 allele of the apolipoprotein E (APOE) gene and an increased risk of Alzheimer's disease (AD) [15] and the related disorder, cerebral amyloid angio- pathy (CAA) [5]. However, subsequent analyses of aged populations indicated that the majority of APOE-14 carriers remained cognitively normal into late life [6,12,13]. These observations focused attention on other genetic factors that may modulate the AD risk associated with APOE-14. One interesting possibility is that polymorphisms in regulatory regions of APOE alter the risk of AD, particularly in APOE heterozygotes. The hypothesis is that some APOE-13/4 individuals have decreased expression of the APOE-14 allele due to a promoter polymorphism, and this may lower their risk of AD [9]. Three common polymorphisms have been identi®ed in the APOE promoter region, at posi- tions 2491, 2427, and 2219 (numbered relative to the transcription start site) [1]. Another polymorphism was identi®ed in the APOE intron 1 enhancer (IE-1) region (1113) [11]. Several studies have addressed whether the APOE 2491 and 2427 polymorphisms are associated with altered risks of AD, with some reports supporting an association [3,7,10], and others not [14,16,17]. The APOE 2219 polymorphism was analyzed in only one large study [7], showing an increased risk of AD associated with the T allele. The APOE IE-1 polymorphism was associated with AD, possi- bly because it is strongly linked to APOE-14 [11]; an APOE-14-independent effect of the IE-1 polymorphism on AD was reported in another study [8]. Analyzing whether these APOE promoter/enhancer polymorphisms affect the risk of AD is complicated by the possibility that each is genetically linked to the APOE-12/3/4 alleles and those polymorphic sites affect the risk of AD. In this work, we analyzed the linkage of the 2219 and the IE-1 polymorph- isms with the APOE-12/3/4 alleles, and tested whether they independently affect the risk of AD. DNA was isolated from blood or brain tissue samples of AD patients and control individuals described in earlier work [4,6]. Patients with probable CAA were diagnosed as described [5]. A standard PCR protocol was used to Neuroscience Letters 272 (1999) 155±158 0304-3940/99/$ - see front matter q 1999 Elsevier Science Ireland Ltd. All rights reserved. PII: S0304-3940(99)00602-3 www.elsevier.com/locate/neulet * Corresponding author. Tel.: 11-617-724-8329; fax: 11-617- 726-5677. E-mail address: rebeck@helix.mgh.harvard.edu (G.W. Rebeck)