Apolipoprotein E 4, and the Risk of Late-Onset Alzheimer Disease in Af

ORIGINAL CONTRIBUTION Variants in the ATP-Binding Cassette Transporter (ABCA7), Apolipoprotein E ␧4, and the Risk of Late-Onset Alzheimer Disease in African Americans Christiane Reitz, MD, PhD Importance Genetic variants associated with susceptibility to late-onset Alzheimer Gyungah Jun, PhD disease are known for individuals of European ancestry, but whether the same or dif- Adam Naj, PhD ferent variants account for the genetic risk of Alzheimer disease in African American individuals is unknown. Identification of disease-associated variants helps identify tar- Ruchita Rajbhandary, MPH gets for genetic testing, prevention, and treatment. Badri Narayan Vardarajan, PhD Objective To identify genetic loci associated with late-onset Alzheimer disease in Li-San Wang, PhD African Americans. Otto Valladares, MS Design, Setting, and Participants The Alzheimer Disease Genetics Consortium Chiao-Feng Lin, PhD (ADGC) assembled multiple data sets representing a total of 5896 African Americans (1968 case participants, 3928 control participants) 60 years or older that were col- Eric B. Larson, MD, MPH lected between 1989 and 2011 at multiple sites. The association of Alzheimer disease Neill R. Graff-Radford, MD with genotyped and imputed single-nucleotide polymorphisms (SNPs) was assessed in case-control and in family-based data sets. Results from individual data sets were Denis Evans, MD combined to perform an inverse variance–weighted meta-analysis, first with genome- Philip L. De Jager, MD, PhD wide analyses and subsequently with gene-based tests for previously reported loci. Paul K. Crane, MD, MPH Main Outcomes and Measures Presence of Alzheimer disease according to stan- dardized criteria. Joseph D. Buxbaum, PhD Results Genome-wide significance in fully adjusted models (sex, age, APOE geno- Jill R. Murrell, PhD type, population stratification) was observed for a SNP in ABCA7 (rs115550680, allele=G; Towfique Raj, PhD frequency, 0.09 cases and 0.06 controls; odds ratio [OR], 1.79 [95% CI, 1.47-2.12]; ϫ Ϫ9 Nilufer Ertekin-Taner, MD, PhD P=2.2 10 ), which is in linkage disequilibrium with SNPs previously associated with Alzheimer disease in Europeans (0.8ϽD'Ͻ0.9). The effect size for the SNP in ABCA7 Mark Logue, PhD was comparable with that of the APOE ε4–determining SNP rs429358 (allele=C; fre- Ϫ Clinton T. Baldwin, PhD quency, 0.30 cases and 0.18 controls; OR, 2.31 [95% CI, 2.19-2.42]; P=5.5ϫ10 47). Several loci previously associated with Alzheimer disease but not reaching signifi- Robert C. Green, MD, MPH cance in genome-wide analyses were replicated in gene-based analyses accounting Lisa L. Barnes, PhD for linkage disequilibrium between markers and correcting for number of tests per- Ͻ Ͻ Laura B. Cantwell, MPH formed per gene (CR1, BIN1, EPHA1, CD33; 0.0005 empirical P .001). M. Daniele Fallin, PhD Conclusions and Relevance In this meta-analysis of data from African American participants, Alzheimer disease was significantly associated with variants in ABCA7 and Rodney C. P. Go, PhD with other genes that have been associated with Alzheimer disease in individuals of Patrick Griffith, MD European ancestry. Replication and functional validation of this finding is needed be- fore this information is used in clinical settings. Thomas O. Obisesan, MD JAMA. 2013;309(14):1483-1492 www.jama.com Jennifer J. Manly, PhD Kathryn L. Lunetta, PhD Kathleen S. Hall, PhD Gerard D. Schellenberg, PhD M. Ilyas Kamboh, PhD Alison M. Goate, PhD Richard Mayeux, MD, MSc Oscar L. Lopez, MD Goldie S. Byrd, PhD for the Alzheimer Disease Genetics David A. Bennett, MD Consortium Walter A. Kukull, PhD Hugh Hendrie, MB, ChB, DSc Tatiana M. Foroud, PhD Author Affiliations and a List of Members of the Alzheimer Disease Genetics Consortium appear at the See also pp 1527 and 1533. Jonathan L. Haines, PhD end of this article. Corresponding Author: Richard Mayeux, MD, MSc, Author Video Interview available at Lindsay A. Farrer, PhD Gertrude H. Sergievsky Center, Columbia University, www.jama.com. 630 W 168th St, New York, NY 10032 (rpm2 Margaret A. Pericak-Vance, PhD @columbia.edu).

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

ATE-ONSET ALZHEIMER DISEASE Disorders Association criteria.36 Clas- (LOAD) is the most common sification of participants as African Box. Glossary of Terms cause of dementia, increasing in American was based on self-report frequency from 1% at age 65 using the format of the 1990 US cen- Genome-wide analysis: A genetic yearsL to more than 30% for people older sus.37 A detailed description of the origi- study evaluating the potential link- than 80 years.1 As much as 20% of the nal cohorts contributing samples is pro- age of genetic markers located disease-attributable risk is related to the vided in the eMethods, available at throughout the genome to a spe- ε4 variant in APOE.2 A series of large http://www.jama.com. A glossary of cific trait. This approach has been used for mendelian (single-gene) genome-wide association studies terms used in this article is provided in disorders as well as complex traits (GWASs) identified several additional the BOX. (genome-wide association study). variants that affect disease susceptibil- All participants provided written in- Haplotype: The combination of ity in non-Hispanic whites of Euro- formed consent, and the data sets for linked marker alleles (may be poly- pean ancestry, including CR1, CLU, the study were approved for analysis by morphisms or mutations) for a given PICALM, BIN1, CD2AP, CD33, EPHA1, the relevant institutional review boards. region of DNA on a single chromo- MS4A6A/MS4E4, and ABCA7.3-7 In some. addition, SORL1 was identified as Censoring Age Imputation: A statistical method a susceptibility gene in candidate gene Information on age at onset for case for inferring genotypes that are not and functional studies.8,9 However, participants and age at examination or directly measured. Linkage disequilibrium: Refers to LOAD heritability estimates are high death for control participants was alleles at loci close enough together 2 Ϸ (h 60%-80%), and a large part of the available for most cohorts. However, that they remain inherited together genetic contribution to LOAD re- surrogate age information was avail- through many generations because 10 mains unexplained. able for other data sets including age their extreme close proximity makes The incidence of LOAD among Afri- at ascertainment (Indiana University), recombination (crossing over) be- can Americans is higher than among age at diagnosis (Chicago Health and tween them highly unlikely. whites living in the same commu- Aging Project [CHAP], Minority For a complete list of genomic nity,11 and the reported risk for the dis- Aging Research Study/Clinical Minor- terms, see the Appendix in this is- ease associated with APOE ε4 hetero- ity Core [MARS/CORE]), or age at sue. zygosity is inconsistent in African death (subset of autopsy-confirmed Americans compared with whites.12 samples in the University of Miami/ African Americans and other minori- Vanderbilt University [UM/VU] ties are understudied, and it is unclear cohort). Age at death was used for LightCycler 480 instrument (Roche whether any of the recently identified autopsied participants. To restrict the Diagnostics)38 and LightMix Kit ApoE loci modify risk of LOAD in racial or analyses to case participants with C112R R158 (TIB MOLBIOL); for the ethnic groups other than whites. LOAD, persons younger than 60 years University of Pittsburgh, Washington To identify genetic variants associated at last evaluation, symptom onset, or Heights Columbia Aging Project, and withLOADinAfricanAmericans,theAlz- death were excluded. Indianapolis cohorts, they were deter- heimer Disease Genetics Consortium mined by pyrosequencing39 or analy- (ADGC) performed a GWAS among the Genotyping sis of restriction fragment length poly- largest sample, to our knowledge, of Afri- GWAS genotypes were from a variety morphisms40,41; for the Religious Orders can Americans ever assembled for genetic of Illumina arrays (eTable 1). For all Study/Rush Memory and Aging Proj- studies of Alzheimer disease. data sets, case and control samples were ect (ROS/MAP) and MARS/CORE they randomly plated to minimize poten- were determined by high-throughput METHODS tial batch effects. For the Alzheimer Dis- sequencing of codons 112 and 158 in Study Samples ease Centers, Adult Changes in APOE by Agencourt Bioscience Corpo- Participants were recruited from sev- Thought, National Institute in Aging– ration; for the Washington University eral independent community-based LOAD/National Cell Repository for Alz- samples they were determined using a case-control and family studies of heimer Disease (NIA-LOAD/NCRAD), taqman-based assay from Applied Bio- African Americans collected over a pe- UM/VU, CHAP, Columbia University, systems. Single-nucleotide polymor- riod of approximately 30 years be- and Mayo Clinic cohorts, APOE geno- phisms were annotated based on the tween 1989 and 2011.12-35 All partici- types were based on haplotypes de- National Center for Biotechnology In- pants underwent rigorous phenotyping rived from single-nucleotide polymor- formation (NCBI) Reference Se- for LOAD, and diagnoses were made by phisms (SNPs) rs7412 and rs429358. quence database and the GRCh37/ National Institute of Neurological and For the MIRAGE and GenerAAtions co- hg19 genome build; genes were Communicative Disorders and Stroke– horts, APOE genotypes were deter- annotated using NCBI Entrez Gene ac- Alzheimer’s Disease and Related mined using the Roche Diagnostics cession number.

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

Quality Control Procedures respect to African American ancestry sex, and population substructure (using Single-nucleotide polymorphisms with were removed from the sample. Then, for each cohort the appropriate num- minor allele frequencies (MAFs) less the data were reevaluated using ber of principal components) (TABLE 1). than 0.01, call rates less than 98%, or EIGENSTRAT to derive loadings for the Results from the individual data sets not in Hardy-Weinberg equilibrium first 10 principal components. Princi- were combined using an inverse vari- (PϽ10Ϫ6 in controls) were excluded. pal component analysis was used to ance–weighted meta-analysis ap- Participants whose reported sex dif- model for each assessed marker ances- proach implemented in METAL (http: fered from the sex assignment deter- try differences in frequency between case //genome.sph.umich.edu/wiki mined by analysis of the X-chromo- and control participants. The resulting /METAL). The meta-analysis P value some SNPs using PLINK version 1.07 information can be used to adjust for was estimated by the summarized test (http://pngu.mgh.harvard.edu/~purcell population substructure, which mini- statistic after applying a genomic con- /plink/) were excluded. For cohorts mizes spurious associations and maxi- trol within each individual study. genotyped on multiple chips (MIRAGE, mizes power to detect true associations. Heterogeneity of effect estimates across UM/VU), quality control was per- data sets (I2) was tested with the ␹2 dis- formed separately for the subsets of in- Genotype Imputation tributed Q statistic.45,46 All analyses were dividuals genotyped using different Genome-wide imputation of allele dos- repeated adjusting for the number of chips. Latent relatedness among par- ages was performed using the June 2011 APOE-ε4 alleles (0, 1, or 2). The thresh- ticipants within and across the case- panel from 1000 Genomes build 37 for old for genome-wide significance was control cohorts was identified by the es- imputation of genotypes (http://www calculated as PՅ5ϫ10Ϫ8, taking link- timated proportion of alleles (␲) shared .1000genomes.org/announcements age disequilibrium between markers identical by descent (IBD) using PLINK. /june-2011-data-release-2011-06-23) into account. The genomic inflation fac- The proportion IBD is calculated by es- and the IMPUTE2 (http://mathgen.stats tors (␭) for each model are estimated timating the probability of sharing 0, .ox.ac.uk/impute/impute_v2.html) soft- based on the concept that apart from a 1, or 2 alleles IBD for any 2 individu- ware applying strict prephasing, small number of SNPs showing a true als (␲=P [IBD=2]ϩ0.5ϫP [IBD=1], preimputation filtering, and variant po- association with the disease, the test sta- where P indicates probability). One sition and strand alignment control.43 tistics for other SNPs should follow the participant from each duplicate The reference panel used is a multi- distribution under the null hypothesis pair (␲Ͼ0.95) or relative pair reference panel specifically developed of no association and thus reflect cryp- (0.4Յ␲Ͻ0.95) was included in the for imputation of nonwhite popula- tic population stratification, related- sample used for association analyses, tions and shown to impute genotypes ness, or genotyping errors. These fac- prioritizing based on nonmissing dis- in African Americans with high accu- tors were between 0.87 and 1.03, ease status and then higher SNP call racy.43,44 Only imputed SNP dosages indicating that there was no substan- rate. Relationships among individuals with an imputation quality estimate of tial inflation of the test statistics in either in the family-based cohorts (MIRAGE, R2Ն0.50 were included in the final SNP meta-analysis (eFigure 1). All find- NIA-LOAD/NCRAD) were confirmed set for analysis. ings with P Յ 10Ϫ6 in the fully ad- by pairwise genome-wide estimates of justed model were compared with re- IBD allele sharing. All discrepancies Association Analyses sults obtained in whites.5 were reviewed with clinical and pedi- Association of LOAD with genotyped Because of the a priori hypothesis of gree data to determine the most likely and imputed SNPs (allele dosages) that an involvement with LOAD, associations relationship consistent with IBD esti- had passed quality control was as- of SNPs in previously reported LOAD mates. sessed using logistic regression meth- genes (CR1 [NCBI Entrez Gene 1378], ods for case-control data sets and lo- BIN1 [NCBI Entrez Gene 274], PICALM Population Substructure gistic generalized estimating equations [NCBI Entrez Gene 8301], CLU [NCBI Population substructure was evaluated for family data sets as implemented in Entrez Gene 1191], EPHA1 [NCBI En- in each cohort separately using PLINK. All analyses were performed trez Gene 2041], MS4A6A cluster [NCBI EIGENSTRAT (EIGENSOFT version using an additive genetic model (ie, Entrez Gene 64231], CD2AP [NCBI En- 3.0) (http://genepath.med.harvard genotyped SNPs were coded 0, 1, or 2 trez Gene 23607], and CD33 [NCBI En- .edu/~reich/EIGENSTRAT.htm).42 First, based on the number of minor alleles trez Gene 945]), were analyzed with a genetic profiles for all participants in the [with 0 being homozygous for the ref- versatile gene-based association study case-control data sets and a group of un- erence allele, 1 being heterozygous, and (VEGAS47), adding 50 kilobases (kb) to related participants in the MIRAGE fam- 2 being homozygous for the minor al- each side. Gene-based tests for associa- ily-based data set were compared with lele], and imputed SNPs were coded tion are a useful complement to GWASs, those in the HapMap reference panel of based on the posterior probability of the because gene-based tests consider asso- African Americans (African ancestry in minor allele [0–2]). The primary association between a trait and all SNPs the Southwest USA), and outliers with ciation analyses were adjusted for age, within a gene rather than each marker

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

individually. Depending on the under- D' is not influenced by differences in some 5q35.2 that is not near any genes lying genetic architecture, gene-based ap- allele frequencies between ethnic with a known function (OR, 2.03 [95% proaches can be more powerful than groups. CI, 1.54-2.67]; P =5.1ϫ 10Ϫ7), and traditional single-SNP–based GWASs, rs115550680 in ABCA7 (NCBI Entrez in particular if a gene contains several RESULTS Gene 10347) (OR, 1.78 [95% CI, 1.28- SNPs with marginal levels of signifi- We performed the GWAS using data 1.82]; P =1.4ϫ 10Ϫ6). After adjust- cance that are often indistinguishable from 1968 African American case par- ment for APOE, the associations with from random noise in the initial GWAS. ticipants with LOAD and 3928 cogni- ELMO1 and SOX13 SNPs diminished, For the specific gene assessed, VEGAS tively normal elderly control partici- whereas the association for incorporates linkage disequilibrium in- pants. Fifty percent of the cohort had rs115550680 in ABCA7 (OR, 1.79 [95% formation from a set of reference indi- preexisting genome-wide genotyping, CI, 1.47-2.12]; P =2.21ϫ 10Ϫ9) be- viduals from HapMap, determines the and another 1074 cases and 1908 con- came stronger (TABLE 2). The associa- number of tagging SNPs, and calcu- trols were genotyped specifically for this tion of rs145848414 on chromosome lates the empirical P value for the gene project. Several characteristics of the in- 5q35.2 with LOAD also became stron- by using simulations from the multi- dividual data sets are shown in Table 1. ger but did not fully reach genome- variate normal distribution.47 Accord- The final SNP set included a total of wide significance (OR, 2.29 [95% CI, ingly, the P value threshold for signifi- 17 332 474 genotyped and imputed 1.69-3.09]; P =6.9ϫ 10Ϫ8). The in- cance differs between genes depending variants. The association with the low- creases in effect size were accompa- on the linkage disequilibrium struc- est P value was with APOE (NCBI En- nied by decreases in P value, which were ture and number of tagging SNPs trez Gene 348). In models adjusting for most pronounced in the larger data sets assessed. age, sex, and population stratification, (ADGC, CHAP, MIRAGE660, India- Strength of linkage disequilibrium— numerous SNPs in the APOE region napolis). which is a measure of the association were significant (eg, rs429358, In African Americans, the SNP in of 2 alleles at different loci—between P=5.5ϫ10Ϫ47) for association with ABCA7 (rs115550680) is in linkage dis- different SNPs observed in the same LOAD. Excluding SNPs in the APOE re- quilibrium with 2 other ABCA7 SNPs gene in this African American sample gion, the strongest associations were ob- previously associated with LOAD at the and the white samples was deter- served for rs10247412 in ELMO1 (NCBI genome-wide significance level in non- mined by estimating D'.D' ranges from Entrez Gene 9844) (odds ratio [OR], Hispanic whites of European ancestry 0 to 1, with 0 indicating no linkage (ie, 0.66 [95% CI, 0.56-0.77]; (rs3764650 [Hollingworth et al3] and fully independent transmission from P =2.9ϫ 10Ϫ7), rs885330 in SOX13 rs3752246 [Naj et al5], 0.8ϽD'=0.9) parent to offspring) and 1 indicating (NCBI Entrez Gene 9580) (OR, 1.25 (FIGURE 1) and showed the same di- perfect linkage (ie, completely linked [95% CI, 1.17-1.33]; P=3.9ϫ10Ϫ7), an rection of effect. The effect size for transmission from parent to offspring) intergenic SNP (rs145848414) at rs115550680 in ABCA7 (OR, 1.79 [95% between 2 markers. In contrast to R2, 174 014 114 base pairs on chromo- CI, 1.47-2.12]; P=2.21ϫ10Ϫ9)was

Table 1. Characteristics of Data Sets12-35 No. (%)

Total ADC1/ NIA-LOAD/ Mirage Mirage No. of Characteristic ACT ADC2 ADC3 CHAP Indianapolis NCRAD ADGCa 300k 660k GenerAAtions Participants Individuals Affected 32 (33.0) 59 (44.7) 166 (59.7) 115 (20.9) 173 (14.7) 35 (36.5) 907 (35.1) 51 (44.0) 188 (44.3) 242 (54.3) 1968 Unaffected 65 (67.0) 73 (55.3) 112 (40.3) 435 (79.1) 1002 (85.3) 61 (63.5) 1675 (64.9) 65 (56.0) 236 (55.7) 204 (45.7) 3928 Women 62 (63.9) 94 (71.2) 211 (75.9) 362 (65.8) 771 (65.6) 70 (72.9) 1879 (72.8) 81 (69.1) 305 (71.9) 260 (58.3) 4095 Age at last 80.5 (6.1) 74.2 (7.6) 77.6 (7.8) 78.8 (6.7) 83.0 (5.5) 73.9 (6.8) 75.6 (8.5) 69.5 (13.9) 71.4 (9.4) 79.4 (6.7) evaluation, mean (SD) APOE genotype Ϫ/Ϫb 57 (58.8) 59 (44.7) 101 (36.3) 328 (59.6) 748 (63.7) 46 (47.9) 1362 (52.7) 42 (36.2) 190 (44.8) 206 (46.2) 3139 Ϫ/4 32 (33.0) 58 (43.9) 117 (42.1) 194 (35.3) 373 (31.7) 39 (40.6) 810 (31.4) 61 (52.6) 183 (43.2) 175 (39.2) 2042 4/4 4 (4.1) 10 (7.6) 21 (7.6) 17 (3.1) 54 (4.6) 11 (11.5) 131 (5.1) 13 (11.2) 49 (11.5) 32 (7.2) 342 Missing 4 (4.1) 5 (3.8) 39 (14.0) 11 (2.0) 0 0 225 (8.7) 0 2 (0.5) 33 (7.4) 319 Abbreviations: ACT, Adult Changes in Thought; ADC, Alzheimer Disease Center; ADGC, Alzheimer Disease Genetics Consortium; APOE, apolipoprotein E; CHAP, Chicago Health and Aging Project; NIA-LOAD/NCRAD, National Institute on Aging–Late-Onset Alzheimer Disease/National Cell Repository for Alzheimer’s Disease. a Samples genotyped by the ADGC for this project were received from the African American Genetics Study, the ADCs, CHAP, Mayo Clinic, Mount Sinai School of Medicine, NIA-LOAD/NCRAD, Religious Orders Study/Rush Memory and Aging Project/Minority Aging Research Study/Clinical Minority Core, University of Miami/Vanderbilt University, University of Pittsburgh, Washington Heights Columbia Aging Project, and Washington University. b All no-APOE*4−containing genotypes (APOE 3/3, APOE 2/3, APOE 2/2).

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

comparable with that observed for gional association plots for ABCA7 in in Naj et al5 showed more widespread APOE (OR, 2.31 [95% CI, 2.19-2.42]; this African American sample and the associations among African Ameri- Ϫ P =5.5ϫ 10 47). Comparison of re- non-Hispanic white sample described cans (FIGURE 2). Consistent with this

Table 2. Genome-Wide Meta-analysis Results of Fully Adjusted Model for Single-Nucleotide Polymorphisms with P Յ 10Ϫ8 Excluding the APOE Regiona,b Base-Pair Gene SNP Chromosome Position Function Allele 1 Allele 2 MAF OR (95% CI) P Value ABCA7 rs115550680 19 1 050 420 Intron G A 0.07 1.79 (1.47-2.12) 2.21 ϫ 10Ϫ9 HMHA1 rs115553053 19 1082 844 Coding-synonymous T C 0.06 1.86 (1.49-2.32) 3.14 ϫ 10Ϫ8 GRIN3B rs115882880 19 1 001 777 Intron A C 0.11 1.55 (1.32-1.81) 6.34 ϫ 10Ϫ8 – rs145848414 5 174 014 114 Intergenic A G 0.04 2.29 (1.69-3.09) 6.90 ϫ 10Ϫ8 Abbreviations: MAF, minor allele frequency; OR, odds ratio; SNP, single-nucleotide polymorphism. aAdjusted for age, sex, APOE genotype, and population stratification. bOdds ratio greater than 1 for all data sets except Mirage300k and Mirage660k, which were not included in the meta-analyses because rs145848414 on chromosome 5 did not pass the minor allele frequency cutoff during the postimputation quality control. The direction of effects in the individual data sets is in the following order: ACT, ADC1ϩ2, ADC3, CHAP, ADGC, GenerAAtions, Indianapolis, NIA-LOAD/NCRAD, Mirage300k, Mirage660k.

Figure 1. Linkage Disequilibrium Pattern of Single-Nucleotide Polymorphisms in ABCA7 Based on the HapMap Reference Sample (African Americans in the Southwest USA) and NCBI36/hg18 Genome Build

ABCA7 (19p13.3)

Chromosome 19 q p

990 kb 1000 kb 1010 kb

NM_033308 5 3 NM_019112 5 3

Hollingworth et al.3 African American Naj et al.5

rs115550680 rs3752246 rs2020000 rs10419707 rs10426279 rs3795065 rs3752228 rs3752232 rs3764647 rs3764650 rs3752237 rs4147912 rs3752240 rs3829687 rs3752243 rs10413245 rs10402406 rs4147916 rs4147918 rs2279796 rs4147932 rs4147937 rs2242436 Block 1 Block 2 (2 kb) Block 3 Block 4 Block 5 (0 kb) (1 kb) (2 kb) (0 kb) 1 2 3 4 5 7 8 91011 12 13 14 15 16 17 18 19 20 21 22 95 87 96 94 0 7 89 52 90 91 91 58 33 77 43 89 80 54 79 91 77 29 30 80 56 54 80 79 94 94 37 56 57 31 51 89 93 36 57 55 15 74 87 45 55 55 62 33 86 44 48 15 75 62 30 35 46 10 40 47 30 51 5 5 78 18 51 52 68 27 55 52 6 71 16 5 10 6 73 1 5 58 39 3 67 57 66 70 21 70 60 27 70 14 14 14

Black arrows indicate single-nucleotide polymorphisms (SNPs) previously reported to be associated with Alzheimer disease in whites3,5 (the top hit reported by Hol- lingworth et al [rs3752228] may have changed if the entire cohort had been genotyped in stages 2 and 3). Pink arrow indicates the location of rs115550680 associated with Alzheimer disease in the present study.The SNPs shown in blue are not represented in HapMap. Kb indicates kilobase.

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

correcting for the number of indepen- Figure 2. Regional Association Plot of the ABCA7 Region (Ϯ100 Kilobases) in the African American Sample and the White Sample Described in Naj et al5 Based on the GRCh37/hg19 Genome Build dent tests per gene, SNPs in CR1 (rs146366639: OR, 0.82 [95% CI, 0.73- 0.00000000001 ADGC Whites 0.92]; empirical P =.0005), BIN1 ADGC African Americans (rs55636820: OR, 1.89 [95% CI, 1.31- 0.0000000001 2.75]; empirical P =.0007), EPHA1 0.000000001 (rs6973770: OR, 0.70 [95% CI, 0.56- 0.87]; empirical P=.001), and CD33 0.0000001 (rs114282264: OR, 0.61 [95% CI, 0.47- 0.000001 0.81]; empirical P=.0007) were significantly associated with LOAD, al- 0.00001 though the most significant SNPs Value

P 0.0001 differed from the top-ranked SNPs in Europeans. 0.001

0.01 DISCUSSION To our knowledge, the present study 0.10 is the largest GWAS for the study of

1 LOAD in African Americans ever as-

0.95 1.00 1.05 1.10 1.15 sembled. Aside from SNPs associated Position on Chromosome 19 (Megabases) with APOE, the top-ranked SNP observed in this study was located in WDR18 C19orf6 ABCA7 POLR2E SBNO2 ABCA7 (rs115550680) and had an effect size comparable with that of APOE ARID3A GRIN3B CNN2 HMHA1 GPX4 ε4. This observation differs from the Dashed black line indicates the threshold typically applied in genome-wide association studies for genome- previous GWAS in whites. The re- Ϫ wide significance (PՅ5ϫ10 8). ported ABCA7 SNPs in non-Hispanic whites have lower effect sizes finding, in this African American ants largely differ between popula- (rs3752246: OR, 1.13 [95% CI, 1.03- sample, SNPs at 2 adjacent loci on chro- tions of European and African descent 1.25]; rs3764650: OR, 1.23 [95% CI, mosome 19p (GRIN3B [NCBI Entrez (MAF for rs3764650, 0.25 in African 1.17-1.28]),3,5 as do all other genes re- Gene 116444] and HMHA1 [NCBI En- Americans and 0.11 in Europeans; MAF ported in whites (CR1, BIN1, PICALM, trez Gene 23526]) were associated with for rs3752246, 0.04 in African Ameri- CLU, EPHA1, MS4A cluster, CD2AP, LOAD at PՅ10Ϫ8 in the fully adjusted cans and 0.19 in Europeans). In turn, CD33).3-6 model (Table 2). ABCA7, GRIN3B, and rs115550680, significant in this Afri- It remains possible that this could be HMHA1 span a 81-kb region on chro- can American data set, is monomor- attributable to population differences mosome 19p and are in linkage dis- phic in Europeans. However, as de- in the frequencies of the causative vari- equilibrium (0.8ϽD'Ͻ0.95) (Table 2). scribed above, the direction of effects ant(s) tagged by the associated SNPs Further analyses conditioned on of rs115550680, rs3764650, and (rs115550680 in ABCA7 is monomor- rs115550680 in ABCA7 revealed that rs3752246 were similar. phic in non-Hispanic whites; the MAF the associations in GRIN3B and HMHA1 The susceptibility loci previously for rs3752246 is 0.04 in African Ameri- were not independent (eTable 2) associated with LOAD in whites, cans and 0.19 in non-Hispanic whites; The imputation quality (R^2) for which did not reach the P value cutoff the MAF for rs3764650 is 0.25 in Afri- rs115550680 in ABCA7, the signifi- for genome-wide significance in this can Americans and 0.11 in non- cant SNPs in GRIN3B, HMHA1, and the African American data set (CR1, BIN1, Hispanic whites) or the result of a bias novel locus on chromosome 5q35.2 was PICALM, CLU, EPHA1, MS4A cluster, in the estimated effect of a newly iden- high (0.87-0.99) across all data sets in- CD2AP, CD33), were further explored tified allele on disease (also termed cluded in the analyses (eTable 3). For- in gene-based analyses adding 50 kb “winner’s curse”). est plots (eFigure 2) indicated the con- to both sides of each gene.3-7 TABLE 3 However, it is also possible that the sistency of results across data sets. The shows the genes significant in these large difference between whites and ABCA7 SNPs previously reported in gene-based tests and reports informa- African Americans in the effect size of whites (rs37646503 and rs37522465) tion on the number of tagging SNPs the ABCA7 locus on the relative odds did not reach genome-wide signifi- assessed in each gene and the corre- of being diagnosed with LOAD is ex- cance in this African American data set. sponding P value threshold needed to plained by population-specific caus- However, the MAFs for these 2 vari- reach statistical significance. After ative variants with variable influence on

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

Table 3. Known Genetic Loci Associated With Alzheimer Disease in the African American Data Set in a Versatile Gene-Based Association Study (VEGAS47)a No. of P Value Smallest P Value Risk Tagging Threshold for Detected in Gene SNP Chromosome Base-Pair Locationb Allele MAF SNPs Significance Current Data Set CR1 rs146366639 1 207 649 473-207 835 110 G 0.26 44 .001 .0005 BIN1 rs55636820 2 127 785 603-127 884 931 G 0.02 38 .001 .0007 EPHA1 rs6973770 7 143 067 382-143 125 985 G 0.06 30 .002 .001 CD33 rs114282264 19 51 708 320-51 763 274 G 0.03 24 .002 .0007 Abbreviations: MAF, minor allele frequency; SNP, single-nucleotide polymorphism. a Adjusted for age, sex, APOE genotype, and population stratification. VEGAS incorporates linkage disequilibrium information for the assessed genes from a set of reference individuals from HapMap, determines the number of tagging SNPs, and calculates the empirical P value for the gene by using simulations from the multivariate normal distribution. b Including 20 kilobases to each side; based on genome build 37.3.

protein structure or function. The link- emia and cardiovascular and cerebro- sortium comprising whites from the age disequilibrium block in which vascular diseases are well-recognized United Kingdom, Europe, and the rs115550680 is located spans across risk factors for LOAD,51,52 and the United States had similar findings and several introns and exons (Figure 1), LOAD-related genes SORL1, CLU, and first reported the association between implying that rs115550680 is in dis- APOE are also involved in lipid me- SNPs in ABCA7 and Alzheimer disequilibrium with exonic variants that tabolism. If confirmed, focusing on the ease.3 Logue et al29 reported nominal could be potentially causative. Thus, al- role of lipid metabolism in LOAD may significance for the ABCA7 SNP though the findings of this study re- have significant effects on disease man- rs3764650 reported by Hollingworth et quire replication in an independent agement. al3 in a well-characterized cohort of 513 African American sample with enough ABCA7 also affects the transport of African American persons with Alzhei- power to detect small ORs as well as other important proteins, including mer disease and 496 cognitively nor- functional confirmation, support for our amyloid precursor protein,49 through mal controls. As described above, the findings comes from the previous stud- the cell membrane and is involved in effect sizes for the association be- ies in whites observing ABCA7 as a risk host defense through effects on phago- tween ABCA7 and LOAD in these stud- locus in Alzheimer disease, albeit with cytosis by macrophages of apoptotic ies is small compared with the effect size marginal effects.3,5 cells.48 Thus, there are multiple ways observed in the current study. In the If validated by future replication and in which ABCA7 might affect risk of current study CR1, BIN1, EPHA1, and functional studies, identification of LOAD. CD33 were replicated with signifi- ABCA7 as a risk gene in LOAD among Compared with the findings de- cance in gene-based analyses. Differ- African Americans not only may help scribed in Naj et al5 among non- ences in disease-associated SNPs in elucidate the disease etiology but also Hispanic whites, the area including sig- these loci between the white and Afri- may have major implications for de- nificant SNP associations in the ABCA7 can American consortium data sets also veloping targets for genetic testing, pre- region was broader in the African reflect differences in degree of varia- vention, and treatment. ABCA7 is an in- American sample. It is possible that this tion and size of haplotype blocks, which tegral transmembrane adenosine broad region of association in African in turn is helpful in identifying the true triphosphate–binding cassette trans- Americans is attributable to a large, an- causative variants. porter that belongs to the ABC family cestral risk haplotype recently intro- This study has limitations. Because proteins and that mediates the biogen- duced by admixture with white (“Eu- of the paucity of available African esis of high-density lipoprotein with cel- ropean”) Americans and has remained American data sets for LOAD, we could lular lipid and helical apolipopro- substantially intact within African not divide the assembled data sets into teins.48 It binds apolipoprotein A1 and Americans because of the relatively discovery and replication data sets but functions in apolipoprotein-mediated short time since its introduction. In con- rather used the ADGC white race data phospholipid and cholesterol efflux trast, the risk allele may exist on sev- set for replication. Thus, this study re- from cells.49 eral different haplotypes in non- quires replication in an independent The findings of the current study sug- Hispanic whites (ie, may be older), only African American sample. In addition, gest that lipid metabolism is a promi- a subset of which was introduced into we had limited power to detect asso- nent pathway of LOAD in African the African American population. ciations with small effect sizes and as- Americans. This is consistent with the In a previous study,5 the ADGC re- sociations with rare variants. Al- fact that cardiovascular and cerebro- ported genome-wide associations for though all data sets included in the vascular diseases are more prominent variants in MSA4, CD2AP, CD33, and analytic sample used accepted clinical in African Americans than in non- EPHA1 among individuals of white Eu- or pathological criteria to define LOAD, Hispanic whites.50 Moreover, dyslipid- ropean ancestry. A cohort-based con- phenotypic heterogeneity between

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

samples may have limited our ability to Logue, Baldwin, and Farrer), Biostatistics (Drs Jun, Analysis and interpretation of data: Reitz, Jun, Vardarajan, Lunetta, and Farrer), Ophthalmology Naj, Rajbhandary, Vardarajan, Wang, Valladares, detect some associations. (Drs Jun and Farrer), Epidemiology (Dr Farrer), and Graff-Radford, De Jager, Crane, Buxbaum, Raj, In addition, the top-ranked SNP ob- Neurology (Dr Farrer), Boston University, Boston, Ertekin-Taner, Logue, Manly, Lunetta, Bennett, Massachusetts; The John P. Hussman Institute for Hendrie, Farrer, Pericak-Vance, Schellenberg, served in ABCA7 was not directly geno- Human Genomics, University of Miami, Miami, Mayeux. typed but imputed in all data sets. How- Florida (Drs Naj and Pericak-Vance and Ms Rajb- Drafting of the manuscript: Reitz, Naj, De Jager, Raj, ever, several facts make it unlikely that handary); Department of Pathology and Laboratory Cantwell, Pericak-Vance, Mayeux. Medicine, University of Pennsylvania Perelman Critical revision of the manuscript for important in- the observed association was caused by School of Medicine, Philadelphia (Drs Wang, Lin, tellectual content: Reitz, Jun, Naj, Rajbhandary, imputation error. First, as stated above and Schellenberg and Mr Valladares and Ms Vardarajan, Wang, Valladares, Lin, Larson, Cantwell); Department of Medicine (Drs Larson and Graff-Radford, Evans, Crane, Buxbaum, Murrell, and shown in Figure 1, rs115550680 Crane) and National Alzheimer’s Coordinating Cen- Ertekin-Taner, Logue, Baldwin, Green, Barnes, Fallin, is in linkage disequilibrium with the 2 ter and Department of Epidemiology (Dr Kukull), Go, Griffith, Obisesan, Manly, Lunetta, Kamboh, ABCA7 SNPs reported by Naj et al5 University of Washington, Seattle; Group Health Lopez, Bennett, Hendrie, Hall, Goate, Byrd, Kukull, Research Institute, Group Health, Seattle (Dr Lar- 3 Foroud, Haines, Farrer, Pericak-Vance, Schellenberg, and Hollingworth et al in non-His- son); Departments of Neuroscience (Drs Graff- Mayeux. panic whites of European ances- Radford, and Ertekin- Taner) and Neurology (Drs Statistical analysis: Reitz, Jun, Naj, Rajbhandary, Graff-Radford and Ertekin- Taner), Mayo Clinic, Vardarajan, Raj, Logue, Hall, Lunetta, Hendrie, Haines, try (rs3764650 and rs3752246, Jacksonville, Florida; Rush Institute for Healthy Farrer, Pericak-Vance. 0.8ϽD'=0.9) that make this finding Aging, Department of Internal Medicine (Dr Evans), Obtained funding: Larson, Evans, Murrell, Green, plausible. Second, the imputation qual- Departments of Neurological Sciences (Drs Barnes Barnes, Fallin, Go, Manly, Kamboh, Bennett, Goate, and Bennett) and Behavioral Sciences (Dr Barnes), Byrd, Haines, Pericak-Vance, Schellenberg, Mayeux. ity (R^2) of this SNP is high across all and Rush Alzheimer’s Disease Center (Dr Bennett), Administrative, technical, or material support: Naj, data sets (0.89ϽR^2Ͻ0.99) (eTable 3). Rush University Medical Center, Chicago, Illinois; Wang, Valladares, Lin, Larson, Crane, Buxbaum, Program in Translational Neuropsychiatric Genom- Murrell, Ertekin-Taner, Baldwin, Green, Cantwell, Third, the MAF of rs115550680 in our ics, Department of Neurology, Brigham & Women’s Fallin, Obisesan, Kamboh, Lopez, Bennett, Hall, Goate, African American sample is 7%. Al- Hospital, Boston, Massachusetts (Dr De Jager); Har- Byrd, Kukull, Foroud, Farrer, Schellenberg, Mayeux. though in general the imputation er- vard Medical School, Boston (Drs De Jager and Study supervision: Go, Obisesan, Bennett, Hendrie, Raj); Program in Medical and Population Genetics, Byrd, Foroud, Farrer, Schellenberg, Mayeux. ror rate increases with decreasing MAF, The Broad Institute, Cambridge, Massachusetts (Dr Conflict of Interest Disclosures: All authors have com- several recent studies suggest that SNPs De Jager); Department of Medical and Molecular pleted and submitted the ICMJE Form for Disclosure Genetics, Indiana University (Drs Murrell and of Potential Conflicts of Interest. Dr Baldwin re- with MAFs less than 5% are especially Foroud), Indiana University Center for Aging ported serving as a consultant for the Center for Hu- 36 prone to imputation errors. The re- Research (Dr Hendrie), and Department of Psychia- man Genetics Inc. Dr Go reported receiving travel sup- try, Indiana University School of Medicine (Drs cent study by Hancock et al,53 which port from the National Institutes of Health (NIH). Dr Hendrie and Hall), Indianapolis; Division of Genet- Griffith reported receiving payment for lectures from specifically assessed genotype imputa- ics, Department of Medicine, and Partners Center Eisai and Pfizer. Dr Manly reported serving as a board tion performance using 1000 Ge- for Personalized Genetic Medicine, Brigham and member for the International Neuropsychological So- Women’s Hospital and Harvard Medical School, ciety; receiving grants or grants pending from the Alz- nomes reference panels in African Boston (Dr Green); Departments of Psychiatry (Dr heimer’s Association and the National Institute on Ag- Americans, determined that the thresh- Buxbaum), Genetics and Genomics Sciences (Dr ing (NIA); and receiving travel expenses from the Buxbaum), and Neuroscience (Dr Buxbaum) and Alzheimer’s Association. Dr Kamboh reported receiv- old for high imputation lies at MAF 2% the Friedman Brain Institute (Dr Buxbaum), Mount ing travel support from the NIH. Dr Lopez reported or greater, applying the software and Sinai School of Medicine, New York, New York; receiving consulting fees or honoraria from Mertz and reference panel used in the present Department of Epidemiology, Johns Hopkins Uni- Lundbeck. Dr Bennett reported receiving travel sup- versity School of Public Health, Baltimore, Maryland port from the NIH. Dr Goate reported serving as a con- study. (Dr Fallin); School of Public Health, University of sultant for Finnegan; providing expert testimony in The variant associations reported Alabama at Birmingham (Dr Go); Department of cases involving the genetics of Alzheimer disease; re- Neurology, Meharry Medical College, Nashville, ceiving grants or grants pending from Genentech and herein reflect a portion of the genetic Tennessee (Dr Griffith); Division of Geriatrics, How- Pfizer; receiving payment for lectures from Pfizer, Ge- influences of common alleles on LOAD ard University Hospital, Washington, DC (Dr Obis- nentech, and Amgen; and receiving patent royalties esan); Department of Human Genetics (Dr Kam- from Taconic for a tau mutation. Dr Pericak-Vance re- in African Americans. Among these, boh) and Alzheimer’s Disease Research Center (Drs ported receiving revenues from Athena Diagnostics. ABCA7 and APOE genotype were the Kamboh and Lopez), University of Pittsburgh, Pitts- No other authors reported disclosures. strongest risk factors that both sub- burgh, Pennsylvania; Department of Psychiatry and Funding/Support: The NIA supported this work Hope Center Program on Protein Aggregation and through grants U01-AG032984, RC2-AG036528, stantially increased the risk of LOAD Neurodegeneration, Washington University School U01-AG016976 (Dr Kukull); U24 AG026395, U24 (OR, 1.79 and 2.31, respectively). Iden- of Medicine, St Louis, Missouri (Dr Goate); Depart- AG026390, R01AG037212, R37 AG015473 (Dr May- ment of Biology, North CarolinaA&TUniversity, eux); K23AG034550 (Dr Reitz); U24-AG021886 (Dr tification of the genetic risk variants by Winston-Salem (Dr Byrd); Department of Molecular Foroud); R01AG009956, RC2 AG036650 (Dr Hall); resequencing and validation by func- Physiology and Biophysics and Vanderbilt Center UO1 AG06781, UO1 HG004610 (Dr Larson); R01 for Human Genetics Research, Vanderbilt Univer- AG009029 (Dr Farrer); 5R01AG20688 (Dr Fallin); P50 tional studies would allow refinement sity, Nashville (Dr Haines); and Regenstrief Institute AG005133, AG030653 (Dr Kamboh); R01 AG019085 of risk estimates and diagnostic and pre- Inc, Indianapolis (Dr Hendrie). (Dr Haines); R01 AG1101, R01 AG030146, RC2 Author Contributions: Dr Mayeux had full access to AG036650 (Dr Evans); P30AG10161, R01AG15819, dictive testing protocols specific for all of the data in the study and takes responsibility for R01AG30146, R01AG17917, R01AG15819 (Dr Ben- African Americans. the integrity of the data and the accuracy of the data nett); R01AG028786 (Dr Manly); R01AG22018, analysis. P30AG10161 (Dr Barnes); P50AG16574 (Dr Ertekin- Author Affiliations: Taub Institute for Research on Study concept and design: Reitz, Buxbaum, Fallin, Taner, Dr Graff-Radford), R01 AG032990 (Dr Ertekin- Alzheimer’s Disease and the Aging Brain (Drs Reitz, Griffith, Obisesan, Manly, Bennett, Haines, Farrer, Taner), KL2 RR024151 (Dr Ertekin-Taner); R01 Manly, and Mayeux), Gertrude H. Sergievsky Cen- Pericak-Vance, Schellenberg, Mayeux. AG027944, R01 AG028786 (Dr Pericak-Vance); P20 ter (Drs Reitz, and Mayeux), and Departments of Acquisition of data: Reitz, Valladares, Lin, Larson, MD000546, R01 AG28786-01A1 (Dr Byrd); Neurology (Drs Reitz, Manly, and Mayeux), Psy- Graff-Radford, Evans, Crane, Buxbaum, Murrell, AG005138 (Dr Buxbaum); P50 AG05681, P01 chiatry (Dr Mayeux), and Epidemiology (Dr May- Ertekin-Taner, Baldwin, Green, Barnes, Cantwell, AG03991, P01 AG026276 (Dr Goate); and eux), College of Physicians and Surgeons, Columbia Fallin, Go, Obisesan, Manly, Kamboh, Lopez, Bennett, P30AG019610, P30AG13846, U01-AG10483, University, New York, New York; Departments of Hendrie, Hall, Goate, Byrd, Kukull, Foroud, Haines, R01CA129769, R01MH080295, R01AG017173, Medicine (Genetics Program) (Drs Jun, Vardarajan, Farrer, Pericak-Vance, Schellenberg, Mayeux. R01AG025259, R01AG33193, P50AG008702,

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

P30AG028377, AG05128, AG025688, P30AG10133, Amanda G. Smith, Joshua A. Sonnen, Salvatore Spina, Wilson RS. Mild cognitive impairment is related to Alz- P50AG005146, P50AG005134, P01AG002219, Robert A. Stern, Rudolph E. Tanzi, John Q. Tro- heimer disease pathology and cerebral infarctions. P30AG08051, MO1RR00096, UL1RR029893, janowski, Juan C. Troncoso, Debby W. Tsuang, Vivi- Neurology. 2005;64(5):834-841. P30AG013854, P30AG008017, R01AG026916, anna M. Van Deerlin, Linda J. Van Eldik, Harry V. 16. Bennett DA, Schneider JA, Buchman AS, Men- R01AG019085, P50AG016582, UL1RR02777, Vinters, Jean Paul Vonsattel, Sandra Weintraub, Kath- des de Leon C, Bienias JL, Wilson RS. The Rush Memory R01AG031581, P30AG010129, P50AG016573, leen A. Welsh-Bohmer, Jennifer Williamson, Randall and Aging Project: study design and baseline charac- P50AG016575, P50AG016576, P50AG016577, L. Woltjer, Clinton B. Wright, Steven G. Younkin, teristics of the study cohort. Neuroepidemiology. 2005; P50AG016570, P50AG005131, P50AG023501, Chang-En Yu, and Lei Yu. 25(4):163-175. P50AG019724, P30AG028383, P50AG008671, Online-Only Material: eTables 1-3, eFigures 1 and 17. Bennett DA, Wilson RS, Schneider JA, et al. Natu- P30AG010124, P50AG005142, P30AG012300, 2, eMethods, and Author Video Interview are avail- ral history of mild cognitive impairment in older persons. AG010491, AG027944, AG021547, AG019757, able at http://www.jama.com. Neurology. 2002;59(2):198-205. P50AG005136 (Alzheimer Disease GeneticsConsor- 18. Berg L, McKeel DW Jr, Miller JP, et al. Clinico- tium [ADGC]). We thank Creighton Phelps, Stephen pathologic studies in cognitively healthy aging and Alz- Synder, and Marilyn Miller from the NIA, who are ex- REFERENCES heimer’s disease: relation of histologic markers to de- officio members of the ADGC. Support was also pro- mentia severity, age, sex, and apolipoprotein E vided by the Alzheimer’s Association (IIRG-08- 1. Fratiglioni L, De Ronchi D, Agu¨ero-Torres H. World- genotype. Arch Neurol. 1998;55(3):326-335. 89720 [Dr Farrer] and IIRG-05-14147 [Dr Pericak- wide prevalence and incidence of dementia. Drugs 19. Bienias JL, Beckett LA, Bennett DA, Wilson RS, Vance]), National Institute of Neurological Disorders Aging. 1999;15(5):365-375. Evans DA. Design of the Chicago Health and Aging and Stroke grant NS39764, National Institute of Men- 2. Slooter AJ, Cruts M, Kalmijn S, et al. Risk esti- Project (CHAP). J Alzheimers Dis. 2003;5(5):349- tal Health grant MH60451, GlaxoSmithKline, and the mates of dementia by apolipoprotein E genotypes from Office of Research and Development, Biomedical Labo- a population-based incidence study: the Rotterdam 355. ratory Research Program, US Department of Veter- Study. Arch Neurol. 1998;55(7):964-968. 20. Carrasquillo MM, Zou F, Pankratz VS, et al. Ge- ans Affairs Administration. For the ADGC, biological 3. Hollingworth P, Harold D, Sims R, et al; Alzhei- netic variation in PCDH11X is associated with suscep- samples and associated phenotypic data used in pri- mer’s Disease Neuroimaging Initiative; CHARGE tibility to late-onset Alzheimer’s disease. Nat Genet. mary data analyses were stored at principal investi- Consortium; EADI1 Consortium. Common variants at 2009;41(2):192-198. gators’ institutions and at the National Cell Reposi- ABCA7, MS4A6A/MS4A4E, EPHA1, CD33 and 21. Edwards TL, Scott WK, Almonte C, et al. Genome- tory for Alzheimer’s Disease (NCRAD) at Indiana CD2AP are associated with Alzheimer’s disease. Nat wide association study confirms SNPs in SNCA and the University, funded by the NIA. Associated pheno- Genet. 2011;43(5):429-435. MAPT region as common risk factors for Parkinson typic data used in secondary data analyses were stored 4. Lambert JC, Heath S, Even G, et al; European Alz- disease. Ann Hum Genet. 2010;74(2):97-109. at the National Alzheimer’s Coordinating Center and heimer’s Disease Initiative Investigators. Genome- 22. Evans DA, Bennett DA, Wilson RS, et al. Inci- at the NIA Alzheimer’s Disease Data Storage Site at wide association study identifies variants at CLU and dence of Alzheimer disease in a biracial urban com- the University of Pennsylvania, funded by the NIA. CR1 associated with Alzheimer’s disease. Nat Genet. munity: relation to apolipoprotein E allele status. Arch Contributors to the genetic analysis data included prin- 2009;41(10):1094-1099. Neurol. 2003;60(2):185-189. cipal investigators on projects ndividually funded by 5. Naj AC, Jun G, Beecham GW, et al. Common vari- 23. Green RC, Cupples LA, Go R, et al; MIRAGE Study the NIA, other NIH institutes, or private entities. ants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 Group. Risk of dementia among white and African Role of the Sponsor: The funding organizations and are associated with late-onset Alzheimer’s disease. Nat American relatives of patients with Alzheimer disease. sponsors had no role in the design and conduct of the Genet. 2011;43(5):436-441. JAMA. 2002;287(3):329-336. study; the collection, management, analysis, and in- 6. Seshadri S, Fitzpatrick AL, Ikram MA, et al; CHARGE 24. Haroutunian V, Perl DP, Purohit DP, et al. Re- terpretation of the data; or the preparation, review, Consortium; GERAD1 Consortium; EADI1 Consortium. gional distribution of neuritic plaques in the nonde- or approval of the manuscript. Genome-wide analysis of genetic loci associated with mented elderly and subjects with very mild Alzhei- Members of the Alzheimer’s Disease Genetics Con- Alzheimer disease. JAMA. 2010;303(18):1832- mer disease. Arch Neurol. 1998;55(9):1185-1191. sortium: Marilyn S. Albert, Roger L. Albin, Liana G. 1840. 25. Jun G, Naj AC, Beecham GW, et al; Alzheimer’s Apostolova, Steven E. Arnold, Robert Barber, Michael 7. Harold D, Abraham R, Hollingworth P, et al. Ge- Disease Genetics Consortium. Meta-analysis con- M. Barmada, Thomas G. Beach, Gary W. Beecham, nome-wide association study identifies variants at CLU firms CR1, CLU, and PICALM as Alzheimer disease risk Duane Beekly, Eileen H. Bigio, Thomas D. Bird, Debo- and PICALM associated with Alzheimer’s disease. Nat loci and reveals interactions with APOE genotypes. Arch rah Blacker, Bradley F. Boeve, James D. Bowen, Adam Genet. 2009;41(10):1088-1093. Neurol. 2010;67(12):1473-1484. Boxer, James R. Burke, Guiqing Cai, Nigel J. Cairns, 8. Reitz C, Cheng R, Rogaeva E, et al; Genetic and 26. Kamboh MI, Minster RL, Demirci FY, et al. As- Chuanhai Cao, Chris S. Carlson, Regina M. Carney, Environmental Risk in Alzheimer Disease 1 Consortium. sociation of CLU and PICALM variants with Alzhei- Steven L. Carroll, Helena C. Chui, David G. Clark, Da- Meta-analysis of the association between variants in mer’s disease. Neurobiol Aging. 2012;33(3):518- vid H. Cribbs, Elizabeth A. Crocco, Carlos Cruchaga, SORL1 and Alzheimer disease. Arch Neurol. 2011; 521. Charles DeCarli, Steven T. DeKosky, F. Yesim Demirci, 68(1):99-106. 27. Kukull WA, Higdon R, Bowen JD, et al. Demen- Malcolm Dick, Kelley M. Faber, Kenneth B. Fallon, Mar- 9. Rogaeva E, Meng Y, Lee JH, et al. The neuronal tia and Alzheimer disease incidence: a prospective co- tin R. Farlow, Steven Ferris, Matthew P. Frosch, Doug- sortilin-related receptor SORL1 is genetically associ- hort study. Arch Neurol. 2002;59(11):1737-1746. las R. Galasko, Mary Ganguli, Marla Gearing, Daniel ated with Alzheimer disease. Nat Genet. 2007; 28. Lee JH, Cheng R, Graff-Radford N, Foroud T, H. Geschwind, Bernardino Ghetti, John R. Gilbert, Sid 39(2):168-177. Mayeux R; National Institute on Aging Late-Onset Alz- Gilman, Jonathan D. Glass, John H. Growdon, Ha- 10. Gatz M, Pedersen NL, Berg S, et al. Heritability heimer’s Disease Family Study Group. Analyses of the kon Hakonarson, Ronald L. Hamilton, Kara L. Ham- for Alzheimer’s disease: the study of dementia in Swed- National Institute on Aging Late-Onset Alzheimer’s Dis- ilton-Nelson, Vahram Haroutunian, Lindy E. Harrell, ish twins. J Gerontol A Biol Sci Med Sci. 1997; ease Family Study: implication of additional loci. Arch Elizabeth Head, Lawrence S. Honig, Christine M. Hu- 52(2):M117-M125. Neurol. 2008;65(11):1518-1526. lette, Bradley T. Hyman, Gail P. Jarvik, Gregory A. Ji- 11. Tang MX, Cross P, Andrews H, et al. Incidence 29. Logue MW, Schu M, Vardarajan BN, et al; Multi- cha, Lee-Way Jin, Anna Karydas, John S. K. Kauwe, of AD in African-Americans, Caribbean Hispanics, and Institutional Research on Alzheimer Genetic Epidemi- Jeffrey A. Kaye, Ronald Kim, Edward H. Koo, Neil W. Caucasians in northern Manhattan. Neurology. 2001; ology (MIRAGE) Study Group. A comprehensive ge- Kowall, Joel H. Kramer, Patricia Kramer, Frank M. netic association study of Alzheimer disease in African LaFerla, James J. Lah, Rosalyn Lang-Walker, James B. 56(1):49-56. Leverenz, Allan I. Levey, Ge Li, Andrew P. Lieber- 12. Tang MX, Stern Y, Marder K, et al. The APOE- Americans. Arch Neurol. 2011;68(12):1569-1579. man, Constantine G. Lyketsos, Wendy J. Mack, Dan- epsilon4 allele and the risk of Alzheimer disease among 30. Morris JC, Roe CM, Xiong C, et al. APOE pre- iel C. Marson, Eden R. Martin, Frank Martiniuk, Debo- African Americans, whites, and Hispanics. JAMA. 1998; dicts amyloid-beta but not tau Alzheimer pathology rah C. Mash, Eliezer Masliah, Wayne C. McCormick, 279(10):751-755. in cognitively normal aging. Ann Neurol. 2010; Susan M. McCurry, Andrew N. McDavid, Ann C. 13. Barnes LL, Shah RC, Aggarwal NT, Bennett DA, 67(1):122-131. McKee, Marsel Mesulam, Bruce L. Miller, Carol A. Schneider JA. The Minority Aging Research Study: on- 31. Morris JC, Weintraub S, Chui HC, et al. The Uni- Miller, Joshua W. Miller, Thomas J. Montine, John C. going efforts to obtain brain donation in African Ameri- form Data Set (UDS): clinical and cognitive variables Morris, John M. Olichney, Joseph E. Parisi, Elaine Pe- cans without dementia. Curr Alzheimer Res. 2012; and descriptive data from Alzheimer disease centers. skind, Ronald C. Petersen, Aimee Pierce, Wayne W. 9(6):734-745. Alzheimer Dis Assoc Disord. 2006;20(4):210-216. Poon, Huntington Potter, Joseph F. Quinn, Ashok Raj, 14. Beecham GW, Martin ER, Li YJ, et al. Genome- 32. Murrell JR, Price B, Lane KA, et al. Association of Murray Raskind, Eric M. Reiman, Barry Reisberg, John wide association study implicates a chromosome 12 apolipoprotein E genotype and Alzheimer disease in M. Ringman, Erik D. Roberson, Howard J. Rosen, Roger risk locus for late-onset Alzheimer disease. Am J Hum African Americans. Arch Neurol. 2006;63(3):431- N. Rosenberg, Mary Sano, Andrew J. Saykin, Julie A. Genet. 2009;84(1):35-43. 434. Schneider, Lon S. Schneider, William W. Seeley, 15. Bennett DA, Schneider JA, Bienias JL, Evans DA, 33. Scott WK, Nance MA, Watts RL, et al. Complete

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013 LATE-ONSET ALZHEIMER DISEASE IN AFRICAN AMERICANS

genomic screen in Parkinson disease: evidence for mul- 40. Hixson JE, Vernier DT. Restriction isotyping of hu- wide association studies. Am J Hum Genet. 2010; tiple genes. JAMA. 2001;286(18):2239-2244. man apolipoprotein E by gene amplification and cleav- 87(1):139-145. 34. Storandt M, Grant EA, Miller JP, Morris JC. Lon- age with HhaI. J Lipid Res. 1990;31(3):545-548. 48. Tanaka N, Abe-Dohmae S, Iwamoto N, Yokoyama gitudinal course and neuropathologic outcomes in origi- 41. Lai E, Riley J, Purvis I, Roses A. A 4-mb high- S. Roles of ATP-binding cassette transporter A7 in cho- nal vs revised MCI and in pre-MCI. Neurology. 2006; density single nucleotide polymorphism−based map lesterol homeostasis and host defense system. J Ath- 67(3):467-473. around human APOE. Genomics. 1998;54(1):31- eroscler Thromb. 2011;18(4):274-281. 35. Meier IB, Manly JJ, Provenzano FA, et al. White 38. 49. Chan SL, Kim WS, Kwok JB, et al. ATP-binding matter predictors of cognitive functioning in older 42. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, cassette transporter A7 regulates processing of amy- adults. J Int Neuropsychol Soc. 2012;18(3):414- Shadick NA, Reich D. Principal components analysis loid precursor protein in vitro. J Neurochem. 2008; 427. corrects for stratification in genome-wide association 106(2):793-804. 36. McKhann G, Drachman D, Folstein M, Katzman studies. Nat Genet. 2006;38(8):904-909. 50. Roger VL, Go AS, Lloyd-Jones DM, et al; Ameri- R, Price D, Stadlan EM. Clinical diagnosis of Alzhei- 43. Howie B, Fuchsberger C, Stephens M, Marchini can Heart Association Statistics Committee and Stroke mer’s disease: report of the NINCDS-ADRDA Work J, Abecasis GR. Fast and accurate genotype im- Statistics Subcommittee. Heart disease and stroke Group under the auspices of Department of Health putation in genome-wide association studies statistics—2012 update: a report from the American and Human Services Task Force on Alzheimer’s Disease. through pre-phasing. Nat Genet. 2012;44(8):955- Heart Association. Circulation. 2012;125(1):e2- Neurology. 1984;34(7):939-944. 959. e220. 37. US Census Bureau. 1990 Census of Population 44. Chanda P, Yuhki N, Li M, et al. Comprehensive 51. Breteler MM. Vascular risk factors for Alzhei- and Housing Summary File 1. Washington, DC: US evaluation of imputation performance in African mer’s disease: an epidemiologic perspective. Neuro- Census Bureau; 1991. Americans. J Hum Genet. 2012;57(7):411-421. biol Aging. 2000;21(2):153-160. 38. Wittwer CT, Ririe KM, Andrew RV, David DA, 45. Higgins JP, Thompson SG. Quantifying hetero- 52. Shepardson NE, Shankar GM, Selkoe DJ. Cho- Gundry RA, Balis UJ. The LightCycler: a microvolume geneity in a meta-analysis. Stat Med. 2002;21 lesterol level and statin use in Alzheimer disease, I: re- multisample fluorimeter with rapid temperature control. (11):1539-1558. view of epidemiological and preclinical studies. Arch Biotechniques. 1997;22(1):176-181. 46. Higgins JP, Thompson SG, Deeks JJ, Altman DG. Neurol. 2011;68(10):1239-1244. 39. Ahmadian A, Gharizadeh B, Gustafsson AC, et al. Measuring inconsistency in meta-analyses. BMJ. 2003; 53. Hancock DB, Levy JL, Gaddis NC, et al. Assess- Single-nucleotide polymorphism analysis by 327(7414):557-560. ment of genotype imputation performance using 1000 pyrosequencing. Anal Biochem. 2000;280(1):103- 47. Liu JZ, McRae AF, Nyholt DR, et al; AMFS Genomes in African American studies. PLoS One. 2012; 110. Investigators. A versatile gene-based test for genome- 7(11):e50610.

JAMA Medical Student Elective in Medical Editing

—JAMA offers a 4-week elective in medical editing to third- and fourth-year US medical students. The elective is full- time and must be taken for academic credit. For information and an application, please contact Robert M. Golub, MD ([email protected]).

Downloaded From: http://jama.jamanetwork.com/ by a Indiana University School of Medicine User on 08/22/2013