© 2011 Nature America, Inc. All rights reserved. *A *A full list of authors and affiliations appears at the end of the paper. genome-wide CR1 showed with association sample for evidence 1) significant Initiative Disease Alzheimer’s GWAS disease Alzheimer’s pendent and the 1 ), receptor complement ( chance by We more variants with observed also ( gene assembly clathrin binding ( clusterin loci: susceptibility significant genome-wide new two we identified which in 1), Consortium Disease Alzheimer’s in (Genetic Risk GERAD1 Environmental and designated sample a in (GWAS) disease study Alzheimer’s of association genome-wide a published we 2009, onset disease In late with increase disease Alzheimer’s to of form known common the gene for risk only the was E) apolipoprotein recently, until but cases, of minority a in disease 79% to up (ref. of heritability shows and complex genetically is disease Alzheimer’s risk. to contributing factors genetic and environmental Alzheimer’s is disease the most common form of with dementia, both P ADGC P CD2AP which, for susceptibility ADGC MS4A 1 compelling a at for associated wide paper. Disease and disease We CD33 Common variants at Nature Ge Nature Received 9 September 2010; accepted 10 March 2011; published online 3 April 2011;

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© 2011 Nature America, Inc. All rights reserved. disease casesand21,258 controls. a Chr., ; MAF, minorallelefrequency. rs744373 rs3818361 rs670139 rs610932 rs3764650 SNP T the in association for loci risk stage new 3 sample and showed further evidence of replication implicating (rs3764650, SNPs three the P 2 stage (rs610932, cluster gene 2 stage (rs3764650, at SNPs to addition In for threshold Bonferroni-adjusted of significance a using replication for dence excluding SNPs, (10 BIN1 2 stage in replication for forward taken were Table 2 GERAD2, to the most significant SNPs at each locus ( of analysis our limited susceptibility loci that had previously been tested in GERAD2, and we 3. stage in samples EADI2 the in rs381861 elsewhere presented been have consortium CHARGE the 1 Figure s r e t t e l  GERAD1, EADI1,ADNIand TGEN1,lessthan6,688casesand13,685controls. able able 1 = 1.1 × 10 × 1.1 = ie f h 1 SP tse i sae soe sgiiat evi significant showed 2 stage in tested SNPs 12 the of Five known excluded we 2, stage in testing for SNPs selecting When Stage 2:primaryreplicatio Stage 3:secondaryreplicatio Genotyped inGERAD2 Stage 1:meta-analysisofavailableGWASdat and and 13,685 controls 496,763 SNPs ). ). Following pruning for linkage disequilibrium (LD), 12 SNPs

4,903 controls 21,258 controls 6,688 case 4,896 case R GERAD+ study design. *Data for rs744373 and rs3818361 in rs3818361 and rs744373 for *Data design. study GERAD+ BIN1 CR1 MS4A4E MS4A6A ABCA7 8,286 case Only mostsignificantSNPsin 12 SNPs Closest CR1 esults esults of the G 3 SNPs gene −3 ) showed evidence of replication in stage 2. We tested We 2. tested stage in replication of evidence showed ) ).

P * s s Chr. 11 11 19 s = × 4.2 10 APOE, CLU 2 1 Non-independent SNPs(LD)excluded(8 Meta-analysis ofGERAD+Stages1,2and 0.29 0.19 0.41 0.42 0.10 ADNI MAF P n d GERAD1 andGERAD2,EADI1 andEADI2,ADNI,TGEN1,deCODE,AD-IG,CHARGE andMayo2,lessthan19,870Alzheimer’s diseasecases and39,846controls. = 1.9 × 10 × 1.9 = BIN1 n 19,870 cases,39,846controls and 1.5 × 10 3.2 × 10 1.0 × 10 1.8 × 10 2.6 × 10 ER BIN1 61 SNPswith 5 SNPswith −3 AD+ AD+ study PICALM 12 SNPsselecte P and and ( Meta-analysis

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−5 P OR P a BI ≤ CR1, 1 < ) and two SNPS at the the at SNPS two and ) 1 N 0.05 , which had not been tested in in tested been not had which , and and a genotyped(6SNPsexcluded) × d 1.11–1.22 1.14–1.27 1.06–1.16 0.85–0.92 1.13–1.32 10 95% CI one SNP within within SNP one –5 Supplementary Table 3 Supplementary TGEN −3 ; and rs670139, stage 2 stage rs670139, ; and 3 3.8 × 10 1.4 × 10 1.1 × 10 1.6 × 10 1.9 × 10 In silic Genotyped inMayo2 b Genotyped inEADI2 ) GERAD2, deCODEandAD-IG, 4,896Alzheimer’s diseasecasesand4,903 controls. In silico ) EADI 1 P deCOD Supplementary Supplementary 5 in CHARG AD-IG o , as has data for for data has , as replication −5 −3 −3 −3 −5 1 replication Stage 2 E 1.17 1.14 1.11 0.90 1.28 OR E ABCA7 MS4A b 1.08–1.25 1.05–1.23 1.04–1.19 0.84–0.96 1.14–1.44 95% CI ). ). -

D BIN1 ( date to identified variants significant genome-wide the of any between epistasis of evidence find not did we indeed, and between action 10 × 3.8 with association signal. lying D rs610932, with top our SNP (rs4938933 is in LD with locus the at SNP ADGC significant most the that noteworthy is It results. ADGC and GERAD+ the of analysis combined the tively,in P the at SNPs two samples), and combining results GERAD+ removing (after ADGC overlapping (meta P vided strong evidence for association with rs3764650 at from stages 1, 2 and 3 ( 3 stage 3 stage if rs3764650 is associated with the expression of of expression the with associated is rs3764650 if lines cell lymphoblastoid from (derived data from used two We expression quantitative published trait datasets (eQTL) loci variant. functional relevant the be to unlikely is and change benign a be to predicted is which protein, posi the of at 1527 tion substitution alanine to glycine a encodes rs3752246 1.17). (GERAD2 disease Alzheimer’s with associated of out rs3764650 with HapMap LD all highest the showed which gene, the of 32 exon in SNP non-synonymous a rs3752246, for sample GERAD2 an associated functional variant at the in the included GWAS. However, attempt in a to preliminary identify others and SNP not this between is LD of levels which low the given criterion, unexpected 1 stage our passed that gene the in only the variant was SNP This 13. intron in located is which rs3764650, is sette, sub-family A, member 7) locus ( The of samples. first is these the tibility loci, which replicate over a number of independent case rs744373, Alzheimer’s of (rs3764650, onset disease at age and loci these between association for ( ated variants had on little effect the results of one the analysis of the three newly associ least at of presence the for adjusting Likewise, 3.2 × 10 2.1 × 10 2.9 × 10 = 1.2 × 10 × 1.2 = = 4.5 × 10 × 4.5 = ′ ′ = 0.89). This variant (which was not in genotyped stage 1) was also = 0.86), and thus both datasets may be detecting the same under same the detecting be may datasets both thus and 0.86), = This study also provides additional independent support for for support independent additional provides also study This data of meta-analysis weighted variance inverse Wean conducted This This study therefore identifies two new Alzheimer’s suscep disease NA NA P , , P CR1 P −3 −5 −7 P −5 = 1.8 × 10 × 1.8 = Stage 3 = × 2.9 10 = 3.2 × 10 × 3.2 = 1.06 0.91 1.22 ; see see ; ABCA7 P OR NA NA , , = 0.87; and rs3818361, rs3818361, and 0.87; = −16 −17 PICALM ABCA7 c Supplementary Table 4b Supplementary 1.02–1.11 0.87–0.95 1.13–1.32 (OR = 0.91) and and 0.91) = (OR Table 95% CI ) and two SNPs at the the at SNPs two and ) a APOE MS4A NA NA CR1 DVANCE ONLINE PUBLICATION ONLINE DVANCE had had −7 −14 −3 P -coding variants based on on based variants -coding ; rs610932, stage 3 stage ; rs610932, 1 (stage 2 2 (stage = 0.17; rs670139, rs670139, 0.17; = , , ; ; Table and the new variants identified in this study, this in identified variants new the and ) and rs670139 (meta (meta rs670139 and ) for meta-analysis.) We did not observe inter We observe not did meta-analysis.) for gene cluster, rs610932 and rs670139, showed showed rs670139, and rs610932 cluster, gene P 2.6 × 10 3.7 × 10 1.4 × 10 1.8 × 10 4.5 × 10 Table Table CLU = 5.0 × 10 × 5.0 = Meta-analysis ofGERAD+ and stage1,23 P or or 1 −14 −14 −9 −14 −17 and 1 c EADI2, CHARGEandMayo2, lessthan8,286Alzheimer’s P and and APOE = 1.4 × 10 × 1.4 = ABCA7 P 1.17 1.18 1.09 0.90 1.23 OR = 1.1 × 10 × 1.1 = Supplementary Table 3 −21 P Supplementary Table 3 Table Supplementary = 0.58). = ABCA7 Fig. Fig. 2 1.12–1.21 1.13–1.24 1.06–1.12 0.87–0.92 1.18–1.30 (odds ratio (OR) = 1.22). The The 1.22). = (OR) ratio (odds ) ( ) 95% CI MS4A P (encoding ATP-binding (encoding cas ). ). We no found evidence also 1 P Supplementary Table 4a Table Supplementary 7 = × 2.1 10 d = 0.38; rs610932, rs610932, 0.38; = and brain and −3 a

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r P 2 NA NA Nature Ge Nature = 1 × 10 × 1 = GERAD+ andADGC ABCA7 values ( values P BIN1 Meta-analysis of −5 1 −10 −16 −21 ABCA7 8 APOE ; and rs670139, ; and rs670139, ) to determine determine to ) ABCA7 (stage 2 2 (stage 1.08 0.91 1.23 OR NA NA ). This pro . However, . −9 r r

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© 2011 Nature America, Inc. All rights reserved. GERAD1, EADI1, deCODE and AD-IG GWASand AD-IG deCODE (up to 6,992 EADI1, datasets GERAD1, rs3865444, ADGC with LD first to show for suggestive evidence the were study another from researchers Similarly, on here. reported 0.28, (rs11771145, ease dis Alzheimer’s with association of evidence suggestive showing as viously. Members of were this collaboration the first to report with association suggestive EPHA1 10 × (1 10 disease Alzheimer’s with for association evidence the for SNPs at datasets different the in association depicting forest plots sample. same the in locus this at variant significant ( association for evidence weaker This variants SNP was rs2304933. was in analyzed stage 1 but showed significant genome-wide the with associated strongly most was that SNP non-synonymous The lines. cell or pons lymphoblastoid cortex, cortex (0.01 < ciation with expression levels of and of MS4A6E MS4A prising the 4-domains membrane-spanning subfamily A by (encoded (chr11: 59,814,287–60,107,105) and includes 6 of 16 known genes com ( cluster gene locus. at this variant(s) causal the identify to required be will ( no association we observed data are at provided the of bottom where each with on SNP each lines chip indicating schematic genotyped the is 610-quad Illumina represented. by indicated the red The lines. chart and The graph. stage GERAD+ 1, 2 and 3 meta-analysis gene The black boxes exons region. indicate and −log of the untranslated transcription, directions of the 2 Figure Nature Ge Nature meta-analysis. variance inverse using controls), 13,472 and cases a −8 We combined data from the GERAD+ dataset, comprising the the comprising dataset, GERAD+ the from data combined We We also sought to follow up four additional loci showing suggestive Second, we implicate the MS4A6A

ABCA7 –log P MS4A6A

) from the ADGC GWAS ADGC the from ) 10 D 10.00 15.00 MS4A ). These ). are These 5.00 ′ , ,

= 0.75) = 0 Schematic of the associated variants reported in to of reported reference ( variants Schematic the associated CD2AP . . The SNPsassociated are found in the 3 n (rs3764650) and (rs3764650) gene cluster. are shown positions at the Chromosome top indicate arrows of (UCSC Feb horizontal the Gene 2009). schematics schematic: (rs610932) and the intergenic region between between region intergenic the and (rs610932) Chr. 19 etics (rs670139). rs610932 showed nominally significant asso Fig. P < 0.05; 1 1 and and , which included the GERAD1 and EADI1 samples samples EADI1 and GERAD1 the included which ,

MS4A2 2

1,030k P ABCA7 b = 1.7 × 10 × 1.7 = ADVANCE ONLINE PUBLICATION ONLINE ADVANCE ). The association spans an LD block of 293 kb 293 of block LD an spans association The ). ARID5B Supplementary TableSupplementary 5 Meta , , MS4A3 MS4A 1,040k EPHA1 r D rs3764650 MS4A Supplementary Table 5 Supplementary 2 P ′ = 0.13, 0.13, = 1 LD of block structure =4.5 . It should be noted that evidence for for evidence that noted be should It . 2 −6 MS4A6A . These loci included those in in those included loci These . (encoding membrane-spanning 4A) ; LD with ADGC rs11767557, rs11767557, ADGC with LD ; , , P × and (rs610932 and rs670139) loci. and rs670139) (rs610932 MS4A4A 10 1,050k = 0.006) than the genome-wide genome-wide the than 0.006) = CD33 –1 D 7 ′ CD33 = 1.0) = in cer (rs3826656, (rs3826656, 1,060k , , MS4A4E has been reported pre reported has been ) ) but not in the 1 e 9 bellum bellum and temporal ′ . untranslated region ABCA7 1,070k

Figure Figure ). Further work Further ). , , P MS4A6A = 4.0 × 10 P plus the surrounding region and chr11: 59.81Mb–60.1Mb according to according the CEPH HapMap and region plus 59.81Mb–60.1Mb the chr11: surrounding −6 values for rs3764650 ( for values rs3764650

≥ MS4A4E 3 1,080k

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b of expression of of expression of product of which is known to clear apoptotic and cells, the high levels surface cell apoptotic the on protein receptor complement C1q the through mediated by macrophages cells of apoptotic phagocytosis modulates overexpressing cells cultured in secretion inhibit and processing APP regulate to shown been has ABCA7 In addition, molecules. these between interaction biological ( loci genetic three the between interactions epistatic for evidence no by CLU. followed are APOE brain in We lipoproteins main observed Notably, the particles. lipoprotein to cells from lipids of efflux the in CA1 the neurons hippocampal cell membranes superfamily has roles in transporting a transporter wide range of substrates ABC across The transporter. (ABC) cassette ATP-binding an loci. susceptibility disease Alzheimer’s five tional TableSupplementary 6 Table meta ADGC and (GERAD+ overall ADGC by reported that to opposite was (rs2588969, observed nominally significant evidence of association with with of association evidence significant nominally observed rs11767557, GERAD+ and ADGC meta meta ADGC and GERAD+ rs3865444, disease Alzheimer’s meta ADGC with and GERAD+ (rs9349407, association for evidence genome-wide EPHA1 10 with association for support observed We analyses. set and covery were thus particular from excluded these We included the TGEN1, ADNI and Mayo1 datasets in the ADGC dis

Supplementary Table 4a Table Supplementary –log10 P and ( −4 Taken together, these results show compelling evidence for an addi When these data were combined with the ADGC data, we observed 10.0 15.0 5.00 , OR = 1.11), 1.11), = OR , 0 0 0 2 b 2 for results of the GERAD+ and ADGC combined analyses and (rs11767557, (rs11767557, ABCA7 Chr. 11 3 ) chromosomal region chr11: 59.81Mb–60.1Mb members harboring . . ABCA7 P PLAC1L = 3.3 × 10 ), rs610932 ), ( rs610932 59.8 Mb MS4A 2 10 ABCA7 0 . . is an ortholog of ortholog an is CD33

ABCA7 MS4A P 3 of the in SNPs analyzed stage 1 are shown in the P 2 = 3.4 × 10 × 3.4 = −2 for results ofSNPs additional atloci. these (rs3865444, (rs3865444, in microglia are consistent with such a role. a such with consistent are microglia in , , OR = 1.06); however, the direction of effect 59.9 Mb Meta is highly expressed in brain, in particularly MS4A6A ), however, this is not a prerequisite for for prerequisite a not is this however, ), MS4A6A rs610932 P 2 = 1.8 1 MS4A4E and microglia Meta rs670139 −4 ) ) and ( rs670139 × Caenorhabditis elegans ced-7 elegans Caenorhabditis , OR = 0.90). = OR , 10 60.0 Mb P P P –1 = 3.6 × 10 × 3.6 = = 1.4 = 2.2 × 10 × 2.2 = CD2AP P MS4A4A 4 = 6.0 × 10 P P 1 APP = 1.6 × 10 × 1.6 = × 2 = 8.6 × 10 × 8.6 = 10 and was not significant significant not was and MS4A6E –9 (rs9349407, (rs9349407, (ref. (ref. 2 60.1 Mb 2 . ABCA7 . is ABCA7 involved −1 −4 −10 MS4A4E MS4A , OR = 0.99). See See 0.99). = OR , s r e t t e l , OR = 0.89) and and 0.89) = OR , ABCA7 23). 23). MS4A14 , OR = 0.90). We −9 −9 7 , OR = 0.91; 0.91; = OR , , OR = 1.11; 1.11; = OR , ABCA7 MS4A β ) ) are 60.2 Mb - -amyloid MS4A encodes encodes P ARID5B 5 = 8.0 × 8.0 = 1 also also , the , the  - -

© 2011 Nature America, Inc. All rights reserved. a Chr., chromosome; MAF, minorallelefrequency;LD, linkagedisequilibrium. rs3865444 rs4948288 rs2588969 rs11767557 rs9296559 rs9349407 SNP T suggestive showing loci three for support independent provide also with We samples. disease case-control independent of Alzheimer’s number a over replication to susceptibility with associated cluster inflammation motility and morphology cell tissues epithelial in mainly expressed is EPHA1 guidance axon and cell in roles play which are tors membrane-bound recep Eph and Ephrins subfamily. receptor ephrin the of member a is EPHA1 membrane. the across molecules of transduction and tion genes susceptibility established recently the and disease, Alzheimer’s for receptor-mediated endocytosis of regulation the in involved also protein a tin, a is protein) clathrin of independent through mechanism endocytosis a mediating receptors, endocytic as act CD33, adaptive and innate systems the immune in cells of functions regulate and inter actions cell-cell promote to thought is which family, (Siglec) lectins functions. specific known no have receptors IgE affinity high proteins cell-surface of family a of part to be are likely they that indicating domains, transmembrane including family, the of members other all with structure genomic at the 3 Figure s r e t t e l  Naj GERAD1, EADI1,deCODE and AD-IG. Cochran’ All data *excluding overlappingsampleswithADGC ADGC MAYO2 CHARG EADI2 AD-IG deCOD GERAD ADNI EADI1 GERAD Stud able able 2 Our study has identified variants at at variants identified has study Our CD33 is a immunoglobulin-like member of the sialic-acid-binding The genes in the et al. y * 1 E ABCA7 * 2 1 E 2 PICALM s .

d No. cases,control Q Data imputedinthedeCODE dataset. d b c b Forest plots showing association in for datasets the SNPs association plots Forest showing different R test, 3 25900, 4158 0 esults esults of the combined analysis of the G 1239, 1081 9015, 7603 2490, 4114 2751, 2620 3262, 3320 2025, 5328 3333, 6026 and in synaptic development and plasticity and development synaptic in and 709, 97 925, 61 151, 17 Closest gene 2 (rs3764650) and (rs3764650)

P 9 CD33 ARID5B ARID5B EPHA1 CD2AP CD2AP scaffold adaptor protein adaptor scaffold . It is striking that these two new susceptibility genes genes susceptibility new two these that striking is It . 3 = 0.82 5 and and have also been proposed. been also have 1 2 7 2 4 3 6 MS4A . Most members of the Siglec family, including including family, Siglec the of members Most . s BIN1 1.23 [1.17–1.28 1.20 [1.11–1.30 1.24 [1.10–1.41 1.09 [0.92–1.29 1.31 [1.15–1.50] 1.15 [0.83–1.59] 1.23 [0.93–1.64] 1.32 [1.15–1.51] 1.01 [0.58–1.75] 1.21 [1.08–1.37] 1.24 [1.12–1.38] OR I 2 Chr. 19 10 10 = b Results generatedfromimputed data.TheresultsfromthetopgenotypedSNPare alsoshown.See 7 6 6 cluster on 11 chromosome have a common , are all implicated in cell-cell communica cell-cell in implicated all are , 0 95% CI 2 5 . The remaining genes in the LD block block LD the in genes remaining The . MS4A 3 3 . Additional roles in apoptosis in roles Additional . 0.31 0.26 0.40 0.21 0.29 0.29 MAF 2 ] ] ] ] 4 0.6 . . (rs610932 and rs670139) loci. and rs670139) (rs610932 MS4A2 P =5.0 2 8 LD withthetopADGC 2 that associates with cortac with associates that ABCA7 0.55 0.71 7

N/A N/A N/A N/A × SNP ateachloci . CD2AP (CD2-associated (CD2-associated CD2AP . r 0.8 10 2 encodes the the encodes –21 Odds rati and the the and 1.0 3 2 0.78 0.95 N/A N/A N/A N/A where it regulates regulates it where D ER ′ o 1.2 AD+ AD+ consortia with the ADGC GWA rs3764650, 3 β 1 MS4A subunit of of subunit . However, . 1.4 6,283 6,992 6,283 6,283 6,283 6,283 Cases 1.6 3 ABCA gene gene 4 and and 1. 8 7 - - - ­ Controls 13,472 12,935 Cochran’ All data *excluding overlappingsampleswithADGC ADGC MAYO2 CHARG EADI2 AD-IG deCOD GERAD TGEN ADNI EADI1 GERAD Stud 7,165 7,165 7,165 7,165 deCOD GERAD TGEN ADNI EADI1 GERAD Stud Cochran’ All data *excluding overlappingsampleswithADGC ADGC MAYO2* CHARGE EADI2 AD-IG understanding the pathogenesis of Alzheimer’s disease. Alzheimer’s of pathogenesis the understanding at aimed studies focused for impetus new provide therefore findings A and neurodegeneration in roles strong play would processes these that conceivable is It processing. and endocytosis, ing and have putative functions in the immune system; Finally,significance. we provide replication further evidence for of levels the data when were showed genome-wide combined, which, in a evidence disease susceptibility loci in in loci susceptibility disease tion of the genes Five identified. of the Alzheimer’srecently identified func putative in consistency emerging the is findings our about ing and y y * E * GERAD+ consortia 2 1 * E s E CR1 CD2AP 2 1

s Q No. cases,control

No. cases,control Q test, 2.2 ×10 3.6 ×10 3.3 ×10 3.4 ×10 1.5 ×10 8.0 ×10 28183, 46911 test, 28484, 46850 9980, 9092 2501, 4141 1367, 12904 2751, 2620 3262, 3320 2025, 5328 3941, 7414 loci as Alzheimer’s disease susceptibility loci. What is strik loci. susceptibility as Alzheimer’s disease loci 3262, 3320 2025, 5328 3333, 6026 9980, 9092 3410, 5468 1367, 1290 2751, 2620 709, 97 925, 61 571, 33 151, 17 925, 61 571, 33 151, 17 709, 97 P P P = 0.20 are involved in processes at the cell membrane, includ membrane, cell the at processes in involved are S = 0.4

−4 −3 −2 −4 −3 −4 upplementary companion paper companion 1 2 2 7 2 2 7 1 a 6 4 a DVANCE ONLINE PUBLICATION ONLINE DVANCE s S s 0.89 1.07 1.06 0.90 1.10 1.11 × 0.92 [0.88–0.96] 0.91 [0.88–0.93] I 0.91 [0.84–0.98 0.95 [0.88–1.03 0.90 [0.83–0.97 0.79 [0.65–0.96 0.81 [0.70–0.95 0.94 [0.87–1.02 0.74 [0.60–0.90 0.88 [0.64–1.22 0.93 [0.86–1.00 0.87 [0.82–0.92 OR 2 OR 1.15 [0.99–1.35] 1.10 [1.02–1.19] 1.26 [1.03–1.54] 1.08 [0.78–1.49] 1.06 [0.99–1.14] 1.13 [1.06–1.21] 1.02 [0.94–1.11] 1.13 [0.93–1.38] I 1.08 [1.06–1.11 1.05 [1.01–1.10 1.11 [1.04–1.18 1.05 [0.96–1.15 OR 2 =25.9 = APOE T c c able 6 0 95% CI 95% CI forfulldetails. 0.84–0.95 1.03–1.15 1.01–1.13 0.85–0.95 1.04–1.17 1.04–1.18 95% CI , , CLU CLU ] ] ] ] ] ] ] ] ] ] ] ] ] ] 1 0. 2 P =1.1 P =1.2 : loci in : loci 0 8 , , and and β CR1 clearance from the brain. These These brain. the from clearance c Opposite directionofeffect tothatreportedby 0. × × 1.6 ×10 3.6 ×10 6.0 ×10 8.6 ×10 0 7 10 .9 10 ABCA7 , , –10 ABCA7 CD33 –16 NA NA P 1.0 .8 −9 −1 −10 −9 GERAD+ andADGC Odds rati PICALM , , are involved in lipid lipid in involved are Odds rati 1.1 meta-analysis

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© 2011 Nature America, Inc. All rights reserved. H.-E.W. contributed to clinical sample ascertainment, diagnosis collection, and G.L., N.J.B., H.G., A.M., M.T., T.W.M., M.M.N., S. Moebus, K.-H.J., N.K. and D.R., I.G., J.S.K.K., C.C., P.N., J.C.M., K. Mayo, K. Sleegers, K.B., S.E., P.P.D., C.V.B., H.v.d.B., I.H., J.K., J. Wiltfang, M. Dichgans, L.F., H.H., M. Hüll, J.G., A.M.G., J.H., S. Mead, N.C.F., M. Rossor, J. Collinge, W.M., F.J., B.S., H.K., R.H., E.R., K. Morgan, K.S.B., P.A.P., D. Craig, B.M., S.T., C.H., D.M., A.D.S., S. Love, P.G.K., C. is J.based. Williams, P.H.,R.A., A.G., R.S., C.W., J. Chapman, K.D., N.J., A.S., preparation, genotyping and/or conduct of the GWAS upon which this study M.O.D. and M.J.O. All authors contributed to the sample samplecollection, responsibilityprimary for drafting the manuscript, assisted by A.G., R.S., R.A., helped by P.H., A.G., L.J.R.S., R.A., and D. Harold. J. Williams, P.H. and D.H. took J. Williams directed this study, assisted by M.J.O. and M.O.D. and was also sampleLeeds was collection funded by the Health Foundation. partly funded by the NIHR Biomedical Research Centre Programme, Oxford. The and Sports; European Commission and the Municipality of Rotterdam. G.W. was of Ministry Education, Elderly; Culture and for Ministry Science; Health, Welfare the Health Research and Development; the Research Institute for in Diseases the Netherlands organization for research;scientific Netherlands Organization for of Research; Scientific Netherlands Genomics Initiative; Erasmus Medical Center; Dawson Robert Kidney EvansDiseases; Endowment; Netherlands Organisation Heart Lung and Institute;Blood National Institute of Diabetes and Digestive and andDeafness Other Communication Disorders; Hjartavernd; Althingi; National Network; forGerman Ministry Education and Research; National Institute on Research and Education; Dana Foundation; German National Genome Research Foundation for the National Institutes of Health Northern InstituteCalifornia for Alzheimer’s Foundation;Drug Discovery US Food and Drug Administration; Hoffman-La Synarc;Roche; Schering-Plough; Wyeth; Alzheimer’s Association; Innogenetics; Johnson and Johnson;Medpace; Eli Merck;Lilly; Novartis; Pfizer; Schering Pharma; Bristol-Myers Squibb; Elan; Genentech; GE; GlaxoSmithKline; Institute of Biomedical Imaging Abbott;Bioengineering; BayerAstraZeneca, the Ministerio de Sanidad y Consumo; Fundación Ramón Areces; National of Ministry Health; Fondazione Monzino; Ministerio de Educación y Ciencia Neurodegeneration; Italian of Ministry Research; Carimonte Foundation; Italian Research Council of the Academy of Finland; Nordic Centre of Excellence in Research/Institute national de la santé et de la recherché Eisai; medicale; Health and Bourgogne Regional FondationCouncils; de France; French of Ministry Longévité; Agence Française de SanitaireSécurité des Produits de Santé; Aquitaine Maladie des Travailleurs Direction de Salariés, Générale la Sant; Institut de la National de Génotypage; Fondation pour la Recherche Médicale Caisse; Nationale Research; Carl Edward and Susan Bass Bolch Gift; Institut Pasteur de Centre Lille; Postdoctoral Fellowship and AD Research Program; Palumbo Professorship in AD National Institute of Neurological Disorders and Stroke; and Robert Clarice Smith InteruniversityOffice Attraction Poles program; Mayo AD Research Center; for Alzheimer Research; Methusalem Excellence grant; Federal PolicyScience UniversityServices; of Antwerp, Fund for Research-Flanders; Scientific Foundation Program of the National Institute of Ageing Department of Health and Human KruppDementia; Alfried von und Bohlen Halbach-Stiftung; Intramural Research Research Competence Network Dementia and Competence Network Degenerative Biomedical Centre; Lundbeck; German ofFederal Ministry Education and Alzheimer’s Research Initiative; University College London (UCL) Hospital/UCL Institutes of Health, the Barnes Jewish Foundation; Charles and Joanne Knight Trust; Bristol Research into Alzheimer’s and CareUS Nationalof the Eldery; Northern Ireland Royal R&D Office; College of Physicians; Medical Dunhill Institute for Research on Ageing; Alzheimer’s Ulster Garden Society; Villages; (UK); Alzheimer’s Research UK; the Welsh Assembly Government; Mercer’s groups who contributed to this Wellcomestudy: Trust; Medical Research Council individuals and families who took part in this research and who those funded the For complete acknowledgments, please see the Note: Supplementary information is available on the online the at http://www.nature.com/naturegenetics/. paper the of in ­version available are references asso Nature Ge Nature preparation of samples from the independent GERAD2 sample genotyped as part AU Acknowledgments

et Thomas, S. Lovestone, J.P., P. Proitsi, M.K.L., C. Brayne, D.C.R., M.G., B.L., A.L., T H ho O ADNI database, database, ADNI R R ds CONT n http://adn etics RIBU

T ADVANCE ONLINE PUBLICATION ONLINE ADVANCE I i.loni.ucla.edu/wp-c ONS h f . ttp://www.loni.ucla. Supplementary Supplementary Note ontent/uploads/how_t Nature Genetic edu/ADN

s website. . . We thank the I ; ADNI ADNI ; o_apply/

reprintsandpermissions/. http://npg.nature.com/ at online available is information permissions and Reprints Published online at http://www.nature.com/naturegenetics/. HTML version of the paper at The authors declare competing interests:financial details accompany the full-text P.A.H. All authors the discussed results and approved the manuscript. control and produced association statistics under the supervision of J. Williams and and analysis of the deCODE GWAS. D. Harold and P.H. completed statistical quality K. Stefansson, J.S., S.B. and P.V.J were responsible for sample collection, conduct conduct and analysis of the AD-IG GWAS. S. Steinberg, T.J., H. Stefansson, S. Schreiber, M. Mayhaus, S.N. and S.W. were responsible for sample collection, and analysis of the Mayo2 sample. M. Riemenschneider, T.M.F., P.F., C.R., M.K., R.C.P., K. Morgan and S.G.Y. in sample collection, sample preparation, genotyping H.B., D.W., G.W., N.M.H., E.R.L.C.V., S.B.S., J.O.A., M.B., Z.K.W., D.W.D.,contributed clinical N.R.G.R., and genotypic data. M.M.C. played a leading role, along with contributed clinical and genotypic data to the CHARGE GWAS. J.-C.L. and P.A. Sample. S.S., A.L.D., O.L. and L.J.L., as well as M.A.I., C.M.v.D. and M.M.B.B. for sample collection, sample preparation, genotyping and analysis of the EADI2 E.S., D.G., A.B., D. Hannequin, F.L., H. Soininen, J.-C.L. and P.A. were responsible G.S., M. Mancuso, F. Panza, B.N., S. Sorbi, P. Bossù, P. Piccardi, B.A., G.A., D.S., D.Z., M. Delepine, M.J.B., F. Pasquier, I.M., A.F.-G., E.P., O.H.,related toE. genotyping Coto, the GERAD2 sample. V.C.,V.A., B.G.-B., M. Hiltunen,P. O.C., Bosco, of this study. D.R.S., Harold, A.G., D.R. and I.G. were responsible for procedures 22. 21. 20. 19. 18. 17. 16. 15. 14. 13. 12. 11. 10. 9. 8. 7. 6. 5. 4. 3. 2. 1. COM

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45 , , , 110 5 33 , , , n 38 107 , etics , , 77 88 , , , © 2011 Nature America, Inc. All rights reserved. of of Public Health, University of Cambridge, Cambridge, UK. Foundation Trust and Institute of Psychiatry, Kings College, London, UK. Florida, USA. F-59019, Lille, France. Medicine Psychological and Neurology, School of Medicine, Cardiff University, Cardiff, UK. 1 Nature Ge Nature Neuroscience, Norwegian Neuroscience, University of Science and Technology, NTNU, 7491 Trondheim Norway. Informatics, Mayo Clinic and Mayo Foundation, Rochester, Minnesota, USA. Biometry and Epidemiology, Munich, Germany. Ludwig-Maximilians-Universität, of Epidemiology, Helmholtz Zentrum München, German Research Center for Health, Environmental Neuherberg, Germany. Bonn, Germany. Bethesda, Maryland, USA. of Neurology, Aristotle University of Greece. Thessaloniki, Thessaloniki, 47 of Mental Health Sciences, University College London, London UK. Antwerpen, Biotechnologie, Belgium. University of Antwerp, Antwerpen, Belgium. Washington University School of Medicine, St Louis, Missouri, USA. Medicine, St Louis, Missouri, USA. and Section of and Gerontopsychiatry Neuropsychology, University of Freiburg, Freiburg, Germany. University, Frankfurt, Germany. Faculty Mannheim, University of Heidelberg, Mannheim, Germany. and Dementia Research, Klinikum der Universität München, Munich, Germany. Psychotherapy, University Essen, Duisburg-Essen, Germany. of Psychiatry and Psychotherapy, University of Erlangen, Nuremberg, Germany. Primary Medical Care, University Medical Center Hamburg, Germany.Hamburg-Eppendorf, Bonn, Germany. University of Bonn, Bonn, Germany. Neurology, London, UK. (NHS) Trust, Stott Lane, Salford, UK. Biology, Faculty of Biological Sciences, LIGHT University Laboratories, of Leeds, Leeds, UK. Oxford, UK. University of Oxford, John Radcliffe Hospital, Oxford, UK. Based Medicine, University of Manchester, Hope Hospital, Stott Lane, Salford, Manchester, UK. School Neurosciences, of Medicine, University of Southampton, Southampton, UK. UK. for Research on Aging, St. James Hospital and Trinity College, Dublin, Ireland. contributed contributed equally to this work. should Correspondence be addressed to or M.J.O. ([email protected]) J.W. ([email protected]). 108 107 106 IRCCS, Ospedale Maggiore, Mangiagalli e Regina Elena, Milan, Italy. Pharmacology, Department of University Neuroscience, of Cagliari, Cagliari, Italy. Florence, Italy. Center for Aging Brain, Memory Unit, University of Bari, Policlinico, Bari, Italy. e Cura a Carattere Scientifico Oasi Maria SS, Troina, Italy. Department of Geriatrics, Broca Hospital, Paris, France. La Paz (UAM), Madrid, Spain. Autonoma, Campus de Cantoblanco, Madrid, Spain. 91 90 Finland and Kuopio University Hospital, Kuopio, Finland. of Iceland, Faculty of Medicine, Reykjavik, Iceland. and Epidemiology, Klinikum Rechts der Isar, Technische Universität, München, Germany. Christian-Albrechts-University, Kiel, Germany. Medical Informatics and Statistics, Christian-Albrechts-University, Kiel, Germany. France. Genotypage, Institut Genomique, Commissariat à l’énergie Atomique, Evry, France. Université Paris Descartes, Paris, France. Montpellier, France. Washington DC, USA. Medicine, Pittsburgh, USA. Pennsylvania, School of Medicine, Pittsburgh, USA. Pennsylvania, of Epidemiology, University of Washington, Seattle, Washington, USA. Medicine, Boston, USA. Massachusetts, The Netherlands. report. See URLs for a complete listing of the ADNI investigators. As such, the investigators within the ADNI contributed to the design and implementation of ADNI and/or provided data but Minnesota, USA. did not participate in analysis or writing of this Neurology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA. Centre, Polish Academy of Sciences, Warsaw, Poland. Medical Medical Research Council (MRC) Centre for Genetics Neuropsychiatric and Genomics, and Neurosciences Mental Health Research Institute, Department of MRC MRC Centre for Research, Department Neurodegeneration of Clinical King’sNeuroscience, College London, Institute of Psychiatry, London, UK. Centre Centre National de Genotypage, Institut Genomique, Commissariat à l’énergie Atomique, Evry, France. Centro Biomedica Investigacion en Red ‘Marqués de Enfermedades Neurodegenerativas Valdecilla’ University Hospital (University of Cantabria), Santander, Spain. INSERM, INSERM, UMR_S679, Hopital de la salpétirère, Paris, France. Department of Neurological Sciences, Università degli Studi di Milano, Fondazione IRCCS, Ospedale Maggiore, Mangiagalli e Regina Elena, Milan, Italy. Geriatric Unit and Research Laboratory,Gerontology-Geriatric Department of Medical Science, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy. 12 Ageing Ageing Group, Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, UK. 80 Department Department of Psychiatry and Psychotherapy, des Universitätsklinikum Saarlandes, Universität des Saarlandes Saarbruecken Germany. 17 n 6 Dementia Dementia Research Group, University of Bristol Institute of Clinical Frenchay Neurosciences, Hospital, Bristol, UK. National National Institute for Health Research Biomedical Research Centre for Mental Health at the South London and Maudsley National Health Service etics 102 52 26 63 65 Department Department of Clinical and Behavioral Neurology, IRCCS Santa Lucia Foundation, Roma, Italy. Institute Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Essen, Duisburg-Essen, Germany. Department of Psychiatry, University of Göttingen, Göttingen, Germany. Data Data used in the preparation of this article were obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database (see URLs). Netherlands Netherlands Consortium for Healthy Aging, Leiden, The Netherlands. 74

72 INSERM INSERM U614, Faculté de de Médecine-Pharmacie Rouen, Rouen, France. 4 ADVANCE ONLINE PUBLICATION ONLINE ADVANCE Department Department of Neurology, Boston University School of Medicine, Boston, USA. Massachusetts, 22 Université Université de Lille Nord de France, F-59000 Lille, France. Department Department of Disease, Neurodegenerative University College London, Institute of Neurology, London, UK. 50 Department Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany. 95 36 Department Department of Experimental Pathology, School of Medicine, University of Bologna, Bologna, Italy. Department Department of Primary Care and Public Health, School of Medicine, Cardiff University, Cardiff, UK. 39 24 Department Department of Neurology, Washington University School of Medicine, St Louis, Missouri, USA. 44 20 German German Centre for Diseases, Bonn, Neurodegenerative Bonn, Germany. Memory Memory Clinic and Department of Neurology, Antwerpen, Middelheim, Antwerpen, ZiekenhuisNetwerk Belgium. Department Department of Molecular Institute Neuroscience, of Neurology, London, UK. 67 76 71 The The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, USA. Massachusetts, INSERM INSERM U897, Victor Segalen University, Bordeaux, France. 43 Neuroepidemiology Section, Neuroepidemiology Laboratory of Epidemiology, Demography and Biometry (LJL), National Institute on Aging, 83 Neurodegenerative Brain Neurodegenerative Diseases group, Department of Molecular Genetics, Vlaams Instituut voor Interuniversitair Institute Institute for Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany. 87 93 70 Faculty Faculty of Medicine, University of Iceland, Reykjavik, Iceland. 60 Centre Centre Hospitalier Régional de Universitaire Lille, Lille, France. Department Department of Psychiatry, The Alzheimer’s Disease Research Center, University of Pittsburgh School of Department Department of Neurology, Mayo Clinic College of Medicine, Florida, Jacksonville, USA. 97 89 16 99 Genetic Genetic Molecular Unit, Hospital Central Universitario de Asturias, Oviedo, Spain. 9 Neurology Neurology Service, ‘Marqués de Valdecilla’ University Hospital (University of Cantabria), Santander, Spain. Nuffield Nuffield Department of Clinical Medicine, Medical Sciences Division. University of Oxford, Headington, Department Department of Neurological Neuroscience, Clinic, University of Pisa, Italy. 32 Cambridge Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.

Department Department of Neurology, Klinikum der Universität München, Munich, Germany. 64 109 35 46 Department Department of Epidemiology, Erasmus Medical Center, University Medical Center, Rotterdam, 41 105 INSERM INSERM U614, Faculté de de Médecine-Pharmacie Rouen, Rouen, France. Department Department of Psychiatry, Psychsomatic Medicine and Psychotherapy, Johann Wolfgang Goethe- The The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK. 69 Department Department of Biology, Brigham Young University, Provo, Utah, USA. 49 Department Department of Clinical Medicine and Prevention, University of Monza, Milano-Bicocca, Italy. Department Department of Neurology, The Alzheimer’s Disease Research Center, University of Pittsburgh 7 62 Laboratory Laboratory of National Neurogenetics, Institute on Aging, National Institutes of Health, Department Department of Institute Neuroscience, of Psychiatry, Kings College, London, UK. Mayo Mayo Alzheimer Disease Research Center, Mayo Clinic College of Medicine, Rochester, 57 Department Department of Neurology, St. Olav’s Hospital, Trondheim, Norway. 11 101 31 34 55 Institute Institute of Genetics, Queen’s Medical Centre, University of Nottingham, Nottingham, Landschaftsverband Rheinland-Hospital Essen, Rheinland-Hospital Department of Landschaftsverband Psychiatry and 104 Department Department of Geriatric Psychiatry, Central Institute of Mental Health, Medical 82 Department Department of Neurological and Psychiatric Sciences, University of Florence, Klinikum Klinikum Grosshadern, Munich, Germany. 79 14 Biobank Biobank Popgen, Institute of Experimental Medicine, Section of Epidemiology, 5 Department Department of Internal Medicine, Università degli Studi di Milano, Fondazione Department Department of Mayo Neuroscience, Clinic College of Medicine, Jacksonville, The The Foundation Jean d’Etude Dausset-Centre du Humain, Polymorphisme Paris, Neurodegeneration and Neurodegeneration Mental Health Research Group, School of Community 66 85 27 29 2 Departments Departments of Neurology and Boston Biostatistics, University School of deCODE deCODE Genetics, Reykjavik, Iceland. INSERM INSERM U744, F-59019 Lille, France. Department Department of Psychiatry, Royal Derby Hospital, Derby, UK. 19 Department Department of Psychiatry, Charité Berlin, Berlin, Germany. Cerebral Cerebral Function Unit, Salford Royal National Health Service 15 59 38 Oxford Oxford Project to Investigate Memory and Ageing (OPTIMA), 75 Department Department of Disorders, Medical Neurodegenerative Research Department Department of Psychiatry, Washington University School of Unité Unité Mixte de Recherche 894, Inserm Faculté de Médecine, 92 77 Centro Centro de Biologia Molecular Severo Ochoa, Universidad INSERM INSERM U708, Paris, France. 25 Institute Institute for Molecular Psychiatry, University of Bonn, 103 51 Institute Institute of Human Genetics, University of Bonn, 21 Lab Lab of Molecular Genetics, Section of Clinical 88 94 Reta Reta Lilla Weston Institute Laboratories, of Department Department of Neurology, University of Eastern 73 Servicio Servicio de Neurologia, Hospital Universitario INSERM INSERM U888, Hôpital La Colombière, 54 Institute Institute of Medical Informatics, 56 Division Division of Biomedical Statistics and 18 86 96 Institute Institute of Molecular and Cellular 40 3 deCODE deCODE Genetics and University University University Paris Descartes, 23 37 Institut Institut Pasteur de Lille, Department Department of Genetics, 84 100 Department Department of Psychiatry, Centre Centre for Geriatric Medicine Institute Institute of Medical Statistics Department Department of Geriatrics, 78 42 Centre Centre National de 98 Institute Institute Born-Bunge, Istituto Istituto Di Ricovero 61 33 13 58 Department Department of 81 10 Institute Institute for Stroke 110 48 Division Division of Clinical s r e t t e l Department Department of Institute Institute of Mercer’s Institute Third Third Department These These authors 45 30 28 68 Department Department Department Department Institute Institute of Department Department 53 8 Institute Institute

Institute Institute



© 2011 Nature America, Inc. All rights reserved. for significance, accounting for 12 tests, of of tests, 12 for accounting significance, for 4,896 cases and 4,903 controls). We employed a to Bonferroni-adjusted threshold up of sample (total meta-analysis effects fixed inverse-variance–weighted an using combined were samples three these from Data 2. stage in included and meta-analyses. final and 3 2, Stage ( for genotyping selected SNPs other the with LD high in were that SNPs 8 Weexcluded excluded). SNPs (6 sample 2 stage the in tested been previously not had they of ing sample GERAD2 the in reported already were data variants at the and also for Alzheimer’s disease, gene susceptibility is a known as this SNPs), the at variants exclude to chose we 2, stage in replication for at disease Alzheimer’s with associated cantly signifi remained SNPs using Sixty-one repeated meta-analysis. was variance-weighted analysis inverse the and SNPs, 67 these for consortium EADI ( at disease Alzheimer’s with combined associated were the SNPs In 67 array). analysis, 500K Affymetrix the employed studies, other the unlike (which, sample TGEN the in SNPs these of 457,509 imputed cessfully GWAS.Wesuc EADI1 and ADNI GERAD1, the of each in control quality passed SNPs These SNPs. autosomal 496,795 tested analysis combined The able The datasets. TGEN P and ADNI GERAD1, the in disease Alzheimer’s with for to association test used was meta-analysis effects fixed variance-weighted GWAS. disease Alzheimer’s four of analysis combined 1: Stage in found be can ples the in found be can of and control all descriptions methods samples, genotyping quality measures Full 2 and 4; approved 27 July 2007). Amendment 04/09/030; (MREC disease approval to use these samples to search for genes susceptibility for Alzheimer’s ethical We obtained studies. association genetic the in part take to assent or sample the EADI2 (ref. comprised 8,286 cases and 21,258 controls, which included new genotyping in ( aged predominantly stage 2 control group (55.1% female, mean age at ascertainment, 70.0 years) cases werewith Alzheimer’s weredisease 72.3 years and 76.8 years, respectively. The in at age ascertainment mean the and onset female at age disease mean The (63.4%). predominantly were cases disease Alzheimer’s disease. Alzheimer’s ADRDA to NINCDS- according were GWASdiagnosed and AD-IG cases All datasets. and sample GERAD2 the of genotyping application. upon researchers to available are 1 stage of results meta-analysis controls genome-wide complete The unscreened years). 48.6 based collection, at age mean female, population (50.8% study GERAD1 5,770 the from and years) 74.5 collection, ( aged 7,915 of total a included 1 Stage respectively. years, 77.3 and years 71.6 were disease mean The Alzheimer’s with cases of at ascertainment (62.4%). age mean and onset at disease age female predominantly were cases disease Alzheimer’s (CERAD) Alzheimer’s Disease for Registry a Establish to Consortium the or (DSM-IV) ADRDA) (NINCDS- Association Disorders Related and Disease Alzheimer’s the and Stroke and Disorders Communicative and Neurological of Institute National ADNI and (ref. GERAD1 including: controls) 13,685 and cases (6,688 GWAS datasets disease Alzheimer’s four of meta-analysis a Sample ascertainment, diagnostic criteria and genotyping. O doi:10.1038/ng.803 Supplementary Table 2 Table Supplementary values from this meta-analysis were then combined with the publicly avail publicly the with combined then were meta-analysis this from values NLINE Stage 2 included 4,896 cases and 4,903 controls, which comprised individual in silico P values from the EADI1 study using Fisher’s combined probability test. test. probability Fisher’s using combined study EADI1 the from values CRI 1 1 3 . All individuals included in these analyses provided written consent consent written provided analyses in these included . individuals All 3 6 3 6 , DSM-IV or CERAD or DSM-IV ,

and and 7 1 MET , The Diagnostic and Statistical Manual of Mental Disorders IV IV Disorders Mental of Manual Statistical and Diagnostic The , replication (deCODE and GWASReimenschneider datasets) were criteria for either probable or definite Alzheimer’s disease. disease. Alzheimer’s definite or probable either for criteria 4 Supplementary Table 2 Supplementary . All Alzheimer’s disease cases were diagnosed according to to according diagnosed were cases disease Alzheimer’s All . CLU 4 BIN1 ≥ ) ) and Mayo2 samples and HO 0 er) cend otos 5.% eae ma ae at age mean female; (59.9% controls screened years) 60 and Supplementary Note Supplementary Supplementary Table 1 Supplementary SNPs to the most significant markers at each locus, as as locus, each at markers significant most the to SNPs DS ≥ PICALM 60 years) and screened for dementia (77.2%). Stage 3 Stage (77.2%). dementia for screened and years) 60 ). Full summary statistics were obtained from the the from obtained were statistics summary Full ). loci (1 SNP and 8 SNPs, respectively), as these 3 7 criteria for possible, probable or definite definite or probable possible, for criteria Both new genotyping data (GERAD2) (GERAD2) data genotyping new Both ). in silico in . Clinical characteristics of all sam of all characteristics . Clinical in silico 3 ), EADI1 ), (ref. EADI1 P . = 4.2 × 10 × 4.2 = P

≤ replication in the deCODE deCODE the in replication 1 × 10 × 1 replication in the CHARGE 3 . We restricted genotyp We . restricted −3 −5 4 . For the three new new three the For . . In selecting SNPs selecting In . ), TGEN1 ), (ref. TGEN1 Stage 1 comprised APOE P

An inverse inverse An ≤ locus (26 (26 locus 1 × 10 × 1 1 3 −5 - - - - - )

Table 5b Table of Inclusion of framework. a regression within allele or presence logistic absence one least at of presence the for adjusting while disease Alzheimer’s P (rs3764650, diesase Alzheimer’s of onset at age these and loci between association for evidence no Wefound origin. of country for to allow analysis regression in logistic the were included Covariates assumed. was model an and additive analysis, regression a in linear variable dependent age at Towith onset. tionships as the was used age end, at years) this (in onset analyses. Secondary in shown are in shown is SNP I Cochran’s a stages, all at meta-analyses For trols). sample of (total up and con to cases meta-analysis 39,846 19,870 effects fixed deCODE, AD-IG, Mayo2 and CHARGE) using an inverse-variance–weighted TGEN, ADNI, EAD2, and EAD1 GERAD2, and (GERAD1 datasets all from of tests, three for accounting significance, for threshold adjusted Bonferroni a employing controls), 21,258 and cases 8,286 to up fixed of sample (total meta-analysis effects inverse-variance–weighted an in combined were studies EADI2 and CHARGE and Mayo2 EADI2, the from variances) and ORs (including data SNPs that showed evidence for association in stage 2 ( 38. 37. 36. 2). or 1 0, SNP: at each alleles minor of number the as (coded genotypes SNP on level expression normalized of sion papers in original the as described publications original the in presented as used were data Genotype BeadChips. Expression HumanRef-8 Illumina using performed was analysis Expression (Illumina). subject. Genotyping was performed using Infinium HumanHap550 BeadChips each for cortices) temporal and frontal and pons, (cerebellum, regions brain of European subjects ancestry. Frozen samples were from tissue four obtained dataset eQTL second The BeadChip. Illumina’s using whole genome commercial performed expression array, Human-6the Sentrix Expression was analysis Expression individuals. HapMap CEU European unrelated 60 from generated lines cell lymphoblastoid from leagues col and by Stranger published first, The datasets. eQTL two within analyzed analysis. (eQTL) loci trait quantitative Expression in presented are test 1-degree-of-freedom term, interaction the represents that and components); principal and origin of Y respectively; B and A at SNPs alleles minor of number the representing ables where ι term SNP interaction × SNP a SNP, and each of effects main covariates, for terms including BIN1 in SNPs significant genome-wide of combinations Y 2 = and 0.38; rs610932, 1 was calculated to assess heterogeneity. The total sample size tested for each tested size sample total The heterogeneity. to assess calculated was 6 to to Finally, we combined full summary data (including ORs and variances) variances) and ORs (including data summary full combined we Finally, ln( APOE

+ + Myers,A.J. S.S. Mirra, McKhann, G. 1494–1499 (2007). 1494–1499 disease. (CERAD). Part II. Standardization of the neuropathologic assessment of Alzheimer’s Human and Health of Department of Disease. Alzheimer’s on auspices TaskForce Services the under Group Work ADRDA κ , , are regression coefficients. We are coefficient the regression coefficients. regression whether tested Y P κ CR1 P /(1 − − /(1 6 X 1 is the probability of having the disease; correspond to the covariates included in the main analysis (country (country analysis main the in included covariates the to correspond 7 A

, consists of profiles generated using RNA extracted RNA using extracted generated profiles of , consists gene expression ). Finally, we tested for genetic interactions between all pairwise pairwise all between interactions genetic for tested we Finally, ). ε X , , 4 as a covariate had little effect on the results ( results the on effect little had covariate a as 4 Neurology B ABCA7 17,18,38 Supplementary Table 8 Supplementary etal. P P t al. et )) = = )) = 0.0167. = et al. Supplementary Table 7 Supplementary Asurvey of genetic human cortical gene expression. . . The expression data were and normalized log transformed h Cnotu t Etbih Rgsr fr lhie’ Disease Alzheimer’s for Registry a Establish to Consortium The and and

Clinical diagnosis of Alzheimer’s disease: report of the NINCDS- α 41 We tested the genome-wide significant SNPs for rela for SNPs significant genome-wide the Wetested + + P , 479–486 (1991). 479–486 , MS4A = We0.95). tested the also SNPs with for association β X A + + . Logistic regression analyses were performed performed were analyses regression Logistic . γ 17,18,38 X B + + . 1 κ α 8 , equals zero or not. not. or zero equals , analyzed 143 neurologically normal normal neurologically 143 analyzed is a constant; and and constant; a is . eQTLs were tested by linear regres by linear were . tested eQTLs δ . Summary statistics for all datasets datasets all for statistics Summary . Y Supplementary Table 5a Supplementary Neurology 1 + + X ε A Y and Q 2 Expression profiles were profiles Expression + + P test was performed and and performed was test

34 APOE < 4.2 × 10 X ζ , 939–944 (1984). 939–944 , B Nature Ge Nature Y correspond to vari P 3 β = 0.17; rs670139, rs670139, 0.17; = + + , , , , P Supplementary Supplementary CLU γ values for this this for values , , η Nat.Genet. δ −3 Y , , ), ), summary , , ε 4 + + , , PICALM APOE . ζ n , , θ etics η Y , ,

5 θ 39

+ ε , , 4 - - - - - ι , ,