Supplementary Table 1: GWE Studies in AD

Supplementary Table 1: GWE studies in AD

Reference / Age (yrs) [mean ± S.D and/or range] / Postmortem Interval (PMI) (hrs) / Featured Differentially Expressed Genes / Validation Method / Genes/Proteins Validated
AD / Control / AD / Control / Up−regulated genes / Down−regulated genes
Miller et al., 2013 [231] / 77.3 ± 9.1 / 81.7 ± 6.9 / 11.2 ± 6.3 / 10.8 ± 6.8 / NRIP3, ABHD12, TMEM158, TSPAN18, TOMM34, CCDC109A, HOMER2, CPNE4, LINGO1, HMGCR, S100A6, GEM, PFKFB3, SERPINA3, TPST1, SPARC, CAB39L, RCN1, DMN, BCL2 / SPARCL1, CYP1B1, PPP1R16B, KCNH3, EPHB1, STOX1, MT1M, ID2, SOX2, GPAM, SEPT5, CSPG5, WFDC1, KCNIP1, CXCL14, ANKRD20A1, SEC14L5, LOC648639, ARPP-21, ADRA1B / qPCR, ISH / SPARCL1, NRIP3, ABHD12, TSPAN18, CXCL14, SEC14L5, S100A6, GEM
Bossers et al., 2010 [260] / 82.3 ± 4.9 (BS4) 74.3 ± 6.5 (BS5) 70.3 ± 7.8 (BS6) / 70.6 ± 9.6 (BS0) 80.3 ± 5.6 (BS1) 76.7 ± 7.8 (BS2) 85.0 ± 6.4 (BS3) / 5.0 ± 1.6 (BS4) 5.4 ± 1.2 (BS5) 4.8 ± 0.9 (BS6) / 6.8 ± 1.4 (BS0) 5.9 ± 0.9 (BS1) 7.3 ± 1.6 (BS2) 6.2 ± 2.6 (BS3) / POGK, TLE4, MRGPRF, KIAA1737, GTF3C5, PPP1R1A, SIRT1, PHYHIPL, KEAP1, CENTD2, STARD10, CP110, STARD7, TAF4, MRAS, MTSS1, LRRC1, MID1IP1, CAPS, CASC3, ZC3H11A, EFHD1, CAB39l, POGK, HNRPH3, IGFBP5, LEAP−2, FZD7, DVL2, RAF1, CSRP1, HSPA2, OR7A5, RPRM / SCG3, SPON2, CRYBA2, PCSK1, IMP4, MRPS25, NDUFA7, PCIA1, BOLA3, MGC4172, RASGRF1 / qPCR, IB, IHC / PSEN2, ZNT3, RER1
Avramopoulos et al., 2010 [248] / − / − / − / − / REPIN1, GLTP, ARHGEF10, COBL, ZFYVE26, RERE, M6PRBP1, ZNFX1, NYREN18, FKBP5, HS1BP3, HYPB, SGK, ID3, STAT5B, MGST2, HBP1, VAMP3, PBX3, SUPT6H, AKT1, CRKL, DLST, IL13RA1, TPST2, DDR1, SLTM, PPFIA1, ZNF319, IGF2R, PARP9, IFI16, TMEM43, SOX10, LLGL1, DDX23, CRK, RHOU, SLC44A1, RAP80, ZNF395, UNC84B, BFAR, DDIT4, LSS, FAM54B, PCF11, AGPAT3, ANKRD40, KLF15, TCFL5, PDK4, ZNF398, OBFC2B, DIP2B, CASC3, ZNF22, YIPF6, BAZ2B, ZNF664, CYP27A1, ESRRA, EP300, GNG7, BCAR3, RAB7L1, ZFAND3, AIP, HSP90AA1, RAB6IP1, LHFPL2, DVL3, LASP1, TFIP11, MVP, ZCCHC3, ARIH2, SNX27, FGR, CHST3, GLE1L, ZMPSTE24, GIMAP4, INPPL1, KLK6, TM4SF11 / RAB3C, CACNB1, EPPB9, WNT10B, CACNB1, RBM9, PYDC1, BAIAP2L2, LY6H, PRPF18, SLBP, IMMP2L, CRH, BYSL, WIF1, CRHBP, STX1A, GLRA2, B3GNT4, WDR69, LMTK2, HES4, TYRP1, KLK7, RPP40, UROS, SLC1A6, KCTD16, MAP1LC3A, KDELR3, GPI, PDE1A, ZDHHC23, BSCL2, DPYSL4, ATP5G3, HRAS, GYPE, NALP2, YWHAB, KCNC2, CLYBL, MAP6, KCNK1, RSPO3, COL22A1, NPTXR, LRRC7, KCNMA1, CPNE5, NTSR1, MT, RPS7, SIDT1, GABARAPL1, M6PR, EID−3, WDR50, SLC30A3, PRKCE, PHF14, RHBDD2, POLR3F, R3HDM2, PEX13, SLC22A18, CGI−96, BZRAP1, FBLN2, RP1−32F7.2, GPRASP1, ABC1, LCMT1, ADAMTS3, EDF1, RASGRF1, CHCHD6, FARP2, GNG4, UBQLN1 / qPCR / VGF, RBP4, ADCYAP1 (FDR<0.05) SOX10, NPTXR, VMD2, SP1, BDNF (FDR 0.2)
Tan et al., 2010 [243] / 79.9 ± 1.8 / 80.1 ± 2.5 / 45.9 ± 11 / 43.2 ± 6 / AQP1, CSDA, SLC7A2, ITPKB, ANKRD49, HSPB1, MT2A, TIGD3, KIF1C, MID1IP1, MLLT7, ANKRD40, RASL12, SASH1, SAMD4A, RANBP3L, SH3PXD2B, PARD3, CD44, TRIP10, ADAM12, BACE2, GSN, HTR1B, IL1R1, NFKB2, TGFB1, GNA12, MAPK4, HSPB1, HSPB2 / GOLGA8B, RPH3A, PVALB, NRN1, GOLGA8A, PCSK1, NEUROD6, GPRASP2, MDH1, RBM3, MCHR2, GAD2, EXTL2, GAD1, CHGB, TAF9, SMYD2, GOT2, NAP1L5, NPTX2, APLP2, APPBP1, DRD1IP, GRIK1, GRIK4, HTR2A, HTR3B, CAMK2G, CSNK2A1, GSK3B, PLCB1, PPP2R1B, PRKCD, PRKCE, PRKCZ, PTPN5, RGS4, HSPB3, BDNF, GFRA2, SNAP25, STX12, SYT11, SYT12, VAMP1 / IB / AKT3, CAMKII, GAD65, GSK3B, PP2AC, AQP1

Supplementary Table 1 (Continued)

Reference / Age (yrs) [mean ± S.D and/or range] / Postmortem Interval (PMI) (hrs) / Featured Differentially Expressed Genes / Validation Method / Genes/Proteins Validated
AD / Control / AD / Control / Up−regulated genes / Down−regulated genes
Liang et al., 2010 [232] / 79.9 ± 6.9 (AD) 86.6 ± 5.3 (NDAD) / 79.8 ± 9.1 / 2.5 mean / − / RPS4X, TNIP2, MSRB3, NOTCH2, SOX6, SOX8, ZFP36L1, RPS6KA2, FLJ20097, ACYP2, CSDE1, FBXW2, DC12, B3GALT2, VPS54, LYRM2 (FLJ22222), CCDC25, UBE2I, ANKH, THUMPD2, ZFAND2A, SPIRE1, SEC22L1, PANK4, HINT1, DJ122O8.2, NSDHL, ATP5L, SOX9, VIL2, ANGPT1, CASR, GPR30, MARK1, TTBK2, APP, STX6, ABI2, EFNB2, GRM7, LAMB1, PRKACB, VDAC3, SYN3 / CTSD, ACOT8, KIAA1688, AURKAIP1, TM6SF1, TUBB2, SLC25A6, MRAP, UBR1, NRXN1, ENOSF1, GPHN, HGF, GAS7, ADK, RPL7A, ADARB1, NAPA, DIO1, LMBR1, DHX15, KLF6, SNX5, TPI1, STOML1, CCS, MAGED4, HADH2, CTNNBIP1, MFN2, DHX38, GNPAT, CAPNS1, MGC3040, EIF2S1, RBM8A, FAM11A, RPS27A, ALKBH5 (FLJ20308), MAPT, MARK3, MARK4, CDK5, PINK1, BACE1, PSEN1, PSEN2, STX1A, STX3A, STX1B2, STX8, SYN1, SYNGR1, SYNGR3, SYT1, SYT3, SYT5, SYT12, SYT13, VAMP3, APOE, CHST10, CTNND2, EGR1, FYN, GM2A, MAPT, PRKCB1, PTN, S100B, SHC3, SNAP25, STX10, STX16, STX17, SYN2, SYT6, SYT11, SYT17, VAMP1, VAMP3, VAMP4 / qPCR / MAP1B, GRIA1, GRIA3, APOE, APP, BACE1, COX5B, MAP4
Nunez−Iglesias et al., 2010[233] / 85(75-92) / 91.8(90-95) / 5.87(3.75-10.1) / SLC5A6, FLT1, LZTS2 / CREBL2, SELT, LIN7C, RAB10, TSPAN31, TMED2, PIK3C2A, C6orf62 / − / −
Ginsberg et al., 2010 [261] / 86.7 ± 7.7 (AD) 86.2 ± 5.2 (MCI) 80-101 (AD) 80-97 (MCI) / 82.1 ± 7.9
67-92 / 7.3 ± 4.1 (AD) 6.7 ± 4.2 (MCI) / 8.3 ± 8.7 / RAB4,RAB5,RAB7,RAB24, CTSD, EEA1, P44, DNCLC1 / RAB3, CAST, NPC1, VPP1, TRKB, TRKC, TRKA / RT-PCR, IB, IHC, RNA silencing / RAB and TRK Proteins
Katsel et al., 2009 [240] / 76.8 ± 8.4 (MD 86-) 80.8 ± 7.1 (SD 86-) 90.8 ± 3.9 (MD 87+) 92.9 ± 4.8 (SD 87+) / 75.2 ± 8.6 (CNT 86-) 94.2 ± 4.6 (CNT 87+) / 4 ± 1.2 (MD 86-) 5.31 ± 5.26 (SD 86-) 5.45 ± 5.28 (MD 87+) 3.55 ± 1.40 (SD 87+) / 8.68 ± 6.18 (CNT 86-) 4.03 ± 1.53 (CNT 87+) / HIPK2, MCTP1, RUFY2 / HLA−DPA1, TYROBP, C3, HLA−DRB1,3, , GPNMB, C1QC, CD74, C4A, C4B, HLA−B, HLA−DRB11, HLA−A, LY96, LGALS1, RARRES3, HLA−F, SERPING1, CCR1, FCER1G, HLA−G, HLA−E, PSMB9, LGALS3BP, PSME2, IFI44, IFITM1, SERPINA3, TNFSF13B, ISGF3G, DTNA, HAMP, SPP1, VEGF, MX1 / qPCR IB / CD74, HLA-DPA1, C3, LY96/MD-2, CX3CR1, TYROBP/ DAP-12, C1QC, ITGB2, CX3CR1, HLA−DPA1, CD74
Bronner et al., 2009 [234] / 72-82 / 72-82 / 3.5-5.3 / 4.3-7.7 / FOXC1, ZNF500, ZNF703, SASH1 / NT5E, SLC1A2, BZRAP1, MOXD1, ZNF589, LOC200383 / qPCR / MOXD1, ZNF589, FOXC1, SASH1, ACAD2, SEPT2, PNPLA2, TNPO1, CBL, GOLPH4, NRD1, PARD3, PTEN, NPIP, BTBD14A, CENTB5
Williams et al., 2009 [262] / − / − / − / − / CHRM3, GRIA2, NRGN, SLC1A2, HOMER1, EPHA4, HTR2A, THY1, NRXN1, GPR51, CAMK2B, RAB14, APOE, SV2A, GAP43, SCN1B, ARNT2, PRKCZ, LPPR4, PUM1 / − / qPCR, IB / GRIA2

Supplementary Table 1 (Continued)

Reference / Age (yrs) [mean ± S.D and/or range] / Postmortem Interval (PMI) (hrs) / Featured Differentially Expressed Genes / Validation Method / Genes/Proteins Validated
AD / Control / AD / Control / Up−regulated genes / Down−regulated genes
Qin et al., 2009 [253] / 69-98 / 59-102 / 0.7-1201 / 240-1665 / PC / GAPD, GPI, PFKM, PGK1, ACLY, CS, COX6C, MTATP6, PCK2, PDHA1, PDK3, PPARGC1A (PGC−1α), UCP2 / qPCR, IB / PPARGC1A (PGC−1α)
Liang et al., 2008 [235] / 79.9 ± 6.9 / 79.8 ± 9.1 / mean PMI 2.5hrs / mean PMI 2.5hrs / COX4I2, COX7B2, COX8C, NDUFB9, UQCR / ATP5A1, ATP5B, ATP5C1, ATP5D, ATP5F1, ATP5G1, ATP5G2, ATP5G3, ATP5H, ATP5I, ATP5J, ATP5J2, ATP5L, ATP5O, COX4I1, COX5A, COX5B, COX6A1, COX6A2, COX6B1, COX6C, COX7A2L, COX7B, COX7C, COX8A, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA13, NDUFA2, NDUFA3, NDUFA4, NDUFA5, NDUFA6, NDUFA7, NDUFA8, NDUFA9, NDUFAB1, NDUFAF1, NDUFB1, NDUFB10, NDUFB11, NDUFB2, NDUFB3, NDUFB4, NDUFB5, NDUFB6, NDUFB7, NDUFB8, NDUFC1, NDUFC2, NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS5, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, NDUFV3, SDHA, SDHB, SDHC, SDHD, CYC1, CYCS, UCRC, TIMM17B, TIMM22, TIMM23, TIMM44, TIMM50, TIMM8B, TIMM9, TOMM20, TOMM22, TOMM34, TOMM40, TOMM7, TOMM70A / IB / Mitochondrially
encoded ND6 subunit of Complex1, 30 kDa Fe-S subunit of complex II, core 2 subunit of complex III, COX2 of complex IV, F1-alpha sununit of ATP synthase (complex V)
Wilmot et al., 2008 [252] / 89.74 ± 4.33 / 93.03 ± 12.19 (BS 0/1)
90.85 ± 0.21 (BS 3/4)
93.57 ± 1.59 (BS 5/6) / − / − / ITSN1, NFKBIA, PDGFRB, ITGB5, PER1, GPR125, BCL2, CPT1B, ITGA10, PARD3, MXD4, ROCK1, ABCA1, HDAC7A, ATP8B1, DDR2, BAZ2B, PRKY, SH3BP2, FOXO1A, PLCE1, CDC14A, PRKX, YES1, TM4SF6 / ATP6V1G2, MFTC, PFKM, SGNE1, ATP5J, NDUFA5, SRD5A1, GNG3, ACTR1A, LGALS8, MAPBPIP, RGS7, DLGAP1, EIF2B3, CAMK1G, GAP43, PSMB2, TPI1, SNRPA1, CD200, MAPK9, PDHB, APEX1, TDE1, BEX1, IDH3B, CGI−51, TCEAL2, POLR2K, KCNJ3, ARPP−19, IDS, SYNJ1, ATP5C1, AP2M1, GOLT1B, FAM127B, ATP5J2, SNX10, IARS, ENSA, NIFUN, PCP4, SH3GLB2, GPI, ATP5L, CAPNS1, BSCL2, NELL1, SCG3, SYNCRIP, SLC25A6, POP7, CRI1, BNIP3, VARS2, CCNA1, ACSL3, CDC5L, UBE2N, DIRAS2, B4GALT6, MDH2, CUL2, ASAH1, PSMB3, NDUFA4, QP−C, FKBP1B, FBXL2, TUBB2, LDHA, ATP2B2, PSMD14, MRPS15, CACYBP, SCN2A2, RAD51C, RUSC1, KPNB1, RAB6A, NARS, NRXN1, GGCX, COX7A2, OSBPL10, CYCS, ATP5E, MTHFD1, TUBG2, SNCG, CBARA1, STXBP1, STAF65, NDUFB4, PIK4CA, UBE2G1, NEUROD6, UQCR, ARF3, MYT1L, SYNGR3, STMN2, NEF3, MRPS10, TRIM32, ANAPC13, VSNL1, TCTE1L, AF1Q, CDK5, GPR22, TTC1, TA−LRRP, TBCA, CAP1, TNFSF5IP1, INA, R3HDM, STXBP5L, PH−4, ELAVL4, PAM, ALDOC, RSU1, SUMO1, ATP6V1F / qPCR / ITSN1

Supplementary Table 1 (Continued)

Reference / Age (yrs) [mean ± S.D and/or range] / Postmortem Interval (PMI) (hrs) / Featured Differentially Expressed Genes / Validation Method / Genes/Proteins Validated
AD / Control / AD / Control / Up−regulated genes / Down−regulated genes
Katsel et al., 2007 [241] / 83.4 ± 2.4 (CDR 0.5) 85.2 ± 2.2 (CDR 1) 88.1 ± 1.2 (CDR 2) 90.2 ± 1.4 (CDR 3) 85.4 ± 1.6 (CDR 4-5) / 83.6 ± 2.5 (CDR 0) / 4.8 ± 0.7 (CDR 0.5)
5.8 ± 1.4 (CDR 1)
5.3 ± 1.0 (CDR 2)
4.1 ± 0.5 (CDR 3)
4.6 ± 0.8 (CDR 4-5) / 7.9 ± 1.4 (CDR 0) / PPAP2B, SGPL1, LASS1, UGT8, LASS2, SPTLC2, TMEM23, PPAP2A, GALC, SMPD1, NSMAF / UGCGL2, CERK, ASAH1, UGCG, LASS6, PTDSS1, B4GALT6 / − / −
Grünblatt et al., 2007 [242] / 70.3 ± 3.3 / 69.0 ± 1.8 / 2.0 ± 0.6 / 2.1 ± 0.6 / IDE, IGF1R, SYN2, SYT5, STXBP3, OR2W3, CNR2, H1ST1H4E, APBA3, VPS26, VPS25, VPS41, SYT4,SNX2 / GPX5, GSTM1, SOD2, ALDH1L2, TFRC, FTH1, TF, CYP2E1, IRS4, SYN1, PALM, COG2, CHRNA6, GFAP, HTR4, APP, BACE1, SNX7, CHK, CHPT1, VPS35, SYT4, SNX2 / q RT-PCR / SYT1, SYT4, SYN2, COG2, VPS35, VPS41, OR10H3, CHRNA6, H5HT4b, CNR2, APP, SNX2, APBA3, BACE1, IDE, IGF1R, IRS4, TF, FTH1, GSTM1, GFAP, H1ST1H3E
Weeraratna et al., 2007 [244] / 73–95 / 74–91 / <3 / CCL27, CCR3, CCR5, CXCR2, CXCR4, IL28A, YEATS2, ZZZ3, KNTC2, LRP3, AGA, WBSCR22, RNF141, SCIN, ADRA2B, APOF, MNX1, MYO6, ZNF740, VTA1, SCD, HLA−DQB1, FXR1,NDFIP1, AQP1 / SENP3, ECE2, PEX6, CUEDC2, MANEA, RSC1A1, PASK, TLE1, LGALS2, RPL36, NCOR2, ZNF295, RGPD2, CHD2, CDH2, TBL2, NUFIP1, GRIK2, TSC2, GUK1, CHAF1B, WASF3 / qPCR, IHC / AQP1, LRP3, SENP3, ECE2, CCR3, CXCR4
Brooks et al., 2007 [251] / 60-83 / 48-89 / (4-21) / (7-21) / − / GAPD, GPI, LDHA, ACLY, FH, MDH1, MDH2, SUCLA2, ATP5B, COX4I1, COX6A1, NDUFS4, UQCRC2, SLC25A14, GOT1 / qPCR / GAPD, GOT1, LDHA, OXCT, UQCRC2, PDK3, MDH1
Cui et al., 2007 [246] / 69.0±1.8 Moderate 70.3±3.3 Late / 70.8±4.2 / 2.5±0.6 Moderate 2.6±0.5 Late / 2.2±0.4 / DAXX, APP, COX2, IL-1B, cPLA2, FAS / − / IB / DAXX, APP, COX2, cPLA2

Supplementary Table 1 (Continued)

Reference / Age (yrs) [mean ± S.D and/or range] / Postmortem Interval (PMI) (hrs) / Featured Differentially Expressed Genes / Validation Method / Genes/Proteins Validated
AD / Control / AD / Control / Up−regulated genes / Down−regulated genes / AD / Control
Parachikova et al., 2007 [254] / 85.3 ± 5.1
77-93 / 83.7 ± 8.1 70-95 / 2.55 ± 0.93 / 2.86±0.90 / IL15RA, PPBP, LCP1, FCGR3B, FCGR1A, FCGBP, IFI16, HLA−DQB1, LY96, TLR2, ICAM2, CX3CR1, OLR1, HLA−A, IFITM1, CD74, TGFBR2, FCGR3B, CD14, CD53, ICAM2, ITGAM, IL10RB, CD37, TGFB1, HLA−DPB1, IL1RN, CCR2, HLA−C, NFKBIA, HLA−DRB3, CCL2, CD59, HLA−E, HLA−F, CD59, HLA−G, IFI30, HLA−DPA1, HLA−DQB1, BLNK, HLA−DOA / − / IHC, IB, Dot Blot / MHC II proteins
Emilsson et al., 2006 [245] / 49-97 / 41-72 / 33 (4-103) / 45 (8-96) / ITPKB, SLC1A3, AQP1, THG1, RPS27, CDK8, IFITM3, ATP1A2, MT1G, IFITM1, KRTHB6, S100B, GRSF1, C4A, PRKACB, VIM, BST2, BOK, CDC14B, C1QG / RGS4, CAP2, RAB3A, NELL2, PARG1, RNAHP, PRKCZ, PAK1, TPI1, SULT4A1, HBACH, ENO2, GABRD, CRYM, STMN1, ENC1, SYNGR3, RTN1, OLFM1, BASP1, COTL1, MDH1, AOC2, PTPRN, NSF, STX1A, NP25, DKFZp547D, KIAA1045, KIAA0750, HSA243396, C1orf15, KIAA1183 / RT-PCR / GABRD, STX1A, STMN1, SYNGR3, PRKCZ, ATP1A2, PRKACB
Dunckley et al., 2006 [250] / 84.7 ± 7.5 / 80.1 ± 7.9 / − / − / APOJ, CSNK2B, TIMP3, IRAK1, CD44, RAP2A, ICAM2, ITGA7, HLA−DRB3, SLC6A12, RPS6, ITSN1, HMGA2, H2AFJ, TCEA3, RPL13A, CRISPLD2, STAB1, IL13RA1, RPS2, APOE, ADD3, SLC21A9, ATP6V0D2, IFI27, RPS6, HDAC7A, HIPK2, SEPT8, EPAS1, DERP6, CXCL32, PRKCN, YAP1, PECAM1, LAPTM5, KCTD2, BZRP, RAB31, IL12B, FAM38A, FBXO32, MRVI1, HIGD1B, SLC21A3, ARH, M54A7, TU3A, ADAMTS1, LIM, ITGB5, TAZ, CHST6, SP100, VWF / CAPN7, PAK7, LNX, ACHE, WSX1, EGR4, SLC17A6, RNF123, ATP9B, KCNG1, SUHW2, PAIP1, ZNF546, NRCAM, CHD5, FAT3, CDKL1, RICS, PAK1, RANBP3, LRP3, BRUNOL5, NPTXR, PAK7, GRAMD4, CAMK2D, PBX4, HOMER1, SLC39A4, GAP43, SCN3B, MBNL2, ATP6V1H, CACNA1A, SCN3A, CACNG2, PAM, THY1, OLFM3, ARPC4, NBEAL1, ATF6, P2RX5, GPR24, ELAVL4, SEZ6, RGS7, NHLH1 / IHC / APOJ, CSNK2B, TIMP3, IRAK1, CD44, RAP2A, CAPN7, PAK7
Small et al., 2005 [263] / 33-98 / 33-98 / − / − / − / VPS35 / qPCR, IHC, IB / VPS35, VPS26
Ricciarelli et al., 2004 [258] / 85.0 ± 7.0 / 74.0 ± 10 / − / − / ACTB, EIF5A, GLS, IFITM3, ACTR1A, FAIM2, TUBB, GAP43 / RPL21, PPP1R8, ALOX15B, ACTA2, PLEKHA1, FXYD6, FOXN1, SGCB, ZBTB24, RPS24, RPL41, JAK3, TDGF1P3, S100, CECR2 / RT-PCR / ACTB, CES, IFTM3, S24, S100, ZF450
Blalock et al., 2004 [249] / 90.0 ± 2.1 (Incipient) 83.4 ± 1.1 (Moderate) 84.0 ± 4.0 (Severe) / 85.3 ± 2.7 / 3.3 ± 0.6 (Incipient) 3.2 ± 0.2 (Moderate) 3.0 ± 0.1 (Severe) / 2.6 ± 0.2 / IFNA5, IFNG, IL10RA, IL10RB, IL13RA1, IL17R, IL18, IL2RG, IL6R, CAST, DAPK2, EP300, S100A4, AIM1, CDK2AP1, FZR1, GSK3B, SFRP1, TGFBR3 / ACAD8, ALDH2, COX7A2L, COX7C, HADH, NDUFB3, PDHA1, PDHX, SDHA, SLC25A6, AHSA1, CCT2, CCT3, CCT4, CCT5, DNAJA1, HSP90AB1, HSP90AA2,HSP90AA1, PDIA6 / − / −

Supplementary Table 1 (Continued)

Reference / Age (yrs) [mean ± S.D and/or range] / Postmortem Interval (PMI) (hrs) / Featured Differentially Expressed Genes / Validation Method / Genes/Proteins Validated
AD / Control / AD / Control / Up−regulated genes / Down−regulated genes / AD / Control
Walker et al., 2004 [264] / − / − / (4-8) / (4-8) / DTNA, B2M, APLP1, C4B, LIMS2, IGHM, ATF4, RANGAP, GSTM2, TU3A, ADD3, FTL, HBB, CLU, HBG2, AGT, PLP1, PRDX1, PTS, HBG1, PCSK1N, RPL31, MT1G, CHN2, FTL, OSBPL3, EEF1A1, HLA−B, RAP1GDS1, CD81, CDC10, TSPAN−3, NEDD5 / GRP58, DMPK, PCL1, PLEKHB1 / − / −
Yao et al., 2003 [265] / 72-90 / 57-91 / 4.25-16.5 / 4-18.5 / − / DNM1, STX1A, SYT1, AMPH, AP3µ3B / qRT-PCR, IB, IHC / DNM1
Colangelo et al., 2002 [247] / 70.3 ± 3.3 67-76 / 69.0 ± 1.8 66-71 / 2.0 ± 0.6 / 2.1 ± 0.6 / APP, B94, CEX1, DPP1, HB15, HUMJE, IFNIND, IL1A, IL1B, NFIL6, PLA2G4A, PTGS2, CDP5, DAXX, FAS, HER2B, cPLA2, NF-kBp100, KIAA1088, NF-kBp52 / NFKBIA, RELB, CHAT, CSPG5, NFL, SLIT2, SYN1, SYP, ADAM9, BDNF, P2XR, HSP27, MDC9, NCP, ISGF, GATA-2, LYL-1, 1RELA, GATA-4, MAD3A, PCAF65B, MTF-1, MET3 / − / na
Loring et al., 2001 [256] / 79-87 / 47-85 / <24 / Apr-23 / C3, HLA−DRB5, CD74, CD99, AHNAK, PPAP2C, RGS5 / COX4I1, TPI1, TPIP1, LMO4, NDUFS5, LOC100130794, LOC652797, PKM2, ENO3, UQCRC2, OXCT1, SLC25A4, CHL1, COPS8, ENSA, FKBP52, GSK3A, ITPR1, MAPK10, MAP2K1, MAP3K6, NOMO3, NOMO1, NPTN, NR4A1, PGRMC1, PIP4K2B, PPP2CA, PRKACG, PRKCZ, PTK2, RAN, RCAN2, RUNDC3A, SIRPA, YWHAB / − / nc
Hata et al., 2001 [259] / 71-86 / 81-91 / 1.0-3.0 / 2.0-2.5 / PPP3CB, RANBP1, GNA11, CSN1S1, MS4A2/ FCER1A/ FCER1G, S100A4, ART3, FGL2, CLCNKB, ACSL4, RPS15, GBP2, RPS27, PHKG2, AVPR1A, PSMB7, EFEMP1 / HMMR, LAMB1, POU2F1, MYH8, TM4SF5, ADORA2B, COL11A1, PDCD11, TGM4, PCK2, TBC1D10A, LCK, TNFRSF8, DPYS, EGR2, COL10A1, CD36, CAV2, DEFA1, AKAP8 / RT PCR, ISH-HC / PPP3CB
Ho et al., 2001 [266] / 73-94 / 73-89 / 2.5-22.7 / 3.4-49.3 / − / SYN2 / IB / SYN2
Ginsberg et al., 2000 [255] / 77.2 ± 3.3 / 73.2 ± 4.4 / 10.6 ± 2.2 / 10.8 ± 3.0 / CTSD / ARC, SLC6A3, DRD1, DRD2, DRD3, DRD4, DRD5, GRIA1, GRIA2, GRIN2B, SYN1, SYP, SNCA, SNCB, SYTx, NF−L, NF−M, NF−H, TUBB, ERK1, ERK2, FAK, GSK3B, NOS2, PPP1CA, PPP1CC, PPP2R1A, PPP2CA / ISH-HC / −

HIP: Hippocampus; PFC: prefrontal cortex; MFG: medial frontal gyrus; STL (BA 22): superior temporal lobe (Brodman area 22); LCM: laser capture microdissected; EC: entorhinal cortex, MTG: middle temporal gyrus; PC: posterior cingulate cortex; SFG: superior frontal gyrus; VCX: primary visual cortex; FC: Frontal cortex; PC: Parietal cortex; TC: Temporal cortex; OC: Occipital cortex; IPL: inferior parietal lobe; DG: dentate gyrus; AMY: amygdale; CC: cingulate cortex; CDR: clinical dementia rating; MMSE: mini–mental state examination

Table S2: Distribution of characteristic features among GWE studies

Reference / Brain region / Diagnostic criteria / Braak stage / Samples / Age range (yrs) / Postmortem Interval (PMI) (hrs) / Dataset - MIAME compliant / Score
AD / Control / AD [M/F] / Control [M/F] / AD / Control / AD / Control
Miller et al., 2013 [231] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / 7
Bossers et al., 2010 [260] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / 6
Avramopoulos et al., 2010 [248] / ✓ / ✓ / ✓ / − / ✓ / ✓ / − / − / − / − / − / 4
Tan et al., 2010 [243] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / 6
Liang et al., 2010 [232] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / ✓ / 7
Nunez−Iglesias et al., 2010 [233] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / 7
Ginsberg et al., 2010 [261] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / 6
Katsel et al., 2009 [240] / ✓ / ✓ / − / − / − / − / ✓ / ✓ / ✓ / ✓ / − / 4
Bronner et al., 2009 [234] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / 7
Williams et al., 2009 [262] / ✓ / ✓ / ✓ / − / ✓ / ✓ / − / − / − / − / ✓ / 5
Qin et al., 2009 [253] / ✓ / ✓ / − / − / − / − / ✓ / ✓ / ✓ / ✓ / − / 4
Liang et al., 2008 [235] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / 7
Wilmot et al., 2008 [252] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / − / − / 5
Katsel et al., 2007 [241] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / 6
Grünblatt et al., 2007 [242] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / 6
Weeraratna et al., 2007 [244] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / 6
Brooks et al., 2007 [251] / ✓ / ✓ / − / − / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / 5
Cui et al., 2007 [246]
Parachikova et al., 2007 [254] / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / ✓ / − / 6

Table S2 (Continued)

Supplementary Table 3: GWAS studies in AD

Reference / Gene symbol / SNP / Non-APOE hits / APOE-related hits / SNP / APOE-related hits
P value / Odds ratio / Gene symbol / P value / Odds ratio
Nelson et al., 2014 [301] / BMPER
SLC8A1-AS1 / rs17169634
rs75847378 / 1.2 × 10-7
7.1 × 10-7 / - / TOMM40 / rs2075650 / 4.2 × 10-13 / -
Perez-Palma
et al., 2014 [302] / KRT19P2 - NDUFA12
PGBD3P2 - HPRTP2
MS4A3
FANCD/ FANCD2OS / rs249153
rs13178362
rs474951
rs528823
rs1552244
rs9849434 / 4.4 × 10-7
6.6 × 10-7
1.3 × 10-6
1.6 × 10-6
1.6 × 10-6
1.9 × 10-6 / 1.41
0.75
0.79
0.79
0.76
0.71 / TOMM40 / rs2075650 / 8.5 × 10-116 / 4.48
Cruchaga et al., 2013 [303] / GEMC1 – OSTN
GLIS3
TREM gene cluster / rs9877502
rs514716
rs6922617 / 4.9 × 10⁻⁹ ( CSF tau)
1.07 × 10⁻⁸ (CSF tau)
3.2 × 10⁻⁹ (CSF p-tau)
3.6 × 10⁻⁸ (CSF p-tau) / - / APOE / rs769449 / 2.6 × 10-18
(p-tau)
2.0 × 10-16
(tau) / -
Lambert et al., 2013 [290] / CR1
BIN1
CD2AP
EPHA1
CLU
MS4A6A
PICALM
ABCA7
CD33
HLA-DRB5/HLA-DRB1
PTK2B
SORL1
SLC24A4-RIN3
DSG2
INPP5D
MEF2C
NME8
ZCWPW1
CELF1
FERMT2
CASS4 / rs6656401
rs6733839
rs10948363
rs11771145
rs9331896
rs983392
rs10792832
rs4147929
rs3865444
rs9271192
rs28834970
rs11218343
rs10498633
rs8093731
rs35349669
rs190982
rs2718058
rs1476679
rs10838725
rs17125944
rs7274581 / 5.7 × 10−24
6.9 × 10−44
5.2 × 10−11
1.1 × 10−13
2.8 × 10−25
6.1 × 10−16
9.3 × 10−26
1.1 × 10−15
3.0 × 10−6
2.9 × 10−12
7.4 × 10−14
9.7 × 10−15
5.5 × 10−9
1.0 × 10−4
3.2 × 10−8
3.2 × 10−8
4.8 × 10−9
5.6 × 10−10
1.1 × 10−8
7.9 × 10−9
2.5 × 10−8 / 1.18
1.22
1.10
0.90
0.86
0.90
0.87
1.15
0.94
1.11
1.10
0.77
0.91
0.73
1.08
0.93
0.93
0.91
1.08
1.14
0.88 / APOE / - / < 5.0 × 10−8 / -

Supplementary Table 3 (Continued)

Reference / Gene symbol / SNP / Non-APOE hits / APOE-related hits / SNP / APOE-related hits
P value / Odds ratio / Gene symbol / P value / Odds ratio
Boada et al., 2013 [304] / ATP5H/KCTD2 / rs11870474 / 4.7 × 10-9 / 1.53 / - / - / - / -
Reitz et al., 2013[283] / ABCA7
HMHA1
GRIN3B
- / rs115550680
rs115553053
rs115882880
rs145848414 / 2.2× 10–9
3.1 × 10–8
6.3 × 10–8
6.9 × 10–8 / 1.79
1.86
1.55
2.29 / APOE / rs429358 / 5.5 × 10–47 / 2.31
Miyashita et al., 2013 [305] / SORL1 / rs11218343
rs3781834 / 2.2 × 10-9
9.9 × 10-9 / 0.81
0.78 / PVRL2 / rs519113 / 5.0 × 10-39 (Japanese) / 2.09
Kamboh et al., 2012[289] / BIN1
PICALM
PPP1R3B
MMP3/MMP12
—
FLJ37543
— / rs7561528
rs17817600
rs3748140
rs12808148
rs6856768
rs11738335
rs1357692 / 6.0 × 10-11
2.2 × 10-8
3.0 × 10-7
1.2 × 10-6
4.6 × 10-6
4.7 × 10-6
9.3 × 10-6 / 1.25
1.33
2.43
0.81
0.85
0.83
0.86 / APOE/
TOMM40/
APOC1 / rs4420638 / 7.9 x10–149 / 0.29
Cummings et al., 2012 [282] / MPZL1
-
-
-
-
ATXN7L1
ATXN7L1
-
-
LUZP2
CDON
-
PCNX
-
- / rs4145462
rs41458646
rs41476545
rs6738181
rs7638995
rs679974
rs11983798
rs6468852
rs9969729
rs12361953
rs472926
rs4937314
rs11848070
rs17767225
rs6085820 / 1.2 × 10-6
8.4 × 10-6
9.0 × 10-6
5.0 × 10-6
1.8 × 10-6
8.7 × 10-6
1.5 × 10-6
1.1 × 10-6
1.9 × 10-6
7.9 × 10-7
3.3 × 10-6
7.0 × 10-6
5.6 × 10-6
7.9 × 10-6
9.3 × 10-6 / -
-
-
-
-
-
-
-
-
-
-
-
-
-
- / - / - / - / -

Supplementary Table 3 (Continued)

Reference / Gene symbol / SNP / Non-APOE hits / APOE-related hits / SNP / APOE-related hits
P value / Odds ratio / Gene symbol / P value / Odds ratio
Logue et al., 2011 [306] / -
-
SLC4A1AP
-
POLN
CNTNAP2
-
-
-
-
STK24 / rs340849
rs11889338
rs17006206
rs2221154
rs1923775
rs10273775
rs956225
rs3888908
rs10850408
rs17511627
rs912330 / 7.5 × 10-6
8.9 × 10-6
2.3 × 10-6
2.6 × 10-6
5.6 × 10-6
8.9 × 10-6
8.7 × 10-6
9.5 × 10-6
9.3 × 10-7
5.0 × 10-6
3.8 × 10-6 / 0.59
1.55
2.05
0.57
1.60
1.52
0.30
1.72
0.63
1.75
0.54 / PVRL2 / rs6859 / 5.4 × 10-7 / 1.58
Lee et al. 2011 [280] / -
HPCAL1,ODC1
-
-
-
-
-
-
-
DGKB
-
-
-
GHITM, C10orf99, PCDH21, LRT2, LRT1, RGR -
-
-
-
-
-
-
-
- / rs7525939
rs4669573
rs10197851
rs1402752
rs11711889
rs919289
rs4895298
rs2973413
rs10271466
rs1117750
rs11786902
rs6477258
rs10758939
rs7908652
rs978769
rs978770
rs11213703
rs11617026
rs11630802
rs4843359
rs9945493
rs6135782
rs2403771 / 5.3 × 10−6
5.3 × 10−5
1.0 × 10−4
6.6 × 10−4
7.0 × 10−6
4.7 × 10−4
4.8 × 10−4
5.7 × 10−4
1.1 × 10−4
8.0 × 10−6
1.3 × 10−4
7.2 × 10−6
4.8 × 10−6
3.6 × 10−6
2.9 × 10−6
1.5 × 10−6
2.4 × 10−6
9.1 × 10−4
4.9 × 10−6
2.8 × 10−4
1.7 × 10−7
6.2 × 10−6
6.2 × 10−6 / 0.58
1.42
0.71
1.48
0.50
0.71
0.71
0.71
1.52
1.87
0.69
1.51
0.67
1.50
0.66
0.65
0.66
0.54
0.66
1.69
0.33
0.50
0.54 / - / - / - / -

Supplementary Table 3 (Continued)

Reference / Gene symbol / SNP / Non-APOE hits / APOE-related hits / SNP / APOE-related hits
P value / Odds ratio / Gene symbol / P value / Odds ratio
Antunez et al., 2011 [307] / MS4A
BIN1
PICALM
CLU / rs1562990
rs744373
rs536841
rs569214 / 4.4 × 10−11
2.1 × 10−9
3.0 × 10−9
4.1 × 10−8 / 0.88
1.18
0.86
0.88 / TOMM40 / rs157580 / 8.2 × 10-89 / 0.59
Wijsman et al., 2011 [281] / CELF2 (CUGBP2) / rs201119 / 1.5 × 10−8 / 4.02 / TOMM40 / rs2075650 / 3.2 × 10-81 / -
Hu et al., 2011 [279] / BIN1 / rs12989701
rs744373 / 1.3 ×10-10
3.2 × 10-10 / 1.19
1.23 / - / - / - / -
Hollingworth et al., 2011 [285] / ABCA7
CD2AP
CD33
EPHA1
MS4A4E
MS4A6A
ARID5B / rs3764650
rs9349407
rs3865444
rs11767557
rs670139
rs610932
rs2588969 / 5.0 × 10-21
8.6 × 10-9
1.6 × 10-9
6.0 × 10-10
1.1 × 10-10
1.2 × 10-16
3.6 × 10-1 / 1.23
1.11
0.91
0.90
1.08
0.91
0.99 / - / - / - / -
Naj et al., 2011 [287] / MS4A4A
EPHA1
CD2AP
CD33
BIN1
CLU
CR1
PICALM / rs4938933
rs11767557
rs9349407
rs3865444
rs7561528
rs1532278
rs6701713
rs561655 / 8.2 × 10-12
6.0 × 10-10
8.6 × 10-9
1.6 × 10-9
4.2 × 10-14
8.3 × 10-8
4.6 × 10-10
7.0 × 10-11 / 0.89
0.90
1.11
0.91
1.17
0.89
1.16
0.87 / - / - / - / -
Kim et al., 2010 [308] / CCDC134
EPC2 / rs7364180
rs2121433
rs4499362 / 1.0 × 10-6
(Aβ42)
1.0 × 10-6
(t-tau)
1.0 × 10-6
(t-tau/
Aβ42) / - / TOMM40
APOE
LOC100129500 / rs157580
rs2075650
rs429358
rs439401 / 1.0 × 10-6 (Aβ42)
1.0 × 10-6
(p-tau181p/Aβ42,
t-tau/Aβ42)
1.0 × 10-6
(Aβ42, p-tau181p,
p-tau181p/Aβ42,
t-tau/Aβ42)
1.0 × 10-6 (Aβ-42) / -

Supplementary Table 3 (Continued)

Reference / Gene symbol / SNP / Non-APOE hits / APOE-related hits / SNP / APOE-related hits
P value / Odds ratio / Gene symbol / P value / Odds ratio
Naj et al., 2010 [309] / MTHFD1L
Chr 2q13
Chr 2q13 / rs11754661
rs4676049
rs17034806 / 2 × 10-10
4.3 × 10-7
5.1 × 10-8 / 2.1
1.76
1.75 / TOMM40
PVRL2 / rs2075650
rs6859 / 5.0 × 10-36
9.6 × 10-8 / 2.94
1.41
Seshadri et al., 2010 [288] / CLU
PICALM
BIN1
EXOC3L2
EPHA1
LTBP2
PRSS7 / rs11136000
rs3851179
rs744373
rs597668
rs11771145
rs2043948
rs2825544 / 1.6 × 10-16
3.2 × 10-12
1.6 × 10-11
6.5 × 10-9
1.7 × 10-6
4.5 × 10-4
2.1 × 10-5 / 0.85
0.87
1.15
1.17
0.91
1.13
1.09 / TOMM40 / rs2075650 / 1.0 × 10-295 / 2.53
Potkin et al., 2009 [278] / ARSB
CAND1
EFNA5
EFNA5
EFNA5
MAGI2
PRUNE2
-
-
-
-
-
-
-
MAL2
RP11-232A1.1
ETS1
ARID2 - SFRS2IP
-
-
-
C20orf132
RPN2
ZBP1
FDPSP / rs337847
rs1082714
rs10074258
rs12654281
rs1265723
rs11525066
rs10781380
rs4845552
rs682748
rs7727656
rs6881634
rs9918508
rs2124799
rs10276619
rs1364705
rs10867752
rs6590322
rs1373549
rs9301535
rs4773460
rs11626056
rs8115854
rs6031882
rs2073145
rs1888414 / 6.7 × 10-6
4.9 × 10-6
2.2 × 10-7
3.7 × 10-7
8.9 × 10-6
2.9 × 10-6
7.1 × 10-7
6.2 × 10-6
8.1 × 10-6
8.3 × 10-6
1.9 × 10-6
8.5 × 10-6
8.5 × 10-6
2.9 × 10-6
8.9 × 10-6
3.1 × 10-6
9.4 × 10-6
7.8 × 10-6
7.9 × 10-6
1.9 × 10-6
1.2 × 10-6
2.1 × 10-6
6.2 × 10-6
2.1 × 10-6
2.4 × 10-7 / -
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- / TOMM40
APOE / rs2075650
rs11556505
rs157580
rs429358
rs7412 / 7.5 × 10-7
3.0 × 10-5
1.1 × 10-3
2.3 × 10-16
5.0 × 10-4 / -
-
-
-
-

Supplementary Table 3 (Continued)

Reference / Gene symbol / SNP / Non-APOE hits / APOE-related hits / SNP / APOE-related hits
P value / Odds ratio / Gene symbol / P value / Odds ratio
Heinzen et al., 2009 [310] / RFC3
TTLL7
PAX2
SASH1
RCAN2
Q0VG70_HUMAN
PRKG1
PDXDC2
SSBP3
Q0VG70 HUMAN
TTLL7
GSC
ZCCHC2
GHITM
NP_835466.1
DBC1
MN1 / rs690705
rs7539409
rs4509693
rs9390537
rs4530856
rs9659297
rs1915678
rs998109
rs6697414
rs11583706
rs10747407
rs10484049
rs11152349
rs11200713
rs4075205
rs1360806
rs2267106 / 6.3 × 10-7
1.2 × 10-6
6.3 × 10-6
8.2 × 10-6
1.3 × 10-5
1.4 × 10-5
1.4 × 10-5
1.6 × 10-5
2.2 × 10-5
2.4 × 10-5
3.0 × 10-5
3.0 × 10-5
3.2 × 10-5
3.6 × 10-5
3.7 × 10-5
4.0 × 10-5
4.1 × 10-5 / TOMM40 / rs2075650
rs157580 / 3.2 × 10-11
6.8 × 10-6
Lambert et al., 2009 [286] / CLU
CR1 / rs11136000
rs6656401 / 7.5 × 10-9
3.7 × 10-9 / 0.86
1.21 / APOE / 5.1 × 10-7 to
<2.0 × 10-16 / -
Harold et al., 2009[284] / CLU
PICALM / rs11136000
rs3851179 / 8.5 × 10-10
1.3 × 10-9 / 0.86
0.86 / TOMM40
TOMM40
PVRL2
TOMM40
APOE / rs2075650
rs157580
rs6859
rs8106922
rs405509 / 1.8 × 10-157
9.6 × 10-54
6.9 × 10-41
5.4 × 10-39
4.9 × 10-37 / 2.53
0.63
1.46
0.68
0.70
Carrasquillo et al., 2009 [277] / PCDH11X / rs5984894
rs2573905 / 2.2 × 10-7
1.6 × 10-7 / 1.3
1.3 / - / - / - / -
Feulner et al., 2009 [311] / - / - / - / - / TOMM40
APOE / rs157580
rs8106922 / < 1.0 × 10-40
<1.0 × 10-6 / -

Supplementary Table 3 (Continued)

Reference / Gene symbol / SNP / Non-APOE hits / APOE-related hits / SNP / APOE-related hits
P value / Odds ratio / Gene symbol / P value / Odds ratio
Poduslo et al., 2009 [276] / TRPC4AP / rs6087664
rs6088692
rs1885119
rs6120816
rs2065108
rs6088727
Haplotype / 5.6 × 10-11
5.6 × 10-11
5.6 × 10-11
7.0 × 10-11
3.9 × 10-10
3.9 × 10-10
0.03 / -
-
-
-
-
-
1.56 / - / - / - / -
Beecham et al., 2009 [275] / 12q13 (FAM113B) / rs11610206 / 3.5 × 10-7 / - / - / - / - / -
Betram et al., 2008 [274] / CD33
chr14q31.2 chr18p11.31
ATXN1 / rs3826656
rs11159647
rs2049161
rs179943 / 6.0 × 10-6
2.0 × 10-6
6.0 × 10-3
8.0 × 10-3 / 1.1 to 1.4 / APOC1 / rs4420638 / 5.7 × 10-14 / -
Abraham et al., 2008 [273] / LRAT / rs727153
rs201825 / 3.4 × 10-6
6.1 × 10-7 / 1.2
1.3 / TOMM40
APOE / rs8106922
rs405509 / 4.0 × 10-14
4.8 × 10-6 / -
Li et al., 2008 [272] / GOLM1 (GOLPH2)
chr9p24.3
chr15q21.2 / rs7019241
rs10868366
rs9886784
rs10519262 / 2.4 × 10-4 (Canadian);
1.2 × 10-3 (UK)
2.9 × 10-4 (Canadian);
9.8 × 10-3 (UK)
3.1 × 10-4 (Canadian);
4.3 × 10-2 (UK)
4.5 × 10-6 (Canadian);
3.3 × 10-2 (UK) / 0.55
0.46
0.54
0.51
3.23
2.90
1.89
1.45 / APOC1 / rs4420638 / 2.3 × 10-44 / -

Supplementary Table 3 (Continued)

Reference / Gene symbol / SNP / Non-APOE hits / APOE-related hits / SNP / APOE-related hits
P value / Odds ratio / Gene symbol / P value / Odds ratio
Webster et al., 2007 [312] / - / - / - / - / APOC1 / rs4420638 / 1.1 × 10-39 / -
Reiman et al., 2007 [271][ / GAB2 / rs2373115 / 9.7 × 10-11 / 4.06 / - / - / - / -
Coon et al., 2007[292] / - / - / - / - / APOC1 / rs4420638 / 1.1 × 10-39 / 4.01
Grupe et al., 2007 [270] / GALP
TNK1
Chr14q32.13
PCK1
LMNA
PGBD1
LOC651924
Chr7p15.2
THEM5
MYH13
CTSS
UBD
BCR
ACAN
TRAK2
EBF3 / rs3745833
rs1554948
rs11622883
rs8192708
rs505058
rs3800324
rs6907175
rs1859849
hCV22274641
rs2074877
hCV15746640
rs444013
rs9608099
rs2882676
rs13022344
rs11016976 / 5.0 × 10-5
6.3 × 10-5
9.4 × 10-5
9.9 × 10-5
2.0 × 10-4
3.2 × 10-4
4.7 × 10-4
5.8 × 10-4
6.1 × 10-4
7.2 × 10-4
7.8 × 10-4
7.9 × 10-4
9.7 × 10-4
1.0 × 10-3
1.0 × 10-3
1.0 × 10-3 / 1.2
1.19
1.19
1.29
1.35
1.43
1.16
1.15
1.24
1.12
1.21
1.11
1.09
1.07
1.07
1.07 / TOMM40
APOE
APOC2 / rs157581
rs405509
rs1132899 / 1.0 × 10-8
1.0 × 10-8
7.6 × 10-5 / 2.73
1.43
1.19

Supplementary Table 4: Summary of studies with Epigenomic modifications in AD

Reference / Samples (N) / Brain tissue/cell type / Plateform/Methodology / Primary finding / Top-hits/associated gene
Global DNA Methylation
Mastroeni D et al. , 2009 [326] / A pair of monozygotic twins discordant for AD / Temporal neocortex / Immunohistochemistry / Reduced level of global 5mC methylation in AD twin / ─
Mastroeni D et al., 2010 [327] / 20 AD and 20 controls / EC / Immunohistochemistry / Reduced level of global methylation (2 markers of DNA methylation and 8 methylation maintenance factors) / ─
Bradley-Whitman MA et al. 2013[328] / 5 Age-matched controls, 5 preclinical AD, and 7 late-stage AD / HIP/HPG, CER / Dot blot immunochemistry / Increased levels of 5mC and 5hmC, and decreased levels of 5fC and 5caC in the HPG of AD subjects / ─
Chouliaras L et al., 2013 [325] / 10 AD and 10 age-matched controls; and a pair of monozygotic twins discordant for AD / HIP / Immunohistochemistry and
image analysis / Decrease in the hippocampal
levels of 5mC and 5hmC in
AD hippocampus / ─
Coppieters N et al., 2014 [329] / 13 AD (MFG) and 13 age matched controls; 29 AD (MTG) and 29 age-matched controls / MFG and MTG / Immunohistochemistry / Hypermethylation and increased level of 5hmC in both AD MFG and MTG / ─
Di Francesco A et al. 2015 [331] / 37 LOAD and 44 controls / PBMCs / Luminometric methylation assay / DNA hypermethylation in LOAD / ─
Lashley T et al. 2014 [330] / 12 AD cases and 14 neurologically normal controls / EC / immunohistochemistry / No change in 5mC and 5hmC between AD cases and controls / ─

Supplementary Table 4 (Continued)

Reference / Samples (N) / Brain tissue/cell type / Plateform/Methodology / Primary finding / Top-hits/associated gene
Genome-wide MicoRNA profiling
Nunez−Iglesias et al., 2010 [233] / 4 AD and 4 age-matched controls / PFC / Custom µ-Paraflo array / miRNA and target mRNA associations are changed in AD / ─
Tan L et al., 2014 [337] / Discovery sampleset -50AD patients and 50 controls
Validation sampleset- 158 patients and 155 controls / Serum / Illumina HiSeq 2000 sequencing (discovery) and qRT-PCR (validation) / 6 miRNAs - MiR-98-5p, miR-885-5p, miR-483-3p, miR-342-
3p, miR-191-5p, and miR-let-7d-5p displayed significantly different expression levels in AD patients compared with controls / miR-342-3p

EC: entorhinal cortex; HIP: Hippocampus; HPG: parahippocampal gyrus; CER: cerebellum; MFG: medial frontal gyrus; MTG: medial temporal gyrus; PBMCs: peripheral blood mononuclear cells; PFC: prefrontal cortex