Summary-based methylome-wide association analyses suggest potential genetically driven epigenetic heterogeneity of Alzheimer’s disease Alireza Nazarian*, Anatoliy I. Yashin, and Alexander M. Kulminski* Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA *Corresponding Authors: Alireza Nazarian and Alexander M. Kulminski Duke University Social Science Research Institute Biodemography of Aging Research Unit Erwin Mill Building, 2024 W. Main St. Durham, NC 27705 Emails: [email protected] and [email protected] 1 Supporting Acknowledgment This research was supported by Grants No. P01AG043352, R01AG047310, and R01AG065477 from the National Institute on Aging. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. This manuscript was prepared using limited access datasets obtained though dbGaP (accession numbers: phs000287.v5.p1 (CHS), phs000007.v28.p10 (FHS), phs000428.v2.p2 (HRS), and phs000168.v2.p2 (LOADFS) at https://www.ncbi.nlm.nih.gov/gap) and the University of Michigan. Phenotypic HRS data are available publicly and through restricted access from http://hrsonline.isr.umich.edu/index.php?p=data. The Cardiovascular Health Study (CHS) was supported by contracts HHSN268201200036C, HHSN268200800007C, N01-HC-85079, N01-HC-85080, N01-HC-85081, N01-HC-85082, N01-HC-85083, N01-HC-85084, N01-HC-85085, N01-HC-85086, N01-HC-35129, N01 HC-15103, N01 HC-55222, N01-HC- 75150, N01-HC-45133, and N01-HC-85239; grant numbers U01 HL080295 and U01 HL130014 from the National Heart, Lung, and Blood Institute (NHLBI), and R01 AG-023629 from the National Institute on Aging, with additional contribution from the National Institute of Neurological Disorders and Stroke. A full list of principal CHS investigators and institutions can be found at https://chs-nhlbi.org/pi. This manuscript was not prepared in collaboration with CHS investigators and does not necessarily reflect the opinions or views of CHS, or the NHLBI. Support for the genotyping through the CARe Study was provided by NHLBI Contract N01-HC-65226. Additional support for infrastructure was provided by HL105756 and additional genotyping among the African-American cohort was supported in part by HL085251. DNA handling and genotyping at Cedars-Sinai Medical Center was supported in part by National Center for Research Resources grant UL1RR033176, now at the National Center for Advancing Translational Technologies CTSI grant UL1TR000124; in addition to the National Institute of Diabetes and Digestive and Kidney Diseases grant DK063491 to the Southern California Diabetes Endocrinology Research Center. The Framingham Heart Study (FHS) is conducted and supported by the National Heart, Lung, and Blood Institute (NHLBI) in collaboration with Boston University (Contract No. N01-HC-25195 and HHSN268201500001I). This manuscript was not prepared in collaboration with investigators of the FHS and does not necessarily reflect the opinions or views of the FHS, Boston University, or NHLBI. Funding for SHARe Affymetrix genotyping was provided by NHLBI Contract N02-HL-64278. SHARe Illumina genotyping was provided under an agreement between Illumina and Boston University. Funding for CARe genotyping was provided by NHLBI Contract N01-HC-65226. Funding support for the Framingham Dementia dataset was provided by NIH/NIA grant R01 AG08122. Funding support for the Framingham Inflammatory Markers was provided by NIH grants R01 HL064753, R01 HL076784 and R01 AG028321. Funding support for the Framingham C-reactive Protein dataset was provided by NIH grants R01 HL064753, R01 HL076784 and R01 AG028321. Funding support for the Framingham Adiponectin dataset was provided by NIH/NHLBI grant R01-DK-080739. Funding support for the Framingham Interleukin-6 dataset was provided by NIH grants R01 HL064753, R01 HL076784 and R01 AG028321. The Health and Retirement Study (HRS) genetic data is sponsored by the Genetics Resource with HRS April 21, 2010, version G Page 5 of 7 National Institute on Aging (grant numbers U01AG009740, RC2AG036495, and RC4AG039029) and was conducted by the University of Michigan. This manuscript 2 was not prepared in collaboration with HRS investigators and does not necessarily reflect the opinions or views of HRS. Funding support for the Late Onset Alzheimer’s Disease Family Study (LOADFS) was provided through the Division of Neuroscience, NIA. The LOADFS includes a genome-wide association study funded as part of the Division of Neuroscience, NIA. Assistance with phenotype harmonization and genotype cleaning, as well as with general study coordination, was provided by Genetic Consortium for Late Onset Alzheimer’s Disease. This manuscript was not prepared in collaboration with LOADFS investigators and does not necessarily reflect the opinions or views of LOADFS. 3 Tables Table S1: Blood-based methylome-wide association results ProbeID Chr ProbePos Gene SNP Pos A1 Freq PGWAS PmQTL bSMR SESMR PSMR PHEIDI NHEIDI Current? Previous? Region? Plan 1: All Subjects cg20486877 6p22.1 29626704 GABBR1 rs12530421 29581666 C 0.072 2.11E-04 3.47E-66 -0.284 0.057 5.17E-07 5.21E-02 20 N N N cg12893697 11p15.5 970389 AP2A2 rs7395773 970503 C 0.481 1.34E-05 0 -0.168 0.031 6.64E-08 4.36E-01 20 S S S cg06064525 11p15.5 970664 AP2A2 rs7395773 970503 C 0.481 1.34E-05 0 -0.158 0.029 6.30E-08 5.10E-01 20 S S S cg05626073 11p15.5 971527 AP2A2 rs7395773 970503 C 0.481 1.34E-05 1.75E-305 -0.188 0.035 7.49E-08 1.25E-01 20 S S S cg09162537 11p15.5 976950 AP2A2 rs7395402 950293 C 0.447 1.54E-05 4.81E-59 -0.352 0.069 3.04E-07 2.03E-01 20 S S S cg21806090 12p13.33 2088868 CACNA1C rs56401832 2074725 C 0.030 2.28E-03 5.18E-165 -0.141 0.028 3.43E-07 3.63E-01 6 N N N cg00222015 12q24.31 121795469 LINC01089 rs7964357 121893222 C 0.025 3.21E-04 0 -0.130 0.021 1.54E-09 2.50E-01 20 N N N cg06750524 19q13.32 44906698 APOE rs769449 44906745 A 0.112 2.15E-83 9.38E-15 3.617 0.469 1.24E-14 9.03E-02 10 G G G Plan 2: Only Males cg20011360 4p14 37584038 C4orf19 rs2276944 37584048 A 0.106 5.94E-04 3.40E-180 0.366 0.058 2.62E-10 3.04E-01 17 N N N cg23395749 5q35.3 177557245 IGR (FAM193B) rs1001530 177558514 G 0.046 4.38E-03 2.55E-26 -0.559 0.109 2.95E-07 2.48E-01 5 N S S cg04627871 6p21.33 31736144 CLIC1 rs34585796 31778065 T 0.013 2.46E-02 2.57E-54 0.339 0.059 1.09E-08 1.24E-01 10 N G S cg15598276 6p21.32 32980566 BRD2 rs115417321 32973918 C 0.016 6.96E-03 9.03E-38 -0.484 0.073 2.68E-11 2.61E-01 14 N G G cg01991743 6p21.32 33085831 HLA-DPB1 rs11551421 33085832 A 0.039 1.59E-03 0 -0.140 0.025 2.79E-08 2.29E-01 20 N G G cg06527438 6q27 170236746 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 1.44E-25 -0.548 0.098 2.10E-08 4.10E-01 5 N N S cg21205282 6q27 170244045 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 2.90E-16 -0.693 0.134 2.55E-07 8.05E-02 5 N N S cg22883453 6q27 170244276 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 1.09E-19 -0.628 0.117 8.38E-08 5.52E-02 4 N N S cg04505845 6q27 170244461 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 7.99E-22 -0.592 0.108 4.76E-08 2.03E-01 4 N N S cg05526015 6q27 170244757 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 1.13E-35 -0.463 0.079 4.65E-09 2.18E-01 6 N N S cg24651908 6q27 170245433 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 1.52E-18 -0.650 0.123 1.18E-07 5.85E-02 4 N N S cg04386759 6q27 170245707 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 1.36E-25 -0.542 0.097 2.09E-08 5.91E-02 5 N N S cg26180843 6q27 170248014 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 1.75E-21 -0.584 0.107 5.18E-08 1.14E-01 5 N N S cg12035402 6q27 170250189 IGR (LOC154449) rs58691983 170238096 A 0.013 2.95E-02 1.02E-16 -0.692 0.133 2.16E-07 7.79E-02 5 N N S cg05438220 7q21.13 90643046 CDK14 rs17864073 90601202 A 0.022 6.89E-03 0 -0.125 0.023 3.54E-08 2.11E-01 15 N N S cg11399834 8p22 14566901 SGCZ rs7013654 14587192 T 0.047 1.75E-03 6.43E-156 -0.348 0.054 1.20E-10 2.06E-01 20 N N G cg12185975 8q24.22 130761450 IGR (ADCY8) rs79599781 130735526 A 0.057 5.42E-04 2.13E-165 -0.239 0.040 1.73E-09 6.17E-01 20 S S S cg23402755 10p14 7702004 ITIH2 rs76129783 7716283 C 0.027 2.98E-03 1.29E-26 -0.453 0.089 3.85E-07 6.42E-01 12 N G G cg14381908 10q11.21 43202369 RASGEF1A rs35718664 43158746 G 0.056 2.03E-03 1.22E-195 0.204 0.040 4.90E-07 2.63E-01 18 N N N cg25422051 11q13.1 65916842 C11orf68 rs7940700 65903526 T 0.015 2.87E-02 5.91E-26 -0.658 0.094 2.43E-12 3.54E-01 7 N N N cg15007809 12q21.2 75883289 IGR (PHLDA1) rs11180729 75883290 A 0.014 1.08E-02 1.65E-298 -0.190 0.021 8.73E-20 4.99E-01 10 N G G cg19755435 14q31.3 88006657 GPR65 rs1372363 88006834 T 0.076 8.12E-04 2.90E-45 -0.462 0.087 1.04E-07 3.79E-01 20 N N S cg20239174 15q24.1 73780023 IGR (C15orf59) rs1869176 73789242 T 0.010 4.71E-02 3.59E-224 -0.160 0.025 2.42E-10 5.18E-01 7 N N N cg24801087 17q25.3 78485647 DNAH17,DNAH17-AS1 rs654154 78485428 C 0.061 3.39E-03 2.53E-45 -0.573 0.106 6.81E-08 2.09E-01 13 N S S cg08778119 17q25.3 78496484 DNAH17,DNAH17-AS1 rs12944401 78611646 T 0.028 3.54E-03 5.02E-40 -0.483 0.087 3.23E-08 3.68E-01 4 N S S cg06750524 19q13.32 44906698 APOE rs769449 44906745 A 0.112 7.08E-30 9.38E-15 3.651 0.477 1.92E-14 1.39E-01 10 G G G cg05206559 19q13.32 45913997 NANOS2 rs66529687 45914171 A 0.133 1.83E-04 2.84E-41 0.723 0.125 7.67E-09 3.28E-01 20 G G G cg25673584 19q13.32 45914293 NANOS2 rs66529687 45914171 A 0.133