Nelson PT et al, “ABCC9 polymorphism is associated..” Supplemental Methods: 1. AD GWAS (preliminary, to confirm methodology) Definitions of AD cases (N=1,443) and controls (N=99) were as described in detail on Supplemental Tables 1, with inclusion and exclusion criteria below. The AD GWAS confirmed as expected that alleles near the APOE locus on chromosome 19 are strong risk factors for AD pathology. Results for AD SNPs are shown in Supplementary Table 2 and Manhattan plot is Supplemental Fig. 2. 2. Inclusion and exclusion criteria AD GWAS: AD Case: No age cutoff NIARI=1 (Patient meets criteria for AD according to 1997 National Institute of Aging-Reagan Institute criteria) Braak stages = V or VI AD control Age cutoff>74 The following are true: NPNIT (Reagan low pathology or not AD) = 3 or 4 NPCERAD = (CERAD none or low density of amyloid plaques) NPBRAAK = Braak stages 0,I, II, or III ADRDA= 2 HS-AGING GWAS: ADGC HS-AGING CASES: Must have died 2000 or later. An HS case must have at least one of the following NP fields: NPTHPRIM = 11, NPTHSECN = 11, NPPHIPP = 1, NPCHIPP = 1, or NPSCL=1 HS-AGING CONTROLS Death 2000 or later without any of the HS CASE hallmarks We used HS cases having either primary or contributing Hippocampal sclerosis (from NP form) or primary/secondary neuropathological diagnostic classification (from MDS). In sum, controls didn't have any HS hallmark variables. Exclusions from either group related to cases with pathologically-confirmed dementia-inducing disease NP FORM: NPPICK=1 (Pick's disease - Yes) NPCORT=1 (Corticobasal degeneration - Yes) NPPROG=1 (Progressive supranuclear palsy - Yes) NPFRONT=1 (Frontotemporal dementia and Parkinsonism with tau-positive or argyrophilic inclusions - Yes) NPFTD=1 (FTD with ubiquitin-positive (tau-negative) inclusions - FTD with motor neuron disease) NPFTDSPC=1 (Was FTD "not otherwise specified present?" - Yes) NPPRION=1 (Other Prion - Yes) NPPFTLD=1 (FTLD Primary - Yes) NPCFTLD=1 (FTLD Contributing - Yes) NPPPRION=1 (Prion Associated Disease Primary - Yes) NPCPRION=1 (Prion Associated Disease Contributing - Yes) MDS FORM: NPTHPRIM=9 (Primary NP DX - Pick's Disease) NPTHPRIM=10 (-Lobar atrophy without Pick's bodies) NPTHPRIM=12 (-Progressive supranuclear palsy) NPTHPRIM=13 (-Corticobasal degeneration) NPTHPRIM=14 (-Prion-associated disease) NPTHPRIM=15 (-Down Syndrome) NPTHSECN=9 (Secondary NP DX - Pick's Disease) NPTHSECN=10 (-Lobar atrophy without Pick's bodies) NPTHSECN=12 (-Progressive supranuclear palsy) NPTHSECN=13 (-Corticobasal degeneration) NPTHSECN=14 (-Prion-associated disease) NPTHSECN=15 (-Down Syndrome) For reference to the NACC coding guidebook see: https://www.alz.washington.edu/NONMEMBER/PDF/npman8.pdf http://www.alz.washington.edu/NONMEMBER/mdsded06.pdf HS GWAS: ROS-MAP inclusion/exclusion HS Cases 1. Cases with pathologically-verified hippocampal sclerosis. 2. Exclusion: age at death <80; or clinical FTD; or pathological FTLD HS Controls 1. Died past age 85 years. 2. Died with complete neuropathological evaluation 3. Did not have hippocampal sclerosis HS GWAS: ACT Inclusion/exclusion criteria: Inclusion: all with HS pathology, which were compared to all without HS pathology. Exclusion: 1. Individuals dying before age 80 2. Individuals with FTD clinically 3. Individuals with FTLD pathology of any subtype 4. Individuals who withdrew consent after the study started (n=4) 3. Genomic sequencing of ABCC9 in cases and controls Genomic sequencing was performed on DNA from six individuals with autopsy information (GG is linked to risk for HS-Aging): Case 1 2 3 4 5 6 Genotype: rs704180 GG GG GG AA AA AA Age 100 95 96 92 91 94 HS-Aging pathology No No No Yes Yes Yes TDP pathology (Scale 0-2+) 0 0 0 2+ 2+ 2+ Genomic sequencing methods: ABCC9 sequences were captured by using the HaloPlex Target Enrichment System (Agilent Technologies, Santa Clara, CA) to amplify fragments spanning the genomic region chr12:21950273-22094386. The six resulting fragment libraries were run in a single flow cell on a HiSeq 2500. Alignment of the sequence reads with the ABCC9 genomic reference and subsequent variant calling was performed using the CLC Genomics Workbench 6.5. All target capture, sequencing, read mapping and variant calling procedures were performed by Ambry Genetics (Aliso Viejo, CA). Sequence gaps were identified by using the samtools mpileup utility to calculate coverage across the entire ABCC9 gene region. A key gap in the 3’ UTR region was bridged via PCR and the missing sequence information was acquired using standard Sanger methods. The variant files were inspected both manually and with custom Perl scripts to identify mutations that either cause non-synonymous changes in the predicted ABCC9 protein sequence or, alternatively, are predicted to alter transcript splicing. 4. Immunoblot analyses—technical details Hippocampus tissue from postmortem brain autopsies were dissected, weighed and homogenized in 5ml/g Low-salt (LS) buffer (10mM Tris, pH 7.5, 5mM EDTA, 1mM DTT, 10% Sucrose and a cocktail of protease and phosphatase inhibitors) and centrifuged at 20,000Xg for 30 minutes at 4°C. Supernatants were saved as the LS fraction. Pellets from the above sedimentation were subjected to two sequential extractions in 5ml/g Triton-X-100 (TX) buffer (LS+ 1% Triton-X-100+0.5M NaCl) and centrifugation at 20,000Xg for 30 minutes at 4°C. Supernatants from the first of these TX buffer extractions were saved as TX fraction. Pellets were homogenized in 5ml/g Sarkosyl (SARK) buffer (LS+ 1%N-Lauryl-Sarcosine+0.5M NaCl) and incubated at 22°C on a shaker for 1hr before sedimentation at 20,000Xg for 30 minutes at 22°C. Supernatants were saved as the SARK fraction. Remaining pellets were extracted in 1ml/g Urea buffer (7M Urea, 2M Thiourea, 4% CHAPS, 30mM Tris, pH – 8.5) before centrifugation at 25,000Xg for 30 minutes at 22°C. Immunoblot analysis. Equal amounts of protein were loaded to denaturing SDS Polyacrylamide gel prior to immunoblot analysis, for LS and TX fractions. The gels, after run, were washed for 10 minutes in Deionized water before transfer. After transfer onto a nitrocellulose membrane, the nonspecific epitopes were blocked with 5% Nonfat milk, for 1hr at room temp. The antibodies used are as follows: SUR2B (C15): sc-5793, SUR2A (T-19): sc-32461, SUR2 (H-80): sc-25684, all three from Santacruz Biotechnology, Inc, and anti-SUR2B, clone N323A/31 and anti-SUR2A, clone N319A/14 from EMD Millipore Corp, CA. The dilutions used were according to the manufacturers’ instruction. The secondary antibodies were all Alkaline Phosphatase conjugated, from Jackson Immunoresearch. The bands were visualized with the Enhanced Chemi-Luminescence kit from Thermo® . The cases involved including some clinical, genomic, and pathological details, and the order on the gels are as follows: Gel lane Age at death HS-Aging rs704178 Braak stage 1 99 N CC III 2 92 Y GG II 3 94 Y GG 0 4 91 Y GG II 5 90 N CC II 6 93 Y GG II 7 100 N CC IV 8 96 N CC IV 9 92 Y GG II For images of the western western blots, please see file labeled Supplemental Fig. 6 western blots 5. Additional Acknowledgments The Georgia Centenarian Study (Leonard W. Poon, PI) was funded by 1P01-AG17553 from the National Institute on Aging, a collaboration among The University of Georgia, Louisiana State University, Louisiana State University Health Sciences Center, Boston University, University of Kentucky, Emory University, Duke University, Rosalind Franklin University of Medicine and Science, Iowa State University and University of Michigan. ADGC Acknowledgments (contributors) Marilyn S. Albert1, Roger L. Albin2-4, Liana G. Apostolova5, Steven E. Arnold6, Sanjay Asthana7-9, Craig S. Atwood7,9, Clinton T. Baldwin10, Robert Barber11, Michael M. Barmada12, Lisa L. Barnes13,14, Thomas G. Beach15, James T. Becker16, Gary W. Beecham17,18, Duane Beekly19, Eileen H. Bigio20,21, Thomas D. Bird22,23, Deborah Blacker24,25, James D. Bowen27, Adam Boxer28, James R. Burke29, Joseph D. Buxbaum30-32, Nigel J. Cairns33, Laura B. Cantwell34, Chuanhai Cao35, Chris S. Carlson36, Cynthia M. Carlsson8, Regina M. Carney37, Steven L. Carroll39, Helena C. Chui40, David G. Clark41, David H. Cribbs44, Elizabeth A. Crocco37, Carlos Cruchaga45, Charles DeCarli46, Steven T. DeKosky47, F. Yesim Demirci12, Malcolm Dick48, Dennis W. Dickson38, Ranjan Duara49, Nilufer Ertekin-Taner38,50, Kelley M. Faber51, Kenneth B. Fallon39, Martin R. Farlow52, Steven Ferris53, Tatiana M. Foroud51, Matthew P. Frosch54, Douglas R. Galasko55, Mary Ganguli56, Daniel H. Geschwind57, Bernardino Ghetti58, John R. Gilbert17,18, Jonathan D. Glass59, Alison M. Goate45, Neill R. Graff-Radford38,50, John H. Growdon60, Hakon Hakonarson61, Ronald L. Hamilton62, Kara L. Hamilton-Nelson17, Lindy E. Harrell41, Elizabeth Head63, Lawrence S. Honig64, Christine M. Hulette65, Bradley T. Hyman60, Gail P. Jarvik66,67, Lee-Way Jin68, Gyungah Jun10,69,70, Anna Karydas28, John S.K. Kauwe72, Jeffrey A. Kaye73,74, Ronald Kim75, Edward H. Koo55, Neil W. Kowall76,77, Joel H. Kramer78, Brian W. Kunkle17, Frank M. LaFerla79, James J. Lah59, James B. Leverenz80, Allan I. Levey59, Ge Li81, Andrew P. Lieberman82, Chiao-Feng Lin34, Oscar L. Lopez71, Kathryn L. Lunetta69, Constantine G. Lyketsos83, Wendy J. Mack84, Daniel C. Marson41, Eden R. Martin17,18, Frank Martiniuk85, Deborah C. Mash86, Eliezer Masliah55,87, Wayne C. McCormick43, Susan M. McCurry88, Andrew N. McDavid36, Ann C. McKee76,77, Marsel Mesulam21,89, Bruce L. Miller28, Carol A. Miller90, Joshua W. Miller68, John C. Morris33,91, Jill R. Murrell51,58, Adam C. Naj34, John M. Olichney46, Joseph E. Parisi92, Henry L. Paulson2, William Perry17, Elaine Peskind81, Ronald C. Petersen26, Aimee Pierce44, Wayne W. Poon48, Huntington Potter35, Joseph F. Quinn73, Ashok Raj35, Murray Raskind81, Eric M. Reiman42,93,94, Barry Reisberg53,95, Christiane Reitz64,96,97, John M. Ringman5, Erik D. Roberson41, Howard J. Rosen28, Roger N. Rosenberg98, Mark A. Sager8, Mary Sano31, Andrew J. Saykin51,99, Lon S. Schneider40,100, William W. Seeley28, Amanda G. Smith35, Salvatore Spina58, Robert A. Stern76, Rudolph E. Tanzi60, Tricia A. Thornton-Wells101, John Q. Trojanowski34, Juan C. Troncoso102, Debby W. Tsuang23,81, Vivianna M. Van Deerlin34, Badri N. Vardarajan64,96,97, Harry V. Vinters5,103, Jean Paul Vonsattel104, Sandra Weintraub21,105, Kathleen A. Welsh-Bohmer29,106, Jennifer Williamson64, Sarah Wishnek17, Clinton B. Wright107, Steven G. Younkin38, Chang-En Yu43, Lei Yu13 Institutional Affiliations 1 Department of Neurology, Johns Hopkins University, Baltimore, Maryland, 2Department of Neurology, University of Michigan, Ann Arbor, Michigan, 3Geriatric Research, Education and Clinical Center (GRECC), VA Ann Arbor Healthcare System (VAAAHS), Ann Arbor, Michigan, 4Michigan Alzheimer Disease Center, Ann Arbor, Michigan, 5Department of Neurology, University of California Los Angeles, Los Angeles, California, 6Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 7Geriatric Research, Education and Clinical Center (GRECC), University of Wisconsin, Madison, Wisconsin, 8Department of Medicine, University of Wisconsin, Madison, Wisconsin, 9Wisconsin Alzheimer's Institute, Madison, Wisconsin, 10Department of Medicine (Genetics Program), Boston University, Boston, Massachusetts, 11Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, 12Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, 13Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, 14Department of Behavioral Sciences, Rush University Medical Center, Chicago, Illinois, 15Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Phoenix, Arizona, 16Departments of Psychiatry, Neurology, and Psychology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 17The John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, 18Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, Florida, 19National Alzheimer's Coordinating Center, University of Washington, Seattle, Washington, 20Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 21Cognitive Neurology and Alzheimer's Disease Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 22 Department of Neurology, University of Washington, Seattle, Washington, 23VA Puget Sound Health Care System/GRECC, Seattle, Washington, 24Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, 25Department of Psychiatry, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, 26Department of Neurology, Mayo Clinic, Rochester, Minnesota, 27 Swedish Medical Center, Seattle, Washington, 28Department of Neurology, University of California San Francisco, San Francisco, California, 29Department of Medicine, Duke University, Durham, North Carolina, 30Department of Neuroscience, Mount Sinai School of Medicine, New York, New York, 31 Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, 32Departments of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, 33Department of Pathology and Immunology, Washington University, St. Louis, Missouri, 34Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, 35USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, Florida, 36 Fred Hutchinson Cancer Research Center, Seattle, Washington, 37Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, Florida, 38Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, 39Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, 40Department of Neurology, University of Southern California, Los Angeles, California, 41Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, 42Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, 43 Department of Medicine, University of Washington, Seattle, Washington, 44Department of Neurology, University of California Irvine, Irvine, California, 45Department of Psychiatry and Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of Medicine, St. Louis, Missouri, 46Department of Neurology, University of California Davis, Sacramento, California, 47 University of Virginia School of Medicine, Charlottesville, Virginia, 48Institute for Memory Impairments and Neurological Disorders, University of California Irvine, Irvine, California, 49Wien Center for Alzheimer's Disease and Memory Disorders, Mount Sinai Medical Center, Miami Beach, Florida, 50Department of Neurology, Mayo Clinic, Jacksonville, Florida, 51Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, 52Department of Neurology, Indiana University, Indianapolis, Indiana, 53Department of Psychiatry, New York University, New York, New York, 54C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, Charlestown, Massachusetts, 55Department of Neurosciences, University of California San Diego, La Jolla, California, 56 Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, 57Neurogenetics Program, University of California Los Angeles, Los Angeles, California, 58Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, Indiana, 59Department of Neurology, Emory University, Atlanta, Georgia, 60Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, 61Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, 62Department of Pathology (Neuropathology), University of Pittsburgh, Pittsburgh, Pennsylvania, 63Sanders-Brown Center on Aging, Department of Molecular and Biomedical Pharmacology, University of Kentucky, Lexington, Kentucky, 64Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, New York, 65Department of Pathology, Duke University, Durham, North Carolina, 66Department of Genome Sciences, University of Washington, Seattle, Washington, 67Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington, 68Department of Pathology and Laboratory Medicine, University of California Davis, Sacramento, California, 69Department of Biostatistics, Boston University, Boston, Massachusetts, 70Department of Ophthalmology, Boston University, Boston, Massachusetts, 71University of Pittsburgh Alheimer's Disease Research Center, Pittsburgh, Pennsylvania, 72 Department of Biology, Brigham Young University, Provo, Utah, 73Department of Neurology, Oregon Health & Science University, Portland, Oregon, 74Department of Neurology, Portland Veterans Affairs Medical Center, Portland, Oregon, 75Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, 76Department of Neurology, Boston University, Boston, Massachusetts, 77Department of Pathology, Boston University, Boston, Massachusetts, 78Department of Neuropsychology, University of California San Francisco, San Francisco, California, 79Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, 80Department of Pathology, University of Washington, Seattle, Washington, 81Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, 82Department of Pathology, University of Michigan, Ann Arbor, Michigan, 83Department of Psychiatry, Johns Hopkins University, Baltimore, Maryland, 84Department of Preventive Medicine, University of Southern California, Los Angeles, California, 85Department of Medicine - Pulmonary, New York University, New York, New York, 86Department of Neurology, University of Miami, Miami, Florida, 87Department of Pathology, University of California San Diego, La Jolla, California, 88School of Nursing Northwest Research Group on Aging, University of Washington, Seattle, Washington, 89Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 90Department of Pathology, University of Southern California, Los Angeles, California, 91Department of Neurology, Washington University, St. Louis, Missouri, 92Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, 93Arizona Alzheimer’s Consortium, Phoenix, Arizona, 94Banner Alzheimer's Institute, Phoenix, Arizona, 95Alzheimer's Disease Center, New York University, New York, New York, 96 Gertrude H. Sergievsky Center, Columbia University, New York, New York, 97Department of Neurology, Columbia University, New York, New York, 98Department of Neurology, University of Texas Southwestern, Dallas, Texas, 99Department of Radiology and Imaging Sciences, Indiana University, Indianapolis, Indiana, 100Department of Psychiatry, University of Southern California, Los Angeles, California, 101Center for Human Genetics and Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, 102Department of Pathology, Johns Hopkins University, Baltimore, Maryland, 103Department of Pathology & Laboratory Medicine, University of California Los Angeles, Los Angeles, California, 104Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Pathology, Columbia University, New York, New York, 105Department of Psychiatry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 106Department of Psychiatry & Behavioral Sciences, Duke University, Durham, North Carolina, 107Evelyn F. McKnight Brain Institute, Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida ADGC Acknowledgments (Funding) The National Institutes of Health, National Institute on Aging (NIH-NIA) supported this work through the following grants: ADGC, U01 AG032984, RC2 AG036528; NACC, U01 AG016976; NCRAD, U24 AG021886; P01 AG030128, NIA LOAD, U24 AG026395, U24 AG026390; Banner Sun Health Research Institute P30 AG019610; Boston University, P30 AG013846, U01 AG10483, R01 CA129769, R01 MH080295, R01 AG017173, R01 AG025259, R01AG33193; Columbia University, P50 AG008702, R37 AG015473; Duke University, P30 AG028377, AG05128; Emory University, AG025688; Group Health Research Institute, UO1 AG06781, UO1 HG004610; Indiana University, P30 AG10133; Johns Hopkins University, P50 AG005146, R01 AG020688; Massachusetts General Hospital, P50 AG005134; Mayo Clinic, P50 AG016574; Mount Sinai School of Medicine, P50 AG005138, P01 AG002219; New York University, P30 AG08051, MO1RR00096, UL1 RR029893, 5R01AG012101, 5R01AG022374, 5R01AG013616, 1RC2AG036502, 1R01AG035137; Northwestern University, P30 AG013854; Oregon Health & Science University, P30 AG008017, R01 AG026916; Rush University, P30 AG010161, R01 AG019085, R01 AG15819, R01 AG17917, R01 AG30146; TGen, R01 NS059873; University of Alabama at Birmingham, P50 AG016582, UL1RR02777; University of Arizona, R01 AG031581; University of California, Davis, P30 AG010129; University of California, Irvine, P50 AG016573, P50, P50 AG016575, P50 AG016576, P50 AG016577; University of California, Los Angeles, P50 AG016570; University of California, San Diego, P50 AG005131; University of California, San Francisco, P50 AG023501, P01 AG019724; University of Kentucky, P30 AG028383, AG05144; University of Michigan, P50 AG008671; University of Pennsylvania, P30 AG010124; University of Pittsburgh, P50 AG005133, AG030653; University of Southern California, P50 AG005142; University of Texas Southwestern, P30 AG012300; University of Miami, R01 AG027944, AG010491, AG027944, AG021547, AG019757; University of Washington, P50 AG005136; Vanderbilt University, R01 AG019085; and Washington University, P50 AG005681, P01 AG03991. The Kathleen Price Bryan Brain Bank at Duke University Medical Center is funded by NINDS grant # NS39764, NIMH MH60451 and by Glaxo Smith Kline. Samples from the National Cell Repository for Alzheimer’s Disease (NCRAD), which receives government support under a cooperative agreement grant (U24 AG21886) awarded by the National Institute on Aging (NIA), were used in this study. We thank contributors, including the Alzheimer’s Disease Centers who collected samples used in this study, as well as patients and their families, whose help and participation made this work possible. Support was also from the Alzheimer’s Association (LAF, IIRG-08-89720; MP-V, IIRG-05-14147) and the US Department of Veterans Affairs Administration, Office of Research and Development, Biomedical Laboratory Research Program. We thank Drs. D. Stephen Snyder and Marilyn Miller from NIA who are ex-officio ADGC members.