Laura B. Cantwell

Meta-analysis confirms CR1, CLU, and PICALM as alzheimer disease risk loci and reveals interactions with APOE genotypes.

OBJECTIVES To determine whether genotypes at CLU, PICALM, and CR1 confer risk for Alzheimer disease (AD) and whether risk for AD associated with these genes is influenced by apolipoprotein E (APOE) genotypes. DESIGN Association study of AD and CLU, PICALM, CR1, and APOE genotypes. SETTING Academic research institutions in the United States, Canada, and Israel. PARTICIPANTS Seven thousand seventy cases with AD, 3055 with autopsies, and 8169 elderly cognitively normal controls, 1092 with autopsies, from 12 different studies, including white, African American, Israeli-Arab, and Caribbean Hispanic individuals. RESULTS Unadjusted, CLU (odds ratio [OR], 0.91; 95% confidence interval [CI], 0.85-0.96 for single-nucleotide polymorphism [SNP] rs11136000), CR1 (OR, 1.14; 95% CI, 1.07-1.22; SNP rs3818361), and PICALM (OR, 0.89; 95% CI, 0.84-0.94, SNP rs3851179) were associated with AD in white individuals. None were significantly associated with AD in the other ethnic groups. APOE ε4 was significantly associated with AD (ORs, 1.80-9.05) in all but 1 small white cohort and in the Arab cohort. Adjusting for age, sex, and the presence of at least 1 APOE ε4 allele greatly reduced evidence for association with PICALM but not CR1 or CLU. Models with the main SNP effect, presence or absence of APOE ε4, and an interaction term showed significant interaction between presence or absence of APOE ε4 and PICALM. CONCLUSIONS We confirm in a completely independent data set that CR1, CLU, and PICALM are AD susceptibility loci in European ancestry populations. Genotypes at PICALM confer risk predominantly in APOE ε4-positive subjects. Thus, APOE and PICALM synergistically interact.

Genome-wide association study of corticobasal degeneration identifies risk variants shared with progressive supranuclear palsy

Corticobasal degeneration (CBD) is a neurodegenerative disorder affecting movement and cognition, definitively diagnosed only at autopsy. Here, we conduct a genome-wide association study (GWAS) in CBD cases (n=152) and 3,311 controls, and 67 CBD cases and 439 controls in a replication stage. Associations with meta-analysis were 17q21 at MAPT (P=1.42 × 10−12), 8p12 at lnc-KIF13B-1, a long non-coding RNA (rs643472; P=3.41 × 10−8), and 2p22 at SOS1 (rs963731; P=1.76 × 10−7). Testing for association of CBD with top progressive supranuclear palsy (PSP) GWAS single-nucleotide polymorphisms (SNPs) identified associations at MOBP (3p22; rs1768208; P=2.07 × 10−7) and MAPT H1c (17q21; rs242557; P=7.91 × 10−6). We previously reported SNP/transcript level associations with rs8070723/MAPT, rs242557/MAPT, and rs1768208/MOBP and herein identified association with rs963731/SOS1. We identify new CBD susceptibility loci and show that CBD and PSP share a genetic risk factor other than MAPT at 3p22 MOBP (myelin-associated oligodendrocyte basic protein).

Global and local ancestry in African-Americans: Implications for Alzheimer's disease risk.

African‐American (AA) individuals have a higher risk for late‐onset Alzheimers disease (LOAD) than Americans of primarily European ancestry (EA). Recently, the largest genome‐wide association study in AAs to date confirmed that six of the Alzheimers disease (AD)‐related genetic variants originally discovered in EA cohorts are also risk variants in AA; however, the risk attributable to many of the loci (e.g., APOE, ABCA7) differed substantially from previous studies in EA. There likely are risk variants of higher frequency in AAs that have not been discovered.

VCPA: genomic Variant Calling pipeline and data management tool for Alzheimer’s Disease Sequencing Project

Abstract Summary We report VCPA, our SNP/Indel Variant Calling Pipeline and data management tool used for the analysis of whole genome and exome sequencing (WGS/WES) for the Alzheimer’s Disease Sequencing Project. VCPA consists of two independent but linkable components: pipeline and tracking database. The pipeline, implemented using the Workflow Description Language and fully optimized for the Amazon elastic compute cloud environment, includes steps from aligning raw sequence reads to variant calling using GATK. The tracking database allows users to view job running status in real time and visualize >100 quality metrics per genome. VCPA is functionally equivalent to the CCDG/TOPMed pipeline. Users can use the pipeline and the dockerized database to process large WGS/WES datasets on Amazon cloud with minimal configuration. Availability and implementation VCPA is released under the MIT license and is available for academic and nonprofit use for free. The pipeline source code and step-by-step instructions are available from the National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (http://www.niagads.org/VCPA). Supplementary information Supplementary data are available at Bioinformatics online.

THE GCAD CLOUD-BASED WORKFLOW FOR PROCESSING WHOLE EXOME AND WHOLE GENOME DATA FROM THE ALZHEIMER’S DISEASE SEQUENCING PROJECT

membership models to the transcriptome data for clustering genes and identified ones that were characterized in each cluster. We performed Gene Ontology analysis on the characteristic genes in each cluster to examine their biological functions. Results:We found 673 genes that were differentially expressed among the different Braak stages (10% false discovery rate).Among them, genes in clusters related to neurons were downregulated in Braak stage V–VI as expected. Their downregulation appears to be consistent with the timing of tau-related neuropathology spreading into frontal cortex. Interestingly, genes in a cluster related to myelination were greatly altered in the Braak stages III–IV or more. Conclusions: The transcriptome analysis of autopsy brains in this study revealed aberrant expression in genes associated with myelination, which may precede the appearance of neuropathological changes associatedwithAD.Our resultsmay imply thatmyelin alteration could be an early event linking with AD pathogenesis.

THE ALZHEIMER’S DISEASE SEQUENCING PROJECT (ADSP) DATA UPDATE 2017

P3-089 AUTOSOMAL DOMINANT EARLY-ONSET ALZHEIMER’S DISEASE: CHARACTERIZATION OFA BRAZILIAN COHORT Leonel Tadao Takada, Sonia Maria Dozzi Brucki, Roberta Diehl Rodriguez, Jerusa Smid, Valeria S. Bahia, Gerson Chadi, Ricardo Nitrini, Medical School of University of S~ao Paulo, S~ao Paulo, Brazil; University of S~ao Paulo Medical School, S~ao Paulo, Brazil; University of S~ao Paulo, S~ao Paulo, Brazil. Contact e-mail: leonel. takada@gmail.com

ALZHEIMER'S DISEASE SEQUENCING PROJECT: SEARCH FOR ALZHEIMER'S DISEASE RESILIENCE GENES THAT MAY MODIFY DISEASE SUSCEPTIBILITY IN SPECIFIC APOE GENOTYPE BACKGROUNDS

not available. EC-01-04 PHYSIOLOGICAL SUBSTRATES OF BACE1 AND ADAM10: SAFETY ISSUES OR BIOMARKERS? Stefan Lichtenthaler, Technical University of Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.. Contact e-mail: Stefan.Lichtenthaler@dzne.de Background: The beta-secretase BACE1 is a major drug target in Alzheimer’s disease (AD), but also has other functions, e.g. in myelination and axon targeting. BACE1-deficient mice have additional phenotypes in the brain and several BACE1 substrates, referred to as the BACE1 degradome, are emerging in the CNS. This raises the possibility that therapeutic BACE1 inhibition may have mechanism-based side-effects. Additionally, most BACE1 inhibitors also block the homologous protease BACE2 and, thus, may interfere with BACE2 function. Methods: We developed methods for whole proteome analysis of murine tissue, including CSF Results: We used the novel methods to identify BACE1 substrate candidates in murine CSF, but also in neurons and brains. Selected substrate candidates were validated and functionally and mechanistically characterized. Two of the candidates are seizure protein 6 (SEZ6) and SEZ6-like (SEZ6L), which control neurite outgrowth and synapse formation. Both proteins were validated as BACE1 substrates in vitro and in vivo. In CSF, SEZ6 and SEZ6Lwere found to be suitable markers for measuring BACE1 inhibition in vivo. Conclusions: BACE1 has broad functions in the CNS. The presentation will discuss the implication of the substrates a) for the safety of BACE1 inhibitors and b) for the use as companion diagnostics to monitor BACE inhibition in vivo. SUNDAY, JULY 24, 2016 FEATURED RESEARCH SESSIONS F1-01 THE ALZHEIMER’S DISEASE SEQUENCING PROJECT (ADSP): GENE DISCOVERY IN ACTION F1-01-01 STRUCTURALVARIATION (SV) IN HETEROGENOUS WHOLE-GENOME SEQUENCING DATA FROM 111 FAMILIES AT RISK FOR ALZHEIMER DISEASE: ALZHEIMER DISEASE SEQUENCING PROJECT SV STUDY Li Charlie Xia, Stanford University, Stanford, CA, USA; University of Pennsylvania, Philadelphia, PA, USA. Contact e-mail: lixia@stanford.edu Background: The Alzheimer Disease Sequencing Project (ADSP) is a national initiative to identify novel genetic variants involved in determining risk of late-onset Alzheimer disease (AD). Methods: Structural variation was characterized in 111 families of multiple ethnicities comprising 578 individuals diagnosed with or at risk for AD. We developed a statistical framework that leverages pedigree information to assess accuracy and optimize structural variant (SV) calls. The kinship coefficient was used to filter SVs showing excess heterozygosity. We also formulated a metric called the D-score which is an outgroup-based measure of sib-sharing to filter SVs identified by calling algorithms that detect insertion and deletion breakpoints, but do not render genotypes. These metrics also permitted assessment of reliability of individual calling programs for various SV sizes. An in silico procedure was devised to “spike-in” SVs of varying purity into real sequenced libraries, accommodating multi-library designs, and applied it to three samples that were sequenced at all three centers. This comprehensive QC process allowed benchmarking SV callers across the widely differing libraries and combining these callers in a library-specific way for improved specificity and sensitivity. Candidate SV regions were further refined using an ensemble of 12 SV callers with local assembly to provide precise breakpoints for subsequent calling of genotypes. Results:We identified a high-confidence set of deletions, insertions, and complex variants larger than 20 base pairs (bp) genotyped across all 578 individuals. These variants were prioritized based on predicted functional impact and overlap with known AD genes and linkage regions. Thus far, we detected, and confirmed by sequencing, a 44 bp ABCA7 deletion in 11 members (all have AD) of 5 of 67 CaribbeanHispanic families. This finding is consistent with our recent AD association finding of this deletion in a sample containing >2,800 African Americans which results in a frameshift and truncating mutation that could interfere with protein function. Conclusions: A carefully developed pipeline for detecting, genotyping, and filtering SVs from family-based whole genome sequence data permitted discovery of a robust association of AD risk with a rare 44 bp deletion in ABCA7. Amore comprehensive analysis of these data is underway. F1-01-02 ALZHEIMER’S DISEASE SEQUENCING PROJECT: SEARCH FOR ALZHEIMER’S DISEASE RESILIENCE GENES THAT MAY MODIFY DISEASE SUSCEPTIBILITY IN SPECIFIC APOE GENOTYPE BACKGROUNDS Eduardo Marcora, Alan E. Renton, Gary W. Beecham, Eric Boerwinkle, Laura Cantwell, Carlos Cruchaga, Rebecca Cweibel, Adam Felsenfeld, Myriam Fornage, Manav Kapoor, Keoni Kauwe, Mugdha Khaladkar, Dan Kobolt, Yiyi Ma, Richard Mayeux, Marilyn Miller, Adam C. Naj, Amanda B. Partch, Margaret A. Pericak-Vance, Gerard D. Schellenberg, Sudha Seshadri, Badri N. Vardarajan, Li-San Wang, Joshua C. Bis, Lindsay A. Farrer, Alison M. Goate, 1 Icahn School of Medicine at Mount Sinai, New York, NY, USA; 2 University of Miami Miller School of Medicine, Miami, FL, USA; Baylor College of Medicine, Houston, TX, USA; University of Texas Health Science Center at Houston, Houston, TX, USA; 5 University of Pennsylvania, Philadelphia, PA, USA; 6 Washington University in St. Louis, Saint Louis, MO, USA; Washington University School of Medicine, St. Louis, MO, USA; Knight Alzheimer Disease Center, St. Louis, MO, USA; Division of Genome Sciences, National HumanGenome Research Institute, Bethesda,MD, USA; 10 University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA; Brigham Young University, Provo, UT, USA; Washington University in St. Louis, St. Louis, MO, USA; Washington University, St. Louis, MO, USA; 14 The Genome Institute, Washington University in St. Louis, St. Louis, MO, USA; Boston University, Boston, MA, USA; Columbia University, New York, NY, USA; Division of Neuroscience, National Institute on Aging, Bethesda, MD, USA; 18 University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA; Boston University School of Medicine, Boston, MA, USA; 21 University of Washington, Seattle, WA, USA. Contact e-mail: edoardo.marcora@mssm.edu Background:Common variation at the APOE locus is the strongest known genetic risk factor for Alzheimer’s disease (AD). Podium Presentations: Sunday, July 24, 2016 P162

Multiple deletion copy number variants (CNVs) are associated with late-onset Alzheimer's disease: The Alzheimer’s disease genetics consortium

Background:Alzheimer’s disease (AD) is characterized by progressive neuropathology and cognitive decline. Although the neuropathological manifestation of AD is well characterized in postmortem brain, little is known about the underlying risk factors or mechanism(s) involved in disease progression. We recently published the first epigenome-wide association studies (EWAS), demonstrating methylomic variation in AD brain and blood (Lunnon et al., 2014), with the most notable differences occurring in regions of the brain characterised by extensive neuropathology. Following on from these studies, we describe a network approach to identify modules of co-methylated loci associated with amyloid and tau burden using DNA from multiple brain regions in a cohort of 144 samples. Methods: DNA was extracted from 100mg tissue from a cohort of 144 individuals from the Mount Sinai NIH Brain and Tissue Repository (NBTR), with two brain regions (Prefrontal cortex-PFC and Superior temporal gyrus-STG) obtained from each individual. Genomic DNA was bisulfite treated using the Zymo EZ DNA methylation kit and samples were assessed using the Illumina Infinium Human Methylation 450K BeadChip. Following data normalisation and stringent quality control, we identifiedmethylomic variation associatedwith quantitativemeasures of neuropathology (amyloid/tau) using linear models, whilst controlling for the effects of age and gender. We used the R package “WGCNA” to identify groups of co-methylated genes that were associated with (a) neuropathological measures and (b) genetic variants associated with AD from recent large meta-analyses. Results: We identified many differentially methylate positions (DMPs) associated with disease in both the PFC and STG, replicating many of our previous findings. The strongest results were found with amyloid burden and braak staging, where we observed DMPs located in and near previously identified genes containing risk variants, including APOE. UsingWGCNA, we also identified multiple modules of co-methylated loci characterised by consistent associations with disease status and neuropathology measures, as well as polygenic risk status. Conclusions:This study provides further evidence for a role of epigenomic dysfunction in AD, identifying networks of co-methylated loci associated withvarious neuropathological traits. We demonstrate strong evidence for an interaction between genotype and DNA methylation at loci previously implicated in genetic studies of AD.

Association of TREM2 variants with Alzheimer's disease in African-Americans: For the Alzheimer's Disease Genetics Consortium (ADGC)

P1-063 ASSOCIATION OF TREM2 VARIANTS WITH ALZHEIMER’S DISEASE IN AFRICANAMERICANS: FOR THE ALZHEIMER’S DISEASE GENETICS CONSORTIUM (ADGC) Christiane Reitz, Gyungah Jun, Adam Naj, Badri Vardarajan, Li-SanWang, Eric Larson, Neill Graff-Radford, Denis Evans, Philip De Jager, Paul Crane, Joseph Buxbaum, Nilufer Ertekin-Taner, Mark Logue, Robert Green, Laura Cantwell, Danielle Fallin, Jennifer Manly, Kathryn Lunetta, Ilyas Kamboh, Oscar Lopez, David Bennett, Kathleen Steele Hall, Alison Goate, Goldie Byrd, Walter Kukull, Tatiana Foroud, Jonathan Haines, Lindsay Farrer, Margaret Pericak-Vance, Gerard Schellenberg, Richard Mayeux, Columbia University, New York, New York, United States; Boston University School of Medicine, Boston, Massachusetts, United States; University of Miami Hussman Institute for Human Genomics, Miami, Florida, United States; Columbia University, Boston, Massachusetts, United States; University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States; Group Health Research Institute, Seattle, Washington, United States; Mayo Clinic Jacksonville, Jacksonville, Florida, United States; Rush University Medical Center, Chicago, Illinois, United States; Brigham & Women’s Hospital, Boston, Massachusetts, United States; Mt. Sinai Hospital, New York, New York, United States; Mayo, Jacksonville, Florida, United States; Boston University School of Medicine/Biomedical Genetics, Boston, Massachusetts, United States; University of Pittsburgh Schools of Nursing and Medicine, Pittsburgh, Pennsylvania, United States; University of Pennsylvania, Philadelphia, Pennsylvania, United States; Johns Hopkins University, Baltimore, Maryland, United States; Columbia University Medical Center, New York, New York, United States; Boston University School of Public Health, Boston,Massachusetts, United States; University of Pittsburgh, Pittsburgh, Pennsylvania, United States; University of Pittsburgh, Pittsburgh, Pennsylvania, United States; Rush University Medical Center, Chicago, Illinois, United States; Indiana University, Indianapolis, Indiana, United States; Washington University, St. Louis, Saint Louis, Missouri, United States; North Carolina AT National Alzheimer’s Coordinating Center, Seattle, Washington, United States; Indiana University School of Medicine, Indianapolis, Indiana, United States; Vanderbilt University, Nashville, Tennessee, United States; Boston University, Boston, Massachusetts, United States; Vanderbilt University, Nashville, Tennessee, United States; University of Pennsylvania, Philadelphia, Pennsylvania, United States. Contact e-mail: cr2101@columbia.edu