Yiyi Ma

Genome-wide association study of Alzheimer's disease endophenotypes at prediagnosis stages

Genetic associations for endophenotypes of Alzheimers disease (AD) in cognitive stages preceding AD have not been thoroughly evaluated.

Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation

The Alzheimer’s Disease Sequencing Project (ADSP) undertook whole exome sequencing in 5,740 late-onset Alzheimer disease (AD) cases and 5,096 cognitively normal controls primarily of European ancestry (EA), among whom 218 cases and 177 controls were Caribbean Hispanic (CH). An age-, sex- and APOE based risk score and family history were used to select cases most likely to harbor novel AD risk variants and controls least likely to develop AD by age 85 years. We tested ~1.5 million single nucleotide variants (SNVs) and 50,000 insertion-deletion polymorphisms (indels) for association to AD, using multiple models considering individual variants as well as gene-based tests aggregating rare, predicted functional, and loss of function variants. Sixteen single variants and 19 genes that met criteria for significant or suggestive associations after multiple-testing correction were evaluated for replication in four independent samples; three with whole exome sequencing (2,778 cases, 7,262 controls) and one with genome-wide genotyping imputed to the Haplotype Reference Consortium panel (9,343 cases, 11,527 controls). The top findings in the discovery sample were also followed-up in the ADSP whole-genome sequenced family-based dataset (197 members of 42 EA families and 501 members of 157 CH families). We identified novel and predicted functional genetic variants in genes previously associated with AD. We also detected associations in three novel genes: IGHG3 (pu2009=u20099.8u2009×u200910−7), an immunoglobulin gene whose antibodies interact with β-amyloid, a long non-coding RNA AC099552.4 (pu2009=u20091.2u2009×u200910−7), and a zinc-finger protein ZNF655 (gene-based pu2009=u20095.0u2009×u200910−6). The latter two suggest an important role for transcriptional regulation in AD pathogenesis.

Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer’s Disease Sequencing Project

Background/Aims: The Alzheimer’s Disease Sequencing Project (ADSP) aims to identify novel genes influencing Alzheimer’s disease (AD). Variants within genes known to cause dementias other than AD have previously been associated with AD risk. We describe evidence of co-segregation and associations between variants in dementia genes and clinically diagnosed AD within the ADSP. Methods: We summarize the properties of known pathogenic variants within dementia genes, describe the co-segregation of variants annotated as “pathogenic” in ClinVar and new candidates observed in ADSP families, and test for associations between rare variants in dementia genes in the ADSP case-control study. The participants were clinically evaluated for AD, and they represent European, Caribbean Hispanic, and isolate Dutch populations. Results/Conclusions: Pathogenic variants in dementia genes were predominantly rare and conserved coding changes. Pathogenic variants within ARSA, CSF1R, and GRN were observed, and candidate variants in GRN and CHMP2B were nominated in ADSP families. An independent case-control study provided evidence of an association between variants in TREM2, APOE, ARSA, CSF1R, PSEN1, and MAPT and risk of AD. Variants in genes which cause dementing disorders may influence the clinical diagnosis of AD in a small proportion of cases within the ADSP.

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

The Alzheimers Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed consensus calling, to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.

Genome-wide pleiotropy analysis of neuropathological traits related to Alzheimer's disease

BackgroundSimultaneous consideration of two neuropathological traits related to Alzheimer’s disease (AD) has not been attempted in a genome-wide association study.MethodsWe conducted genome-wide pleiotropy analyses using association summary statistics from the Beecham et al. study (PLoS Genet 10:e1004606, 2014) for AD-related neuropathological traits, including neuritic plaque (NP), neurofibrillary tangle (NFT), and cerebral amyloid angiopathy (CAA). Significant findings were further examined by expression quantitative trait locus and differentially expressed gene analyses in AD vs. control brains using gene expression data.ResultsGenome-wide significant pleiotropic associations were observed for the joint model of NP and NFT (NP + NFT) with the single-nucleotide polymorphism (SNP) rs34487851 upstream of C2orf40 (alias ECRG4, P = 2.4 × 10−8) and for the joint model of NFT and CAA (NFT + CAA) with the HDAC9 SNP rs79524815 (P = 1.1 × 10−8). Gene-based testing revealed study-wide significant associations (P ≤ 2.0 × 10−6) for the NFT + CAA outcome with adjacent genes TRAPPC12, TRAPPC12-AS1, and ADI1. Risk alleles of proxy SNPs for rs79524815 were associated with significantly lower expression of HDAC9 in the brain (P = 3.0 × 10−3), and HDAC9 was significantly downregulated in subjects with AD compared with control subjects in the prefrontal (P = 7.9 × 10−3) and visual (P = 5.6 × 10−4) cortices.ConclusionsOur findings suggest that pleiotropy analysis is a useful approach to identifying novel genetic associations with complex diseases and their endophenotypes. Functional studies are needed to determine whether ECRG4 or HDAC9 is plausible as a therapeutic target.

SEX-SPECIFIC ANALYSIS OF THE ADSP CASE-CONTROL WHOLE-EXOME SEQUENCING DATASET

National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, USA; University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Universit e Lille 2, Lille, France; Institut Pasteur de Lille, Lille, France; INSERM, Lille, France; Erasmus University Medical Center, Rotterdam, Netherlands; University of Texas School of Public Health, Houston, TX, USA; University of Texas Health Science Center at Houston, Houston, TX, USA. Contact e-mail: joshbis@uw.edu

NOVEL GENETIC VARIANTS ASSOCIATED WITH FAMILIAL LATE-ONSET ALZHEIMER DISEASE IN THE ALZHEIMER’S DISEASE SEQUENCING PROJECT

Background:The Alzheimer’s Disease Sequencing Project (ADSP) is an initiative to identify rare genetic variation influencing Late Onset Alzheimer’s Disease (LOAD) risk. As part of the ADSP, we performed whole-genome sequencing (WGS) in 67 Caribbean Hispanic (CH) and 44 non-Hispanic white (NHW) extended families multiply affected by LOAD, followed by extensive quality control, variant filtering, and gene-based association tests.Methods: WGS datawere generated for 351 subjects from 67 CH families and 197 subjects from 44 NHW families, including both AD and cognitively intact relatives. Alignment was performed using the Burrows-Wheeler algorithm, followed by genotype calling using a consensus calling pipeline that used both GATK genotype calls and ATLAS genotype calls. Variants were annotated for allele frequency and predicted functional impact, categorized into damaging (e.g., loss of function, high CADD scores, etc) and likely damaging (e.g., non-synonymous, moderate CADD, etc). We performed gene-based association testing, accounting for family structure using the FSKAT software. Association was performed using rare variants (MAF<0.01) and two models (damaging set only; damaging and likely damaging), with CH and NHW sets analyzed separately. Results:Examination of the 30 known LOAD genes (largely identified by GWAS-based meta-analyses) confirmed the role of rare functional variation in a number of genes, including CR1 (p 1⁄40.040 in NHW, p1⁄40.049 in CH; damaging variants only) and SLC24A4 (p1⁄40.002 in NHW, p1⁄40.040 in CH). Other candidate genes showed nominal association in one but not both datasets (AKAP9, FERMT2, GRN, HLA-DRB5, MEF2C in NHW dataset; BIN1, PTK2B in CH). Additional genes showed strong association in the CH dataset, with nominal association in the NHW. These include ATG2A (p1⁄40.0003 in CH, p1⁄40.02 in NHW), a gene involved in both autophagy and lipid droplet formation, and CD69 (p1⁄40.00054 in CH, p1⁄40.02 in NHW), a gene involved in cell proliferation.Conclusions:These results suggest rare, functional variation may influence LOAD risk in multiplex families, even among genes identified through common variation. We also show association with novel genes, ATG2A and CD69, with support from both CH and NHW families. Variants are currently being validated using other technologies, and follow-up and replication analyses are ongoing.

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

RARE DELETERIOUS AND LOSS-OF-FUNCTION VARIANTS IN OPRL1 AND GAS2L2 CONTRIBUTE TO THE RISK OF LATE-ONSET ALZHEIMER’S DISEASE: ALZHEIMER’S DISEASE SEQUENCING PROJECT CASE-CONTROL STUDY

P1-018 RARE DELETERIOUS AND LOSS-OF-FUNCTION VARIANTS IN OPRL1 AND GAS2L2 CONTRIBUTE TO THE RISK OF LATE-ONSETALZHEIMER’S DISEASE: ALZHEIMER’S DISEASE SEQUENCING PROJECT CASE-CONTROL STUDY Xueqiu Jian, Joshua C. Bis, Brian W. Kunkle, Kara L. Hamilton, Gary W. Beecham, William S. Bush, William Salerno, Dan Lancour, Yiyi Ma, Yuning Chen, Anita L. DeStefano, Josee Dupuis, Eric Boerwinkle, Gerard D. Schellenberg, Sudha Seshadri, Adam C. Naj, Myriam Fornage, Lindsay A. Farrer, the Alzheimer’s Disease Sequencing Project, University of Texas Health Science Center at Houston, Houston, TX, USA; University of Washington, Seattle, WA, USA; University of Miami Miller School of Medicine, Miami, FL, USA; Case Western Reserve University, Cleveland, OH, USA; 5 Baylor College of Medicine, Houston, TX, USA; Boston University, Boston, MA, USA; Boston University School of Public Health, Boston, MA, USA; University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA. Contact e-mail: Xueqiu.Jian@uth.tmc.edu