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Background: African Americans (AA) are underrepresented in Alzheimer's disease (AD) brain donation research, making up approximately 2% of brain donations to the National Alzheimer's Coordinating Center (NACC). The objective of this study is to gain insights into the attitudes of Black∖AA individuals toward brain donation and perceptions of medical research that may hinder or facilitate brain donation. Method: A 35‐item survey was developed to understand the attitudes and beliefs about brain donation in a sample of AA, using survey items validated in prior investigations. Electronic and paper and pencil surveys were administered in Florida, New York and North Carolina, United States between November 2021‐January 2022. Descriptive analysis of demographic data and was conducted using SAS® software version 9.4. Result: The racial composition of the 135 respondents was primarily Black/African American (97.58%), with the remaining responses for race as "missing" or "prefer not to answer". Most respondents were women (73.6%). The majority of respondents report having a positive view about medical research (85.5%), while 72.1% believe that medical researchers can be trusted to protect the interests of participants. Many respondents reported wanting to learn more about AD (93.1%). Whereas, 82.0% report not knowing how researchers use a brain for research, 58.9% report knowing that study of the brain is important for advances in AD. Despite 53.1% of respondents reporting being either unlikely or unsure whether they would donate a loved one's brain even if that was their loved ones' wish, only 21.4% of the sample believe that the decision to donate one's brain is mostly a family decision. Overall, 63.8% of the respondents are either unsure or unlikely to donate their own brain. Conclusion: Findings suggest that 1) awareness of brain donation research procedures and processes should be focused on whole family education, and 2) increasing knowledge about AD will be fruitful areas for an educational intervention. Including families in the consenting processes will be pivotal in ensuring that brain donation occurs. Results will be utilized to develop a community‐informed educational program for Black communities about AD research and brain donation. [ABSTRACT FROM AUTHOR]

Background: The hallmark lesions of Alzheimer Disease (AD) include tangles and plaques; however, these seldom appear alone. Lesions of AD‐related dementias such as vascular dementias and Lewy body dementias often co‐occur with AD. These co‐occurring lesions and total lesion burden are associated with a higher likelihood of dementia and severe cognitive impairment. Even amongst other lesions, cerebral amyloid angiopathy (CAA) presents a strong risk for more severe cognitive impairment. CAA also shows moderate correlations to AD (rho = 0.31), suggesting that CAA pathology could present an underlying or related process of AD pathology. We hypothesize that there is a genetic overlap between CAA and AD and therefore we investigate the influence of known AD genes on CAA. Method: Data come from 3,495 autopsied individuals with neuropathology and array data from the National Alzheimer's Coordinating Centers (NACC). CAA was measured according to NACC neuropathology form guidelines. We used ordinal logistic regression to model APOE genotype and 22 other known AD variants with CAA severity while adjusting for sex, age at death, and AD pathology. For the 22 other known AD variants, we tested the lead variants reported by Kunkle et al. and labeled by closest gene. We modeled APOE by carrier status and genotype. Result: We confirmed associations for APOE with CAA severity, when modeling APOE as e4 dosage (OR=2.34, p<0.001) or by genotype (e3/e4: OR=1.96, p<0.001; e4/e4: OR=5.76, p<0.001). However, we did not see a significant association between CAA severity and APOEe2 carriers, as others have reported. Association persisted when including AD pathology terms in the model, even when extending to interaction‐based models. Genetic variations in 7 of the 22 known AD genes (BIN1, HLA‐DRB1, TREM2, CLU, PICALM, SORL1, SLC24A4) showed significant associations with CAA while accounting for AD pathology. Conclusion: We confirmed strong associations of APOEe4 with CAA in a large clinical population. We modeled other known AD genes and 7 of them showed significant associations with CAA, demonstrating genetic overlap between AD and CAA pathologies. This study suggests that there is genetic overlap between CAA and AD pathology that could point to shared disease mechanisms for the targeting and treatment of AD. [ABSTRACT FROM AUTHOR]

Background: The COVID‐19 pandemic has placed a demand on researchers to limit in‐person contact with participants, greatly impacting Alzheimer Disease (AD) research. To address this problem, we describe here an approach to using digital technology to continue nationwide clinical recruitment and ascertainment of biological samples while adhering to COVID‐19 guidelines and travel restrictions. Method: To accomplish this, we considered a videoconferencing approach for remote delivery of cognitive assessments. A multi‐site panel of neurologists and clinical psychologists and a detailed literature review ensured a protocol that captures the best‐practices for administering assessments through videoconferencing while ensuring consistency between remote and in‐person administration. Clinical coordinators underwent training to ensure good agreement with in‐person administration. Most aspects of the cognitive assessments easily transferred to videoconferencing, though Trail Making A and B, and Digit Symbol‐Coding were removed to protect the integrity of the evaluation. Additionally, we coordinated the collection of biological samples with a national company, Quest Diagnostics, to provide phlebotomy services at the participant's residence. All protocols were developed under the guidance of the Human Subjects Research Office at the University of Miami and with approval of local IRB. Result: Our clinical coordinators completed over two dozen remote assessments using these protocols. Both cases and controls were enrolled, across various ethnic populations within our study. The distributions of age and 3MS were similar between in‐person and remote assessments. The uptake of videoconferencing enrollment varied among the age groups, level of impairment, at‐home support system and telemedicine readiness. For example, earlier‐onset groups had the best uptake, while older‐onset groups showed the least uptake due to a higher prevalence of telemedicine unreadiness (Lam et al., 2020; Bossen et al.,2015). Conclusion: This study demonstrates that remote enrollment and ascertainment of biological samples through videoconferencing and partnering with national mobile phlebotomy services is feasible. This approach allows researchers to continue ascertainment efforts while maintaining their participants' autonomy through informed consent and privacy throughout the process and minimizing their exposure to COVID‐19. [ABSTRACT FROM AUTHOR]

Background: A recent study of educational attainment (EA) in African Americans (AA) demonstrated that it is associated with a decreased risk of AD, as previously described in the Non‐Hispanic White population. Several studies have also suggested that EA is a proxy for the concept of cognitive reserve (CR) or the capacity of the brains of some individuals to compensate clinically for the neurodegenerative processes of AD. If true, then EA should also be associated with other aspects of AD, including functional impairment, often measured using the Clinical Dementia Rating scale (CDR). The aim of this study is to test the hypothesis that higher EA is associated with decreased functional impairment in AA. Methods: Participants consisted of 158 AA AD cases with known years of completed education, ascertained for a genetics study of AD. Education levels were stratified into three categories:<8 years, 9‐12 years, >12 years. We used a regression model to test the association between years of education and functional impairment (composite score) with the age at onset and sex as covariates. Using the non‐memory components of the CDR: Judgment and Problem solving, Home and Hobbies, Community Involvement, and Personal Care, we formulated a composite score of 12 totaling the individual score of the 4 components. A composite score of 0 is no functional impairment and 12 equals severe functional impairment. Results: The dataset was 77.2% female with a mean age of exam of 78.8 years and a mean CDR functional composite score of 1.97 and a mean educational attainment of 11.3 years. Our results showed a significant association between education and the composite score (). An increase in the years of education was negatively correlated with functional impairment. Conclusion: Our data support the hypothesis that higher educational attainment is associated with reduced functional impairment. These results extend and support the concept that EA is a measure of CR in AA, extending the role of CR and EA to functional abilities. Further studies on the mechanism by which EA is protective is needed. In addition, our results suggest that EA should be considered when evaluating functional abilities in individuals thought to have AD. [ABSTRACT FROM AUTHOR]

Background: Among older Peruvians (over 65‐years) the prevalence of dementia is 7%, with 56% meeting clinical criteria for Alzheimer Disease (AD). Peruvians, are an admixed population with approximately 80% Amerindian ancestral background. We have ascertained a cohort of Alzheimer Disease (AD) cases and cognitively intact controls for genetic studies. Method: All participants have been recruited since 2019 using community outreach ascertainment strategies and hospital‐based recruitment from Lima, Peru. Cases were assessed by neurologist following NINDS/ADRDA criteria; and completed a comprehensive neurocognitive, neuropsychiatric and functional assessments. Controls were screened using MMSE, Clock drawing test and Pfeffer functional activities questionnaire. IRBs approvals from the participating Peruvian institutions and University of Miami were obtained for this study. Result: A total of 102 AD cases (4 familial cases) and 152 controls were recruited since 2019 to December 2020. For AD cases: age at examination were 76.5±9.09, age at onset were 72.15±8.82, and 63.7% were female, average of 9.9±4.9 year of education. For controls: age at examination were 73.13±6.54, 62.5% were female, average of 11.62±4.41 year of education. Among cases diagnosis was classified as: 62.8% possible AD (two cases screened for Cerebrospinal fluid Abeta42 and tau protein levels) and 37.2% probable AD. Clinical and cognitive assessment profile for cases: MMSE average score was 17.2± 4.9 and Addenbrook's Cognitive Examination average score was 38.5± 21.7 with memory loss predominance. Based on NPI the most frequent neuropsychiatric symptoms were irritability (51%), delusions (46%) and apathy (45%). Severity of dementia were assessed by CDR (CDR=3 for 33.9%, CDR=2 for 32.3%, CDR=1 for 24.2% and CDR=0.5 for 9.7%). Depressive symptoms were assessed with Geriatric Depression Scale with an average of 4.4±3.5. Conclusion: The clinical features of the AD cohort in the Peruvian population are consistent with previous reports. There is a tendency of a higher level of education in the control. Among the Peruvian AD cohort, the main neuropsychiatric symptoms are irritability, delusions and apathy consistent with the predominance of moderate to severe dementia. Reference: Marca V. et al. Dissecting the role of Amerindian genetic ancestry and ApoE ε4 allele on Alzheimer disease in an admixed Peruvian population, Neurobiology of Aging, 2020. [ABSTRACT FROM AUTHOR]

Background: Plasma proteins as biomarkers for the differential diagnosis of AD from other similar neurodegenerative disorders, as well as the identification of preclinical AD, has recently been well supported across several large AD cohorts. However, these are composed primarily of individuals of non‐Hispanic European ancestry. Few studies have been performed in African‐American or Hispanic/Latinx AD populations to determine if plasma biomarkers are also useful in these populations. Given the differences in AD risk loci found across ancestries, the application of these biomarkers in diverse populations is not assured. Therefore, the aim of this study is to explore the utility of plasma biomarkers in AD, MCI and at‐risk family members from diverse ancestral backgrounds. Method: As part of ongoing initiatives to understand AD in individuals of diverse ancestry, we are measuring the plasma level of biomarkers in a cohort of more than 3,000 individuals. This includes: 999 African Americans (248 AD cases, 591 controls, 160 MCI), 581 Puerto Ricans (223 AD cases, 208 controls, 150 MCI), 1052 Puerto Ricans in families (411 AD cases, 413 controls, 228 MCI), 98 Cubans (23 AD cases, 39 controls, 36 MCI), and 117 Peruvians (33 AD cases, 75 controls, 9 MCI). We will also have data on autopsy confirmed European AD cases (37) and a cohort of Amish individuals (∼400 AD cases, ∼200 MCI, and ∼500 controls). Plasma proteins tested are Aβ42, Aβ40, total Tau, and p‐Tau181 using Simoa chemistry assays (Quanterix HD‐X). All measurements are performed in duplicate and data analysis performed using HD‐X Analyzer Software v1.6. Result: Measurement and analysis of biomarkers in this diverse dataset is currently underway and will be completed in a few months. These results will allow a direct comparison of biomarker analysis related to AD diagnosis between European, African, and Amerindian ancestries. Moreover, a family‐based design for over 1000 Puerto Rican individuals will be the first to identify potential heritable trends in biomarker levels. Conclusion: This study is critical to being to understand how plasma biomarkers for AD may vary across diverse ancestries and whether previous findings will be generalizable and useful for all individuals, regardless of ancestry. [ABSTRACT FROM AUTHOR]

Background: Genomic studies of Alzheimer disease (AD) have primarily focused on non‐Hispanic White (NHW) participants affected by the late‐onset form (LOAD; onset age: >65), or the study of early onset AD (EOAD; onset age <=65) cases showing Mendelian inheritance patterns associated with mutations in the APP, PSEN1 and PSEN2 genes. However, mutations in these three genes explain ∼10% of EOAD cases. There are no large‐scale efforts to collect and study EOAD cases not explained by these genes, despite this unexplained category accounting for ∼90% of EOAD cases. Method: To address this, we aim to identify additional EOAD‐associated variants, genes and pathways through a large‐scale whole‐genome sequencing (WGS) study of unexplained EOAD. We will include cases from several AD cohorts, including the Resource for Early‐onset Alzheimer Disease Research (READR), the Knight‐ADRC at Washington University, the Alzheimer's Disease Genetics Consortium (ADGC), and others. Generating and harmonizing a dataset of 200 non‐Hispanic White (NHW) and Caribbean Hispanic (CH) multiplex EOAD families, over 5,400 EOAD singletons and over 13,000 unrelated, cognitive controls, all with WGS, this project will yield the largest EOAD genomics dataset to‐date, improving statistical power for variant identification and allowing us to assess the impact of specific factors such as APOE genotype, vascular risk factors, and neuropsychiatric comorbidities. The inclusion of a large set of Hispanic families and singletons allows the examination of EOAD risk in a significantly understudied population. Analyses will comprise both linkage and association‐based approaches, analyses of polygenic and ancestry effects, and a thorough examination of neurocognitive, neuropsychiatric and cardiovascular endophenotypes. Result: When completed this study will point to novel genetic contributors to EOAD, shed light on the mechanisms of AD and facilitate the development of novel prediction models and therapeutics. Conclusion: Sampling, phenotyping and sequencing analysis protocols will be complementary to and compatible with the existing LOAD genomics resources, such as the Alzheimer Disease Sequencing Project (ADSP) and related studies. This phenotypic and genomic consistency, together with the use of existing AD infrastructure (NIAGADS), allows for immediate integration with the leading efforts on LOAD, enabling rapid large‐scale investigation of a variety of additional critical AD genomics hypotheses. [ABSTRACT FROM AUTHOR]

Background: African Americans (AA) are substantially underrepresented in Alzheimer's disease (AD) genetic studies, yet their admixed genetic ancestry (African and European) provides a unique opportunity to identify novel genetic factors associated with AD related to genetic ancestry. Admixture mapping (AM) provides a more powerful approach than SNP‐based genome‐wide association studies (GWAS) in admixed populations in part due to the lower multiple testing burden. In this study we used AM to identify regions associated with AD in AA individuals. Methods: Our analyses included 10,271 individuals from 17 AD Sequencing Project and AD Genetics Consortium cohorts. We estimated global ancestry (GA) using the GENESIS software. To infer local ancestry (LA), the target AA dataset was combined with appropriate reference‐population samples from HGDP reference panel, and LA was estimated using SHAPEIT followed by RFMix. Then, we performed AM using the GENESIS software separately on each cohort. We meta‐analyzed the AM results with the random effect approach (RE2). We calculated the significance threshold using STEAM software. Finally, we performed logistic regression of genotype on affection status for variants across the prioritized regions from AM for fine‐mapping. The regression model included LA and genotype as main effects and term for their interaction, along with GA, sex and age as covariates, and used permutation‐based testing approach for multiple test correction (N=10,000). Results: AM identified two genome‐wide significant loci on chromosomes 17p13.2 (pv=2.2 x10‐5) and 18q21.33 (pv=1.22x10‐5). 17p13.2 region was identified as a genome‐wide significant in two previous studies in non‐Hispanic White population. To fine map this region we conducted ancestry‐aware regression analysis. LA x genotype interaction model found the MINK1 gene (rs72835013) on the 17p13.2 region significantly associated with AD (pv = 1x10‐4). Conclusions: Our results confirmed an AD associated region on the chromosome 17p13.2 and showed that the 17p13.2 region increases AD risk in AA individuals with the European LA. This region includes genes previously indicated in AD such as SCIMP through association studies and the MINK1 and SLC25A11 genes through brain expression studies. [ABSTRACT FROM AUTHOR]

Background: Recently we demonstrated that local genomic ancestry (LA) drives the difference in AD risk between European (EU) and African (AF) carriers of APOEε4/4. As a follow‐up study using single‐nuclei RNAseq, we found that AD APOEε4 homozygotes with EU Local Ancestry (LA) had a significantly increased APOEε4 expression compared to AD APOEε4/4 homozygotes with AF LA. In two of the EU LA patients, an astrocyte cluster with the highest APOEε4 expression was observed and expressed a panel of genes consistent with A1 reactive astrocytes (A1RA). No such cluster was seen in the AF LA. As a previous study in mice suggested that APOEε4 expression was a contributor to the development of A1RA, we sought to explore the relationship of increased APOEε4 expression and A1RA using inducible pluripotent stem cells (iPSC)‐derived astrocytes. Method: APOEε4/4 astrocytes from one European and one African LA were derived from iPSC lines. The astrocytes were brought to maturity (Day 54 in‐vitro), and then each group was treated with either a cytokine cocktail (IL‐1a, hTNFa, C1q) or overexpressed with APOEε4 by lentiviral transduction for 14‐days (two replicates per line). mRNA was extracted and qPCR was performed to measure changes in APOEε4 and markers of A1RA (C3, GBP2, IFITM3). Result: iPSCs were validated by immunocytochemistry (ICC) and qPCR for Nanog, SOX2 and OCT4 and subsequently differentiated into astrocytes. Astrocyte validation was performed by GFAP and βS100 ICC. Astrocytes treated with the cytokine cocktail had a 100‐ and 600‐fold increase in C3 in EU and AF LA astrocytes respectively, as well as significant increase in GBP2 and IFITM3 compatible with A1RA. When overexpressing APOEε4, a significant increase in C3 was observed in the EU LA astrocytes, while no increase was observed in the AF LA astrocytes. Conclusion: Our preliminary results support the hypothesis that APOEe4 overexpression can increase the conversion of astrocytes to the toxic A1RA state in EU LA astrocytes. It is intriguing that this effect was not seen in the African LA astrocytes. By increasing the sample size, we will increase the significance of the association between APOEe4 overexpression and A1RA induction in EU LA astrocytes compared to their AF counterparts. [ABSTRACT FROM AUTHOR]

Background: We recently published a genome‐wide association study (GWAS) for Alzheimer disease (AD) in African Americans (AA; 2,784 cases, 5,222 cognitively normal individuals) (Kunkle et al. JAMA Neurol. 2021). We now present a GWAS meta‐analysis of this AA data stratified by APOEε4‐genotype. Method: All datasets were imputed to the African Genome Resource panel (∼93 million variants) using the Sanger imputation server. Single‐variant association analysis was conducted in APOEε4‐negative (1,060 cases, 3,247 cognitively normal individuals) and APOEε4‐positive (1,450 cases, 1,808 cognitively normal individuals) groups separately, adjusting for age, sex and principal components. Individual datasets were analyzed applying logistic regression for case‐control datasets and general estimating equations for family‐based datasets. Within‐study results were meta‐analyzed using METAL. Result: Following quality control, ∼14.4 million variants in the APOEε4‐positive group and ∼14.2 million variants in the APOEε4‐negative group with minor allele frequency >=0.01 were analyzed. We identified seven novel candidate loci at P<10‐6 for AD in AA. These include signals in the APOEε4‐negative analysis centered at 16q24.1 (P=3.9x10‐7), 2q22.2 (P=4.3x10‐7), 1p36.32 (P=5.8x10‐7), 2p23.1 (P=8.2x10‐7), 8q21.3 (P=9.4x10‐7), and 4p15.1 (P=9.4x10‐7), and one signal in the APOEε4‐positive analysis centered at 7p15.3 (P=9.6x10‐7). A scan for eQTL's within these loci found an eQTL in the 7p15.3 locus for the gene DECR1, involved in reaction to oxidative stress, in brain cerebellum (P=1.8x10‐5; GTEx.v7). Conclusion: We identified several potential novel candidate loci for AD in AA at P<10‐6 in groups of individuals with and without APOEε4 alleles. In addition to DECR1, these loci contain genes and functions relevant to AD including: FOXL1 (key regulatory molecule associated with transcriptional changes in AD) and an association (P=2x10‐6) with hippocampal volume in ADNI at 16q24.1, LRP1B (APP binding partner; decreases APP processing to Aβ) at 2q22.2, and MMEL1 (clears Aβ; expression and activity are altered in mild‐cognitive impairment) at 1p36.32. Confirmation of these loci in larger studies of AA is necessary and could provide novel therapeutic targets for AD. [ABSTRACT FROM AUTHOR]

Background: Generalization of Alzheimer disease (AD) genetic findings to ancestrally admixed populations, such as African Americans (AA) and Caribbean Hispanics from Puerto Rico (PR), is challenging as they are underrepresented in most studies. There is evidence of differing underlying genetic architecture of AD in these groups, but identification of associated DNA variants is just a first step in understanding underlying biology. We evaluated the gene regulatory architecture by expression quantitative trait loci (eQTL) analysis within and across ancestries in a diverse cohort. Method: We performed RNAseq from peripheral blood and genotyping with the Illumina Global Screening Array in 537 individuals: 241 non‐Hispanic Whites (NHW) (121 AD, 120 cognitively intact controls), 232 AA (115 AD, 117 controls) and 64 PR (34 AD, 30 controls). All individuals had phenotypic adjudication for consensus AD status and were over the age of 65 at last examination and blood draw. We ran eQTL analysis overall and within each ancestry accounting for age and sex. Results were filtered for variant‐gene pairs with p‐values ≤ 1x10‐5. Result: We identified 1846 eQTLs at 737 genes, 2383 eQTLs at 791 genes, and 979 eQTLs in 459 genes in AA, NHW and PR, respectively. 603 eQTLs (∼30%) were significant across all ancestries with the same target gene and direction of effect. Interestingly, >70% of the PR eQTLs were also significant in either or both of the AA and NHW. Among eQTLs in linkage disequilibrium (r2>=0.5) with a significantly associated marker from AD GWAS studies in NHW (Kunkle at el 2019) or AA (Kunkle et all 2020) were two specific to AA for HLA‐DQB1 and C1QTNF4 and three to NHW for C2, CNN2, and PILRB. Analysis of case and control eQTL effects and the role of local ancestry in other admixed populations, including those with Amerindian ancestry, is ongoing. Conclusion: AA, NHW, and PR individuals have overlapping regulatory architecture that likely reflects the admixture in AA (20% European, 80% African) and PR (∼60% European, 20% African, and 20% Amerindian). These results underscore the importance of continuing to include diverse populations in AD genomics and functional studies to identify unique and shared architecture of AD. [ABSTRACT FROM AUTHOR]

Background: Alzheimer disease (AD) is a degenerative brain disease, being the most common cause of progressive dementia and listed as the sixth leading cause of mortality in the USA. It is often described as either early onset (EOAD, age at onset, [AAO] <= 65) or late onset (LOAD, [AAO]>65). Non‐Mendelian EOAD (not monogenic; nmEOAD) has irregular inheritance patterns and fluctuating AAO, characteristics also present in LOAD cases. There is still a lack of evidence in the literature depicting the similarities (if any) between nmEOAD and LOAD forms, being unclear how much genetic etiology is shared by the two forms of AD. To shed light to this question, a genome‐wide association study (GWAS) and heritability analyses of nmEOAD and LOAD were performed. Method: Genetic data on 21,622 individuals from the Alzheimer Disease Genetics Consortium (ADGC) were used: (1,476 nmEOAD, 9,695 LOAD and 10,451 control). Single‐variant association analyses were performed using logistic regression under two models: (1) ancestry plus SNP, and (2) ancestry, sex, APOE dosage, and SNP. nmEOAD and LOAD were considered separately. LD score regression was used to estimate the SNP heritability (h2) and genetic correlation (rg), considering two additional models: (3) ancestry, sex, and SNP and (4) ancestry, APOE dosage and SNP. Result: Several known candidate genes confirmed for LOAD along with novel regions associated with immune and cell‐signaling pathways in nmEOAD models. Gene based tests showed significant association for APOE gene (Chr19): nmEOAD (p=3.89x10‐16 and p=4.29x10‐12) and LOAD (p=1.07x10‐65 and p=1.12x10‐14), models (1) and (2) respectively. Heritability analyses showed higher h2 values for EOAD (h2=0.24, 0.23, 0.25 and 0.24) than LOAD (h2=0.18, 0.14, 0.18, and 0.14) for models (1) to (4) respectively. Genetic correlation showed moderate genetic overlap between EOAD and LOAD only for models: (2) rg=0.35 (p=0.0283) and (4) rg=0.34 (p=0.0261). Conclusion: GWAS and heritability analysis suggest that the genetic etiology of EOAD has a noncomplete genetic overlap with LOAD, with a moderate overlap when APOE dosage is modeled and a minimal overlap otherwise (APOE effect). The results also suggest a stronger polygenic effect in EOAD than LOAD, confirming the need for additional genomics efforts in nmEOAD. [ABSTRACT FROM AUTHOR]

Background: A limited number of studies have looked at the genetics of early onset (≤65 years old) Alzheimer disease (EOAD); hence, there is much unidentified heritability contributing to this form of the disease. This study aims to identify novel genes associated with EOAD risk and investigate its differences compared to late onset AD (LOAD). Method: We have combined five cohorts (Knight‐ADRC, NIA‐LOAD, Cache County, Mayo Clinic and ADSP) to generate the largest to date whole exome sequence (WES) non‐Hispanic white EOAD dataset (1,385 cases and 3,867 controls). Sequence data was aligned against GRCh37 reference genome using BWA and GATKv3.5 was used to perform variant calling and QC. Statistical analyses included single variant, gene‐based association of rare (MAF<1%) and pathogenic (CADD>20) variants, and pathway analyses. Result: We found that EOAD is enriched in rare nonsynonymous variants compared to LOAD cases (OR=5.67, p=2.2×10‐16). We identified novel associations (HOXA1 ‐ OR=2.11, p=4.60×10‐14, ADAM29 ‐ OR=6.77, p=2.58×10‐08, DHX16 OR=1.65, p=3.18×10‐08 ,) and a higher effect of certain variants (TREM2 p.Arg47His, OR=7.28, p=2.02×10‐09) in EOAD compared to previous LOAD studies (OR=2.08‐4.07). We identified nine statistically significant (p<0.5×10‐04) genes (SMG5, BCAM, KCNJ1, UBXN6, MIEN1, FRMPD1, ABCD2, ADAT2 and HADHB) in both the MAF<1% and CADD>20 gene‐based analysis. These genes are involved in fatty‐acid metabolic processes (pval=2.18×10‐04) and in endosome to lysosome transport (p=0.003) and we highlight UBXN6, a known Inclusion Body Myopathy with Paget Disease of Bone and Frontotemporal Dementia gene. Conclusion: We are currently performing replication and meta‐analysis to validate these new signals. [ABSTRACT FROM AUTHOR]

An inverse association between Parkinson disease (PD) and total vitamin D levels has been reported, but whether vitamin D from different sources, that is, 25(OH)D2 (from diet and supplements) and 25(OH)D3 (mainly from sunlight exposure), all contribute to the association is unknown. Plasma total 25(OH)D, 25(OH)D2, and 25(OH)D3 levels were measured by liquid chromatography-tandem mass spectrometry in PD patients (n = 478) and controls (n = 431). Total 25(OH)D was categorized by clinical insufficiency or deficiency; 25(OH)D2 and 25(OH)D3 were analyzed in quartiles. Vitamin D deficiency (total 25[OH]D < 20 ng/mL) and vitamin D insufficiency (total 25[OH]D < 30 ng/mL) are associated with PD risk (odds ratio [OR] = 2.6 [deficiency] and 2.1 [insufficiency]; P < 0.0001), adjusting for age, sex, and sampling season. Both 25(OH)D2 and 25(OH)D3 levels are inversely associated with PD ( Ptrend < 0.0001). The association between 25(OH)D2 and PD risk is largely confined to individuals with low 25(OH)D3 levels ( Ptrend = 0.0008 and 0.12 in individuals with 25[OH]D3 < 20 ng/mL and 25[OH]D3 ≥ 20 ng/mL, respectively). Our data confirm the association between vitamin D deficiency and PD, and for the first time demonstrate an inverse association of 25(OH)D2 with PD. Given that 25(OH)D2 concentration is independent of sunlight exposure, this new finding suggests that the inverse association between vitamin D levels and PD is not simply attributable to lack of sunlight exposure in PD patients with impaired mobility. The current study, however, cannot exclude the possibility that gastrointestinal dysfunction, a non-motor PD symptom, contributes to the lower vitamin D2 levels in PD patients. © 2014 International Parkinson and Movement Disorder Society [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) and related dementias are a major public health challenge and present a therapeutic imperative for which we need additional insight into molecular pathogenesis. We performed a genome-wide association study and analysis of known genetic risk loci for AD dementia using neuropathologic data from 4,914 brain autopsies. Neuropathologic data were used to define clinico-pathologic AD dementia or controls, assess core neuropathologic features of AD (neuritic plaques, NPs; neurofibrillary tangles, NFTs), and evaluate commonly co-morbid neuropathologic changes: cerebral amyloid angiopathy (CAA), Lewy body disease (LBD), hippocampal sclerosis of the elderly (HS), and vascular brain injury (VBI). Genome-wide significance was observed for clinico-pathologic AD dementia, NPs, NFTs, CAA, and LBD with a number of variants in and around the apolipoprotein E gene (APOE). GalNAc transferase 7 (GALNT7), ATP-Binding Cassette, Sub-Family G (WHITE), Member 1 (ABCG1), and an intergenic region on chromosome 9 were associated with NP score; and Potassium Large Conductance Calcium-Activated Channel, Subfamily M, Beta Member 2 (KCNMB2) was strongly associated with HS. Twelve of the 21 non-APOE genetic risk loci for clinically-defined AD dementia were confirmed in our clinico-pathologic sample: CR1, BIN1, CLU, MS4A6A, PICALM, ABCA7, CD33, PTK2B, SORL1, MEF2C, ZCWPW1, and CASS4 with 9 of these 12 loci showing larger odds ratio in the clinico-pathologic sample. Correlation of effect sizes for risk of AD dementia with effect size for NFTs or NPs showed positive correlation, while those for risk of VBI showed a moderate negative correlation. The other co-morbid neuropathologic features showed only nominal association with the known AD loci. Our results discovered new genetic associations with specific neuropathologic features and aligned known genetic risk for AD dementia with specific neuropathologic changes in the largest brain autopsy study of AD and related dementias. [ABSTRACT FROM AUTHOR]

ABSTRACT Background We have reported that intermediate repeat lengths of the C9ORF72 repeat are a risk factor for Parkinson's disease (PD) in a clinically diagnosed data set. Because 10% to 25% of clinically diagnosed PD have different diagnoses upon autopsy, we hypothesized that this may reflect phenotypic heterogeneity or concomitant pathology of other neurodegenerative disorders. Methods We screened 488 autopsy-confirmed PD cases for expansion haplotype tag rs3849942T. In 196 identified haplotype carriers, the C9ORF72 repeat was genotyped using the repeat-primed polymerase chain reaction assay. Results No larger (intermediate or expanded) repeats were found in these autopsy-confirmed PD samples. This absence of larger repeats is significantly different from the frequency in clinically diagnosed datasets ( P = 0.002). Conclusions Our results suggest that expanded or intermediate C9ORF72 repeats in clinically diagnosed PD or parkinsonism might be an indication of heterogeneity in clinically diagnosed PD cases. Further studies are needed to elucidate the potential contribution of the C9ORF72 repeat to autopsy-confirmed PD. © 2014 International Parkinson and Movement Disorder Society [ABSTRACT FROM AUTHOR]

Objective: Genome-wide association (GWAS) methods have identified genes contributing to Parkinson's disease (PD); we sought to identify additional genes associated with PD susceptibility. Methods: A 2-stage design was used. First, individual level genotypic data from 5 recent PD GWAS (Discovery Sample: 4,238 PD cases and 4,239 controls) were combined. Following imputation, a logistic regression model was employed in each dataset to test for association with PD susceptibility and results from each dataset were meta-analyzed. Second, 768 single-nucleotide polymorphisms (SNPs) were genotyped in an independent Replication Sample (3,738 cases and 2,111 controls). Results: Genome-wide significance was reached for SNPs in SNCA (rs356165; G: odds ratio [OR] = 1.37; p = 9.3 × 10−21), MAPT (rs242559; C: OR = 0.78; p = 1.5 × 10−10), GAK/DGKQ (rs11248051; T: OR = 1.35; p = 8.2 × 10−9/rs11248060; T: OR = 1.35; p = 2.0 × 10−9), and the human leukocyte antigen (HLA) region (rs3129882; A: OR = 0.83; p = 1.2 × 10−8), which were previously reported. The Replication Sample confirmed the associations with SNCA, MAPT, and the HLA region and also with GBA (E326K; OR = 1.71; p = 5 × 10−8 Combined Sample) (N370; OR = 3.08; p = 7 × 10−5 Replication sample). A novel PD susceptibility locus, RIT2, on chromosome 18 (rs12456492; p = 5 × 10−5 Discovery Sample; p = 1.52 × 10−7 Replication sample; p = 2 × 10−10 Combined Sample) was replicated. Conditional analyses within each of the replicated regions identified distinct SNP associations within GBA and SNCA, suggesting that there may be multiple risk alleles within these genes. Interpretation: We identified a novel PD susceptibility locus, RIT2, replicated several previously identified loci, and identified more than 1 risk allele within SNCA and GBA.ANN NEUROL 2012; [ABSTRACT FROM AUTHOR]

Likelihood ratios are necessary to properly interpret mixed stain DNA evidence. They can flexibly consider alternate hypotheses and can account for population substructure. The likelihood ratio should be seen as an estimate and not a fixed value, because the calculations are functions of allelic frequency estimates that were estimated from a small portion of the population. Current methods do not account for uncertainty in the likelihood ratio estimates and are therefore an incomplete picture of the strength of the evidence. We propose the use of a confidence interval to report the consequent variation of likelihood ratios. The confidence interval is calculated using the standard forensic likelihood ratio formulae and a variance estimate derived using the Taylor expansion. The formula is explained, and a computer program has been made available. Numeric work shows that the evidential strength of DNA profiles decreases as the variation among populations increases. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

With the advent of publicly available genome-wide genotyping data, the use of genotype imputation methods is becoming increasingly common. These methods are of particular use in joint analyses, where data from different genotyping platforms are imputed to a reference set and combined in a single analysis. We show here that such an analysis can miss strong genetic association signals, such as that of the apolipoprotein-e gene in late-onset Alzheimer disease. This can occur in regions of weak to moderate LD; unobserved SNPs are not imputed with confidence so there is no consensus SNP set on which to perform association tests. Both IMPUTE and Mach software are tested, with similar results. Additionally, we show that a meta-analysis that properly accounts for the genotype uncertainty can recover association signals that were lost under a joint analysis. This shows that joint analyses of imputed genotypes, particularly failure to replicate strong signals, should be considered critically and examined on a case-by-case basis. [ABSTRACT FROM AUTHOR]

Parkinson disease (PD) is a chronic neurodegenerative disorder with a cumulative prevalence of greater than one per thousand. To date three independent genome-wide association studies (GWAS) have investigated the genetic susceptibility to PD. These studies implicated several genes as PD risk loci with strong, but not genome-wide significant, associations. In this study, we combined data from two previously published GWAS of Caucasian subjects with our GWAS of 604 cases and 619 controls for a joint analysis with a combined sample size of 1752 cases and 1745 controls. SNPs in SNCA (rs2736990, p-value = 6.7 × 10−8; genome-wide adjusted p = 0.0109, odds ratio (OR) = 1.29 [95% CI: 1.17–1.42] G vs. A allele, population attributable risk percent (PAR%) = 12%) and the MAPT region (rs11012, p-value = 5.6 × 10−8; genome-wide adjusted p = 0.0079, OR = 0.70 [95% CI: 0.62–0.79] T vs. C allele, PAR%= 8%) were genome-wide significant. No other SNPs were genome-wide significant in this analysis. This study confirms that SNCA and the MAPT region are major genes whose common variants are influencing risk of PD. [ABSTRACT FROM AUTHOR]

Background: There is limited study of the effect of genetically determined ancestral background and diabetic risk on cognitive status in admixed populations. Puerto Ricans are an admixed population with European (EU), African (AF), and Amerindian (AI) backgrounds. We analyzed the impact of ancestry and diabetes on cognitive status in older Puerto Ricans. Method: The dataset consisted of Puerto Ricans > 60 years of age enrolled in the Puerto Rican Alzheimer Diseases Initiative (PRADI). At study entry, all participants were administered the 3MS to screen for cognitive problems. Medical history, including the presence of hypertension, diabetes, and cholesterolemia was also collected at that time. Model building analyses indicated that diabetes was the sole vascular predictor. Admixture proportions were estimated using the ADMIXTURE software. Using a Generalized Estimating Equations (GEE) approach, we modelled the contribution of sex, age at 3MS testing, global ancestry proportion, and diabetes to the participants 3MS score. Result: The dataset consisted of 689 Puerto Ricans (70% female) with a mean age at 3MS of 74.9 years (SD=8 years). Mean global ancestry proportions were highest for EU (71%) followed by AF (18%) and AI (11%). As expected, we found significant associations between age, sex, and an age‐sex interaction and the 3MS score. However, we also found significant interactions between ancestry proportions and diabetes as predictors of 3MS score. Specifically, when compared to the effects of combined EU and AI ancestry on the 3MS score, the effect of diabetes on 3MS score is larger in individuals with higher proportions of AF ancestry (p < 0.01). Conclusion: Cognitive decline can be secondary to many different deleterious factors. Along with Alzheimer disease, small vessel vascular disease is a major contributor to the development of dementia. Indeed, diabetes affects small blood vessels, and these data support the importance of controlling diabetes in the Puerto Rican population, particularly those with a strong AF ancestry. This highlights the importance of looking for a history of diabetes when evaluating cognition in dementia‐related disorders in Hispanic populations with AF admixture. [ABSTRACT FROM AUTHOR]

Background: Late‐onset Alzheimer's disease (AD) is a complex disorder with multiple genetic risk factors. Linkage and association analysis have mapped dozens of loci in pooled analysis of many pedigrees or large numbers of unrelated cases and controls. Identification of the underlying DNA risk variants in the regions of interest (ROIs) has been complicated by both the genetic heterogeneity and the cost, until recently, of comprehensive DNA sequencing in ROIs. The known loci also leave much heritability unexplained. Method: We used the families in the AD Sequencing Project (ADSP) discovery family sample to identify variants of interest from whole genome sequences (WGS), and through the variants, genes implicated in risk. We used SNP‐based multipoint linkage analysis to identify ROIs with rare VOIs, carrying out analysis without trimming pedigrees. We pursued all ROIs with family‐specific lodmax scores >1.9, reducing the variants of interest by several filters. We carried out pedigree‐based genotype imputation from the available WGS data, followed by family‐based association analysis, filtered for low population minor allele frequency. We prioritized genes with a low false‐discovery rate for association of single‐cell transcription in brain with AD disease state (PMID:31209304), and genes with high expression in bulk brain (PMID: 24309898). Result: We obtained 46 distinct ROIs representing lodmax1.9‐3.5 per ROI in each of 26 of the 110 ADSP discovery families analyzed. 29 ROIs further investigated in 16 of the families yielded 59 prioritized genes, with 1‐11 genes/ROI. Only 4 out of 321 variants that passed all filters in these genes were in exons, with minimal overlap with genes identified in AD GWASs. Only one ROI occurred in two families, with evidence for a shared‐haplotype between these families, implicating FBXO2 and FBXO44. Both genes are implicated in ubiquitination, while FBXO2 interacts with BACE1. Multiple pathways, both known and new, are implicated, including the ubiquitin‐proteasome system, neural development and maintenance, and mitochondrial functions. Conclusion: This analysis underscores the evidence for extensive genetic heterogeneity and rare variants underlying AD risk, along with multiple potential mechanisms. The preponderance of prioritize non‐coding variants suggests alterations in gene regulation and/or expression as an aspect of AD genetic risk. [ABSTRACT FROM AUTHOR]

Background: In light of the complex etiology of Alzheimer's disease (AD), classifying AD patients into clinical subtypes is important for precision medicine. We tested whether polygenic risk scores (PRSs) combined with brain expression profiles in AD patients are correlated with clinically defined AD subtypes. Methods: We generated 143 co‐expressed gene networks (modules) using RNA sequencing (RNA‐Seq) data derived from 64 autopsied AD brains from the Framingham Heart Study and Boston University Alzheimer's Disease Center. These modules were validated using brain RNA‐seq data from participants with AD in the Religious Orders Study and Memory and Aging Project (n = 363) and the Mayo Clinic Study of Aging (n = 82). Fourteen AD‐related modules were selected by enrichment analysis using the significant genes (P < 0.001) identified in a genome‐wide association study for neuropathological traits (Beecham, 2015) and then characterized by brain cell‐type specific expression profiles. We computed polygenic risk scores of the AD‐associated genes within each module (module‐based PRSs) using the estimates from Beecham et al. in the 449 AD patients of the Alzheimer's Disease Neuroimaging Initiative. Next, we examined correlations of the 14 module‐based PRSs with (1) scores for 9 different cognitive tests and six cognitively‐defined AD subtypes including memory, language, visuospatial, executive, multi, or no domains (Mukherjee, 2018). Results: Eleven of the 14 AD‐related modules were significantly enriched (P < 0.05) for specific brain cell types including four in neurons (best P = 6.8 × 10−104), four in astrocytes (best P = 5.2 × 10−76), two in endothelial cells (best P = 9.9 × 10−87), and one in microglia (P = 1.7 × 10−129). The most significant correlation between the PRSs from the 14 modules and clinical phenotypes was found with an astrocyte‐specific module and language‐related cognitive functions (correlation r2>0.2; P = 6.7 × 10−3), and this module contained 8 AD genes (best gene: DOCK1, P = 3.4 × 10−5). The individual PRSs of the astrocyte‐module were significantly higher in the language‐specific AD patients compared with in other five subtypes (best P = 0.01 from comparison with AD patients in the no domain group). Conclusion: These findings illustrate for the first time that genetic risk scores integrated with system biology may define clinical subtypes of AD. Our findings will facilitate genome‐guided precision medicine efforts in prevention and treatment of AD. [ABSTRACT FROM AUTHOR]

Background: Alzheimer's disease (AD) has become a burden of social and economic importance, affecting millions of families and society at large. The Puerto Rico Alzheimer and Related Dementias Initiatives (PRADI) cohort was developed to investigate AD and genetics factors of AD in the Puerto Rican population. PRADI recruitment was a snowball sampling, with both island‐wide geographic distribution, as well as extensions to PR communities in the continental US. In this study we assessed the relationship between AD and cardiovascular risk factors of AD in the PR population. Method: We assessed over 700 elderly PR individuals for dementia, as well as medical history. Affection status was assessed using standard AD clinical criteria (NINCDS‐ADRDA) or mild cognitive impairment. All medical history was obtained by a self‐report or informant report. Differences between affected and unaffected were initially tested using a chi‐square test (for sex, diabetes, hypercholesterolemia, heart disease, hypertension, and stroke) and a t‐test for the age of the exam. Follow‐up analyses on stroke were performed using logistic regression with age at exam and sex as covariates in the model. Result: The analysis revealed no differences sex differences between AD and unaffected (p‐value > 0.05). Similarly, affected and unaffected showed similar levels of type 2 diabetes, hypercholesterolemia, heart disease, and hypertension (p‐value > 0.05). Affected individuals did however show an increase in stroke incidence (14.0% vs 5.2%; p‐value = 8.3e‐5). This difference persisted even when controlling for age of exam and sex. We did see a difference in age of exam between cases and controls, but this is likely due to ascertainment scheme. Conclusion: This analysis suggests that stroke may be a contributing factor to dementia in the PR population. However, given biases in the ascertainment scheme, additional assessments need to be performed. Additionally, work is ongoing to assess the role of ancestry and genetic factors in this association. [ABSTRACT FROM AUTHOR]

Background: Increased years of education have been previously associated with a decreased risk of developing Alzheimer disease (AD) with cognitive reserve suggested as the source of the protective effect in Non‐Hispanic Whites (NHW). African Americans (AA) are twice as likely to develop AD compared to NHW. We investigated the hypothesis that education was similarly correlated with risk of AD in the AA population. We also examined the relationship of education and age at onset (AAO) of AD in AA. Method: Participants consisted of 132 AA AD cases and 428 AA cognitively intact (CI) individuals with known years of completed education, ascertained for a genetics study of AD. Education levels were stratified into three categories: <8 years, 9‐12 years, >12 years. We used logistic regression to determine the effect of age, sex, education level and APOE4 status between cases versus controls. Additionally, using a linear model we examined the effect of education on AAO including sex and APOE4 status as covariates. Result: Results showed that increasing years of education had a protective effect on AD risk. Initially including sex and age as covariates, both higher education categories were significant, with 9‐12 years (p = 0.02;OR = 0.461[0.23,0.9])) and >12 years (p = 1.30e0‐04;OR = 0.26[0.13,0.41]). Adding APOE4 dosage (0(Ref), 1,2 alleles) to the model (significant at p = 9.54e‐05; p = 5.27e‐07), the effect of education remained significant (p = 0.03;OR = 0.46[0.23,0.93]) and p = 4.84e‐05;OR = 0.22[0.10,0.46]) for 9‐12 and >12, respectively further supporting its role in AD risk. We examined the effect of education on AAO. Education (8‐12 years) trended in significance (p‐value = 0.07; β = ‐3.76[‐7.82,0.307]) with >12 years significant (p‐value = 1.63e‐04; β = ‐13.07,‐4.25]) supporting later AAO with higher education. The effect of APOE4 on AAO was not significant (p = 0.226). APOE4 added to the model as a covariate did not have a significant effect on AAO, however, education levels continued trending (8‐12; p = 0.07; β = ‐3.76[‐7.86,0.34]) and significant (>12; p = 3.71e‐04; β = ‐8.33[‐12.84,‐3.82]). Conclusion: These data support the hypothesis that higher education results in a decreased risk of AD in AA regardless of APOE4 status. We also found a similar protective effect for a later AAO. Thus, the potential outcome of education on cognitive reserve appears across multiple racial backgrounds. [ABSTRACT FROM AUTHOR]

Background: Addressing the disparity Late Onset Alzheimer's disease (LOAD) prevalence among African Americans (AA) requires deliberate inclusion of this population in Alzheimer's disease (AD) studies. Recruiting AA for research studies remains a significant challenge for AD genetic studies. Recruiting and retaining AA males (AAMs) is an even greater challenge, even when study personnel is AA, many traditional recruitment barriers are removed, and community outreach in AA communities is available and culturally appropriate. In this project, we highlight engagement of African American males in outreach and recruitment in three AD studies, and point to the need for expanded and targeted engagement opportunities for this population. While AA males indicate a willingness to participate equal to women, their actual participation is significantly less and may diminish potential generalization of studies in African Americans. Method: We used culturally relevant approaches to educate and build trust within AA communities and made significant contributions to AA participation in AD genomic studies. For this study, we tracked AAM participation in community engagement activities and enrollment in AD genomic research studies over time. Results: Over the past 5 years, 22% of the participants surveyed at an annual AA AD conference were AAM. Participation of AAM's in large genomic studies such as the Research in African American Alzheimer's Disease Initiative (24%), African American Alzheimer's Disease study (24%), the largest Genome Wide Association Study, with 5896 total participants (30%), consistently fell below their non‐Hispanic White counterparts. The average participation of NHW males was 41% over the same period. Conclusion: We have used culturally relevant strategies to engage AAMs in education and in genomic research studies. Their participation falls far below their representation in the general population and below their NHW counterparts. Implementing evidence‐based strategies that specifically address trust and gender‐specific needs of AAMs will be important in increasing their participation in genomic studies in AD, and thus generalizability of study results. [ABSTRACT FROM AUTHOR]

Background: Genetic studies in Alzheimer disease (AD) are underrepresented in African‐descent populations. The African American (AA),population, with the admixed genetic ancestry (African and European) and high African ancestral background (∼80%), provides a unique opportunity to discover African ancestry‐specific genetic factors in AD. Admixture mapping (AM) is a powerful approach for genetic mapping of complex disease in admixed populations. AM uses local ancestry estimates to identify the genetic regions of specific ancestral origins (African, and European) that are associated with AD. These regions are likely to contain risk or protective genes for AD, and identifying these regions will inform sequence analysis in these and additional datasets. Methods: Analyses included 9050 individuals from 16 ADSP and ADGC cohorts We estimated and inferred global ancestry using the GENESIS software that provides robust inference of genetic ancestry in the presence of known and/or cryptic relatedness. To infer local ancestry the target AA dataset was combined with appropriate reference population samples from HGDP reference panel. Local ancestry was estimated using SHAPEIT followed by RFMix. We performed AM using the GENESIS software separately on 16 different cohorts. To meta‐analyse the admixture mapping results we developed in‐house scripts to align the ancestral blocks across cohorts. We used the METAL software for meta‐analysis and STEAM software to estimate the significance threshold. Results: We estimated significant threshold for admixture mapping analysis in AA dataset as 7.3e‐5 using analytic approximation approach from the STEAM package. The most significant region from the meta‐analysis was found on chromosome 4p16.3 (p‐value = 1.4e‐4) failed to reach genome‐wide significance. However, n two individual cohorts ADC8 (sample size = 850) and ADGC‐CHOP (sample size = 2,869) two regions showed genome‐wide significant association with disease on chromosome 18q21.33 (p‐value = 1.2e‐6) and chromosome 19p13.3 (p‐value<2.1e‐5), respectively. Conclusion: Our results confirm association of AD with the known ABCA7 genetic region on chromosome 19p13.3 through AM and suggest a genetic region for AD in AA population on 18q21.33; however, findings were not consistent across cohorts. We are in the process of analyzing data from additional AA cohorts to increase the power and allow us to dissect heterogeneity of AD in AA population. [ABSTRACT FROM AUTHOR]

Background: To identify LOAD risk genes in Puerto Ricans (PR), a population underrepresented in genetic studies, linkage analysis of whole genome sequencing (WGS) in 23 multiplex PR families identified a peak on chromosome 9p21 (MLOD = 3.9). The 1‐LOD unit down region spans from 31∼38Mb; identity‐by‐descent (IBD) sharing region spans from 23‐39 Mb. Two genes in the linkage region, UNC13B, located in the center of the linkage peak (35.1∼35.4 Mb), and ELAVL2 (23.7∼23.8 Mb), at the edge of the IBD sharing region, are of interest. Both genes have multiple rare variants with low minor allele frequencies (MAF) and high CADD scores that segregate with LOAD in the families. UNC13B encodes a protein involved in Ca2+ release at the synapse, and calcium dysfunction has been associated with LOAD. ELAVL2 encodes a neural‐specific protein involved in RNA processing. Method: Recombinant plasmids for testing overexpression (UNC13B) and promoter activity (ELAVL2) were made by site‐directed mutagenesis and transfected into the neuronal SH‐SY5Y. Result: Two UNC13B missense variants, rs35199210 (Asp238Glu, CADD = 22, MAF = 0.5%) or rs41276043 (Phe1096Leu, CADD = 26.5, MAF = 0.5%) have been cloned into overexpression vectors and are currently being evaluated for their effect on Ca2+ release rates. One promoter variant rs542037226 (CADD = 16.6, MAF = 0.03%) in the ELAVL2 demonstrated strong activity (∼200x higher than the empty vector), and the rare allele showed reduced activity compared to the reference allele (10% reduction, p = 0.03). Conclusion: Two potential new LOAD genes with rare variants have been identified within the linkage 9p21 linkage peak. Using segregation and in‐silico analysis we have prioritized rare variants in each gene for testing. Successful demonstration of functional changes in the ELAVL2 variants provide support for this approach. Evaluation of UNC13B variants are underway. Those variants with functional effects will be further evaluated in our inducible pluripotent stem cell models. [ABSTRACT FROM AUTHOR]

Background: The APOE ε4 allele is a major risk factor for AD whose effect shows strong racial/ethnic differences. Among non‐Hispanic White (NHW) populations APOE shows the strongest effect in Northern European (NEu) (rs429358: OR = 3.32, CI:3.20‐3.45) and has a relatively lower effect in Southern European (SEu; i.e., Iberia, Italy, etc) populations (rs429358: OR = 2.27, CI:2.06–2.50). However, it is not clear if this difference in effect is due to genetic or environmental effects. Hispanic/Latino populations with a large proportion of SEu ancestry provide a unique opportunity to assess both global SEu ancestry (i.e., genome‐wide ancestry) and local SEu ancestry (chromosome/region specific ancestry) in populations with environments distinct from SEu. Our objective is to use data from a Caribbean Hispanic Puerto Rican (CHIPR) population to assess the role of SEu genetic ancestry and the APOE gene on Alzheimer disease (AD) risk. Method: APOE and genome‐wide genotyping were performed in 412 CHIPR (231 cases, 181 controls). Local ancestry was calculated using SHAPEIT and RFMix. Global ancestry was assessed using GENESIS. Association between affection status and APOE genotype was analyzed using logistic regression models by adjusting for age, gender, and population substructure. Result: The admixture analysis showed that CHIPR have a substantial SEu ancestral component (∼67%). At the APOE gene, the local ancestry was 68% SEu, 20% African, and 12% Amerindian. Logistic regression model showed a significant association of the APOE ε4 risk allele with AD (CHIPR: OR = 1.9 CI:1.3‐2.8, p‐value = 4.4e‐4). Conclusion: We found that the effect of the APOE ε4 risk allele in CHIPR with the high SEu ancestral background (∼67%) is similar to the effect observed in Southern European populations, despite having a distinct environment. Our results support the hypothesis that SEu genetic ancestry modulates the risk of APOE in CHIPRs. This suggests that subcontinental ancestry could also play an important role in modulating the risk for other known AD candidate. Studying the sub‐continental (NEu and SEu) ethnic disparity in the genetics of AD, provides critical information to advance the development of novel therapeutic measures. [ABSTRACT FROM AUTHOR]

Background: Genetic risk factors for Alzheimer disease (AD) demonstrate distinct effects across diverse ancestral populations. The ancestral heterogeneity (admixture) of Caribbean Hispanics from Puerto Rico (PR), makes studies of the PR population important in the discovery of ancestry‐specific factors in AD. To expand ongoing genomic investigations of AD in PR individuals, it is necessary to characterize functional downstream effects by studying gene expression and regulation. Here we characterized the differences in gene expression, splicing, and RNA editing of the protein coding transcriptome from peripheral blood in PR individuals. to identify case vs control differential expression, splicing, and RNA editing in this diverse population. Method: Poly‐A selected RNA was from peripheral whole blood of 76 PR individuals over the age of 65 (39 AD, 37 cognitively normal controls) was sequenced and analyzed with a standard bioinformatics pipeline. Differential expression between PR cases and controls was calculated using DESeq2, alternative splicing using LeafCutter software, and RNA editing with REDITools and linear models. All analyses were adjusted for sex, age, and sequencing coverage. For each analysis, pathway enrichment analysis of Gene Ontology Biological Processes and KEGG gene sets were used to identify underlying biological pathways. Result: A total of 761 genes (518 up‐regulated, 243 down‐regulated) were differentially expressed between PR AD and controls (adjusted p ≤ 0.05). At the transcript level, 561 genes had a significant (FDR ≤ 0.05) differential splicing event. We also identified 35,246 total RNA editing sites. While there was no significant difference globally, 422 sites in 159 genes showed nominally significant editing difference (p ≤ 0.05). These genes, isoforms, and RNA editing sites overlap little with previous investigations of the transcriptomes of Non‐Hispanic Whites and African‐American AD with only a few genes in common. However, pathway enrichment across all three PR transcriptomic analyses consistently reveals differences in both the adaptive and innate immune response pathways, consistent with other ancestries. Conclusion: Transcriptomic analyses of diverse populations in AD, shows stark divergence at the single gene level. However, the convergence on immune molecular pathways suggest shared underlying disease etiology and the possibility of broad therapeutic options. [ABSTRACT FROM AUTHOR]

Background: The Alzheimer's Disease Sequencing Project (ADSP) seeks to identify genomic variants contributing to increased risk of and/or protection from Alzheimer's disease (AD) in multi‐ethnic populations. Here we report on statistical modeling considerations and results from 4707 diverse individuals including 2076 non‐Hispanic White, 1030 Black, 1304 Hispanic, and 297 of other ancestry with whole genome sequencing (WGS) in the ADSP. Methods: A total of 4789 individuals were sequenced across 4 sequencing centers and 2 sequencing platforms. Joint calling was carried out by the ADSP data coordinating center GCAD. We evaluated a series of models to explore technical covariate adjustment related to study, sequencing center, and platform and then performed single variant association analysis for AD status adjusting for principal components associated with AD, technical covariates, and a genetic relatedness matrix, limiting to variants with a minor allele count > 30 and a missingness rate ≤ 10%. We also performed gene‐based association of rare (both MAF < 1% and MAF < 5%) coding variants. Results: After quality control, we included over 95 million variants across 4707 individuals (2209 cases, 2498 controls). We replicated association at the APOE locus and identified a locus on chromosome 15 that has a suggestive association with AD status (freq = 0.8%, p‐value = 1 × 10−7). Despite joint genotype calling, adjustment for study, sequencing center and platform are necessary to control type‐I error. In gene‐based tests, we found evidence (p < 0.05) of association for 4 of 8 AD candidate genes with low‐frequency or rare variant associations implicated for AD (TREM2, ABI3, SORL1, and MAPT) as well as suggestive associations (P < 5 × 10−5) for seven genes (ZGRF1 on chr4; C1RL on chr12; NAA30 on chr14; NIPA2 on chr15; and ABCC3, BIRC5 and HIC1 on chr17). Conclusion: We explored covariate models for the WGS data from ADSP and established that despite joint calling, it is necessary to account for technical effects in the model. We found suggestive novel associations with AD status that will require confirmation. [ABSTRACT FROM AUTHOR]

Background: The ApoEε4 allele is a major risk factor for AD whose effect shows strong racial/ethnic differences. Among the populations ApoE shows the strongest effect in East Asians (EA) (ε3/ε4 odds ratio OR: 3.1–5.6; ε4/ε4 OR: 11.8–33.1) and has a relatively lower effect in non‐Hispanic Whites (NHW) (ε3/ε4 OR: 3.2; ε4/ε4 OR: 14.9). The effect of ApoEε4 in populations with Amerindian (AI) ancestry is unknown. Peruvians with high AI (∼80%) genetic ancestry provide an opportunity to assess the effect of ApoEε4 in AD individuals with AI genetic ancestry. Our aim is to use data from the Peruvian population to assess the role of AI genetic ancestry and the ApoE gene on AD. Method: Genotyping including both ApoE and Illumina GSA array was performed in 147 Peruvians (54 AD cases and 93 cognitively intact (CI) controls). PC‐AiR and model‐based ADMIXTURE approach inferred population structure. To assess local ancestry, phasing using SHAPEIT (with 1kGP reference) was followed by RFMix (HGDP reference panels). Association between affection status and ApoEε4 dose was analyzed using logistic regression, adjusting for age, gender, PC1‐3. Result: Admixture analysis showed that Peruvians have a substantial AI (62%) ancestral component (31% European, 4% African and 3% EA genetic ancestry). AD individuals have higher frequency of ApoEε4 allele than CI individuals (7.4% vs 3.7%, respectively, p‐value = 3e‐4). Logistic regression analysis showed ApoEε4 dose significantly associated with AD in Peruvians (OR = 4.92, CI: 2.07‐12.83, p = 6e‐4). The average of the local ancestry proportions around the ApoE were close to the average global ancestry proportions (AI:56%, EU:37% and AF:7%). Conclusion: Our results showed that the risk for AD from ApoEε4 in Peruvians is higher than we have observed in NHW populations. Given the high admixture of AI in the Peruvian population, it suggests that the AI local ancestry is contributing to a strong risk for AD in ApoEε4 carriers. This would align with the current believed migration pattern of AI from East Asia, where ApoEε4 carriers have the highest ApoEε4 risk for AD. Further ascertainment is ongoing to identify additional AI ApoEε4 carriers to directly ascertain risk. [ABSTRACT FROM AUTHOR]

Background: With over 5.1 million individuals, the Puerto Rican population makes up over 1.5% of the US population and is the 2nd largest Hispanic/Latino population in the continental US. There are an estimated of 60,000 cases of AD on the island. The Puerto Rico Alzheimer's and Related Dementias Initiatives (PRADI) cohort will both leverage and complement existing AD Resources, the Alzheimer Disease Sequencing Project (ADSP) with the inclusion of a diverse and underrepresented population. At present, the cohort consists of a total of 935 total participants including individuals from 115 multiplex AD families. There are 418 cases of dementia, 217 mild cognitive impairment, and 300 unrelated and family‐based controls. Method: We examined the most successful strategy to recruit cases and controls as well as multiplex families for both case/control and family‐based genetic studies. We began by engaging a wide range of stakeholders across the island. The core activities of our team include relationship building, partnership development and maintenance, and coalition building. For the community outreach, we utilize mass media like newspapers, radio interviews, and focal group presentations and engaged the following stakeholder groups: Alzheimer disease day care centers, elderly housing in San Juan, senior day care centers, non‐profit organizations, private neurology offices, and other community‐based organizations such as the Alzheimer's Association. Result: The percent of patients recruited through each stakeholder group were 45.76% (428/935) from community outreach, 34.33% (321/935) from private neurologist practices, 18.93% (177/935) from senior day care centers and 0.96% (9/935) from Alzheimer disease day care centers. The mean age and standard deviation of cases and controls were 78.22 years (±9.37) and 70.84 years (±7.92) respectively. Examining the data with respect to multiplex family structure, we found that 53.77% of the families (including the largest families) came from private physician referral. Conclusion: Partnering with diverse stakeholders and building coalitions proved to be effective as an outreach method for recruitment. Private physicians remain an excellent source for the identification of multiplex AD families for family‐based genetics study. Outreach community‐based approaches are highly successful mechanisms to educate and engage participants in genetic research. [ABSTRACT FROM AUTHOR]

APOE ε4, the most significant genetic risk factor for Alzheimer disease (AD), may mask effects of other loci. We re-analyzed genome-wide association study (GWAS) data from the International Genomics of Alzheimer’s Project (IGAP) Consortium in APOE ε4+ (10,352 cases and 9,207 controls) and APOE ε4− (7,184 cases and 26,968 controls) subgroups as well as in the total sample testing for interaction between a SNP and APOE ε4 status. Suggestive associations (P<1x10−4) in stage 1 were evaluated in an independent sample (stage 2) containing 4,203 subjects (APOE ε4+: 1,250 cases and 536 controls; APOE ε4-: 718 cases and 1,699 controls). Among APOE ε4− subjects, novel genome-wide significant (GWS) association was observed with 17 SNPs (all between KANSL1 and LRRC37A on chromosome 17 near MAPT) in a meta-analysis of the stage 1 and stage 2 datasets (best SNP, rs2732703, P=5·8x10−9). Conditional analysis revealed that rs2732703 accounted for association signals in the entire 100 kilobase region that includes MAPT. Except for previously identified AD loci showing stronger association in APOE ε4+ subjects (CR1 and CLU) or APOE ε4− subjects (MS4A6A/MS4A4A/ MS4A6E), no other SNPs were significantly associated with AD in a specific APOE genotype subgroup. In addition, the finding in the stage 1 sample that AD risk is significantly influenced by the interaction of APOE with rs1595014 in TMEM106B (P=1·6x10−7) is noteworthy because TMEM106B variants have previously been associated with risk of frontotemporal dementia. Expression quantitative trait locus analysis revealed that rs113986870, one of the GWS SNPs near rs2732703, is significantly associated with four KANSL1 probes that target transcription of the first translated exon and an untranslated exon in hippocampus (P≤1.3x10−8), frontal cortex (P≤1.3x10−9), and temporal cortex (P≤1.2x10−11). Rs113986870 is also strongly associated with a MAPT probe that targets transcription of alternatively spliced exon 3 in frontal cortex (P=9.2x10−6) and temporal cortex (P=2.6x10−6). Our APOE-stratified GWAS is the first to show GWS association for AD with SNPs in the chromosome 17q21.31 region. Replication of this finding in independent samples is needed to verify that SNPs in this region have significantly stronger effects on AD risk in persons lacking APOE ε4 compared to persons carrying this allele, and if this is found to hold, further examination of this region and studies aimed at deciphering the mechanism(s) are warranted.

Background: Recruiting African Americans in AD studies remains a challenge, particularly during a pandemic, where major health disparities in this population are illuminated. The recruitment literature suggests myriad factors that contribute to the underrepresentation of AAs, including, but not limited to "mistrust" in researchers and their institutions. Maintaining a continuous presence in the AA community builds trust even when traditional outreach methods are not allowed. We continued to provide outreach and recruitment opportunities through COVID education and food for families as we educated them about AD, and opportunities for study participation. Method: While our traditional outreach methods for recruiting AAs were interrupted, we continued to conduct AD outreach using virtual platforms, mobile phone calls, family conference calls and food distributions. We hosted nine webinars on COVID‐19 to maintain a presence in local and national AA communities and to remain connected to existing AD participants. We reached over 160,000 persons through webinars and social media. We established new relationship new faith leaders in the AA community who co‐hosted COVID‐19 webinars and also expressed interest in forming partnerships on AD education. In addition, we hosted food drives in AA communities that not only addressed food insecurity and COVID prevention, but also AD education and AD research opportunities. At the food drives we distributed bags with masks, hand sanitizers, AD brochures, booklets and study participation information. Result: Between October and December of 2020, 64 AAs who attended food drives expressed interest in AD studies that required blood draws and cognitive testing. Fifteen enrolled in our genetic study, 15 requested additional follow‐up and 13 expressed interest in participating in more than one study. Conclusion: Prior research suggests that recruiting AAs into AD studies requires continuous engagement. We used multiple strategies to maintain contact with the AA community and existing research participants, and successfully increased enrollment in the last quarter of the year. Maintaining consistent and continuous engagement facilitates trustworthiness with AAs and yields positive recruitment outcomes, even in a pandemic where traditional recruitment methods are limited. [ABSTRACT FROM AUTHOR]