INTRODUCTION:Recently, the O-6-methylguanine-DNA methyltransferase (MGMT) locus was proposed as influencing the risk of Alzheimer's disease (AD) in women who did not carry the apolipoprotein E ε4 allele. We examined an Amish founder population for any influence of genetic variation in and around the MGMT locus on the risk for dementia. METHODS:Genetic association was performed for single nucleotide polymorphisms (SNPs) surrounding the MGMT locus. A total of 946 individuals of Amish descent between the ages of 76 and 95 who were classified as cognitively impaired or cognitively unimpaired were included. Multiple statistical models were applied to test for replication. RESULTS:The results for the previously associated individual SNPs were not significant. However, a different SNP (rs7909468) generated significant results under a model different from the previous report. DISCUSSION:The MGMT locus may influence the risk of AD, although its genetic mechanisms remain unclear and warrant further study. HIGHLIGHTS:Association analyses around the O-6-methylguanine-DNA methyltransferase (MGMT) locus showed a study-significant single nucleotide polymorphism (SNP), rs7909468, in a female cognitively impaired group lacking the apolipoprotein E ε4 genotype. Functional implications of rs7909468 are relatively unexplored, but in silico analyses indicate it may regulate MGMT expression. rs7909468 was not in linkage disequilibrium with other SNPs found to be significant in this region and appears as a distinct novel association.

INTRODUCTION:Alzheimer's disease (AD) remains a debilitating condition with limited treatments and additional therapeutic targets needed. Identifying AD protective genetic loci may identify new targets and accelerate identification of therapeutic treatments. We examined a founder population to identify loci associated with cognitive preservation into advanced age. METHODS:Genome-wide association and linkage analyses were performed on 946 examined and sampled Amish individuals, aged 76-95, who were either cognitively unimpaired (CU) or impaired (CI). RESULTS:A total of 12 single nucleotide polymorphisms (SNPs) demonstrated suggestive association (P ≤ 5 × 10-4) with cognitive preservation. Genetic linkage analyses identified > 100 significant (logarithm of the odds [LOD] ≥ 3.3) SNPs, some which overlapped with the association results. Only one locus on chromosome 2 retained significance across multiple analyses. DISCUSSION:A novel significant result for cognitive preservation on chromosome 2 includes the genes LRRTM4 and CTNNA2. Additionally, the lead SNP, rs1402906, impacts the POU3F2 transcription factor binding affinity, which regulates LRRTM4 and CTNNA2. HIGHLIGHTS:GWAS and linkage identified over 100 loci associated with cognitive preservation. One locus on Chromosome 2 retained significance over multiple analyses. Predicted TFBSs near rs1402906 regulate genes associated with neurocognition.

Background and ObjectivesAlzheimer disease (AD) has a complex etiology with a strong genetic component. Despite mounting evidence that genetic risk effect sizes vary by population, most research on the genetics of AD has examined only data sets of individuals with European ancestry. In this study, we investigate the variable performance and transferability of polygenic risk scores (PRSs) by deriving a PRS from analyses of AD for various race and ethnic categories and applying this across groups using a k-fold cross-validation approach.MethodsAfter quality control and application of inclusion criteria, we analyzed 11,254 individuals from the Alzheimer's Disease Sequencing Project Release 3 with 3 predominant self-identified race/ethnicity groups: Hispanic individuals (n = 2,207), non-Hispanic Black individuals (n = 2,437), and non-Hispanic White individuals (n = 6,610). For each group, a 5-fold cross-validation approach was used to perform a genome-wide association study (training) and construct PRS estimates (test). This approach allowed for consideration of within-group and across-group PRS performance. Area under the curve (AUC) was calculated for each race/ethnicity-specific PRS within each cross-validation fold. Various PRS criteria were considered, including rare single-nucleotide polymorphisms and the APOE region in calculation, sex-specific PRSs, and different sample sizes of training and test groups, and their effects were examined through goodness-of-fit metrics in reduced and full models.ResultsAcross all participant groups, the PRS trained in the same race/ethnicity category as the test group nearly exclusively outperformed the other PRSs with considerable benefit in the Hispanic group. The range of AUCs across iterations was also greater when applying PRSs from other groups. These findings were consistent after inclusion of APOE, sex, and age covariates and through different PRS generation criteria.DiscussionIn this study, we demonstrated the variable performance of AD PRSs within race/ethnicity groups and the weakness in transferability across groups, accounting for different criteria in PRS calculation. This work provided a framework for improving PRS application for AD and highlighted the importance of recruiting diverse populations in genetic studies.

Alzheimer disease (AD) is the most common type of dementia and is estimated to affect 6 million Americans. Risk for AD is multifactorial, including both genetic and environmental risk factors. AD genomic research has generally focused on identification of risk variants. Using this information, polygenic risk scores (PRSs) can be calculated to quantify an individual's relative disease risk due to genetic factors. The Amish are a founder population descended from German and Swiss Anabaptist immigrants. They experienced a genetic bottleneck after arrival in the United States, making their genetic architecture different from the broader European ancestry population. Prior work has demonstrated the lack of transferability of PRSs across populations. Here, we compared the performance of PRSs derived from genome-wide association studies (GWASs) of Amish individuals to those derived from a large European ancestry GWAS. Participants were screened for cognitive impairment with further evaluation for AD. Genotype data were imputed after collection via Illumina genotyping arrays. The Amish individuals were split into two groups based on the primary site of recruitment. For each group, GWAS was conducted with account for relatedness and adjustment for covariates. PRSs were then calculated using weights from the other Amish group. PRS models were evaluated with and without covariates. The Amish-derived PRSs distinguished between dementia status better than the European-derived PRS in our Amish populations and demonstrated performance improvements despite a smaller training sample size. This work highlighted considerations for AD PRS usage in populations that cannot be adequately described by basic race/ethnicity or ancestry classifications.

A shift in focus from risk to resilience for Alzheimer’s disease (AD) encourages efforts to uncover novel AD biological mechanisms. Rare variants identified through whole genome sequencing (WGS) may represent an important and understudied component of complex trait genetics. While population-based studies are powered to discover associations with common genetic variants, founder populations are better powered for discovery of previously unknown rare alleles that have risen to higher frequency due to genetic drift. We examined WGS data from the Mid-Western Amish population in a genome-wide search for rare coding variants shared only among cognitively-unimpaired (CU) individuals. The cognitive status of each individual was assigned via consensus review of medical history and neuropsychological testing. Allele frequencies were calculated across all samples and for CU and cognitively-impaired (CI) groups separately. We defined rare variants as having an allele frequency <0.05 across all samples. Variants with a minor allele count (MAC)>10 in the CU group, and 0 in the CI group were annotated to determine likely loss of function. After extensive QC, 1,048 samples were available to estimate overall allele frequency. Allele frequencies of rare variants (n = 11,854,817) within 634 CU (mean age = 81.53±6.10, 60% female) and within 184 CI (mean age = 84.77±6.60, 62% female) individuals were compared and 51,616 variants with MAC >10 were found only in CU. There were 316 unique coding variants (288 missense, 4 inframe_insertion, 6 inframe_deletion, 11 frameshift, 4 stop_gained, 3 splice_donor) and 180 synonymous variants located within 425 unique genes. Among them, 7 missense variants and 7 synonymous variants had MAC >20 and the remaining variants had MAC of 11-20. The mean allele frequency of the 7 missense variants was 0.0038 in TOPMed compared to 0.0154 in our data. Two synonymous variants were located within proposed AD genes (NYAP1 and ZNF423). Additionally, several untranslated region or nonsense-mediated decay transcript variants existed within 26 known AD gene regions, among which 8 of them are reported to harbor protective variants for AD. Numerous rare variants potentially impacting gene function were found only in CU individuals, providing a rich resource for further investigation of genes that may provide protection from cognitive impairment.

Background: Verbal and visuospatial memory impairments are common to Alzheimer disease and Related Dementias (ADRD), but the patterns of decline in these domains may reflect genetic and lifestyle influences. The latter may be pertinent to populations such as the Amish who have unique lifestyle experiences. Methods: Our data set included 420 Amish and 401 CERAD individuals. Sex-adjusted, age-adjusted, and education-adjusted Z-scores were calculated for the recall portions of the Constructional Praxis Delay (CPD) and Word List Delay (WLD). ANOVAs were then used to examine the main and interaction effects of cohort (Amish, CERAD), cognitive status (case, control), and sex on CPD and WLD Z-scores. Results: The Amish performed better on the CPD than the CERAD cohort. In addition, the difference between cases and controls on the CPD and WLD were smaller in the Amish and Amish female cases performed better on the WLD than the CERAD female cases. Discussion: The Amish performed better on the CPD task, and ADRD-related declines in CPD and WLD were less severe in the Amish. In addition, Amish females with ADRD may have preferential preservation of WLD. This study provides evidence that the Amish exhibit distinct patterns of verbal and visuospatial memory loss associated with aging and ADRD.

Alzheimer’s Disease (AD) is a leading cause of death in the US, with limited treatment options. Most studies assess risk factors for AD; however, protective mechanisms demonstrate higher success rates as therapeutic targets. Here, we examine the genetics of Amish individuals maintaining cognitive preservation into advanced age, aiming to uncover protective mechanisms against AD. Our dataset consisted of individuals of Amish descent, between 76 – 95 years of age and cognitively unimpaired (CU) with at least one first-degree relative determined to be either CU or cognitively impaired (CI). 946 Amish individuals met our criteria, were genotyped across their genomes, and incorporated into a single 13-generation pedigree containing 8,222 individuals. Their complex familial relationships were considered in linkage and genome-wide association analyses (GWAS). GENESIS was used for GWAS, with XWAS used for the X chromosome. Several parametric and non-parametric linkage analyses were also performed utilizing MERLIN software for the autosomes and MINX for the X chromosome. 106 SNPs (representing 64 loci) reached an initial significance threshold (LOD≥3.3) in linkage analyses. Adjusting for number of independent SNPs in our dataset, no SNPs reached significance after GWAS (P≤6.4×10 −7 ), but 12 loci were suggestive (P≤5×10 −4 ). No loci were suggestive/significant on the X chromosome. For a locus to be further investigated, 1) a significant or suggestive LOD score was required in two or more linkage analyses or 2) one significant LOD score and a suggestive GWAS association within a 10 Mb region were required. After applying these criteria, 8 loci, on chromosomes 1, 2, 3, 7, 11, and 17, were selected for further evaluation. Loci on chromosomes 7 and 11 are within 10 Mb of known AD risk and protective loci, EPHA1 and PICALM, respectively. Significant LOD score results on chromosomes 7, 11, and 17 overlap with coding regions for TBXAS1, DLG2, and SPNS3, respectively. These three loci have been implicated in cognitive impairment relating to neurological disorders. We identified 8 loci potentially harboring genes promoting cognitive preservation. These are under further investigation and represent potential therapeutic targets but require experimental studies identifying their specific mechanisms in relationship to AD.

Mitochondrial dysfunction is an important feature of Alzheimer’s Disease (AD) pathogenesis. Reduced glucose utilization and increased oxidative stress are intermediates through which impaired mitochondria may promote AD-associated brain changes. Association between groups of variants (“haplogroups”) in the mitochondrial genome and AD have been reported for haplogroups U, J, and K. To test these effects in the Amish, we looked for evidence of association between AD-associated haplogroups and cognitive impairment in a sample of aged Amish individuals. Cognitive status in adult Amish participants (n=670) with whole-genome sequence (WGS) data was determined based on modified mini-mental status exam results (3MS). An outcome of cognitively impaired (CI) was assigned to individuals with an education-adjusted 3MS < 87 at any age. A status of cognitively unimpaired (CU) was assigned to those aged ≥ 75 scoring ≥ 87 on the 3MS. Mitochondrial variants detected by WGS were used to derive broad haplogroups for each sample using Haplogrep2. Mixed model association testing was performed in GENESIS with CI as the outcome, and haplogroup (U, J, or K), APOE ε4 carrier status (ε4 vs no ε4), sex, and age as predictors. Based on reports of sex-specific haplogroup U effects on AD, a sex-stratified analysis was conducted. A random-effect kinship matrix was used to account for relationships. Association between mitochondrial haplogroups U, J, or K and CI was not observed at a 5% significance level. The sex-stratified analysis showed the strongest association of CI with haplogroup U (OR 1.8, 95% CI 0.92-3.5) among women. Among men, the estimated effect was 0.77 (95% CI 0.37-1.62). The overall direction of association was opposite in men and women, though neither was statistically significant at 5%. Although significant evidence of a haplogroup effect on cognitive status was not observed, the moderate sex-dependent effect of haplogroup U on impairment warrants further examination in an expanded dataset.Previously, haplogroup U was proposed as an AD risk factor among men, whereas it appears as a risk factor for CI in women in the present study.

As plasma biomarker assays have become more widely available, they are increasingly being used to characterize AD and related dementias. The Old Order Amish are a cultural and genetic isolate in the US that have participated in genetic studies for decades. This study investigated plasma phosphorylated tau at threonine-181 (pTau181) in an Old Order Amish cohort to determine if the association with cognitive status is reproducible in this population. Old Order Amish individuals over age 65 (n=467, mean age = 81.3, 60.6% female) in Indiana and Ohio were examined using a modified Consortium to Establish a Registry for Alzheimer’s Disease (CERAD) battery. Each individual was assigned Impaired (n=155, mean age = 82.5, 56.8% female) or Unimpaired (n=312, mean age = 80.8, 62.5% female) cognitive status via consensus review of these examination results. The level of plasma pTau181 was measured using the pTau181 Advantage V2 assay from Quanterix. Genetic Risk Scores (GRS) were calculated using genome-wide significant variants from Kunkle et al. (2019), weighted by log odds ratio estimates. A t-test was used to compare plasma pTau181 levels between the Impaired and Unimpaired groups. Logistic regression was then used to model the contribution of age, sex, GRS, and plasma pTau181 on cognitive status. We found that the average level of plasma pTau181 was significantly higher in the Impaired group (2.46 pg/mL) compared to the Unimpaired group (2.01 pg/mL) at p<0.0001. A multivariable model found increasing age (OR=1.10, p=0.0002), male sex (OR=1.60, p=0.04), increasing GRS (OR=1.97, p<0.0001), and increasing plasma pTau181 (OR=1.46, p=0.001) associated with impaired cognitive status. The effect of GRS is mostly attributable to APOE . The result of these analyses indicates that pTau181 is associated with impaired cognitive status in the Old Order Amish, adding additional information beyond the known genetic risk factors for AD.

Alzheimer’s disease (AD), the most common type of dementia, has a complex etiology with a strong genetic component. Many genetic risk variants for AD have been identified including APOE , the largest known genetic risk factor. However, most of this research has examined only broad populations of individuals with European ancestry and there is mounting evidence that effect sizes vary by population. Here, we investigate the transferability of polygenic risk scores (PRSs), including a network-specific PRS, in the midwestern Amish and across diverse ancestries. Data from 1,091 Amish adults with AD diagnosis by consensus were considered for analysis from the Collaborative Amish Aging & Memory Project. Genotype data (Illumina GSA and MEGA EX ) were imputed using the Haplotype Reference Consortium panel. We also analyzed 15,745 individuals from the Alzheimer’s Disease Sequencing Project (ADSP) r3 with three predominant race/ethnicity groups: African American (AA; n=2,937), Hispanic (n=3,047), and non-Hispanic White (NHW; n=9,708). An AD network-specific PRS was constructed by including variants from AD-implicated molecular networks in the Kyoto Encyclopedia of Genes and Genomes. A comprehensive pruning and thresholding PRS considering all variants was calculated for comparison. Effect estimates from Kunkle et al. (2019) were used. PRS-only models, sex and age covariate-only, and full models were constructed for each group and the full ADSP data. We observed that PRS-only predictive ability was similar between the comprehensive PRS (AUC=0.56) and the network-specific PRS (AUC=0.55) in the full ADSP r3 data. Network-specific PRS performance was similar in the Amish (AUC=0.55). However, we observed better predictive ability with the comprehensive PRS compared to the network-specific PRS in each of the subgroups (Amish AUC: 0.61 vs. 0.55; NHW: 0.70 vs. 0.53; AA: 0.56 vs. 0.53, Hispanic: 0.61 vs. 0.56). These trends were consistent after inclusion of sex and age covariates. We demonstrated that a network-specific PRS performed similarly to a comprehensive PRS in a combined diverse population and the Amish but confers less predictive ability when investigating individual subgroups. Thus, the network-specific PRS has potential as a component of a risk model in diverse populations because it may successfully account for effects that are consistent across subgroups.

Purpose:The purpose of this study was to identify genetic risk loci for retinal traits, including drusen, in an Amish study population and compare these risk loci to known risk loci of age-related macular degeneration (AMD). Methods:Participants were recruited from Amish communities in Ohio, Indiana, and Pennsylvania. Each participant underwent a basic health history, ophthalmologic examination, and genotyping. A genomewide association analysis (GWAS) was conducted for the presence and quantity of each of three retinal traits: geographic atrophy, drusen area, and drusen volume. The findings were compared to results from a prior large GWAS of predominantly European-ancestry individuals. Further, a genetic risk score for AMD was used to predict the presence and quantity of the retinal traits. Results:After quality control, 1074 participants were included in analyses. Six single nucleotide polymorphisms (SNPs) met criteria for genomewide significance and 48 were suggestively associated across three retinal traits. The significant SNPs were not highly correlated with known risk SNPs for AMD. A genetic risk score for AMD provided significant predictive value of the retinal traits. Conclusions:We identified potential novel genetic risk loci for AMD in a midwestern Amish study population. Additionally, we determined that there is a clear link between the genetic risk of AMD and drusen. Further study, including longitudinal data collection, may improve our ability to define this connection and improve understanding of the biological risk factors underlying drusen development.

INTRODUCTION:Studies of cognitive impairment (CI) in Amish communities have identified sibships containing CI and cognitively unimpaired (CU) individuals. We hypothesize that CU individuals may carry protective alleles delaying age at onset (AAO) of CI.METHODS:A total of 1522 individuals screened for CI were genotyped. The outcome studied was AAO for CI individuals or age at last normal exam for CU individuals. Cox mixed-effects models examined association between age and single nucleotide variants (SNVs).RESULTS:Three SNVs were significantly associated (P < 5 × 10-8 ) with AAO on chromosomes 6 (rs14538074; hazard ratio [HR] = 3.35), 9 (rs534551495; HR = 2.82), and 17 (rs146729640; HR = 6.38). The chromosome 17 association was replicated in the independent National Institute on Aging Genetics Initiative for Late-Onset Alzheimer's Disease dataset.DISCUSSION:The replicated genome-wide significant association with AAO on chromosome 17 is located in the SHISA6 gene, which is involved in post-synaptic transmission in the hippocampus and is a biologically plausible candidate gene for Alzheimer's disease.

Mosaic loss of chromosome Y (mLOY) refers to acquired aneuploidy in a fraction of somatic cells. In aging men, has been suggested as a possible biomarker for increased risk of numerous diseases, including Alzheimer’s disease (AD). We investigated mLOY as a risk factor for AD in the Mid-Western Amish, a founder population with homogeneous lifestyle, reducing the effect of confounding environmental factors. The median of the log R ratio (mLRRY) from SNP array data within the male-specific region of chromosome Y was used to measure the degree of mLOY. A mLRRY value lower than the 99% confidence limit of the experimental distribution was scored to estimate the frequency of mLOY. The cognitive status was assigned via consensus review of cognitive examination results. Men in 3 age groups (65-74, 75-84, >=85) were included. The linear mixed model with a polygenic component to account for relatedness and a transformation to address non-normality was used to estimate familial correlations and heritability. A likelihood ratio test of association was performed with age at blood sampling and age of cognitive exam as covariates. After extensive QC, 533 participants (mean age=75.42±6.17) were included and 39 (7.9%) had a detectable level of mLOY. mLOY frequency increased with age (p<1.0x10 -6 ): 1.0% (65-74; n=103), 8.4% (75-84; n=334) and 14.3% (85+; n=96). Heritability of mLOY was 0.53 and the residual sibling correlation was 0.27 (n=201, p<1.0x10 -2 ). A subset of 423 individuals were assigned to the cognitively impaired (n=134) or unimpaired (n=289) groups and mLOY was significantly higher in the cognitively impaired group (p<0.0001). . The sibling correlation was significant for mLOY. We observed the same trend as reported in other European descent populations: mLOY increased with age and was more frequent in cognitively impaired individuals. The frequency of mLOY in Amish was lower than reported, overall and in each age stratum. Our results along with the lower prevalence of AD in Amish reinforces as a promising biomarker for the risk of AD.

Alzheimer’s Disease (AD) is the most common form of dementia and has limited treatments. While AD risk has a large genetic component, under 50% of the genetic risk has been identified. By focusing on identifying genetic variants that delay or prevent the onset of AD, our goal is to identify new associated genes and variants. To detect such loci, we studied cognitive preservation in the Midwestern Amish, a genetically and culturally isolated population of European descent. We studied 946 Amish individuals (ages 76-95) from Ohio and Indiana. Participants were classified as cognitively impaired (33.8%) or cognitively unimpaired (66.2%) by consensus review of cognitive examinations. These individuals were all connected in a 15-generation 8,222-person pedigree. This pedigree was divided into 104 sub-pedigrees via PedCut for linkage analysis. MERLIN was used for autosomal linkage analysis, while MINX was used for X-chromosome linkage analysis. The association analysis, corrected for genetic relationship, used GENESIS for autosomes and XWAS for the X chromosome. Over 250,000 SNPs were used for association and two-point linkage analyses, and a subset of 5,294 uncorrelated SNPs was used for multipoint linkage analyses. on 15 different chromosomes, with the highest two-point heterogeneity LOD score (HLOD = 5.85) on chromosome 2 (∼79Mb) and highest multipoint HLOD (3.55) on chromosome 12 (∼25Mb), neither overlapping with known AD genes. Two linkage results overlapped with known AD genes (Chr 6: CD2AP; Chr 11: PICALM) and do not overlap with association results. Significant (p ≤ 6.4x10 -7 ) and suggestive (p ≤ 1x10 -4 ) thresholds for association were determined using SimpleM. While no significant associations were found, suggestive associations were found for 103 SNPs (11 loci) across 10 chromosomes. Three of these (chr 11: MS4A2; chr 14: SLC24A4; chr 16: IQCK) fall near known AD genes. These significant and suggestive regions are being followed up currently with fine mapping. Preliminary analyses suggest that using cognitive preservation as our phenotype of interest identifies both known AD loci and novel regions that warrant further evaluation and may lead to a further understanding of both AD and cognitive preservation.

Alzheimer disease (AD) is the most common type of dementia and is currently estimated to affect 6.2 million Americans. It ranks as the sixth leading cause of death in the United States, and the proportion of deaths due to AD has been increasing since 2000, while the proportion of many other leading causes of deaths have decreased or remained constant. The risk for AD is multifactorial, including genetic and environmental risk factors. Although APOE ε4 remains the largest genetic risk factor for AD, more than 26 other loci have been associated with AD risk. Here, we recruited Amish adults from Ohio and Indiana to investigate AD risk and protective genetic effects. As a founder population that typically practices endogamy, variants that are rare in the general population may be of a higher frequency in the Amish population. Since the Amish have a slightly lower incidence and later age of onset of disease, they represent an excellent and unique population for research on protective genetic variants. We compared AD risk in the Amish and to a non-Amish population through APOE genotype, a non-APOE genetic risk score of genome-wide significant variants, and a non-APOE polygenic risk score considering all of the variants. Our results highlight the lesser relative impact of APOE and differing genetic architecture of AD risk in the Amish compared to a non-Amish, general European ancestry population.

ABSTRACTBackgroundStudies of cognitive impairment (CI) in Amish communities have identified sibships containing multiple CI and cognitively unimpaired (CU; unaffected after age 75) individuals. We hypothesize that these CU individuals may carry protective alleles delaying age at onset (AAO) of CI, preserving cognition in older age despite increased genetic risk. As well, the genetic and cultural isolation in the Amish since the early 1800s may have reduced the complexity of the genetic architecture of CI, increasing the power to detect protective alleles in this population. With this in mind we conducted a genome-wide study (GWAS) to identify loci associated with AAO of CI in a sample of Amish adults over age 75.Methods1,522 individuals aged 43-99 (mean age 73.1, 42% men) screened at least once for CI using the Modified Mini-Mental State exam (3MS) were genotyped using Illumina chipsets. Genotypes were imputed for 7,815,951 single nucleotide variants (SNV) with minor allele frequency (MAF) > 1%. The outcome studied was age, defined as 1) age at the first 3MS result indicating impairment (AAO; 3MS <87; 362 CI individuals) or 2) age at last normal exam (3MS >=87, 1,160 CU individuals). Cox mixed-effects models examined association between age and each SNV, adjusting for sex and familial relationships. To replicate genome-wide significant findings, SNVs in a 1 Megabase region centered on the peak SNV were examined for association with age using these same methods in the NIA-LOAD family study dataset (1,785 AD cases, 1,565 unaffected controls, mean age 73.5.ResultsThree SNV were significantly associated (p<5 x 10-8) with AAO in the Amish, on chromosomes 6 (rs14538074; HR=3.35), 9 (rs534551495; HR=2.82), and 17 (rs146729640; Hazard Ratio (HR)=6.38). Each region found the common allele associated with later AAO. Replication analysis detected association at rs146729640, with nominal statistical significance (HR=1.49, p=0.02).ConclusionsThe replicated genome-wide significant association with AAO on chromosome 17 suggest this may be novel locus associated with delayed onset of AD. The associated SNP is located in the SHISA6 gene, which is involved in post-synaptic transmission in the hippocampus and is a biologically plausible candidate gene for AD.

Previous studies have identified genetic risk factors for Alzheimer Disease (AD). In the Amish community, many individuals maintain normal cognitive function at older ages, despite having relatively high genetic risk of AD. These individuals may carry protective alleles that buffer the genetic risk. To find such loci, we utilized the Amish family structures to apply a modified genetic linkage analytical tool that considered genetic risk of AD.Cognitive status in adult Amish subjects (n=1,855) was assigned using the modified mini-mental status exam (3MS). Individuals aged ≥ 75 with 3MS ≥ 87 were classified as CN. Those with 3MS < 87 were classified impaired (CI), regardless of age. Genome-wide genotypes were used to impute ∼7 million variants using the HRC imputation reference panel. For genome-wide linkage analysis, we selected 2,167 SNPs and analyzed 110 sibships with ≥ 2 CN members. Adjusting for known genetic risk, we applied ordered subsets analysis (OSA) to rank families by mean Genetic Risk Score (GRS) of CN members. GRS was derived from 27 genome-wide AD loci (Kunkle et al, 2019). Regions with significant increases in linkage (LOD*) were assessed by mixed model genetic association testing.Ranking sibships by high-to-low mean GRS, significant increases in the LOD* after OSA were observed at ∼40 Mb on chromosome (Chr) 19 (peak LOD*=2.176, p=0.009) and ∼49 Mb on chr 18 (peak LOD*=2.23, p=0.03). While linkage to chr 19 may result from known AD loci, the observed linkage to chr 18 does not overlap known risk loci. Mixed model association testing within a 5 Mb region of the peak linkage to chr 18 was performed in 1,036 SNPs with minor allele frequency ≥ 0.01. Individuals with a GRS ≥ 3.65, corresponding to the GRS in the 17 families with the strongest LOD* increase, were considered (n=236). The strongest association occurred at rs12969463 (p=0.002, OR = 2).This study detected increased evidence of linkage and association for protective AD loci on chr 18, considering CN individuals with the highest risk from known AD loci. One or more protective alleles that buffer this increased risk may be located in this region.

Speech sound disorders (SSD) manifest as difficulties in phonological memory and awareness, oral motor function, language, vocabulary, reading, and spelling. Families enriched for SSD are rare, and typically display a cluster of deficits. We conducted a genome-wide association study (GWAS) in 435 children from 148 families in the Cleveland Family Speech and Reading study (CFSRS), examining 16 variables representing 6 domains. Replication was conducted using the Avon Longitudinal Study of Parents and Children (ALSPAC). We identified 18 significant loci (combined p < 10 −8 ) that we pursued bioinformatically. We prioritized 5 novel gene regions with likely functional repercussions on neural pathways, including those which colocalized with differentially methylated regions in our sample. Polygenic risk scores for receptive language, expressive vocabulary, phonological awareness, phonological memory, spelling, and reading decoding associated with increasing clinical severity. In summary, neural-genetic influence on SSD is primarily multigenic and acts on genomic regulatory elements, similar to other neurodevelopmental disorders.

Disorders of cognition are important from both personal and public health perspectives. The Modified Mini-Mental State (3MS) examination is a brief mental status test designed to detect cognitive impairment and widely used as a screening test for dementia including Alzheimer's disease (AD). The Old Order Amish have a homogeneous lifestyle with similar years of formal education, reducing the effect of confounding environmental factors for genetic studies. We carried out a genome-wide association study (GWAS) of 3MS score as a measurement of cognitive function in the Mid-Western Amish.After extensive QC, 1,873 subjects with both 3MS score and single nucleotide variant (SNV) data from Illumina chipsets were analyzed. The education adjusted 3MS score at baseline was used with age at exam, sex, and the first two values from principal components analysis in related samples as covariates. The annual rate of 3MS score change from 1st to 2nd exam was used as the measurement of cognitive decline. 933 people with available follow-up data were used with an additional covariate, baseline 3MS score. A linear mixed model was used to test for association.For the cognitive decline with rate of 3MS score change, LHPP gene on chromosome 10 was genome-wide significance (p=6.4×10-9 ). There were 6 more loci with suggestive associations (TMEM182; p=2.5×10-6 , NFIB; p=3.7×10-6 , HRAT17; p=4.0×10-6 , CDH13; p=5.1×10-6 , SDK1; p=5.7×10-6 , CECR2; p=6.6×10-6 ). For the baseline 3MS measurement, no SNPs reached genome-wide significance. However, we identified 5 loci with suggestive associations. They are either in known protein coding genes or regulatory region variants (TMEM229B; p=2.1×10-7 , TMEM178B; p=2.6×10-7 , CSMD1; p=1.0×10-6 , MTCO1P57; p=5.9×10-6 , LINC02122; p=8.9×10-6 ).We identified one genome-wide significant and 6 suggestive loci for the cognitive decline along with 5 more loci potentially associated with the cognitive status measured by 3MS score. LHPP is a protein coding gene that is overexpressed in the brain, associated with brain activity in Major Depression Disorder, and involved in a regulation pathway of cancer cells. In a previous study screening chromosome 10 for late-onset Alzheimer disease (LOAD), LHPP was one of the genes selected for putative functional mutation.