Cognitive performance is central to health and quality of life. Studying the factors that sustain performance may offer insights into maintaining cognitive function into advanced ages and may inform strategies to promote healthy cognitive aging. To identify single nucleotide polymorphisms (SNPs) underlying cognitive function, we performed genome-wide association studies (GWAS) of nine neuropsychological test scores capturing performance in three cognitive domains in 2,455 participants of the Long Life Family Study (LLFS). We identified 12 variants in seven tests and three domains that reached genome-wide significance (p < 5e-8). Three rare (minor allele frequency, European population MAF < 0.01) protective, intronic variants, rs190287985 (CCSER1), rs75730801 (FHOD3), and rs552842447 (LINC00508), were uniquely associated with semantic fluency, phonemic fluency and number span forward, respectively. Two rare deleterious variants, rs556333682 and rs188304645, were associated with performance on the Hopkins Verbal Learning Test-Revised (HVLT-R) learning trials and lie in ischemia-related genes SH3TC1 and RPH3A. Another variant, rs180691759, associated with HVLT-R delayed recall, was proximal to RSPO3 and linked to decreased ECHDC1 expression, implicating ischemic and unexplained Ethylmalonic acid (EMA) pathways. We compared the results with GWASs of a general cognitive factor (GCF) and reaction time (RT) in the UK Biobank and meta-analysis results of the UK Biobank, CHARGE and COGENT by Davies et al. We found that rs535509651 associates with HVLT-R delayed recall in the LLFS and nominally associates (p < 0.05) with GCF, and that rs10424537 associates with Immediate Logical Memory in the LLFS and nominally associates with RT. Furthermore, we identified 5 genome-wide significant loci in Davies et al. that reached loci adjusted significance in the LLFS (GCF p < 0.05/128 and RT p < 0.05/39). Each locus was associated with a single cognitive domain in the LLFS. We annotated the genome-wide significant results with quantitative trait loci (QTL) analyses of whole blood transcriptomic, serum metabolomic data, and gene set enrichment analyses (GSEA) using all nominally significant transcripts (p < 0.05/12). QTL analyses discovered 1 SNP-transcript (ECHDC1, p < 3e-6), no SNP-lipid (p < 2e-4), and no SNP-polar metabolite (p < 2 x 10-4) associations. Gene set enrichment analyses identified three pathways at FDR < 0.05. Our findings provide insight into the domain-specific genetic architecture of cognitive function. ### Competing Interest Statement The authors have declared no competing interest. National Institutes of Health, NIA cooperative agreement, U19-AG063893, UH2/UH3-AG064704

Purpose: To identify single nucleotide polymorphisms (SNPs) and their likely target genes associated with steroid-induced ocular hypertension (SI-OHT), and to conduct functional annotation analyses. Design: Genome-wide association study (GWAS). Participants: Patients with Fuchs endothelial corneal dystrophy were enrolled after corneal transplantation at a single clinical practice (N = 439). Patients self-administered 1% prednisolone acetate eyedrops after surgery. Intraocular pressure (IOP) was measured at baseline and at 1, 3, 6, and 12 months postsurgery. Methods: Saliva samples were collected, and DNA was extracted and genotyped. A GWAS was then conducted, with maximum change in IOP serving as the quantitative trait (QT). Replication analysis employed 4 independent cohorts (N = 49–103) with participants that had been previously genotyped. Main Outcome Measures: Linear regression analysis was performed to determine association between QT and genotype using the Haplotype Reference Consortium reference panel for imputation. Results: A total of 46 SNPs of genome-wide significance (P < 5E-08) clustered at 29 different risk loci in a total of 623 SNPs of suggestive significance (P < 5E-06) clustered at 323 risk loci. Most SNPs are rare or of low frequency with large effect sizes. A list of 441 prioritized target genes was validated by comparison to gene profiling study results and by annotation analyses. Of the top 29 risk loci, 31% colocalize with those for other high-tension OHT phenotypes, and 2 more are linked to OHT by biological evidence for a total of 38% overlap. Three of the discovered SNPs were independently replicated. Many of the prioritized target genes are not expressed in trabecular meshwork or juxtacanalicular tissue, contrary to the current disease paradigm. Annotation analyses suggest novel pathophysiologic mechanisms. Conclusions: Why some individuals develop SI-OHT, but others do not, has remained unknown since glucocorticoids were first used to treat eye disease in the early 1950s. Results of this study demonstrate a genetic basis for SI-OHT, support a relationship with other high-tension OHT phenotypes, and provide hypothesis-generating information for laboratory follow-up. Discovered and replicated SNPs may be valuable for SI-OHT risk prediction and prioritized target genes might be targeted for SI-OHT management. Financial Disclosures: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Dupuytren Disease (DD) is a chronic progressive disease that can cause disabling hand deformities. The most common treatments have either high complication rates or high early recurrence rates. Dupuytren lacks a staging biomarker profile to inform the development of preventive therapeutics to improve long-term outcomes. This multi-omic study aimed to create a DD blood proteomic biomarker profile by comparing DD plasma with that of a healthy control group. We measured circulating collagen metabolism peptides and found normal Collagen I synthesis but impaired Collagen I degradation in DD. We measured 6995 serum protein aptamers and identified 68 proteins that showed statistically significant differences compared with the control group. We developed two Diagnostic Proteomic Risk Scores (DPRS) based on hypothesis-free and hypothesis-based analyses. In independent data, our hypothesis-free and hypothesis-based DPRS distinguished Dupuytren from control subjects with accuracies of 76.5% and 70.6%, respectively. Our hypothesis-based DPRS also distinguished DD subjects with different disease progression rates by age at their first corrective procedure (p = 0.0018). This pilot study is the first to provide evidence to suggest that Collagen I accumulation in DD results from impaired degradation rather than increased collagen synthesis. It also describes novel DPRS that have potential use as diagnostic and staging biomarker panels for Dupuytren disease.

Adverse drug reactions are a frequent cause of worldwide morbidity and mortality. Glucocorticoids (GCs), commonly used to treat inflammatory diseases, alter gene expression with both beneficial and adverse consequences. When used in the eye, GCs cause steroid-induced ocular hypertension (SIOH) in 30-50% of patients, leading to steroid-induced glaucoma. Evidence suggests that predisposition to SIOH is genetically determined. Here we took a pharmacogenomic approach to discover DNA variants associated with SIOH. We identified 44 SNPs of genome-wide significance (p<5E-08) located at 26 risk loci out of a total of 531 SNPs of suggestive significance (p<5E-06) at 262 risk loci. Unlike SNPs identified in complex disease which are overwhelmingly common in frequency, most SNPs found here were rare or of low frequency, likely discoverable because of their large effect sizes. Follow-up analyses provide insight into the pathogenetic relationship of SIOH to high-tension glaucomas and suggest a new mechanistic paradigm for SIOH pathophysiology.

Cognitive impairment is a growing healthcare and quality-of-life challenge as more individuals reach older ages. Without effective interventions, the prevalence of decline will continue to rise. To identify genetic factors underlying cognitive function, we performed GWAS on nine neuropsychological test scores in the Long Life Family Study (LLFS). We then compared results with UK Biobank GWAS of general cognitive ability and reaction time, conducted quantitative trait locus (QTL) analyses of whole blood transcriptomic and serum metabolomic data for genome-wide significant variants (p < 5e-8), and performed gene set enrichment analyses of nominally significant transcripts. We identified 12 genome-wide significant variants across 7 tests in LLFS. Comparison with UK Biobank data revealed test-specific replication patterns, suggesting that loci for general cognitive function and reaction time reflect distinct cognitive domains. QTL analyses identified one SNP–transcript association (p < 0.05/16,300) but no significant SNP–lipid or SNP–polar metabolite associations. Three rare protective variants—rs190287985, rs75730801, and rs552842447—were linked to semantic fluency (animal), phonemic fluency (FAS), and digit span forward, respectively. Two rare deleterious variants, rs556333682 and rs188304645, associated with performance on the Hopkins Verbal Learning Test (HVLT) total recall, lie in ischemia-related genes SH3TC1 and RPH3A. Another variant, rs180691759, associated with HVLT delayed recall, was proximal to RSPO3 and linked to decreased ECHDC1 expression, implicating ischemic and unexplained ethylmalonic acid pathways. Gene set enrichment identified three pathways (FDR < 0.05), including KEGG JAK-STAT signaling and oxidative phosphorylation. These findings highlight domain-specific mechanisms of cognitive resilience and decline.

Using whole-genome sequencing (WGS) might offer insights into rare genetic variants associated with healthy aging and extreme longevity (EL), potentially pointing to useful therapeutic targets. In this study, we conducted a genome-wide association study using WGS data from the Long Life Family Study and identified a novel longevity-associated variant rs6543176 in the SLC9A2 gene. This SNP also showed a significant association with reduced hypertension risk and an increased, though not statistically significant, cancer risk. The association with cancer risk was replicated in the UK Biobank and FinnGen. Metabolomic analyses linked the rs6543176 longevity allele to higher serine levels, potentially associated with delayed mortality. Our findings warrant further investigation of SLC9A2’s role in both longevity and cancer susceptibility, and they highlight the need for careful evaluation in developing anti-aging therapies based on EL-associated alleles.

Quantitative trait loci (QTL) denote regions of DNA whose variation is associated with variations in quantitative traits. QTL discovery is a powerful approach to understand how changes in molecular and clinical phenotypes may be related to DNA sequence changes. However, QTL discovery analysis encompasses multiple analytical steps and the processing of multiple input files, which can be laborious, error prone, and hard to reproduce if performed manually. To facilitate and automate large-scale QTL analysis, we developed the yQTL Pipeline, where the ‘y’ indicates the dependent quantitative variable being modeled. Prior to the association test, the pipeline supports the calculation or the direct input of pre-defined genome-wide principal components and genetic relationship matrix when applicable. User-specified covariates can also be provided. Depending on whether familial relatedness exists among the subjects, genome-wide association tests will be performed using either a linear mixed-effect model or a linear model. The options to run an ANOVA model or testing the interaction with a covariate are also available. Using the workflow management tool Nextflow, the pipeline parallelizes the analysis steps to optimize run-time and ensure results reproducibility. In addition, a user-friendly R Shiny App is developed to facilitate result visualization. It can generate Manhattan and Miami plots of phenotype traits, genotype-phenotype boxplots, and trait-QTL connection networks. We applied the yQTL Pipeline to analyze metabolomics profiles of blood serum from the New England Centenarians Study (NECS) participants. A total of 9.1M SNPs and 1,052 metabolites across 194 participants were analyzed. Using a p-value cutoff 5e-8, we found 14,983 mQTLs associated with 312 metabolites. The built-in parallelization of our pipeline reduced the run time from ~90 min to ~26 min. Visualization using the R Shiny App revealed multiple mQTLs shared across multiple metabolites. The yQTL Pipeline is available with documentation on GitHub at https://github.com/montilab/yQTLpipeline.

Metabolites that mark aging are not fully known. We analyze 408 plasma metabolites in Long Life Family Study participants to characterize markers of age, aging, extreme longevity, and mortality. We identify 308 metabolites associated with age, 258 metabolites that change over time, 230 metabolites associated with extreme longevity, and 152 metabolites associated with mortality risk. We replicate many associations in independent studies. By summarizing the results into 19 signatures, we differentiate between metabolites that may mark aging-associated compensatory mechanisms from metabolites that mark cumulative damage of aging and from metabolites that characterize extreme longevity. We generate and validate a metabolomic clock that predicts biological age. Network analysis of the age-associated metabolites reveals a critical role of essential fatty acids to connect lipids with other metabolic processes. These results characterize many metabolites involved in aging and point to nutrition as a source of intervention for healthy aging therapeutics.

We performed a genome-wide association study (GWAS) of human extreme longevity (EL), defined as surviving past the 99th survival percentile, by aggregating data from four centenarian studies. The combined data included 2304 EL cases and 5879 controls. The analysis identified a locus in CDKN2B-AS1 (rs6475609, p = 7.13 × 10−8) that almost reached genome-wide significance and four additional loci that were suggestively significant. Among these, a novel rare variant (rs145265196) on chromosome 11 had much higher longevity allele frequencies in cases of Ashkenazi Jewish and Southern Italian ancestry compared to cases of other European ancestries. We also correlated EL-associated SNPs with serum proteins to link our findings to potential biological mechanisms that may be related to EL and are under genetic regulation. The findings from the proteomic analyses suggested that longevity-promoting alleles of significant genetic variants either provided EL cases with more youthful molecular profiles compared to controls or provided some form of protection from other illnesses, such as Alzheimer’s disease, and disease progressions.

Canine hemangiosarcoma (HSA) is an aggressive cancer of endothelial cells with short survival times. Understanding the genomic landscape of HSA may aid in developing therapeutic strategies for dogs and may also inform therapies for the rare and aggressive human cancer angiosarcoma. The objectives of this study were to build a framework for leveraging real-world genomic and clinical data that could provide the foundation for precision medicine in veterinary oncology, and to determine the relationships between genomic and clinical features in canine splenic HSA. One hundred and nine dogs with primary splenic HSA treated by splenectomy that had tumour sequencing via the FidoCure (R) Precision Medicine Platform targeted sequencing panel were enrolled. Patient signalment, weight, metastasis at diagnosis and overall survival time were retrospectively evaluated. The incidence of genomic alterations in individual genes and their relationship to patient variables including outcome were assessed. Somatic mutations in TP53 (n = 44), NRAS (n = 20) and PIK3CA (n = 19) were most common. Survival was associated with presence of metastases at diagnosis and germline variants in SETD2 and NOTCH1. Age at diagnosis was associated with somatic NRAS mutations and breed. TP53 and PIK3CA somatic mutations were found in larger dogs, while germline SETD2 variants were found in smaller dogs. We identified both somatic mutations and germline variants associated with clinical variables including age, breed and overall survival. These genetic changes may be useful prognostic factors and provide insight into the genomic landscape of hemangiosarcoma.

We conducted a genome-wide association study (GWAS) of Digit Symbol Substitution Test (DSST) scores administered in 4207 family members of the Long Life Family Study (LLFS). Genotype data were imputed to the HRC panel of 64,940 haplotypes resulting in ~15M genetic variants with quality score > 0.7. The results were replicated using genetic data imputed to the 1000 Genomes phase 3 reference panel from two Danish twin cohorts: the study of Middle Aged Danish Twins and the Longitudinal Study of Aging Danish Twins. The GWAS in LLFS discovered 20 rare genetic variants (minor allele frequency (MAF) < 1.0%) that reached genome-wide significance (p-value < 5×10 −8 ). Among these, 18 variants had large protective effects on the processing speed, including rs7623455, rs9821776, rs9821587, rs78704059 on chromosome 3, which were replicated in the combined Danish twin cohort. These SNPs are located in/near two genes, THRB and RARB , that belonged to thyroid hormone receptors family that may influence speed of metabolism and cognitive aging. The gene-level tests in LLFS confirmed that these two genes are associated with processing speed.

With the goal of identifying metabolites that significantly correlate with the protective e2 allele of the apolipoprotein E ( APOE ) gene, we established a consortium of five studies of healthy aging and extreme human longevity with 3545 participants. This consortium includes the New England Centenarian Study, the Baltimore Longitudinal Study of Aging, the Arivale study, the Longevity Genes Project/LonGenity studies, and the Long Life Family Study. We analyzed the association between APOE genotype groups E2 (e2e2 and e2e3 genotypes, N = 544), E3 (e3e3 genotypes, N = 2299), and E4 (e3e4 and e4e4 genotypes, N = 702) with metabolite profiles in the five studies and used fixed effect meta-analysis to aggregate the results. Our meta-analysis identified a signature of 19 metabolites that are significantly associated with the E2 genotype group at FDR < 10%. The group includes 10 glycerolipids and 4 glycerophospholipids that were all higher in E2 carriers compared to E3, with fold change ranging from 1.08 to 1.25. The organic acid 6-hydroxyindole sulfate, previously linked to changes in gut microbiome that were reflective of healthy aging and longevity, was also higher in E2 carriers compared to E3 carriers. Three sterol lipids and one sphingolipid species were significantly lower in carriers of the E2 genotype group. For some of these metabolites, the effect of the E2 genotype opposed the age effect. No metabolites reached a statistically significant association with the E4 group. This work confirms and expands previous results connecting the APOE gene to lipid regulation and suggests new links between the e2 allele, lipid metabolism, aging, and the gut-brain axis.

Abstract It has been shown that some longevity variants including the APOE variants have ethnicity-specific effects on EL within European ethnicities. The goal of the present study is to identify genetic variants whose effects vary by ethnicity by conducting a genome-wide association study of extreme longevity (EL: defined as living past the age at which less than 1% individuals from the 1900 - 1920 birth year cohorts survived) that includes the SNP-by-ethnicity interaction terms using a consortium of four centenarian studies: the New England Centenarian Study, the Long Life Family Study, the Southern Italian Centenarian Study, and the Longevity Gene Project. We used the Uniform Manifold Approximation and Projection (UMAP), a non-linear dimension reduction technique, to identify distinct ethnic clusters. The UMAP analysis revealed four distinct ethnic groups (Danish, Italian, Ashkenazi Jewish, and middle European) in the aggregated data set with 2223 cases and 5673 controls. Using a mixed effects logistic model with SNP-by-ethnicity interaction terms, we found 29 loci, in which the test of any interaction effect produced p< 10-5. The results showed that some variants had ethnicity-specific effects on EL. We sought for replication in two independent studies of longevity: the Danish Longevity Study and the Italian Longevity Study. In the Italian Longevity Study, rs7907949 (PFKP), rs11667516 (intergenic: RAB11B;MARCHF2), rs13245505 (intergenic: ZC3HC1;KLHDC10) replicated with a nominal significance level of 0.05. In the Danish Longevity Study, rs79853795 (PLCB1) and rs4072601 (SLC39A11) replicated. Future drug development should account for ethnic-specific differences in the genetic effects for higher efficacy for more diverse populations.

Novel drug targets for sustained reduction in body mass index (BMI) are needed to curb the epidemic of obesity, which affects 650 million individuals worldwide and is a causal driver of cardiovascular and metabolic disease and mortality. Previous studies reported that the Arg95Ter nonsense variant of GPR151, an orphan G protein-coupled receptor, is associated with reduced BMI and reduced risk of Type 2 Diabetes (T2D). Here, we further investigate GPR151 with the Pakistan Genome Resource (PGR), which is one of the largest exome biobanks of human homozygous loss-of-function carriers (knockouts) in the world. Among PGR participants, we identify eleven GPR151 putative loss-of-function (plof) variants, three of which are present at homozygosity (Arg95Ter, Tyr99Ter, and Phe175LeufsTer7), with a cumulative allele frequency of 2.2%. We confirm these alleles in vitro as loss-of-function. We test if GPR151 plof is associated with BMI, T2D, or other metabolic traits and find that GPR151 deficiency in complete human knockouts is not associated with clinically significant differences in these traits. Relative to Gpr151+/+ mice, Gpr151-/- animals exhibit no difference in body weight on normal chow and higher body weight on a high-fat diet. Together, our findings indicate that GPR151 antagonism is not a compelling therapeutic approach to treatment of obesity.

ABSTRACT Background Canine hemangiosarcoma (HSA) is an aggressive cancer of endothelial cells associated with short survival times. Understanding the genomic landscape of HSA is critical to developing more effective therapeutic strategies. Objectives To determine the relationships between genomic and clinical features including treatment and outcome in canine splenic HSA. Animals 109 dogs with primary splenic HSA treated by splenectomy that had tumor sequencing via the FidoCure® Precision Medicine Platform targeted sequencing panel. Methods Patient signalment, weight, metastasis at diagnosis, treatment, and survival time were retrospectively evaluated. The incidence of genomic alterations in individual genes and their relationship to patient variables and outcome were assessed. Results Somatic mutations in TP53 (n = 45), NRAS (n = 20), and PIK3CA (n = 19) were most common. Survival was associated with metastases at diagnosis, germline variants in SETD2 and NOTCH1 , and nominally with breed. Age at diagnosis was associated with NRAS mutations and breed. TP53 and PIK3CA mutations were found in larger dogs, germline SETD2 variants in smaller dogs. Doxorubicin (DOX) treatment did not significantly improve survival time, while targeted therapies had a significant early survival benefit. Conclusions and clinical importance DOX treatment may provide limited clinical benefit for dogs with splenic HSA, while targeted therapy may provide early survival benefit. Genetic signatures associated with splenic HSA may be useful in guiding targeted therapy to improve outcomes. Germline variants, age, size, and breed may be useful prognostic factors and provide insight into the genomic landscape of the tumor.

Abstract Mosaic chromosomal alterations (mCAs) are structural alterations that are associated with mortality, age, cancer, cardiovascular disease, and diverse infections. The distribution of mCAs in long-lived subjects and individuals with familial longevity is not well described. We applied MOsaic CHromosomal Alteration (MoChA) caller on genome-wide genotype samples of 2025 centenarians, their siblings, and offspring and 273 unrelated controls from the New England Centenarian Study (NECS) and 3642 subjects with familial longevity and 920 controls from the Long-Life Family Study (LLFS). MoChA utilizes a Hidden Markov Model to detect mCA-induced deviations in allelic balance at heterozygous sites with Log R Ratio and B-allele frequency (BAF) with phased genotype information. We analyzed somatic mCAs in samples with genome-wide BAF phase concordance less than 0.51, LOD score greater than 10, and estimated cell fraction less than 50%. The results in the two studies showed that autosomal mCAs spanning over 100 kbase pairs increase with older age until approximately 102 years. However, the prevalence of the subjects with mCAs tends to plateau after that age, suggesting that the accumulation of mCAs is less prevalent in long-lived subjects. We also found that offspring and siblings of centenarians accumulate less autosomal mCAs (fixed-effect meta-analysis for NECS and LLFS: RR=0.78, p=0.033) compared to unrelated controls. In addition, consistent with results from other studies, mCAs are associated with increased risk for mortality (HR=1.08, p=0.02) and sex (Male RR=1.37, p=4.15e-05), and impact incident events of cancer, dementia, diabetes, and cardiovascular diseases even at extreme old ages.

Abstract Extreme longevity (EL) runs in families which supports the hypothesis that this is a genetically regulated trait. However, with the exception of APOE, genome-wide association studies (GWAS) of EL have not identified many genetic variants that replicate in independent studies. The majority of GWAS of EL have used imputed genotype data. Recently, the Long Life Family Study has generated the largest whole-genome sequencing data of centenarians and matched controls. We perform single-variant and gene-based tests of EL in these data using the nf-gwas-pipeline with the saddle point approximation adjustment of the p-values. These analyses suggest that, in addition to the APOE/TOMM40 region, some uncommon variants of GRM7 (chr3), AUTS2 (chr7), KIF13B (chr8), SLC2A14 (chr12), and ADCY9 (chr16) genes, and other intergenic SNPs in chromosomes 5, 10, and 20 may be implicated with EL.