We present Gene-Embedded Multi-modal Networks (GEM-Net), a semi-supervised framework for constructing multi-modal networks centered on genes. GEM-Net uses gene-level modules and selectively incorporates heterogeneous omics profiles using a correlated meta-analysis strategy that accounts for scale imbalance, missingness, and intra-modular correlation. Prior to network inference, we developed a harmonized data processing protocol that adjusts each omic layer independently through a shared mathematical workflow involving transformation, dimensionality reduction, and regression-based covariate adjustment. GEM-Net modules were inferred and benchmarked against unsupervised methods using transcriptomic, metabolomic, and lipidomic data from the Long Life Family Study (LLFS), a unique cohort enriched for exceptional familial longevity and health. GEM-Net modules were more diverse and biologically interpretable, with stronger support from protein-protein interactions, transcriptional regulation, and metabolic annotations. Applying GEM-Net to metabolic health in LLFS revealed an axis between the microbiome-derived metabolite N-acetylglycine and immune genes (FCER1A, HDC, CPA3, MS4A2) associated with improved insulin sensitivity and reduced inflammation in healthy older individuals. GEM-Nets offer a reusable reference from a long-lived population and a generalizable framework for multi-omics discovery. https://doi.org/10.5281/zenodo.15003731.

Objectives: The purpose of this study is to determine an individual’s age-specific prevalence of total knee arthroplasty (TKA) and revision TKA after ACL reconstruction (ACLr) and to identify clinical and genetic risk factors associated with undergoing TKA. Methods: The UK Biobank – a prospective cohort of 500,000 adults (age 40-69 at time of enrollment) containing health, physical measures, genotyping data, and linked data on hospitalizations – was utilized to identify individuals with a history of ACL surgery (i.e., “cruciate ligament surgery”) during initial health interviews. Individuals were considered to have progressed to end-stage knee osteoarthritis requiring arthroplasty (i.e., “osteoarthritis”) if they endorsed a procedural history of TKA at time of enrollment or underwent hospitalization with a procedural code for TKA after enrollment in the Biobank cohort. To define an individual’s relative risk of TKA following ACLr, age-specific cumulative incidence of TKA was compared between patients WITH and WITHOUT a history of ACLr. To determine clinical risk factors associated with undergoing TKA after ACLr, age-adjusted logistic regression modeling was utilized to calculate odds ratios (OR) for undergoing TKA. A Manhattan plot was constructed to analyze the relationship between single nucleotide polymorphisms and risk of TKA after ACLr. Results: A total of 2,576 individuals with a history of ACLr were identified, with 290 (11.3%) undergoing TKA. In patients with prior ACLr, prevalence of TKA was 0.75% at 45 years of age, 9.1% at 65 years of age, and 20.43% at 80 years of age (Figure 1). Patients with prior ACLr were 4.6x more likely to have undergone TKA by age 55. In the ACLr cohort, BMI >30 kg/m2 (odds ratio = 4.01, 95% confidence interval = 2.74–5.87) (Table 1), a job that always involved heavy manual or physical labor (odds ratio=2.72, 95% confidence interval=1.57-4.71) or walking and standings (odds ratio=2.58, 95% confidence interval=1.58–4.20) were associated with greater TKA prevalence. After adjusting for age, no difference was noted in revision rates between individuals with TKA after ACLr and individuals undergoing TKA without a history of ACLr (Figure 2). No SNP was associated with undergoing TKA after ACLr (Figure 3). Conclusions: Patients with prior ACLr are 4.6x more likely to undergo TKA by age 55 than the general population. Patients with BMI >30 and jobs that involve heavy manual labor or walking/standing are at greatest risk for undergoing TKA. These data can be used to counsel patients at time of index ACLr on both their life-time risk of TKA and lifestyle modifications that may limit the need for future TKA. After adjusting for age, ACLr was not independently associated with revision TKA. [Figure: see text][Figure: see text][Figure: see text]

Aims The purpose of this study is to determine an individual's age- specific prevalence of total knee arthroplasty (TKA) after cruciate ligament surgery, and to identify clinical and genetic risk factors associated with undergoing TKA. Methods This study was a retrospective case- control study using the UK Biobank to identify individuals reporting a history of cruciate ligament surgery. Data from verbal history and procedural codes recorded through the NHS were used to identify instances of TKA. Patient clinical and genetic data were used to identify risk factors for progression from cruciate ligament surgery to TKA. Individuals without a history of cruciate ligament reconstruction were used for comparison. Results A total of 2,576 individuals with a history of cruciate ligament surgery were identified, with 290 (11.25%) undergoing TKA. In patients with prior cruciate ligament surgery, prevalence of TKA was 0.75% at age 45 years, 9.10% at age 65 years, and 20.43% at age 80 years. Patients with prior cruciate ligament surgery were 4.6 times more likely to have undergone TKA by age 55 years than individuals without prior cruciate ligament surgery. In the cruciate ligament surgery cohort, BMI > 30 kg/m(2) (odds ratio (OR) 4.01 (95% confidence interval (CI) 2.74 to 5.87)), a job that always involved heavy manual or physical labour (OR 2.72 (95% CI 1.57 to 4.71)), or a job that always involved walking and standing (OR 2.58 (95% CI 1.58 to 4.20)) were associated with greater TKA odds. No single- nucleotide polymorphism (SNP) was associated with risk of TKA following cruciate ligament surgery. Conclusion Patients with a history of prior cruciate ligament surgery have substantially higher risk of TKA and undergo arthroplasty at a relatively younger age than individuals without a history of prior cruciate ligament surgery. Physically demanding work and obesity were associated with higher odds of TKA after cruciate ligament surgery, but no SNP was associated with risk of TKA.

For atraumatic rotator cuff tears, genetics contributes to symptomatic tear risk and may influence rotator cuff healing after surgical repair. But little is known about how genetic factors influence rotator cuff tear patient characteristics at presentation. We collected saliva samples for genotyping from atraumatic rotator cuff tear patients. We examined nine single nucleotide polymorphisms (SNPs) associated with cuff tears in prior literature. We estimated associations of SNP dosage with (1) age at tear diagnosis, (2) bilateral atraumatic tear prevalence, and (3) tear size. Linear regression was used to estimate associations with diagnosis age adjusted for sex and principal components. Logistic regression and ordinal logistic regression were used to estimate associations with bilateral tear prevalence and tear size category, respectively, adjusting for age, sex, and principal components. Of 344 eligible patients, 336 provided sufficient samples for genotyping. Median age at tear diagnosis was 61, 22% (N = 74) had bilateral atraumatic tears, and 9% (N = 29) had massive tears. SNP rs13107325 in the SLC39A8 gene and rs11850957 in the STXBP6 gene were associated with younger diagnosis age even after accounting for multiple comparisons (rs13107325: -4 years, 95% CI = -6.5, -1.4; rs11850957: -2.7 years, 95% CI = -4.3, -1.1). No other significant associations were observed with diagnosis age, tear size, or bilateral tear prevalence. SLC39A8 encodes a Mn transporter. STXBP6 may play a role in inflammatory responses by altering phagocytosis and antigen presentation of monocytes and macrophages. Further research is needed to determine if genetic markers can be used alongside patient characteristics to aid in identifying optimal surgical repair candidates.

Study Design. Cohort study. Objective. We aimed to evaluate the associations of genetic and nongenetic factors with degenerative cervical myelopathy (DCM). Summary of Background Data. There is mounting evidence for an inherited predisposition for DCM, but uncertainty remains regarding specific genetic markers involved. Similarly, nongenetic factors are thought to play a role. Materials and Methods. Using diagnosis codes from hospital records linked to the UK Biobank cohort, patients with cervical spondylosis were identified followed by the identification of a subset with DCM. Nongenetic variables evaluated included age, sex, race, Townsend deprivation index, body mass index, occupational demands, osteoporosis, and smoking. Genome-wide association analyses were conducted using logistic regression adjusted for age, sex, population principal components, and follow-up. Results. A total of 851 DCM cases out of 2787 cervical spondylosis patients were identified. Several nongenetic factors were independently associated with DCM including age [odds ratio (OR)=1.11, 95% CI=1.01–1.21, P=0.024], male sex (OR=1.63, 95% CI=1.37–1.93, P<0.001), and relative socioeconomic deprivation (OR=1.03, 95% CI=1.00–1.06, P=0.030). Asian race was associated with lower DCM risk (OR=0.44, 95% CI=0.22–0.85, P=0.014). We did not identify genome-wide significant (≤5×10−8) single-nucleotide polymorphisms (SNPs) associated with DCM. The strongest genome-wide signals were at SNP rs67256809 in the intergenic region of the genes LINC02582 and FBXO15 on chromosome 18 (P=1.12×10−7) and rs577081672 in the GTPBP1 gene on chromosome 22 (P=2.9×10−7). No SNPs reported in prior DCM studies were significant after adjusting for replication attempts. Conclusions. Increasing age, male sex, and relative socioeconomic deprivation were identified as independent risk factors for DCM, whereas Asian race was inversely associated. SNPs of potential interest were identified in GTPBP1 and an intergenic region on chromosome 18, but these associations did not reach genome-wide significance. Identification of genetic and nongenetic DCM susceptibility markers may guide understanding of DCM disease processes, inform risk, guide prevention and potentially inform surgical outcomes. Level of Evidence. Prognostic level III.

Supplementary Table 1 from The CHRNA5-CHRNA3-CHRNB4 Nicotinic Receptor Subunit Gene Cluster Affects Risk for Nicotine Dependence in African-Americans and in European-Americans

Supplementary Table 2 from The CHRNA5-CHRNA3-CHRNB4 Nicotinic Receptor Subunit Gene Cluster Affects Risk for Nicotine Dependence in African-Americans and in European-Americans

Many transposable elements (TEs) contain transcription factor binding sites and are implicated as potential regulatory elements. However, TEs are rarely functionally tested for regulatory activity, which in turn limits our understanding of how TE regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1 and C/EBP-related binding motifs as drivers of enhancer activity. Functional analysis of evolutionarily reconstructed ancestral sequences revealed that LTR18A elements have generally lost regulatory activity over time through sequence changes, with the largest effects occurring due to mutations in the AP-1 and C/EBP motifs. We observed that the two motifs are conserved at higher rates than expected based on neutral evolution. Finally, we identified LTR18A elements as potential enhancers in the human genome, primarily in epithelial cells. Together, our results provide a model for the origin, evolution, and co-option of TE-derived regulatory elements.

Many transposable elements (TEs) contain transcription factor binding sites and are implicated as potential regulatory elements. However, TEs are rarely functionally tested for regulatory activity, which in turn limits our understanding of how TE regulatory activity has evolved. We systematically tested the human LTR18A subfamily for regulatory activity using massively parallel reporter assay (MPRA) and found AP-1- and CEBP-related binding motifs as drivers of enhancer activity. Functional analysis of evolutionarily reconstructed ancestral sequences revealed that LTR18A elements have generally lost regulatory activity over time through sequence changes, with the largest effects occurring owing to mutations in the AP-1 and CEBP motifs. We observed that the two motifs are conserved at higher rates than expected based on neutral evolution. Finally, we identified LTR18A elements as potential enhancers in the human genome, primarily in epithelial cells. Together, our results provide a model for the origin, evolution, and co-option of TE-derived regulatory elements.

Tobacco and alcohol use are heritable behaviours associated with 15% and 5.3% of worldwide deaths, respectively, due largely to broad increased risk for disease and injury 1 – 4 . These substances are used across the globe, yet genome-wide association studies have focused largely on individuals of European ancestries 5 . Here we leveraged global genetic diversity across 3.4 million individuals from four major clines of global ancestry (approximately 21% non-European) to power the discovery and fine-mapping of genomic loci associated with tobacco and alcohol use, to inform function of these loci via ancestry-aware transcriptome-wide association studies, and to evaluate the genetic architecture and predictive power of polygenic risk within and across populations. We found that increases in sample size and genetic diversity improved locus identification and fine-mapping resolution, and that a large majority of the 3,823 associated variants (from 2,143 loci) showed consistent effect sizes across ancestry dimensions. However, polygenic risk scores developed in one ancestry performed poorly in others, highlighting the continued need to increase sample sizes of diverse ancestries to realize any potential benefit of polygenic prediction.

Introduction The purpose of this study is to examine the predictive utility of polygenic risk scores (PRSs) for smoking behaviors. Aims and Methods Using summary statistics from the Sequencing Consortium of Alcohol and Nicotine use consortium, we generated PRSs of ever smoking, age of smoking initiation, cigarettes smoked per day, and smoking cessation for participants in the population-based Atherosclerosis Risk in Communities (ARIC) study (N = 8638), and the Collaborative Genetic Study of Nicotine Dependence (COGEND) (N = 1935). The outcomes were ever smoking, age of smoking initiation, heaviness of smoking, and smoking cessation. Results In the European ancestry cohorts, each PRS was significantly associated with the corresponding smoking behavior outcome. In the ARIC cohort, the PRS z-score for ever smoking predicted smoking (odds ratio [OR]: 1.37; 95% confidence interval [CI]: 1.31, 1.43); the PRS z-score for age of smoking initiation was associated with age of smoking initiation (OR: 0.87; 95% CI: 0.82, 0.92); the PRS z-score for cigarettes per day was associated with heavier smoking (OR: 1.17; 95% CI: 1.11, 1.25); and the PRS z-score for smoking cessation predicted successful cessation (OR: 1.24; 95% CI: 1.17, 1.32). In the African ancestry cohort, the PRSs did not predict smoking behaviors. Conclusions Smoking-related PRSs were associated with smoking-related behaviors in European ancestry populations. This improvement in prediction is greatest in the lowest and highest genetic risk categories. The lack of prediction in African ancestry populations highlights the urgent need to increase diversity in research so that scientific advances can be applied to populations other than those of European ancestry. Implications This study shows that including both genetic ancestry and PRSs in a single model increases the ability to predict smoking behaviors compared with the model including only demographic characteristics. This finding is observed for every smoking-related outcome. Even though adding genetics is more predictive, the demographics alone confer substantial and meaningful predictive power. However, with increasing work in PRSs, the predictive ability will continue to improve.

Objective Occupations requiring high physical demands may lead to greater risk of rotator cuff disease (RCD) and corresponding surgical treatment. We linked a job-exposure matrix (JEM) to the UK Biobank to measure physical occupational exposures and estimate associations with incident RCD surgery. Methods Job titles at baseline and UK Standard Occupational Classification (SOC) codes were recorded during a verbal interview. Lifetime job histories were captured through a web-based survey. UK SOC codes were linked to a JEM based on the US O*NET database. O*NET-based scores for physical demands were assigned to jobs including: static strength, dynamic strength, general physical activities, handling/moving objects (range=1–7), time spent using hands, whole body vibration, and cramped/awkward positions (range=1–5). RCD surgeries were identified through national hospital inpatient records. Cox regression was used to calculate hazard ratios (HRs) as estimates of associations with RCD surgery accounting for confounders. Among those with lifetime job histories, associations were estimated with duration of time with high exposure (i.e. above cut-offs identifying approximately the top quartile of exposure). Results Job titles were available for 277,808 people, of which 1,345 (0.5%) had a subsequent inpatient RCD surgery. After adjusting for age, sex, race, education, deprivation, and body mass index, all O*NET variables considered were associated with RCD surgery (HR per point increase range=1.10–1.45, all P<0.005). More frequent occupational manual labor self-reported in the UK Biobank verbal interview was also associated with RCD surgery (HR for ‘Always’ vs. ‘Never/rarely’=2.12; 95%CI=1.79–2.50). Lifetime job histories were available for 100,929 people, in which high exposures were significantly associated with RCD surgery after more than 10 years of work (Ex. HR for 11–20 years vs. 0 years with static strength score≥4=2.06, 95%CI=1.39–3.04). Conclusion Numerous occupational physical exposures were associated with incident RCD surgery. Associations were strongest in workers with more than a decade of high exposure.

BACKGROUND:Hypertension has been implicated as a smoking-related risk factor for cardiovascular disease but the dose-response relationship is incompletely described. Hispanics, who often have relatively light smoking exposures, have been understudied in this regard. METHODS:We used data from a 6-year follow-up study of US Hispanic adults aged 18-76 to address the dose-response linking cigarette use with incident hypertension, which was defined by measured blood pressure above 140/90 mm Hg or initiation of antihypertensive medications. Adjustment was performed for potential confounders and mediators, including urinary albumin-to-creatinine ratio which worsened over time among smokers. RESULTS:Current smoking was associated with incident hypertension, with a threshold effect above 5 cumulative pack-years of smoking (vs. never smokers, hazard ratio for hypertension [95% confidence interval] of 0.95 [0.67, 1.35] for 0-5 pack-years, 1.47 [1.05, 2.06] for 5-10 pack-years, 1.40 [1.00, 1.96] for 10-20 pack-years, and 1.34 [1.09, 1.66] for ≥20 pack-years, P = 0.037). In contrast to current smokers, former smokers did not appear to have increased risk of hypertension, even at the highest cumulative pack-years of past exposure. CONCLUSIONS:The results confirm that smoking constitutes a hypertension risk factor in Hispanic adults. A relatively modest cumulative dose of smoking, above 5 pack-years of exposure, raises risk of hypertension by over 30%. The increased hypertension risk was confined to current smokers, and did not increase further with higher pack-year levels. The lack of a smoking-hypertension association in former smokers underscores the value of smoking cessation.

Background: While evidence indicates that familial predisposition influences the risk of developing degenerative rotator cuff disease (RCD), knowledge of specific genetic markers is limited. We conducted a genome-wide association study of RCD surgery using the UK Biobank, a prospective cohort of 500,000 people (40 to 69 years of age at enrollment) with genotype data. Methods: Cases with surgery for degenerative RCD were identified using linked hospital records. The cases were defined as an International Classification of Diseases, Tenth Revision (ICD-10) code of M75.1 determined by a trauma/orthopaedic specialist and surgery consistent with RCD treatment. Cases were excluded if a diagnosis of traumatic injury had been made during the same hospital visit. For each case, up to 5 controls matched by age, sex, and follow-up time were chosen from the UK Biobank. Analyses were limited to European-ancestry individuals who were not third-degree or closer relations. We used logistic regression to test for genetic association of 674,405 typed and >10 million imputed markers, after adjusting for age, sex, population principal components, and follow-up. Results: We identified 2,917 RCD surgery cases and 14,158 matched controls. We observed 1 genome-wide significant signal (p < 5 × 10−8) for a novel locus tagged by rs2237352 in the CREB5 gene on chromosome 7 (odds ratio [OR] = 1.17, 95% confidence interval [CI] = 1.11 to 1.24). The single-nucleotide polymorphism (SNP) rs2237352 was imputed with a high degree of confidence (info score = 0.9847) and is common, with a minor allele frequency of 47%. After expanding the control sample to include additional unmatched non-cases, rs2237352 and another SNP in the CREB5 gene, rs12700903, were genome-wide significant. We did not detect genome-wide significant signals at loci associated with RCD in previous studies. Conclusions: We identified a novel association between a variant in the CREB5 gene and RCD surgery. Validation of this finding in studies with imaging data to confirm diagnoses will be an important next step. Clinical Relevance: Identification of genetic RCD susceptibility markers can guide understanding of biological processes in rotator cuff degeneration and help inform disease risk in the clinical setting. Level of Evidence: Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.

AIMS:Few risk factors for rotator cuff disease (RCD) and corresponding treatment have been firmly established. The aim of this study was to evaluate the relationship between numerous risk factors and the incidence of surgery for RCD in a large cohort.METHODS:A population-based cohort of people aged between 40 and 69 years in the UK (the UK Biobank) was studied. People who underwent surgery for RCD were identified through a link with NHS inpatient records covering a mean of eight years after enrolment. Multivariate Cox proportional hazards regression was used to calculate hazard ratios (HRs) as estimates of associations with surgery for RCD accounting for confounders. The risk factors which were considered included age, sex, race, education, Townsend deprivation index, body mass index (BMI), occupational demands, and exposure to smoking.RESULTS:Of the 421,894 people who were included, 47% were male. The mean age at the time of enrolment was 56 years (40 to 69). A total of 2,156 people were identified who underwent surgery for RCD. Each decade increase in age was associated with a 55% increase in the incidence of RCD surgery (95% confidence interval (CI) 46% to 64%). Male sex, non-white race, lower deprivation score, and higher BMI were significantly associated with a higher risk of surgery for RCD (all p < 0.050). Greater occupational physical demands were significantly associated with higher rates of RCD surgery (HR = 2.1, 1.8, and 1.4 for 'always', 'usually', and 'sometimes' doing heavy manual labour vs 'never', all p < 0.001). Former smokers had significantly higher rates of RCD surgery than those who had never smoked (HR 1.23 (95% CI 1.12 to 1.35), p < 0.001), while current smokers had similar rates to those who had never smoked (HR 0.94 (95% CI 0.80 to 1.11)). Among those who had never smoked, the risk of surgery was higher among those with more than one household member who smoked (HR 1.78 (95% CI 1.08 to 2.92)). The risk of RCD surgery was not significantly related to other measurements of secondhand smoking.CONCLUSION:Many factors were independently associated with surgery for RCD, including older age, male sex, higher BMI, lower deprivation score, and higher occupational physical demands. Several of the risk factors which were identified are modifiable, suggesting that the healthcare burden of RCD might be reduced through the pursuit of public health goals, such as reducing obesity and modifying occupational demands. Cite this article: Bone Joint J 2020;102-B(3):352-359.

Smoking is a major contributor to lung cancer and chronic obstructive pulmonary disease (COPD). Two of the strongest genetic associations of smoking-related phenotypes are the chromosomal regions 15q25.1, encompassing the nicotinic acetylcholine receptor subunit genesCHRNA5-CHRNA3-CHRNB4, and 19q13.2, encompassing the nicotine metabolizing geneCYP2A6. In this study, we examined genetic relations between cigarettes smoked per day, smoking cessation, lung cancer, and COPD. Data consisted of genome-wide association study summary results. Genetic correlations were estimated using linkage disequilibrium score regression software. For each pair of outcomes, z-score-z-score (ZZ) plots were generated. Overall, heavier smoking and decreased smoking cessation showed positive genetic associations with increased lung cancer and COPD risk. The chromosomal region 19q13.2, however, showed a different correlational pattern. For example, the effect allele-C of the sentinel SNP (rs56113850) withinCYP2A6was associated with an increased risk of heavier smoking (z-score = 19.2;p = 1.10 x 10(-81)), lung cancer (z-score = 8.91;p = 5.02 x 10(-19)), and COPD (z-score = 4.04;p = 5.40 x 10(-5)). Surprisingly, this allele-C (rs56113850) was associated with increased smoking cessation (z-score = -8.17;p = 2.52 x 10(-26)). This inverse relationship highlights the need for additional investigation to determine howCYP2A6variation could increase smoking cessation while also increasing the risk of lung cancer and COPD likely through increased cigarettes smoked per day.

Eating disorders and substance use disorders frequently co-occur. Twin studies reveal shared genetic variance between liabilities to eating disorders and substance use, with the strongest associations between symptoms of bulimia nervosa and problem alcohol use (genetic correlation [rg ], twin-based = 0.23-0.53). We estimated the genetic correlation between eating disorder and substance use and disorder phenotypes using data from genome-wide association studies (GWAS). Four eating disorder phenotypes (anorexia nervosa [AN], AN with binge eating, AN without binge eating, and a bulimia nervosa factor score), and eight substance-use-related phenotypes (drinks per week, alcohol use disorder [AUD], smoking initiation, current smoking, cigarettes per day, nicotine dependence, cannabis initiation, and cannabis use disorder) from eight studies were included. Significant genetic correlations were adjusted for variants associated with major depressive disorder and schizophrenia. Total study sample sizes per phenotype ranged from ~2400 to ~537 000 individuals. We used linkage disequilibrium score regression to calculate single nucleotide polymorphism-based genetic correlations between eating disorder- and substance-use-related phenotypes. Significant positive genetic associations emerged between AUD and AN (rg = 0.18; false discovery rate q = 0.0006), cannabis initiation and AN (rg = 0.23; q < 0.0001), and cannabis initiation and AN with binge eating (rg = 0.27; q = 0.0016). Conversely, significant negative genetic correlations were observed between three nondiagnostic smoking phenotypes (smoking initiation, current smoking, and cigarettes per day) and AN without binge eating (rgs = -0.19 to -0.23; qs < 0.04). The genetic correlation between AUD and AN was no longer significant after co-varying for major depressive disorder loci. The patterns of association between eating disorder- and substance-use-related phenotypes highlights the potentially complex and substance-specific relationships among these behaviors.

To provide insights into the biology of opioid dependence (OD) and opioid use (i.e., exposure, OE), we completed a genome-wide analysis comparing 4503 OD cases, 4173 opioid-exposed controls, and 32,500 opioid-unexposed controls, including participants of European and African descent (EUR and AFR, respectively). Among the variants identified, rs9291211 was associated with OE (exposed vs. unexposed controls; EUR z = −5.39, p = 7.2 × 10–8). This variant regulates the transcriptomic profiles of SLC30A9 and BEND4 in multiple brain tissues and was previously associated with depression, alcohol consumption, and neuroticism. A phenome-wide scan of rs9291211 in the UK Biobank (N > 360,000) found association of this variant with propensity to use dietary supplements (p = 1.68 × 10–8). With respect to the same OE phenotype in the gene-based analysis, we identified SDCCAG8 (EUR + AFR z = 4.69, p = 10–6), which was previously associated with educational attainment, risk-taking behaviors, and schizophrenia. In addition, rs201123820 showed a genome-wide significant difference between OD cases and unexposed controls (AFR z = 5.55, p = 2.9 × 10–8) and a significant association with musculoskeletal disorders in the UK Biobank (p = 4.88 × 10–7). A polygenic risk score (PRS) based on a GWAS of risk-tolerance (n = 466,571) was positively associated with OD (OD vs. unexposed controls, p = 8.1 × 10–5; OD cases vs. exposed controls, p = 0.054) and OE (exposed vs. unexposed controls, p = 3.6 × 10–5). A PRS based on a GWAS of neuroticism (n = 390,278) was positively associated with OD (OD vs. unexposed controls, p = 3.2 × 10–5; OD vs. exposed controls, p = 0.002) but not with OE (p = 0.67). Our analyses highlight the difference between dependence and exposure and the importance of considering the definition of controls in studies of addiction.

The implementation of pharmacogenomic (PGx) testing in psychiatry remains modest, in part due to divergent perceptions of the quality and completeness of the evidence base and diverse perspectives on the clinical utility of PGx testing among psychiatrists and other healthcare providers. Recognizing the current lack of consensus within the field, the International Society of Psychiatric Genetics assembled a group of experts to conduct a narrative synthesis of the PGx literature, prescribing guidelines, and product labels related to psychotropic medications as well as the key considerations and limitations related to the use of PGx testing in psychiatry. The group concluded that to inform medication selection and dosing of several commonly-used antidepressant and antipsychotic medications, current published evidence, prescribing guidelines, and product labels support the use of PGx testing for 2 cytochrome P450 genes (CYP2D6, CYP2C19). In addition, the evidence supports testing for human leukocyte antigen genes when using the mood stabilizers carbamazepine (HLA-A and HLA-B), oxcarbazepine (HLA-B), and phenytoin (CYP2C9, HLA-B). For valproate, screening for variants in certain genes (POLG, OTC, CSP1) is recommended when a mitochondrial disorder or a urea cycle disorder is suspected. Although barriers to implementing PGx testing remain to be fully resolved, the current trajectory of discovery and innovation in the field suggests these barriers will be overcome and testing will become an important tool in psychiatry.