Determining the stability of genome-wide factors in BMI between ages 40 to 69 years.

Genome-wide association studies (GWAS) have successfully identified common variants associated with BMI. However, the stability of aggregate genetic variation influencing BMI from midlife and beyond is unknown. By analysing 165,717 men and 193,073 women from the UKBiobank, we performed BMI GWAS on six independent five-year age intervals between 40 and 72 years. We then applied genomic structural equation modeling to test competing hypotheses regarding the stability of genetic effects for BMI. LDSR genetic correlations between BMI assessed between ages 40 to 73 were all very high and ranged 0.89 to 1.00. Genomic structural equation modeling revealed that molecular genetic variance in BMI at each age interval could not be explained by the accumulation of any age-specific genetic influences or autoregressive processes. Instead, a common set of stable genetic influences appears to underpin genome-wide variation in BMI from middle to early old age in men and women alike.

Effects of aerobic exercise on neurocognitive function in postmenopausal women receiving endocrine therapy for breast cancer: The Exercise Program in Cancer and Cognition randomized controlled trial.

Objective: The Exercise Program in Cancer and Cognition (EPICC) Study was a randomized controlled trial (RCT) designed to determine whether six months of moderate-intensity aerobic exercise improves neurocognitive function in women with breast cancer (BC) receiving endocrine therapy (ET). Methods: Postmenopausal women with hormone receptor+, early-stage BC, within two years post-primary therapy were randomized to the exercise intervention (six months, ≥150 minutes of moderate-intensity aerobic exercise/week) or usual care control condition. Outcomes were assessed at pre-randomization and after intervention completion. Groups were compared using linear mixed-effects modeling. Results: Participants (N=153) were X ¯ = 62.09 ± 8.27 years old, with stage I BC (64.1%) and a median of 4.7 months post-diagnosis. We found a group-by-time interaction (p=0.041) and a trend for the main effect of time (p=0.11) for processing speed with improved performance in the exercise group and no change in the controls. Similar main effects of time were observed for learning and memory (p=0.024) and working memory (p=0.01). Better intervention adherence was associated with improved processing speed (p=0.017). Conclusions: Six months of moderate-intensity aerobic exercise improves processing speed in postmenopausal women with BC receiving ET who initiate exercise within two years of completing primary therapy (surgery +/- chemotherapy). This is the first large-scale study to examine the effects of aerobic exercise on neurocognitive function in women with BC. Additional research is needed to address the long-term effects of aerobic exercise on cognitive function.

Associations between polygenic liability to psychopathology and non-suicidal versus suicidal self-injury.

Little is known about how non-suicidal and suicidal self-injury are differentially genetically related to psychopathology and related measures. This research was conducted using the UK Biobank Resource, in participants of European ancestry (N = 2320 non-suicidal self-injury [NSSI] only; N = 2648 suicide attempt; 69.18% female). We compared polygenic scores (PGS) for psychopathology and other relevant measures within self-injuring individuals. Logistic regressions and likelihood ratio tests (LRT) were used to identify PGS that were differentially associated with these outcomes. In a multivariable model, PGS for anorexia nervosa (odds ratio [OR] = 1.07; 95% confidence intervals [CI] 1.01; 1.15) and suicidal behavior (OR = 1.06; 95% CI 1.00; 1.12) both differentiated between NSSI and suicide attempt, while the PGS for other phenotypes did not. The LRT between the multivariable and base models was significant (Chi square = 11.38, df = 2, p = 0.003), and the multivariable model explained a larger proportion of variance (Nagelkerke's pseudo-R2 = 0.028 vs. 0.025). While NSSI and suicidal behavior are similarly genetically related to a range of mental health and related outcomes, genetic liability to anorexia nervosa and suicidal behavior is higher among those reporting a suicide attempt than those reporting NSSI-only. Further elucidation of these distinctions is necessary, which will require a nuanced assessment of suicidal versus non-suicidal self-injury in large samples.

Physical activity, cardiorespiratory fitness, and cognitive function in postmenopausal women with breast cancer.

Physical activity may improve cognitive function in women with breast cancer. In a cross-sectional study, we explored the relationship between cognitive function and physical activity (actigraph) and cardiorespiratory fitness (sub-maximal graded exercise test) in 73 postmenopausal women with early stage breast cancer prior to the initiation of systemic adjuvant therapy. Cognitive function was assessed with a standardized battery of neurocognitive measures assessing eight domains. Data were analyzed using partial correlations, controlling for age and total hours of actigraph wear-time. Women were, on average, 63.71 (± 5.3) years of age with 15.47 (± 2.48) years of education. For physical activity, greater average number of steps per day were associated with better attention (r = .262, p = .032) and psychomotor speed (r = .301, p = .011); greater average hours of moderate and moderate/vigorous intensity physical activity were associated with better visual memory (r = .241, p = .049; r = .241, p = .049, respectively); and greater average daily energy expenditure was associated with better visual memory (r = .270, p = .027) and psychomotor speed (r = .292, p = .017). For fitness, higher peak maximum VO2 was associated with better concentration (r = .330, p = .006), verbal memory (r = .241, p = .048), and working memory (r = .281, p = .019). These results suggest that higher levels of physical activity and cardiorespiratory fitness are associated with better cognitive function in postmenopausal women with breast cancer. Randomized controlled trials (RCT) to examine whether physical activity improves cognitive function in women with breast cancer are warranted. These RCTs should also determine the mechanisms of the influence of physical activity on cognitive function. CLINICAL TRIALS REGISTRATION NUMBER: NCT02793921; Date: May 20, 2016.

Testing Genetic and Environmental Associations Between Personality Disorders and Cocaine Use: A Population-Based Twin Study.

Until now, data have not been available to elucidate the genetic and environmental sources of comorbidity between all 10 DSM-IV personality disorders (PDs) and cocaine use. Our aim was to determine which PD traits are linked phenotypically and genetically to cocaine use. Cross-sectional data were obtained in a face-to-face interview between 1999 and 2004. Subjects were 1,419 twins (µage = 28.2 years, range = 19-36) from the Norwegian Institute of Public Health Twin Panel, with complete lifetime cocaine use and criteria for all 10 DSM-IV PDs. Stepwise multiple and Least Absolute Shrinkage and Selection Operator (LASSO) regressions were used to identify PDs related to cocaine use. Twin models were fitted to estimate genetic and environmental associations between the PD traits and cocaine use. In the multiple regression, antisocial (OR = 4.24, 95% CI [2.66, 6.86]) and borderline (OR = 2.19, 95% CI [1.35, 3.57]) PD traits were significant predictors of cocaine use. In the LASSO regression, antisocial, borderline, and histrionic were significant predictors of cocaine use. Antisocial and borderline PD traits each explained 72% and 25% of the total genetic risks in cocaine use, respectively. Genetic risks in histrionic PD were not significantly related to cocaine use. Importantly, after removing criteria referencing substance use, antisocial PD explained 65% of the total genetic variance in cocaine use, whereas borderline explained only 4%. Among PD traits, antisocial is the strongest correlate of cocaine use, for which the association is driven largely by common genetic risks.

Trajectories of self-reported cognitive function in postmenopausal women during adjuvant systemic therapy for breast cancer.

OBJECTIVE: In a sample of 368 postmenopausal women, we (1) determined within-cohort and between-cohort relationships between adjuvant systemic therapy for breast cancer and self-reported cognitive function during the first 18 months of therapy and (2) evaluated the influence of co-occurring symptoms, neuropsychological function, and other covariates on relationships. METHODS: We evaluated self-reported cognitive function, using the Patient Assessment of Own Functioning Inventory (PAOFI), and potential covariates (e.g., co-occurring symptom scores and neuropsychological function z-scores) in 158 women receiving aromatase inhibitor (AI) therapy alone, 104 women receiving chemotherapy followed by AI therapy, and 106 non-cancer controls. Patients were assessed before systemic therapy and then every 6 months, for a total of four assessments over 18 months. Controls were assessed at matched time points. Mixed-effects modeling was used to determine longitudinal relationships. RESULTS: Controlling for covariates, patients enrolled before chemotherapy reported poorer global cognitive function (p < 0.001), memory (p < 0.001), language and communication (p < 0.001), and sensorimotor function (p = 0.002) after chemotherapy. These patients reported poorer higher-level cognitive and intellectual functions from before chemotherapy to 12 months after initiation of AI therapy (p < 0.001). Higher levels of depressive symptoms (p < 0.001), anxiety (p < 0.001), and fatigue (p = 0.040) at enrollment were predictors of poorer cognitive function over time. PAOFI total score was a predictor of executive function (p = 0.048) and visual working memory (p = 0.005) z-scores, controlling for covariates. CONCLUSIONS: Findings provide further evidence of poorer self-reported cognitive function after chemotherapy and of relationships between co-occurring symptoms and cognitive changes. AI therapy alone does not have an impact on self-reported cognitive function. Copyright © 2015 John Wiley & Sons, Ltd.

The Alternative Splicing of Cytoplasmic Polyadenylation Element Binding Protein 2 Drives Anoikis Resistance and the Metastasis of Triple Negative Breast Cancer.

Triple negative breast cancer (TNBC) represents an anomalous subset of breast cancer with a greatly reduced (30%) 5-year survival rate. The enhanced mortality and morbidity of TNBC arises from the high metastatic rate, which requires the acquisition of AnR, a process whereby anchorage-dependent cells become resistant to cell death induced by detachment. In this study TNBC cell lines were selected for AnR, and these cell lines demonstrated dramatic enhancement in the formation of lung metastases as compared with parental cells. Genetic analysis of the AnR subclones versus parental cells via next generation sequencing and analysis of global alternative RNA splicing identified that the mRNA splicing of cytoplasmic polyadenylation element binding 2 (CPEB2), a translational regulator, was altered in AnR TNBC cells. Specifically, increased inclusion of exon 4 into the mature mRNA to produce the CPEB2B isoform was observed in AnR cell lines. Molecular manipulations of CPEB2 splice variants demonstrated a key role for this RNA splicing event in the resistance of cells to anoikis. Specifically, down-regulation of the CPEB2B isoform using siRNA re-sensitized the AnR cell lines to detachment-induced cell death. The ectopic expression of CPEB2B in parental TNBC cell lines induced AnR and dramatically increased metastatic potential. Importantly, alterations in the alternative splicing of CPEB2 were also observed in human TNBC and additional subtypes of human breast cancer tumors linked to a high metastatic rate. Our findings demonstrate that the regulation of CPEB2 mRNA splicing is a key mechanism in AnR and a driving force in TNBC metastasis.

Psychometric Evaluation of the Patient-Reported Outcomes Measurement Information System Fatigue-Short Form Across Diverse Populations.

BACKGROUND: The need for reliable, valid tools to measure patient-reported outcomes (PROs) is critical both for research and for evaluating treatment effects in practice. The Patient-Reported Outcomes Measurement Information System Fatigue-Short Form v1.0-Fatigue 7a (PROMIS F-SF) has had limited psychometric evaluation in various populations. OBJECTIVES: The aim of the study is to examine psychometric properties of PROMIS F-SF item responses across various populations. METHODS: Data from five studies with common data elements were used in this secondary analysis. Samples from patients with fibromyalgia, sickle cell disease, cardiometabolic risk, pregnancy, and healthy controls were used. Reliability was estimated using Cronbach's alpha. Dimensionality was evaluated with confirmatory factor analysis. Concurrent validity was evaluated by examining Pearson's correlations between scores from the PROMIS F-SF, the Multidimensional Fatigue Symptom Inventory-Short Form, and the Brief Fatigue Inventory. Discriminant validity was evaluated by examining Pearson's correlations between scores on the PROMIS F-SF and measures of stress and depressive symptoms. Known groups validity was assessed by comparing PROMIS F-SF scores in the clinical samples to healthy controls. RESULTS: Reliability of PROMIS F-SF scores was adequate across samples, ranging from .72 in the pregnancy sample to .88 in healthy controls. Unidimensionality was supported in each sample. Concurrent validity was strong; across the groups, correlations with scores on the Multidimensional Fatigue Symptom Inventory-Short Form and Brief Fatigue Inventory ranged from .60 to .85. Correlations of the PROMIS F-SF with measures of stress and depressive mood were moderate to strong, ranging from .37 to .64. PROMIS F-SF scores were significantly higher in clinical samples compared to healthy controls. DISCUSSION: Reliability and validity of the PROMIS F-SF were acceptable. The PROMIS F-SF is a suitable measure of fatigue across the four diverse clinical populations included in the analysis.

Patterns of change in cognitive function with anastrozole therapy.

BACKGROUND: The purpose of this study was to examine and compare the effects of the first 18 months of anastrozole therapy on cognitive function in women with breast cancer. METHODS: This large, longitudinal cohort study was composed of postmenopausal women with early-stage breast cancer who received chemotherapy plus anastrozole (n = 114) or anastrozole alone (n = 173) and a control group (n = 110). Cognitive function was assessed before systemic therapy and 6, 12, and 18 months after therapy initiation and at comparable time points in controls. RESULTS: The chemotherapy-anastrozole and anastrozole-alone groups had poorer executive function than the controls at nearly all time points (P < .0001 to P = .09). A pattern of deterioration in working memory and concentration was observed during the first 6 months of anastrozole therapy for the chemotherapy-anastrozole group (P < .0001 and P < .0009, respectively) and the anastrozole-alone group (P = .0008 and P = .0002, respectively). This was followed by improved working memory and concentration from 6 to 12 months in both groups. The anastrozole-alone group had a second decline in working memory and concentration from 12 to 18 months after the initiation of therapy (P < .0001 and P = .02, respectively). CONCLUSIONS: Women with breast cancer had poorer executive functioning from the period before therapy through the entire first 18 months of therapy. A pattern of decline in working memory and concentration with initial exposure to anastrozole was observed. Women receiving anastrozole alone had a second deterioration in working memory and concentration from 12 to 18 months after therapy initiation. The longer term effects (>18 months) of anastrozole on cognitive function remain to be determined.

Chiral discrimination and writhe-dependent relaxation mechanism of human topoisomerase IIα.

BACKGROUND: Human topoisomerase IIα unlinks catenated chromosomes and preferentially relaxes positive supercoils. RESULTS: Supercoil chirality, twist density, and tension determine topoisomerase IIα relaxation rate and processivity. CONCLUSION: Strand passage rate is determined by the efficiency of transfer segment capture that is modulated by the topoisomerase C-terminal domains. SIGNIFICANCE: Single-molecule measurements reveal the mechanism of chiral discrimination and tension dependence of supercoil relaxation by human topoisomerase IIα. Type IIA topoisomerases (Topo IIA) are essential enzymes that relax DNA supercoils and remove links joining replicated chromosomes. Human topoisomerase IIα (htopo IIα), one of two human isoforms, preferentially relaxes positive supercoils, a feature shared with Escherichia coli topoisomerase IV (Topo IV). The mechanistic basis of this chiral discrimination remains unresolved. To address this important issue, we measured the relaxation of individual supercoiled and "braided" DNA molecules by htopo IIα using a magnetic tweezers-based single-molecule assay. Our study confirmed the chiral discrimination activity of htopo IIα and revealed that the strand passage rate depends on DNA twist, tension on the DNA, and the C-terminal domain (CTD). Similar to Topo IV, chiral discrimination by htopo IIα results from chiral interactions of the CTDs with DNA writhe. In contrast to Topo IV, however, these interactions lead to chiral differences in relaxation rate rather than processivity. Increasing tension or twist disrupts the CTD-DNA interactions with a subsequent loss of chiral discrimination. Together, these results suggest that transfer segment (T-segment) capture is the rate-limiting step in the strand passage cycle. We propose a model for T-segment capture that provides a mechanistic basis for chiral discrimination and provides a coherent explanation for the effects of DNA twist and tension on eukaryotic type IIA topoisomerases.

Attribution of mild cognitive impairment etiology in patients and their care partners.

OBJECTIVE: This study examined the attribution of mild cognitive impairment (MCI) etiology assigned by individuals with MCI and their care partners, and the extent to which the dyads agreed on the attribution of MCI etiology. METHODS: We conducted secondary analyses of cross-sectional data from a cohort of individuals with MCI (n = 60) and their care partners (n = 60). The mean age of the individuals with MCI was 71.0 ± 9.4 years and of care partners 64.2 ± 11.0 years. The primary outcome was attribution assigned to memory deficits on the Illness Perception Questionnaire. We categorized the attribution of MCI etiology as either potentially controllable or uncontrollable factors. We described the distribution of MCI etiology with descriptive and contingency tables. We determined the odds of a patient or care partner choosing one type of MCI etiology over another. RESULTS: Although individuals with MCI and their care partners most frequently attributed MCI to uncontrollable factors (81.7% and 61.0%, respectively), care partners were 28.41 (95% CI, 1.26 to 645.48) times more likely to attribute MCI etiology to potentially controllable factors than individuals with MCI. No significant associations between demographic factors and attribution of MCI etiology were found for the individuals with MCI or the care partners. CONCLUSION: Findings demonstrated that members of the dyad attributed MCI etiology to different causes. Attributions of MCI etiology should be explored by professionals to clarify misconceptions and potentially improve subsequent voluntary actions intended to assist oneself or others.

Patient motivators of postoperative electronic patient-reported outcome symptom monitoring use in thoracic surgery patients: a qualitative study.

BACKGROUND: Electronic patient-reported outcome (ePRO) systems can be used to engage patients in remote symptom monitoring to support postoperative care. We interviewed thoracic surgery patients with ePRO experience to identify factors that influenced use of ePROs to report their symptoms post-discharge. METHOD: This qualitative study used semi-structured telephone interviews with adults who underwent major thoracic surgery at an academic medical center in North Carolina. Individuals who enrolled in symptom monitoring, completed at least one ePRO survey, and were reachable by phone for the interview were included. The ePRO surveys assessed 10 symptoms, including validated Patient-Reported Outcome Common Terminology Criteria for Adverse Events (PRO-CTCAE) measures and thoracic surgery-specific questions. Surveys, offered via web-based and automated telephone options, were administered for four weeks post-discharge with alerts sent to clinicians for concerning symptoms. The interviews were guided by the Capability, Opportunity, Motivation model for behavior change (COM-B) and examined factors that influenced patients' completion of ePRO surveys post-discharge. Team members independently coded interviews and identified themes, informed by COM-B. We report descriptive statistics (demographics, number of surveys completed) and themes organized by COM-B components. RESULTS: Of 28 patients invited, 25 (89%) completed interviews from July to October 2022. Participants were a median 58 years, 56% female, 80% White, and 56% had a history of malignancy. They completed 131/150 (87%) possible ePRO surveys. For capability, participants reported building ePROs into their routine and having the skills and knowledge, but lacking physical and emotional energy, to complete ePROs. For opportunity, participants identified the ease and convenience of accessing ePROs and providers' validation of ePROs. Motivators were perceived benefits of a deepening connection to their clinical team, improved symptom management for themselves and others, and self-reflection about their recovery. Factors limiting motivation included lack of clarity about the purpose of ePROs and a disconnect between symptom items and individual recovery experience. CONCLUSIONS: Patients described being motivated to complete ePROs when reinforced by clinicians and considered ePROs as valuable to their post-discharge experience. Future work should enhance ePRO patient education, improve provider alerts and communications about ePROs, and integrate options to capture patients' complex health journeys.

People who undergo thoracic surgery often experience pain and other symptoms while recovering at home. These symptoms can be severe and may reduce overall quality of life and potentially result in some patients returning to the hospital for future treatment. Electronic Patient-Reported Outcomes can be used as a method for having patients regularly track and report any symptoms they experience while at home, and how severe those symptoms are, using digital technology such as an online survey or automated phone survey. Surgical care team members may then follow up with patients about their symptoms. More information was needed about the patient experience with completing these surveys about their symptoms. In this study, we interviewed patients who had completed Electronic Patient-Reported Outcomes after thoracic surgery to understand what may (or may not) have impelled them to participate and to learn how to improve the use of these surveys for patients. This study found that patients generally felt they were able to complete the symptom surveys. Key motivators included feeling more connected to their surgeon by completing the symptom surveys and having the opportunity to reflect on how their recovery was going at home. However, patients also discussed not having a clear understanding of the purpose of the symptom surveys and how their responses might affect their care. The study findings highlight the need for improved patient education and indicate that improvements to the survey questions and to how surgeons review patients' responses may be needed.

The geometry of DNA supercoils modulates the DNA cleavage activity of human topoisomerase I.

Human topoisomerase I plays an important role in removing positive DNA supercoils that accumulate ahead of replication forks. It also is the target for camptothecin-based anticancer drugs that act by increasing levels of topoisomerase I-mediated DNA scission. Evidence suggests that cleavage events most likely to generate permanent genomic damage are those that occur ahead of DNA tracking systems. Therefore, it is important to characterize the ability of topoisomerase I to cleave positively supercoiled DNA. Results confirm that the human enzyme maintains higher levels of cleavage with positively as opposed to negatively supercoiled substrates in the absence or presence of anticancer drugs. Enhanced drug efficacy on positively supercoiled DNA is due primarily to an increase in baseline levels of cleavage. Sites of topoisomerase I-mediated DNA cleavage do not appear to be affected by supercoil geometry. However, rates of ligation are slower with positively supercoiled substrates. Finally, intercalators enhance topoisomerase I-mediated cleavage of negatively supercoiled substrates but not positively supercoiled or linear DNA. We suggest that these compounds act by altering the perceived topological state of the double helix, making underwound DNA appear to be overwound to the enzyme, and propose that these compounds be referred to as 'topological poisons of topoisomerase I'.

Missingness adapted group informed clustered (MAGIC)-LASSO: a novel paradigm for phenotype prediction to improve power for genetic loci discovery.

Introduction: The availability of large-scale biobanks linking genetic data, rich phenotypes, and biological measures is a powerful opportunity for scientific discovery. However, real-world collections frequently have extensive missingness. While missing data prediction is possible, performance is significantly impaired by block-wise missingness inherent to many biobanks. Methods: To address this, we developed Missingness Adapted Group-wise Informed Clustered (MAGIC)-LASSO which performs hierarchical clustering of variables based on missingness followed by sequential Group LASSO within clusters. Variables are pre-filtered for missingness and balance between training and target sets with final models built using stepwise inclusion of features ranked by completeness. This research has been conducted using the UK Biobank (n > 500 k) to predict unmeasured Alcohol Use Disorders Identification Test (AUDIT) scores. Results: The phenotypic correlation between measured and predicted total score was 0.67 while genetic correlations between independent subjects was high >0.86. Discussion: Phenotypic and genetic correlations in real data application, as well as simulations, demonstrate the method has significant accuracy and utility for increasing power for genetic loci discovery.

Multifaceted risk for non-suicidal self-injury only versus suicide attempt in a population-based cohort of adults.

BACKGROUND: Non-suicidal self-injury and suicide attempt represent significant public health concerns. While these outcomes are related, there is prior evidence that their etiology does not entirely overlap. Efforts to directly differentiate risk across outcomes are uncommon, particularly among older, population-based cohorts. METHODS: This research has been conducted using the UK Biobank. Data on individuals' self-reported history of non-suicidal self-injury only versus suicide attempt (maximum N = 6643) were analyzed. Applying LASSO and standard logistic regression, participants reporting one of these outcomes were assessed for differences across a range of sociodemographic, behavioral, and environmental features. RESULTS: Sociodemographic features most strongly differentiated between the outcomes of non-suicidal self-injury only versus suicide attempt. Specifically, Black individuals were more likely to report a suicide attempt, as were those of mixed race, those endorsing higher levels of depressive symptoms or trauma history, and those who had experienced financial problems (odds ratios 1.02-3.92). Those more likely to engage in non-suicidal self-injury only were younger, female, had higher levels of education, those who resided with a partner, and those who had a recently injured relative. LIMITATIONS: Differences in timing across correlates and outcomes preclude the ability to establish causal pathways. CONCLUSIONS: The factors identified in the current study as differentially associated with non-suicidal self-injury only versus suicide attempt provide further evidence of at least partially distinct correlates, and warrant follow-up in independent samples to investigate causality.

Preliminary assessment of three quantitative approaches for estimating time-since-deposition from autofluorescence and morphological profiles of cell populations from forensic biological samples.

Determining when DNA recovered from a crime scene transferred from its biological source, i.e., a sample's 'time-since-deposition' (TSD), can provide critical context for biological evidence. Yet, there remains no analytical techniques for TSD that are validated for forensic casework. In this study, we investigate whether morphological and autofluorescence measurements of forensically-relevant cell populations generated with Imaging Flow Cytometry (IFC) can be used to predict the TSD of 'touch' or trace biological samples. To this end, three different prediction frameworks for estimating the number of day(s) for TSD were evaluated: the elastic net, gradient boosting machines (GBM), and generalized linear mixed model (GLMM) LASSO. Additionally, we transformed these continuous predictions into a series of binary classifiers to evaluate the potential utility for forensic casework. Results showed that GBM and GLMM-LASSO showed the highest accuracy, with mean absolute error estimates in a hold-out test set of 29 and 21 days, respectively. Binary classifiers for these models correctly binned 94-96% and 98-99% of the age estimates as over/under 7 or 180 days, respectively. This suggests that predicted TSD using IFC measurements coupled to one or, possibly, a combination binary classification decision rules, may provide probative information for trace biological samples encountered during forensic casework.

Differentiation of vaginal cells from epidermal cells using morphological and autofluorescence properties: Implications for sexual assault casework involving digital penetration.

Analysis of DNA mixtures from sexual assault evidence is an ongoing challenge for DNA casework laboratories. There is a significant need for new techniques that can provide information as to the source of DNA, particularly for sexual assault samples that do not involve semen. The goal of this study was to develop a new biological signature system that provides additional probative value to samples comprised of mixtures of epidermal and vaginal cells, as may be observed in cases involving digital penetration. Signatures were based on morphological and autofluorescence properties of individual cells collected through Imaging Flow Cytometry (IFC). Comparisons to reference cell populations from vaginal tissue and epidermal cells collected from hands showed strong multivariate differences across >80 cellular measurements. These differences were used to build a predictive framework for classifying unknown cell populations as originating from epithelial cells associated with digital penetration or epidermal tissue. As part of the classification scheme, posterior probabilities of specific tissue group membership were calculated for each cell, along with multivariate similarity to that tissue type. We tested this approach on cell populations from reference tissue as well as mock casework samples involving digital penetration. Many more cells classifying as non-epidermal tissue were detected in digital penetration samples than control hand swabbings. Minimum interpretation thresholds were developed to minimize false positives; these thresholds were also effective when screening licked hands, indicating the potential utility of this method for a variety of biological mixture types and depositional events relevant to forensic casework. Results showed that samples collected subsequent to digital penetration possessed markedly higher numbers of cells classifying as vaginal tissue as well as higher posterior probabilities for vaginal tissue (≥ 0.90) compared to cell populations collected from hands without prior contact with vaginal tissue. Additionally, digital penetration cell populations may be resolved from saliva cell populations and other non-target tissue types.

Differentiation of vaginal cells from epidermal cells using morphological and autofluorescence properties: Implications for sexual assault casework involving digital penetration.

Analysis of DNA mixtures from sexual assault evidence is an ongoing challenge for DNA casework laboratories. To assist the forensic scientist address source and activity level propositions there is a significant need for new techniques that can provide information as to the source of DNA, particularly for sexual assault samples that do not involve semen. The goal of this study was to develop a new biological signature system that provides additional probative value to samples comprised of mixtures of epidermal and vaginal cells, as may be observed in cases involving digital penetration. Signatures were based on morphological and autofluorescence properties of individual cells collected through Imaging Flow Cytometry (IFC). Comparisons to reference cell populations from vaginal tissue and epidermal cells collected from hands showed strong multivariate differences across > 80 cellular measurements. These differences were used to build a predictive framework for classifying unknown cell populations as originating from epithelial cells associated with digital penetration or epidermal tissue. As part of the classification scheme, posterior probabilities of specific tissue group membership were calculated for each cell, along with multivariate similarity to that tissue type. We tested this approach on cell populations from reference tissue as well as mock casework samples involving hand swabbings following digital vaginal penetration. Many more cells classifying as non-epidermal tissue were detected in digital penetration hand swab samples than control hand swabbings. Minimum interpretation thresholds were developed to minimize false positives; these thresholds were also effective when screening licked hands, indicating the potential utility of this method for a variety of biological mixture types and depositional events relevant to forensic casework. Results showed that samples collected subsequent to digital penetration possessed markedly higher numbers of cells classifying as vaginal tissue as well as higher posterior probabilities for vaginal tissue (≥ 0.90) compared to cell populations collected from hands without prior contact with vaginal tissue. Additionally, digital penetration cell populations may be resolved from saliva cell populations and other non-target tissue types.

Improving the discovery of rare variants associated with alcohol problems by leveraging machine learning phenotype prediction and functional information.

Alcohol use disorder (AUD) is moderately heritable with significant social and economic impact. Genome-wide association studies (GWAS) have identified common variants associated with AUD, however, rare variant investigations have yet to achieve well-powered sample sizes. In this study, we conducted an interval-based exome-wide analysis of the Alcohol Use Disorder Identification Test Problems subscale (AUDIT-P) using both machine learning (ML) predicted risk and empirical functional weights. This research has been conducted using the UK Biobank Resource (application number 30782.) Filtering the 200k exome release to unrelated individuals of European ancestry resulted in a sample of 147,386 individuals with 51,357 observed and 96,029 unmeasured but predicted AUDIT-P for exome analysis. Sequence Kernel Association Test (SKAT/SKAT-O) was used for rare variant (Minor Allele Frequency (MAF) < 0.01) interval analyses using default and empirical weights. Empirical weights were constructed using annotations found significant by stratified LD Score Regression analysis of predicted AUDIT-P GWAS, providing prior functional weights specific to AUDIT-P. Using only samples with observed AUDIT-P yielded no significantly associated intervals. In contrast, ADH1C and THRA gene intervals were significant (False discovery rate (FDR) <0.05) using default and empirical weights in the predicted AUDIT-P sample, with the most significant association found using predicted AUDIT-P and empirical weights in the ADH1C gene (SKAT-O P Default = 1.06 x 10 -9 and P Empirical weight = 6.25 x 10 -11 ). These findings provide evidence for rare variant association of the ADH1C gene with the AUDIT-P and highlight the successful leveraging of ML to increase effective sample size and prior empirical functional weights based on common variant GWAS data to refine and increase the statistical significance in underpowered phenotypes.

Case-only exome variation analysis of severe alcohol dependence using a multivariate hierarchical gene clustering approach.

BACKGROUND: Variation in genes involved in ethanol metabolism has been shown to influence risk for alcohol dependence (AD) including protective loss of function alleles in ethanol metabolizing genes. We therefore hypothesized that people with severe AD would exhibit different patterns of rare functional variation in genes with strong prior evidence for influencing ethanol metabolism and response when compared to genes not meeting these criteria. OBJECTIVE: Leverage a novel case only design and Whole Exome Sequencing (WES) of severe AD cases from the island of Ireland to quantify differences in functional variation between genes associated with ethanol metabolism and/or response and their matched control genes. METHODS: First, three sets of ethanol related genes were identified including those a) involved in alcohol metabolism in humans b) showing altered expression in mouse brain after alcohol exposure, and altering ethanol behavioral responses in invertebrate models. These genes of interest (GOI) sets were matched to control gene sets using multivariate hierarchical clustering of gene-level summary features from gnomAD. Using WES data from 190 individuals with severe AD, GOI were compared to matched control genes using logistic regression to detect aggregate differences in abundance of loss of function, missense, and synonymous variants, respectively. RESULTS: Three non-independent sets of 10, 117, and 359 genes were queried against control gene sets of 139, 1522, and 3360 matched genes, respectively. Significant differences were not detected in the number of functional variants in the primary set of ethanol-metabolizing genes. In both the mouse expression and invertebrate sets, we observed an increased number of synonymous variants in GOI over matched control genes. Post-hoc simulations showed the estimated effects sizes observed are unlikely to be under-estimated. CONCLUSION: The proposed method demonstrates a computationally viable and statistically appropriate approach for genetic analysis of case-only data for hypothesized gene sets supported by empirical evidence.