SigTools: exploratory visualization for genomic signals.

MOTIVATION: With the advancement of sequencing technologies, genomic data sets are constantly being expanded by high volumes of different data types. One recently introduced data type in genomic science is genomic signals, which are usually short-read coverage measurements over the genome. To understand and evaluate the results of such studies, one needs to understand and analyze the characteristics of the input data. RESULTS: SigTools is an R-based genomic signals visualization package developed with two objectives: (i) to facilitate genomic signals exploration in order to uncover insights for later model training, refinement and development by including distribution and autocorrelation plots; (ii) to enable genomic signals interpretation by including correlation and aggregation plots. In addition, our corresponding web application, SigTools-Shiny, extends the accessibility scope of these modules to people who are more comfortable working with graphical user interfaces instead of command-line tools. AVAILABILITY AND IMPLEMENTATION: SigTools source code, installation guide and manual is freely available on http://github.com/shohre73.

Continuous chromatin state feature annotation of the human epigenome.

MOTIVATION: Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These methods take as input a set of sequencing-based assays of epigenomic activity, such as ChIP-seq measurements of histone modification and transcription factor binding. They output an annotation of the genome that assigns a chromatin state label to each genomic position. Existing SAGA methods have several limitations caused by the discrete annotation framework: such annotations cannot easily represent varying strengths of genomic elements, and they cannot easily represent combinatorial elements that simultaneously exhibit multiple types of activity. To remedy these limitations, we propose an annotation strategy that instead outputs a vector of chromatin state features at each position rather than a single discrete label. Continuous modeling is common in other fields, such as in topic modeling of text documents. We propose a method, epigenome-ssm-nonneg, that uses a non-negative state space model to efficiently annotate the genome with chromatin state features. We also propose several measures of the quality of a chromatin state feature annotation and we compare the performance of several alternative methods according to these quality measures. RESULTS: We show that chromatin state features from epigenome-ssm-nonneg are more useful for several downstream applications than both continuous and discrete alternatives, including their ability to identify expressed genes and enhancers. Therefore, we expect that these continuous chromatin state features will be valuable reference annotations to be used in visualization and downstream analysis. AVAILABILITY AND IMPLEMENTATION: Source code for epigenome-ssm is available at https://github.com/habibdanesh/epigenome-ssm and Zenodo (DOI: 10.5281/zenodo.6507585). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Serum inflammation markers associated with altered brain white matter microstructure in people with HIV on antiretroviral treatment.

BACKGROUND: Many studies have reported reduced brain white matter fractional anisotropy (FA) and increased mean diffusivity (MD) on diffusion tensor imaging (DTI) of people with HIV (PWH). Few, however, have linked individual blood inflammatory markers with white matter tract-specific FA and MD. METHODS: PWH 50 years old or older from New York, NY, USA, were invited to a cross-sectional study. Demographic data, blood samples, and brain DTI were obtained. Least absolute shrinkage and selection operator (LASSO) regression was used to examine associations between biomarkers and white matter tract-specific FA and MD. All models included age, sex, race, ethnicity, diabetes, hypertension, smoking, and viral load as control variables. RESULTS: Seventy-two cases were analyzed. Mean age was 60 ± 6 years, 47% were women, 21% were Hispanic, and 78% were black. All had asymptomatic HIV infection and were on antiretroviral therapy. Eighty-nine percent had CD4 count >200 cell/mm3 and 78% were virally suppressed. Vascular endothelial growth factor (VEGF) and macrophage inflammatory proteins (MIP) 1ß and 1α were consistently associated with lower FA and higher MD across white matter tracts. CONCLUSIONS: Elevated serum VEGF, MIP-1α, and MIP-1ß were associated with altered white matter microstructure. These blood biomarkers may help predict HIV-associated white matter damage.

Probing the proteome to explore potential correlates of increased Alzheimer's-related cerebrovascular disease in adults with Down syndrome.

Cerebrovascular disease is associated with symptoms and pathogenesis of Alzheimer's disease (AD) among adults with Down syndrome (DS). The cause of increased dementia-related cerebrovascular disease in DS is unknown. We explored whether protein markers of neuroinflammation are associated with markers of cerebrovascular disease among adults with DS. Participants from the Alzheimer's disease in Down syndrome (ADDS) study with magnetic resonance imaging (MRI) scans and blood biomarker data were included. Support vector machine (SVM) analyses examined the relationship of blood-based proteomic biomarkers with MRI-defined cerebrovascular disease among participants characterized as having cognitive decline (n = 36, mean age ± SD = 53 ± 6.2) and as being cognitively stable (n = 78, mean age = 49 ± 6.4). Inflammatory and AD markers were associated with cerebrovascular disease, particularly among symptomatic individuals. The pattern suggested relatively greater inflammatory involvement among cognitively stable individuals and greater AD involvement among those with cognitively decline. The findings help to generate hypotheses that both inflammatory and AD markers are implicated in cerebrovascular disease among those with DS and point to potential mechanistic pathways for further examination.

Alzheimer-Related Cerebrovascular Disease in Down Syndrome.

OBJECTIVE: Adults with Down syndrome (DS) develop Alzheimer disease (AD) pathology by their 5th decade. Compared with the general population, traditional vascular risks in adults with DS are rare, allowing examination of cerebrovascular disease in this population and insight into its role in AD without the confound of vascular risk factors. We examined in vivo magnetic resonance imaging (MRI)-based biomarkers of cerebrovascular pathology in adults with DS, and determined their cross-sectional relationship with age, beta-amyloid pathology, and mild cognitive impairment or clinical AD diagnostic status. METHODS: Participants from the Biomarkers of Alzheimer's Disease in Down Syndrome study (n = 138, 50 ± 7 years, 39% women) with MRI data and a subset (n = 90) with amyloid positron emission tomography (PET) were included. We derived MRI-based biomarkers of cerebrovascular pathology, including white matter hyperintensities (WMH), infarcts, cerebral microbleeds, and enlarged perivascular spaces (PVS), as well as PET-based biomarkers of amyloid burden. Participants were characterized as cognitively stable (CS), mild cognitive impairment-DS (MCI-DS), possible AD dementia, or definite AD dementia based on in-depth assessments of cognition, function, and health status. RESULTS: There were detectable WMH, enlarged PVS, infarcts, and microbleeds as early as the 5th decade of life. There was a monotonic increase in WMH volume, enlarged PVS, and presence of infarcts across diagnostic groups (CS < MCI-DS < possible AD dementia < definite AD dementia). Higher amyloid burden was associated with a higher likelihood of an infarct. INTERPRETATION: The findings highlight the prevalence of cerebrovascular disease in adults with DS and add to a growing body of evidence that implicates cerebrovascular disease as a core feature of AD and not simply a comorbidity. ANN NEUROL 2020;88:1165-1177.

Classifying multiple sclerosis patients on the basis of SDMT performance using machine learning.

OBJECTIVE: To build a model to predict cognitive status reflecting structural, functional, and white matter integrity changes in early multiple sclerosis (MS). METHODS: Based on Symbol Digit Modalities Test (SDMT) performance, 183 early MS patients were assigned "lower" or "higher" performance groups. Three-dimensional (3D)-T2, T1, diffusion weighted, and resting-state magnetic resonance imaging (MRI) data were acquired in 3T. Using Random Forest, five models were trained to classify patients into two groups based on 1-demographic/clinical, 2-lesion volume/location, 3-local/global tissue volume, 4-local/global diffusion tensor imaging, and 5-whole-brain resting-state-functional-connectivity measures. In a final model, all important features from previous models were concatenated. Area under the receiver operating characteristic curve (AUC) values were calculated to evaluate classifier performance. RESULTS: The highest AUC value (0.90) was achieved by concatenating all important features from neuroimaging models. The top 10 contributing variables included volumes of bilateral nucleus accumbens and right thalamus, mean diffusivity of left cingulum-angular bundle, and functional connectivity among hubs of seven large-scale networks. CONCLUSION: These results provide an indication of a non-random brain pattern mostly compromising areas involved in attentional processes specific to patients who perform worse in SDMT. High accuracy of the final model supports this pattern as a potential neuroimaging biomarker of subtle cognitive changes in early MS.

Education differentially contributes to cognitive reserve across racial/ethnic groups.

INTRODUCTION: We examined whether educational attainment differentially contributes to cognitive reserve (CR) across race/ethnicity. METHODS: A total of 1553 non-Hispanic Whites (Whites), non-Hispanic Blacks (Blacks), and Hispanics in the Washington Heights-Inwood Columbia Aging Project (WHICAP) completed structural magnetic resonance imaging. Mixture growth curve modeling was used to examine whether the effect of brain integrity indicators (hippocampal volume, cortical thickness, and white matter hyperintensity [WMH] volumes) on memory and language trajectories was modified by education across racial/ethnic groups. RESULTS: Higher educational attainment attenuated the negative impact of WMH burden on memory (ß = -0.03; 99% CI: -0.071, -0.002) and language decline (ß = -0.024; 99% CI:- 0.044, -0.004), as well as the impact of cortical thinning on level of language performance for Whites, but not for Blacks or Hispanics. DISCUSSION: Educational attainment does not contribute to CR similarly across racial/ethnic groups.

Mitochondrial DNAs provide insight into trypanosome phylogeny and molecular evolution.

BACKGROUND: Trypanosomes are single-celled eukaryotic parasites characterised by the unique biology of their mitochondrial DNA. African livestock trypanosomes impose a major burden on agriculture across sub-Saharan Africa, but are poorly understood compared to those that cause sleeping sickness and Chagas disease in humans. Here we explore the potential of the maxicircle, a component of trypanosome mitochondrial DNA to study the evolutionary history of trypanosomes. RESULTS: We used long-read sequencing to completely assemble maxicircle mitochondrial DNA from four previously uncharacterized African trypanosomes, and leveraged these assemblies to scaffold and assemble a further 103 trypanosome maxicircle gene coding regions from published short-read data. While synteny was largely conserved, there were repeated, independent losses of Complex I genes. Comparison of pre-edited and non-edited genes revealed the impact of RNA editing on nucleotide composition, with non-edited genes approaching the limits of GC loss. African tsetse-transmitted trypanosomes showed high levels of RNA editing compared to other trypanosomes. The gene coding regions of maxicircle mitochondrial DNAs were used to construct time-resolved phylogenetic trees, revealing deep divergence events among isolates of the pathogens Trypanosoma brucei and T. congolense. CONCLUSIONS: Our data represents a new resource for experimental and evolutionary analyses of trypanosome phylogeny, molecular evolution and function. Molecular clock analyses yielded a timescale for trypanosome evolution congruent with major biogeographical events in Africa and revealed the recent emergence of Trypanosoma brucei gambiense and T. equiperdum, major human and animal pathogens.

Frailty and Its Correlates in Adults With Late Life Depression.

OBJECTIVE: To investigate the rates of frailty and frailty characteristics and examine the clinical and neuropsychological correlates of frailty in adults with late life depression (LLD). METHODS: Data were used from the evaluation of 134 individuals over the age of 60 years (45 men, 89 women) with a depressive diagnosis who enrolled in studies for the treatment of their depression. Depression, neuropsychological functioning, white matter hyperintensity (WMH) burden via magnetic resonance imaging, and characteristics of frailty were assessed. RESULTS: Fried frailty burden (≥3 characteristics) was present in 25% of the sample, with this rate increasing to 45.5% when using clinically meaningful cut-scores for gait speed (<1 m/s) and physical activity levels (<1000 kcal/week). Moreover, 62% of the sample exhibited gait slowing (<1 m/s) or weakness (grip strength), with 29% demonstrating both. Greater frailty burden was associated with greater Hamilton Depression Rating Scale severity in covariate adjusted linear regression models (t127 = 2.41, p = 0.02). Greater frailty burden was not associated with neuropsychological dysfunction, nor was it associated with greater WMH burden. CONCLUSION: Findings from this study show that frailty, specifically physical frailty deficits in mobility and strength, is highly comorbid in adults with LLD, associated with greater depressive symptom severity, and does not appear to be associated with the vascular depression subtype of LLD. Future research should investigate the relationship between frailty and antidepressant treatment response as well as test whether there are age-related biological processes that result in the manifestation of the frail-depressed subtype of LLD.

Numerical integration methods and layout improvements in the context of dynamic RNA visualization.

BACKGROUND: RNA visualization software tools have traditionally presented a static visualization of RNA molecules with limited ability for users to interact with the resulting image once it is complete. Only a few tools allowed for dynamic structures. One such tool is jViz.RNA. Currently, jViz.RNA employs a unique method for the creation of the RNA molecule layout by mapping the RNA nucleotides into vertexes in a graph, which we call the detailed graph, and then utilizes a Newtonian mechanics inspired system of forces to calculate a layout for the RNA molecule. The work presented here focuses on improvements to jViz.RNA that allow the drawing of RNA secondary structures according to common drawing conventions, as well as dramatic run-time performance improvements. This is done first by presenting an alternative method for mapping the RNA molecule into a graph, which we call the compressed graph, and then employing advanced numerical integration methods for the compressed graph representation. RESULTS: Comparing the compressed graph and detailed graph implementations, we find that the compressed graph produces results more consistent with RNA drawing conventions. However, we also find that employing the compressed graph method requires a more sophisticated initial layout to produce visualizations that would require minimal user interference. Comparing the two numerical integration methods demonstrates the higher stability of the Backward Euler method, and its resulting ability to handle much larger time steps, a high priority feature for any software which entails user interaction. CONCLUSION: The work in this manuscript presents the preferred use of compressed graphs to detailed ones, as well as the advantages of employing the Backward Euler method over the Forward Euler method. These improvements produce more stable as well as visually aesthetic representations of the RNA secondary structures. The results presented demonstrate that both the compressed graph representation, as well as the Backward Euler integrator, greatly enhance the run-time performance and usability. The newest iteration of jViz.RNA is available at https://jviz.cs.sfu.ca/download/download.html .

High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils.

Despite being key contributors to biogeochemical processes, archaea are frequently outnumbered by bacteria, and consequently are underrepresented in combined molecular surveys. Here, we demonstrate an approach to concurrently survey the archaea alongside the bacteria with high-resolution 16S rRNA gene sequencing, linking these community data to geochemical parameters. We applied this integrated analysis to hydric soils sampled across a model methane-emitting freshwater wetland. Geochemical profiles, archaeal communities, and bacterial communities were independently correlated with soil depth and water cover. Centimeters of soil depth and corresponding geochemical shifts consistently affected microbial community structure more than hundreds of meters of lateral distance. Methanogens with diverse metabolisms were detected across the wetland, but displayed surprising OTU-level partitioning by depth. Candidatus Methanoperedens spp. archaea thought to perform anaerobic oxidation of methane linked to iron reduction were abundant. Domain-specific sequencing also revealed unexpectedly diverse non-methane-cycling archaeal members. OTUs within the underexplored Woesearchaeota and Bathyarchaeota were prevalent across the wetland, with subgroups and individual OTUs exhibiting distinct occupancy and abundance distributions aligned with environmental gradients. This study adds to our understanding of ecological range for key archaeal taxa in a model freshwater wetland, and links these taxa and individual OTUs to hypotheses about processes governing biogeochemical cycling.

Reducing inequity in primary care clinics treating low socioeconomic Jewish and Arab populations in Israel.

Background: An organization-wide inequity-reduction quality improvement (QI) initiative was implemented in primary care clinics serving disadvantaged Arab and Jewish populations. Using the Chronic Care Model (CCM), this study investigated the types of interventions associated with success in inequity reduction. Methods: Semi-structured interviews were conducted with 80 staff members from 26 target clinics, and information about intervention types was coded by CCM and clinical domains (e.g. diabetes, hypertension and lipid control; performance of mammography tests). Relationships between type and number of interventions implemented and inequity reduction were assessed. Results: Target clinics implemented 454 different interventions, on average 17.5 interventions per clinic. Interventions focused on Decision support and Community linkages were positively correlated with improvement in the composite quality score (P < 0.05). Conversely, focusing on a specific clinical domain was not correlated with a higher quality score. Conclusions: Focusing on training team members in selected QI topics and/or tailoring interventions to meet community needs was key to the interventions' success. Such findings, especially in light of the lack of association between QI and a focus on a specific clinical domain, support other calls for adopting a systems approach to achieving wide-scale inequity reduction.

Persistent effects of Libby amphibole and amosite asbestos following subchronic inhalation in rats.

BACKGROUND: Human exposure to Libby amphibole (LA) asbestos increases risk of lung cancer, mesothelioma, and non-malignant respiratory disease. This study evaluated potency and time-course effects of LA and positive control amosite (AM) asbestos fibers in male F344 rats following nose-only inhalation exposure. METHODS: Rats were exposed to air, LA (0.5, 3.5, or 25.0 mg/m(3) targets), or AM (3.5 mg/m(3) target) for 10 days and assessed for markers of lung inflammation, injury, and cell proliferation. Short-term results guided concentration levels for a stop-exposure study in which rats were exposed to air, LA (1.0, 3.3, or 10.0 mg/m(3)), or AM (3.3 mg/m(3)) 6 h/day, 5 days/week for 13 weeks, and assessed 1 day, 1, 3, and 18 months post-exposure. Fibers were relatively short; for 10 mg/m(3) LA, mean length of all structures was 3.7 µm and 1% were longer than 20 µm. RESULTS: Ten days exposure to 25.0 mg/m(3) LA resulted in significantly increased lung inflammation, fibrosis, bronchiolar epithelial cell proliferation and hyperplasia, and inflammatory cytokine gene expression compared to air. Exposure to 3.5 mg/m(3) LA resulted in modestly higher markers of acute lung injury and inflammation compared to AM. Following 13 weeks exposure, lung fiber burdens correlated with exposure mass concentrations, declining gradually over 18 months. LA (3.3 and 10.0 mg/m(3)) and AM produced significantly higher bronchoalveolar lavage markers of inflammation and lung tissue cytokines, Akt, and MAPK/ERK pathway components compared to air control from 1 day to 3 months post-exposure. Histopathology showed alveolar inflammation and interstitial fibrosis in all fiber-exposed groups up to 18 months post-exposure. Positive dose trends for incidence of alveolar epithelial hyperplasia and bronchiolar/alveolar adenoma or carcinoma were observed among LA groups. CONCLUSIONS: Inhalation of relatively short LA fibers produced inflammatory, fibrogenic, and tumorigenic effects in rats which replicate essential attributes of asbestos-related disease in exposed humans. Fiber burden, inflammation, and activation of growth factor pathways may persist and contribute to lung tumorigenesis long after initial LA exposure. Fiber burden data are being used to develop a dosimetry model for LA fibers, which may provide insights on mode of action for hazard assessment.

Cri du chat syndrome and primary ciliary dyskinesia: a common genetic cause on chromosome 5p.

Cri du chat syndrome (CdCS) and primary ciliary dyskinesia (PCD) are rare diseases that present with frequent respiratory symptoms. PCD can be caused by hemizygous DNAH5 mutation in combination with a 5p segmental deletion attributable to CdCS on the opposite chromosome. Chronic oto-sino-pulmonary symptoms or organ laterality defects in CdCS should prompt an evaluation for PCD.

Personalized gene silencing therapeutics for Huntington disease.

Gene silencing offers a novel therapeutic strategy for dominant genetic disorders. In specific diseases, selective silencing of only one copy of a gene may be advantageous over non-selective silencing of both copies. Huntington disease (HD) is an autosomal dominant disorder caused by an expanded CAG trinucleotide repeat in the Huntingtin gene (HTT). Silencing both expanded and normal copies of HTT may be therapeutically beneficial, but preservation of normal HTT expression is preferred. Allele-specific methods can selectively silence the mutant HTT transcript by targeting either the expanded CAG repeat or single nucleotide polymorphisms (SNPs) in linkage disequilibrium with the expansion. Both approaches require personalized treatment strategies based on patient genotypes. We compare the prospect of safe treatment of HD by CAG- and SNP-specific silencing approaches and review HD population genetics used to guide target identification in the patient population. Clinical implementation of allele-specific HTT silencing faces challenges common to personalized genetic medicine, requiring novel solutions from clinical scientists and regulatory authorities.

Multidimensional Treatment Foster Care for Adolescents in English care: randomised trial and observational cohort evaluation.

BACKGROUND: Children in care often have poor outcomes. There is a lack of evaluative research into intervention options. AIMS: To examine the efficacy of Multidimensional Treatment Foster Care for Adolescents (MTFC-A) compared with usual care for young people at risk in foster care in England. METHOD: A two-arm single (assessor) blinded randomised controlled trial (RCT) embedded within an observational quasi-experimental case-control study involving 219 young people aged 11-16 years (trial registration: ISRCTN 68038570). The primary outcome was the Child Global Assessment Scale (CGAS). Secondary outcomes were ratings of educational attendance, achievement and rate of offending. RESULTS: The MTFC-A group showed a non-significant improvement in CGAS outcome in both the randomised cohort (n = 34, adjusted mean difference 1.3, 95% CI -7.1 to 9.7, P = 0.75) and in the trimmed observational cohort (n = 185, adjusted mean difference 0.95, 95% CI -2.38 to 4.29, P = 0.57). No significant effects were seen in secondary outcomes. There was a possible differential effect of the intervention according to antisocial behaviour. CONCLUSIONS: There was no evidence that the use of MTFC-A resulted in better outcomes than usual care. The intervention may be more beneficial for young people with antisocial behaviour but less beneficial than usual treatment for those without.

The script concordance test for clinical reasoning: re-examining its utility and potential weakness.

CONTEXT: The script concordance test (SCT) assesses clinical reasoning under conditions of uncertainty. Relatively little information exists on Z-score (standard deviation [SD]) cut-offs for distinguishing more experienced from less experienced trainees, and whether scores depend on factual knowledge. Additionally, a recent review highlighted the finding that the SCT is potentially weakened by the fact that the mere avoidance of extreme responses may greatly increase test scores. OBJECTIVES: This study was conducted in order to elucidate the best cut-off Z-scores, to correlate SCT scores with scores on a separate medical knowledge examination (MKE), and to investigate potential solutions to the weakness of the SCT. METHODS: An analysis of scores on pulmonary and critical care medicine tests undertaken during July and August 2013 was performed. Clinical reasoning was tested using 1-hour SCTs (Question Sets 1 or 2). Medical knowledge was tested using a 3-hour, computer-adapted, multiple-choice question examination. RESULTS: The expert panel was composed of 16 attending physicians. The SCTs were completed by 16 fellows and 10 residents. Fourteen fellows completed the MKE. Test reliability was acceptable for both Question Sets 1 and 2 (Cronbach's alphas of 0.79 and 0.89, respectively). Z-scores of - 2.91 and - 1.76 best separated the scores of residents from those of fellows, and the scores of fellows from those of attending physicians, respectively. Scores on the SCT and MKE were poorly correlated. Simply avoiding extreme answers boosted the Z-scores of the lowest 10 scorers on both Question Sets 1 and 2 by ≥ 1 SD. Increasing the proportion of questions with extreme modal answers to 50%, and using hypothetical question sets created from Question Set 1 overcame this problem, but consensus scoring did not. CONCLUSIONS: The SCT was able to differentiate between test subjects of varying levels of competence, and results were not associated with medical knowledge. However, the test was vulnerable to responses that intentionally avoided extreme values. Increasing the proportion of questions with extreme modal answers may attenuate the effect of candidates exploiting the test weakness related to extreme responses.

Intracranial response to capmatinib after progression on crizotinib in a patient with MET exon 14 skipping non-small cell lung cancer-a case report.

Background: Capmatinib, a potent and selective MET tyrosine kinase inhibitor (TKI), holds promise as a therapeutic agent due to its potentially elevated intracranial efficacy in metastatic non-small cell lung cancer (NSCLC) patients harboring exon 14 skipping alterations in MET (MET Proto-Oncogene). This study aims to evaluate a targeted therapeutic approach to an MET exon 14 skipping (METex14) advanced NSCLC patient that progressed on Crizotinib and developed off target resistance alteration in PIK3CA. Case Discription: We present a case of advanced METex14 NSCLC patient wherein central nervous system (CNS) relapse occurred post complete surgical resection and remission of the lung tumor under first-line crizotinib treatment. Subsequent disease monitoring demonstrated a profound intracranial response to capmatinib in a crizotinib-resistant brain lesion. Molecular analysis unveiled the original METex14 D1028N driver mutation and a newly arisen PIK3CA bypass mutation, potentially contributing to off-target resistance. Conclusions: Before capmatinib was approved as a first line treatment option for metastatic NSCLC harboring somatic METex14 mutations, crizotinib conferred a potential option for targeted treatment. Switching to a selective MET-TKI like capmatinib with a better CNS penetration, it appears to be a promising approach for CNS metastasized NSCLC patients with METex14 mutations that failed on crizotinib. Further research is needed to more effectively understand and monitor resistance mechanisms using advanced diagnostic techniques such as DNA-based hybrid-capture (HC) next generation sequencing (NGS) to guide molecularly stratified therapy beyond the first line setting.

Small vessel cerebrovascular disease is associated with cognition in prospective Alzheimer's clinical trial participants.

BACKGROUND: Secondary prevention clinical trials for Alzheimer's disease (AD) target amyloid accumulation in asymptomatic, amyloid-positive individuals, but it is unclear to what extent other pathophysiological processes, such as small vessel cerebrovascular disease, account for participant performance on the primary cognitive outcomes in those trials. White matter hyperintensities are areas of increased signal on T2-weighted magnetic resonance imaging (MRI) that reflect small vessel cerebrovascular disease. They are associated with cognitive functioning in older adults and with clinical presentation and course of AD, particularly when distributed in posterior brain regions. The purpose of this study was to examine to what degree regional WMH volume is associated with performance on the primary cognitive outcome measure in the Anti-Amyloid Treatment in Asymptomatic Alzheimer's Disease (A4) study, a secondary prevention trial. METHODS: Data from 1791 participants (59.5% women, mean age (SD) 71.6 (4.74)) in the A4 study and the Longitudinal Evaluation of Amyloid Risk and Neurodegeneration (LEARN) companion study at the screening visit were used to quantify WMH volumes on T2-weighted fluid-attenuated inversion recovery (FLAIR) MR images. Cognition was assessed with the preclinical Alzheimer cognitive composite (PACC). We tested the association of total and regional WMH volumes with PACC performance, adjusting for age, education, and amyloid positivity status, with general linear models. We also considered interactions between WMH and amyloid positivity status. RESULTS: Increased frontal and parietal lobe WMH volume was associated with poorer performance on the PACC. While amyloid positivity was also associated with lower cognitive test scores, WMH volumes did not interact with amyloid positivity status. CONCLUSION: These results highlight the potential of small vessel cerebrovascular disease to drive AD-related cognitive profiles. Measures of small vessel cerebrovascular disease should be considered when evaluating outcome in trials, both as potential effect modifiers and as a possible target for intervention or prevention.

Association of brain arterial diameters with demographic and anatomical factors in a multi-national pooled analysis of cohort studies.

BACKGROUND AND PURPOSE: Brain arterial diameters are markers of cerebrovascular disease. Demographic and anatomical factors may influence arterial diameters. We hypothesize that age, sex, height, total cranial volume (TCV), and persistent fetal posterior cerebral artery (fPCA) correlate with brain arterial diameters across populations. METHODS: Participants had a time-of-flight MRA from nine international cohorts. Arterial diameters of the cavernous internal carotid arteries (ICA), middle cerebral arteries (MCA), and basilar artery (BA) were measured using LAVA software. Regression models assessed the association between exposures and brain arterial diameters. RESULTS: We included 6,518 participants (mean age: 70 ± 9 years; 41% men). Unilateral fPCA was present in 13.2% and bilateral in 3.2%. Larger ICA, MCA, and BA diameters correlated with older age (Weighted average [WA] per 10 years: 0.18 mm, 0.11 mm, and 0.12 mm), male sex (WA: 0.24 mm, 0.13 mm, and 0.21 mm), and TCV (WA: for one TCV standard deviation: 0.24 mm, 0.29 mm, and 0.18 mm). Unilateral and bilateral fPCAs showed a positive correlation with ICA diameters (WA: 0.39 mm and 0.73 mm) and negative correlation with BA diameters (WA: -0.88 mm and -1.73 mm). Regression models including age, sex, TCV, and fPCA explained on average 15%, 13%, and 25% of the ICA, MCA, and BA diameter interindividual variation, respectively. Using height instead of TCV as a surrogate of head size decreased the R-squared by 3% on average. CONCLUSION: Brain arterial diameters correlated with age, sex, TCV, and fPCA. These factors should be considered when defining abnormal diameter cutoffs across populations.