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Adeel Yang,1,* Hersh Goel,1,* Matthew Bryan,2 Ron Robertson,1 Jane Lim,1 Shehran Islam,1 Mark R Speicher2 1College of Medicine, The University of Arizona, Tucson, AZ, USA; 2Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA *These authors contributed equally to this work Background: Medical students are required to retain vast amounts of medical knowledge on the path to becoming physicians. To address this challenge, multimedia Web-based learning resources have been developed to supplement traditional text-based materials. The Picmonic® Learning System (PLS; Picmonic, Phoenix, AZ, USA) is a novel multimedia Web-based learning platform that delivers audiovisual mnemonics designed to improve memory retention of medical sciences. Methods: A single-center, randomized, subject-blinded, controlled study was conducted to compare the PLS with traditional text-based material for retention of medical science topics. Subjects were randomly assigned to use two different types of study materials covering several diseases. Subjects randomly assigned to the PLS group were given audiovisual mnemonics along with text-based materials, whereas subjects in the control group were given the same text-based materials with key terms highlighted. The primary endpoints were the differences in performance on immediate, 1 week, and 1 month delayed free-recall and paired-matching tests. The secondary endpoints were the difference in performance on a 1 week delayed multiple-choice test and self-reported satisfaction with the study materials. Differences were calculated using unpaired two-tailed t-tests. Results: PLS group subjects demonstrated improvements of 65%, 161%, and 208% compared with control group subjects on free-recall tests conducted immediately, 1 week, and 1 month after study of materials, respectively. The results of performance on paired-matching tests showed an improvement of up to 331% for PLS group subjects. PLS group subjects also performed 55% greater than control group subjects on a 1 week delayed multiple choice test requiring higher-order thinking. The differences in test performance between the PLS group subjects and the control group subjects were statistically significant (P

Introduction: There is a growing concern for physician and medical student well-being and burnout. Growth mindset, or the belief that ability can be developed, as well as students' perception of their instructors' growth mindset, have been associated with better academic outcomes for a wide range of students. The primary purpose of the present study was to investigate the effects of growth mindset on medical student well-being., Method: We recruited all graduating osteopathic medical students in the class of 2023. This survey included items about student demographics (including identifiable items), experiences in medical school, practice plans, along with financial and other information. The survey of 667 items required a median time of 33 min to complete. Our sample consisted of 4,180 students. Students self-reported growth mindset, perception of instructor growth mindset, and four measures of well-being: flourishing, resilience, burnout, and maladaptive psychological symptoms., Results: Growth mindset and perception of instructor growth mindset were significant predictors of medical student well-being. Further, significant interactions showed that these effects were strongest for students from historically marginalized backgrounds., Discussion: Our work provides a first step toward addressing physician burnout by targeting medical students, which could prevent them from beginning their careers already in a state of burnout. We argue that systemic change is needed to improve student well-being, such as emphasizing growth mindset-supportive pedagogy, which places the emphasis on changing systems instead of individuals. Future research should include causal analyses to better understand the effect and persistence of growth mindset-supportive environments on student well-being. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Motivation: The analysis of circulating cell-free DNA (cfDNA) holds immense promise as a non-invasive diagnostic tool across various human conditions. However, extracting biological insights from cfDNA fragments entails navigating complex and diverse bioinformatics methods, encompassing not only DNA sequence variation, but also epigenetic characteristics like nucleosome footprints, fragment length, and methylation patterns., Results: We introduce Liquid Biopsy Feature extract (LBFextract), a comprehensive package designed to streamline feature extraction from cfDNA sequencing data, with the aim of enhancing the reproducibility and comparability of liquid biopsy studies. LBFextract facilitates the integration of preprocessing and postprocessing steps through alignment fragment tags and a hook mechanism. It incorporates various methods, including coverage-based and fragment length-based approaches, alongside two novel feature extraction methods: an entropy-based method to infer TF activity from fragmentomics data and a technique to amplify signals from nucleosome dyads. Additionally, it implements a method to extract condition-specific differentially active TFs based on these features for biomarker discovery. We demonstrate the use of LBFextract for the subtype classification of advanced prostate cancer patients using coverage signals at transcription factor binding sites from cfDNA. We show that LBFextract can generate robust and interpretable features that can discriminate between different clinical groups. LBFextract is a versatile and user-friendly package that can facilitate the analysis and interpretation of liquid biopsy data., Data and Code Availability and Implementation: LBFextract is freely accessible at https://github.com/Isy89/LBF. It is implemented in Python and compatible with Linux and Mac operating systems. Code and data to reproduce these analyses have been uploaded to 10.5281/zenodo.10964406., Competing Interests: A patent application has been filed for aspects of the paper (inventors: I.L.; S.O.H.; M.R.S.). S.O.H. is a co-founder of Vessel FlexCo and is on the advisory board of CureMatch. The remaining authors declare no competing interests., (© 2024 The Authors.)

Importance: Given the high rates of burnout and associated negative mental health outcomes (eg, depression, suicidal ideation, substance abuse) among medical students and physicians, it is imperative to identify strategies for supporting the future health workforce, particularly when considering trends indicating a future shortage of physicians. Understanding the associations of medical school students' learning mindsets (eg, growth mindset, purpose and relevance, and sense of belonging) with indicators of well-being (eg, flourishing) and ill-being (eg, burnout) could provide a foundation for future research to consider when attempting to combat the negative mental health trends among medical students and physicians., Objectives: To understand the associations of medical school students' learning mindsets (ie, their beliefs about themselves as learners and their learning environment) with critical student health outcomes (ie, well-being and ill-being)., Design, Setting, and Participants: This survey study used a nationally representative sample of first-year osteopathic medical school students across the US who responded to a survey of learning mindsets as well as measures of well-being and ill-being in fall 2022. Data were analyzed from January to April 2024., Main Outcomes and Measures: Learning mindsets were categorized as growth mindset, purpose and relevance, and sense of belonging. Well-being was categorized as flourishing and resilience, and ill-being was categorized as burnout and psychological symptoms. Outcomes were regressed on learning mindset and demographics variables, and interactions of demographic variables and learning mindsets were assessed., Results: A total of 7839 students were surveyed, and 6622 students (mean [SD] age, 25.05 [3.20]; 3678 [55.5%] women) responded and were included in analyses. The 3 learning mindsets were significantly associated with flourishing (growth mindset: b = 0.34; 95% CI, 0.23 to 0.45; P < .001; purpose and relevance: b = 2.02; 95% CI, 1.83 to 2.20; P < .001; belonging uncertainty: b = -0.98; 95% CI, -1.08 to -0.89; P < .001) and resilience (growth mindset: b = 0.28; 95% CI, 0.17 to 0.40; P < .001; purpose and relevance: b = 1.62; 95% CI, 1.43 to 1.82; P < .001; belonging uncertainty: b = -1.50; 95% CI, -1.60 to -1.40; P < .001) well-being outcomes and burnout (growth mindset: b = -0.09; 95% CI, -0.11 to -0.07; P < .001; purpose and relevance: b = -0.29; 95% CI, -0.32 to -0.25; P < .001; belonging uncertainty: b = 0.28; 95% CI, 0.26 to 0.30; P < .001) and psychological symptoms (growth mindset: b = -0.22; 95% CI, -0.30 to -0.14; P < .001; purpose and relevance: b = -0.51; 95% CI, -0.64 to -0.38; P < .001; belonging uncertainty: b = 1.33; 95% CI, 1.27 to 1.40; P < .001) ill-being outcomes, even when controlling for important demographic characteristics (eg, race and ethnicity, gender identity, age). Furthermore, several significant interactions indicated that these learning mindsets may be particularly salient for students from historically marginalized communities: there was a significant interaction between growth mindset and race and ethnicity (b = 0.58; 95% CI, 0.08 to 1.09, P = .02), such that growth mindset was more strongly associated with flourishing among American Indian or Alaska Native, Black, Latine, or Native Hawaiian students., Conclusions and Relevance: These findings suggest that identifying strategies for supporting students' learning mindsets may be an effective way to support medical student well-being and reduce ill-being, particularly among students from historically marginalized backgrounds.

Importance: More information is needed to guide referring subspecialists on the appropriate patient evaluation before magnetic resonance defecography (MRD)., Objectives: This study aimed to evaluate how often health care providers perform digital rectal examination (DRE) before ordering MRD to investigate causes of bowel and pelvic floor complaints., Study Design: We conducted a retrospective cohort review, including MRD performed on female patients at an integrated health care system from 2016 through 2020. The primary outcome was the presence or absence of documented rectal examination in the year before defecography by the referring provider or 6 months prior by a primary care physician or pelvic floor physical therapist. We hypothesized that the overall rate of rectal examination would be high and unaffected by the referring provider's subspecialty., Results: Three hundred-four defecography tests were performed, with 209 patients (68.8%) referred by gastroenterology providers and 95 (31.2%) from other specialties. Gastroenterologists performed DRE in 32.8% of patients, in contrast to 84.4% of patients referred by other specialties ( P < 0.001). When comparing subspecialties that most commonly refer patients for MRD (gastroenterology, colorectal surgery and urogynecology), there was a statistically significant difference between gastroenterologists and colorectal surgeons ( P < 0.001) as well as urogynecologists ( P < 0.001) but no difference in the rate of rectal examination between colorectal surgeons and urogynecologists ( P = 1.00)., Conclusions: At our single integrated health system, the rate of DRE before MRD testing varied significantly by specialty. Our findings highlight the need for better understanding of DRE utility in the algorithms for evaluation of bowel and pelvic floor disorders., (Copyright © 2024 American Urogynecologic Society. All rights reserved.)

Background: Cell-free DNA (cfDNA), a broadly applicable biomarker commonly sourced from urine or blood, is extensively used for research and diagnostic applications. In various settings, genetic and epigenetic information is derived from cfDNA. However, a unified framework for its processing is lacking, limiting the universal application of innovative analysis strategies and the joining of data sets., Findings: Here, we describe cfDNA UniFlow, a unified, standardized, and ready-to-use workflow for processing cfDNA samples. The workflow is written in Snakemake and can be scaled from stand-alone computers to cluster environments. It includes methods for processing raw genome sequencing data as well as specialized approaches for correcting sequencing errors, filtering, and quality control. Sophisticated methods for detecting copy number alterations and estimating and correcting GC-related biases are readily incorporated. Furthermore, it includes methods for extracting, normalizing, and visualizing coverage signals around user-defined regions in case-control settings. Ultimately, all results and metrics are aggregated in a unified report, enabling easy access to a wide variety of information for further research and downstream analysis., Conclusions: We provide an automated pipeline for processing cell-free DNA sampled from liquid biopsies, including a wide variety of additional functionalities like bias correction and signal extraction. With our focus on scalability and extensibility, we provide a foundation for future cfDNA research and faster clinical applications. The source code and extensive documentation are available on our GitHub repository (https://github.com/kircherlab/cfDNA-UniFlow)., (© The Author(s) 2024. Published by Oxford University Press GigaScience.)

Analyses of cell-free DNA (cfDNA) are increasingly being employed for various diagnostic and research applications. Many technologies aim to increase resolution, e.g. for detecting early-stage cancer or minimal residual disease. However, these efforts may be confounded by inherent base composition biases of cfDNA, specifically the over - and underrepresentation of guanine (G) and cytosine (C) sequences. Currently, there is no universally applicable tool to correct these effects on sequencing read-level data. Here, we present GCparagon, a two-stage algorithm for computing and correcting GC biases in cfDNA samples. In the initial step, length and GC base count parameters are determined. Here, our algorithm minimizes the inclusion of known problematic genomic regions, such as low-mappability regions, in its calculations. In the second step, GCparagon computes weights counterbalancing the distortion of cfDNA attributes (correction matrix). These fragment weights are added to a binary alignment map (BAM) file as alignment tags for individual reads. The GC correction matrix or the tagged BAM file can be used for downstream analyses. Parallel computing allows for a GC bias estimation below 1 min. We demonstrate that GCparagon vastly improves the analysis of regulatory regions, which frequently show specific GC composition patterns and will contribute to standardized cfDNA applications., (© The Author(s) 2023. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.)

This paper reviews the current literature to examine what elements of osteopathic medicine can be used in psychiatry. The aim of this study was to use the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to conduct a systematic review of studies describing the efficacy of osteopathic manipulative medicine (OMM) in treating psychiatric problems directly and indirectly. The authors searched the databases PubMed, PsycINFO, and CINAHL (Cumulative Index to Nursing and Allied Health Literature), reviewing peer-reviewed articles from 1980 to April 2023. The literature demonstrates that OMM has a positive effect on psychiatric symptoms indirectly when treating certain medical conditions, such as chronic pain, fibromyalgia, and irritable bowel syndrome; however, there are many limitations on these studies, and further research is required prior to making firm recommendations. The evidence is lacking for osteopathic manual medicine being used directly to treat psychiatric conditions. This review demonstrates that in some populations, such as individuals with chronic pain, fibromyalgia, and irritable bowel syndrome, OMM could be considered by an osteopathic psychiatrist as an adjunct treatment. More research should be conducted in this area due to the many limitations in the available studies but current research suggests that the use of OMM by osteopathic psychiatrists could be beneficial for some patient populations., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2023, Bowes et al.)

Background The process for program directors (PDs) to provide feedback to medical schools about their graduates' readiness for postgraduate year 1 (PGY-1) training is burdensome and does not generate national benchmarking data. Objective The Association of American Medical Colleges (AAMC) tested the feasibility of administering a standardized Resident Readiness Survey (RRS) to PDs nationally about their PGY-1 residents' preparedness for residency. Methods In 2020 and 2021, the AAMC invited PDs via email to complete RRSs for their PGY-1s who graduated from participating schools; the AAMC provided schools with reports of identified RRS data for their graduates. Outcome measures included school participation rates, PD response rates, PGY-1s' coverage rates (RRSs completed/RRSs PDs invited to complete), RRS completion time (time-stamp difference: RRS opening-submission), and participating schools' feedback about the process collected via AAMC evaluation questionnaires sent to school leaders. Chi-square tested significance of differences between proportions. Results School participation increased from 43.8% (2020: 77 of 176) to 72.4% (2021: 131 of 181). PD response rates, similar in both years overall (2020: 1786 of 2847 [62.7%]; 2021: 2107 of 3406 [61.9%]; P =.48), varied by specialty ( P <.001; range 65 of 154 [42.2%], neurology; 109 of 136 [80.1%], internal medicine-pediatrics, both years combined). PGY-1s' coverage rates were similar ( P =.21) in 2020 (5567 of 10 712 [52.0%]) and 2021 (9688 of 18 372 [52.7%]). RRS completion time averaged less than 3 minutes. Numerous school leaders reported that RRS data stimulated new, or supported ongoing, curricular quality improvement. Conclusions Administration of a standardized RRS to PDs nationally about PGY-1s preparedness for residency is feasible and will continue.

Prostate cancer (PCa) is a common and fatal type of cancer in men. Metastatic PCa (mPCa) is a major factor contributing to its lethality, although the mechanisms remain poorly understood. PTEN is one of the most frequently deleted genes in mPCa. Here we show a frequent genomic co-deletion of PTEN and STAT3 in liquid biopsies of patients with mPCa. Loss of Stat3 in a Pten-null mouse prostate model leads to a reduction of LKB1/pAMPK with simultaneous activation of mTOR/CREB, resulting in metastatic disease. However, constitutive activation of Stat3 led to high LKB1/pAMPK levels and suppressed mTORC1/CREB pathway, preventing mPCa development. Metformin, one of the most widely prescribed therapeutics against type 2 diabetes, inhibits mTORC1 in liver and requires LKB1 to mediate glucose homeostasis. We find that metformin treatment of STAT3/AR-expressing PCa xenografts resulted in significantly reduced tumor growth accompanied by diminished mTORC1/CREB, AR and PSA levels. PCa xenografts with deletion of STAT3/AR nearly completely abrogated mTORC1/CREB inhibition mediated by metformin. Moreover, metformin treatment of PCa patients with high Gleason grade and type 2 diabetes resulted in undetectable mTORC1 levels and upregulated STAT3 expression. Furthermore, PCa patients with high CREB expression have worse clinical outcomes and a significantly increased risk of PCa relapse and metastatic recurrence. In summary, we have shown that STAT3 controls mPCa via LKB1/pAMPK/mTORC1/CREB signaling, which we have identified as a promising novel downstream target for the treatment of lethal mPCa., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Cell-free circulating DNA (cfDNA) analyses may enable multi-cancer early detection (MCED), but the most suitable method is unknown. In this issue of Cancer Cell, Jamshidi et al. compare ten machine-learning classifiers using various cfDNA features and conclude that cfDNA methylation patterns are most promising for MCED testing., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Background: Mucopolysaccharidoses (MPS) are monogenic metabolic disorders that significantly affect the skeleton. Eleven enzyme defects in the lysosomal degradation of glycosaminoglycans (GAGs) have been assigned to the known MPS subtypes (I-IX). Arylsulfatase K (ARSK) is a recently characterised lysosomal hydrolase involved in GAG degradation that removes the 2-O-sulfate group from 2-sulfoglucuronate. Knockout of Arsk in mice was consistent with mild storage pathology, but no human phenotype has yet been described., Methods: In this study, we report four affected individuals of two unrelated consanguineous families with homozygous variants c.250C>T, p.(Arg84Cys) and c.560T>A, p.(Leu187Ter) in ARSK , respectively. Functional consequences of the two ARSK variants were assessed by mutation-specific ARSK constructs derived by site-directed mutagenesis, which were ectopically expressed in HT1080 cells. Urinary GAG excretion was analysed by dimethylene blue and electrophoresis, as well as liquid chromatography/mass spectrometry (LC-MS)/MS analysis., Results: The phenotypes of the affected individuals include MPS features, such as short stature, coarse facial features and dysostosis multiplex. Reverse phenotyping in two of the four individuals revealed additional cardiac and ophthalmological abnormalities. Mild elevation of dermatan sulfate was detected in the two subjects investigated by LC-MS/MS. Human HT1080 cells expressing the ARSK-Leu187Ter construct exhibited absent protein levels by western blot, and cells with the ARSK-Arg84Cys construct showed markedly reduced enzyme activity in an ARSK-specific enzymatic assay against 2-O-sulfoglucuronate-containing disaccharides as analysed by C18-reversed-phase chromatography followed by MS., Conclusion: Our work provides a detailed clinical and molecular characterisation of a novel subtype of mucopolysaccharidosis, which we suggest to designate subtype X., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Genes implicated in the Golgi and endosomal trafficking machinery are crucial for brain development, and mutations in them are particularly associated with postnatal microcephaly (POM)., Methods: Exome sequencing was performed in three affected individuals from two unrelated consanguineous families presenting with delayed neurodevelopment, intellectual disability of variable degree, POM and failure to thrive. Patient-derived fibroblasts were tested for functional effects of the variants., Results: We detected homozygous truncating variants in ATP9 A. While the variant in family A is predicted to result in an early premature termination codon, the variant in family B affects a canonical splice site. Both variants lead to a substantial reduction of ATP9A mRNA expression. It has been shown previously that ATP9A localises to early and recycling endosomes, whereas its depletion leads to altered gene expression of components from this compartment. Consistent with previous findings, we also observed overexpression of ARPC3 and SNX3 , genes strongly interacting with ATP9A ., Conclusion: In aggregate, our findings show that pathogenic variants in ATP9A cause a novel autosomal recessive neurodevelopmental disorder with POM. While the physiological function of endogenous ATP9A is still largely elusive, our results underline a crucial role of this gene in endosomal transport in brain tissue., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2022. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: The promise of precision cancer medicine presently centers around the genomic sequence of a patient's tumor being translated into timely, actionable information to inform clinical care. The analysis of cell-free DNA from liquid biopsy, which contains circulating tumor DNA (ctDNA) in patients with cancer, has proven to be amenable to various settings in oncology. However, open questions surrounding the clinical validity and utility of plasma-based analyses have hindered widespread clinical adoption., Main Body: Owing to the rapid evolution of the field, studies supporting the use of ctDNA as a biomarker throughout a patient's journey with cancer have accumulated in the last few years, warranting a review of the latest status for clinicians who may employ ctDNA in their precision oncology programs. In this work, we take a step back from the intricate coverage of detection approaches described extensively elsewhere and cover basic concepts around the practical implementation of next generation sequencing (NGS)-guided liquid biopsy. We compare relevant targeted and untargeted approaches to plasma DNA analysis, describe the latest evidence for clinical validity and utility, and highlight the value of genome-wide ctDNA analysis, particularly as it relates to early detection strategies and discovery applications harnessing the non-coding genome., Conclusions: The maturation of liquid biopsy for clinical application will require interdisciplinary efforts to address current challenges. However, patients and clinicians alike may greatly benefit in the future from its incorporation into routine oncology care., (© 2022. The Author(s).)

Budding uninhibited by benzimidazoles (BUB1) contributes to multiple mitotic processes. Here, we describe the first two patients with biallelic BUB1 germline mutations, who both display microcephaly, intellectual disability, and several patient-specific features. The identified mutations cause variable degrees of reduced total protein level and kinase activity, leading to distinct mitotic defects. Both patients’ cells show prolonged mitosis duration, chromosome segregation errors, and an overall functional spindle assembly checkpoint. However, while BUB1 levels mostly affect BUBR1 kinetochore recruitment, impaired kinase activity prohibits centromeric recruitment of Aurora B, SGO1, and TOP2A, correlating with anaphase bridges, aneuploidy, and defective sister chromatid cohesion. We do not observe accelerated cohesion fatigue. We hypothesize that unresolved DNA catenanes increase cohesion strength, with concomitant increase in anaphase bridges. In conclusion, BUB1 mutations cause a neurodevelopmental disorder, with clinical and cellular phenotypes that partially resemble previously described syndromes, including autosomal recessive primary microcephaly, mosaic variegated aneuploidy, and cohesinopathies.

Objective: To develop a valid and reliable instrument for measuring attitudes toward osteopathic medicine., Methods: Participants included 5,669 first-year students from 33 U.S. colleges of osteopathic medicine, who completed an online survey at the beginning of the 2019-2020 academic year. Using data from the nationwide Project in Osteopathic Medical Education and Empathy, we developed a 13-item instrument: Attitudes Toward Osteopathic Medicine Scale (ATOMS) and demonstrated the validity and reliability of its scores. The social desirability response bias was controlled in statistical analyses., Results: The corrected item-total score correlations were all positive and statistically significant, and the effect sizes of item discrimination indices were large. Cronbach's coefficient alpha reliability was 0.83. Construct validity, corroborating face and content validity of the ATOMS, was supported by three components, emerged from factor analysis: "Perspectives on Osteopathic Medicine," "Osteopathic Diagnosis and Treatment," and "Holistic-Integrative Care." Correlations between ATOMS scores and scores of cognitive empathy, emotional empathy; orientation toward interprofessional collaboration; lifelong learning; and burnout were statistically significant in the expected direction, providing validity evidence for the ATOMS. Using the method of contrasted groups, significant differences in the ATOMS scores were found by gender, ethnicity, academic background, and career interest in the expected direction, supporting the validity of the ATOMS scores. National norms were developed to assess individual scores alongside national percentile ranks., Conclusions: The ATOMS, developed in a nationwide study, supported by strong psychometric evidence for measuring orientation toward osteopathic medicine, has implications for the assessment of osteopathic medical education, patient outcomes, and admission decisions.

Purpose: Immune checkpoint inhibitors (ICIs) are increasingly being used in non-small-cell lung cancer (NSCLC), yet biomarkers predicting their benefit are lacking. We evaluated if on-treatment changes of circulating tumor DNA (ctDNA) from ICI start (t 0 ) to after two cycles (t 1 ) assessed with a commercial panel could identify patients with NSCLC who would benefit from ICI., Patients and Methods: The molecular ctDNA response was evaluated as a predictor of radiographic tumor response and long-term survival benefit of ICI. To maximize the yield of ctDNA detection, de novo mutation calling was performed. Furthermore, the impact of clonal hematopoiesis (CH)-related variants as a source of biologic noise was investigated., Results: After correction for CH-related variants, which were detected in 75 patients (44.9%), ctDNA was detected in 152 of 167 (91.0%) patients. We observed only a fair agreement of the molecular and radiographic response, which was even more impaired by the inclusion of CH-related variants. After exclusion of those, a ≥ 50% molecular response improved progression-free survival (10 v 2 months; hazard ratio [HR], 0.55; 95% CI, 0.39 to 0.77; P = .0011) and overall survival (18.4 v 5.9 months; HR, 0.44; 95% CI, 0.31 to 0.62; P < .0001) compared with patients not achieving this end point. After adjusting for clinical variables, ctDNA response and STK11 / KEAP1 mutations (HR, 2.08; 95% CI, 1.4 to 3.0; P < .001) remained independent predictors for overall survival, irrespective of programmed death ligand-1 expression. A landmark survival analysis at 2 months (n = 129) provided similar results., Conclusion: On-treatment changes of ctDNA in plasma reveal predictive information for long-term clinical benefit in ICI-treated patients with NSCLC. A broader NSCLC patient coverage through de novo mutation calling and the use of a variant call set excluding CH-related variants improved the classification of molecular responders, but had no significant impact on survival., Competing Interests: Thomas SchlangeEmployment: Bayer AG, Boehringer IngelheimStock and Other Ownership Interests: Bayer AG Wim TimensConsulting or Advisory Role: Bristol Myers SquibbResearch Funding: MSDTravel, Accommodations, Expenses: MSD Marie-Laure YaspoEmployment: Alacris TheranosticsLeadership: Alacris TheranosticsStock and Other Ownership Interests: Alacris Theranostics T. Jeroen. N. HiltermannConsulting or Advisory Role: BMS, AZD, Roche, MSDResearch Funding: BMS, Roche, AZD Ed SchuuringHonoraria: Bio-Rad, Roche, Agena Bioscience, Illumina, LillyConsulting or Advisory Role: MSD/Merck, Bayer, BMS, Agena Bioscience, Janssen Cilag (Johnson & Johnson), Novartis, Roche, AstraZeneca, Amgen, LillyResearch Funding: Biocartis, Bio-Rad, Roche, Agena Bioscience, CC Diagnostics, Qiagen, Abbott, BMS, AstraZeneca, InVitae/ArcherTravel, Accommodations, Expenses: Roche Molecular Diagnostics, Bio-Rad Ellen HeitzerConsulting or Advisory Role: Roche Pharma AGResearch Funding: Roche Molecular Diagnostics, PreAnalytiX, Freenome Harry J. M. GroenConsulting or Advisory Role: Novartis, Bristol Myers Squibb, Lilly, Roche/Genentech, AstraZenecaResearch Funding: Roche, Boehringer IngelheimNo other potential conflicts of interest were reported.

Humans may share more genomic commonalities with other species than previously thought. According to current estimates, ~5% of the human genome is functionally constrained, which is a much larger fraction than the ~1.5% occupied by annotated protein-coding genes. Hence, ~3.5% of the human genome comprises likely functional conserved noncoding elements (CNEs) preserved among organisms, whose common ancestors existed throughout hundreds of millions of years of evolution. As whole-genome sequencing emerges as a standard procedure in genetic analyses, interpretation of variations in CNEs, including the elucidation of mechanistic and functional roles, becomes a necessity. Here, we discuss the phenomenon of noncoding conservation via four dimensions (sequence, regulatory conservation, spatiotemporal expression, and structure) and the potential significance of CNEs in phenotype variation and disease., Competing Interests: Declaration of interests None declared by authors., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: Molecular profiling (MP) represents an opportunity to match patients to a targeted therapy and when tumor tissue is unavailable, circulating tumor deoxyribonucleic acid (ctDNA) can be harnessed as a non-invasive analyte for this purpose. We evaluated the success of a targeted therapy selected by profiling of ctDNA and tissue in patients with advanced and refractory carcinoma., Patients and Methods: A blood draw as well as an optional tissue biopsy were obtained for MP. Whole-genome sequencing and a cancer hotspot panel were performed, and publicly available databases were used to match the molecular profile to targeted treatments. The primary endpoint was the progression-free survival (PFS) ratio (PFS on MP-guided therapy/PFS on the last evidence-based therapy), whereas the success of the targeted therapy was defined as a PFS ratio ⩾1.2. To test the impact of molecular profile-treatment matching strategies, we retrospectively analyzed selected cases via the CureMatch PreciGENE™ decision support algorithm., Results: Interim analysis of 24 patients yielded informative results from 20 patients (83%). A potential tumor-specific drug could be matched in 11 patients (46%) and eight (33%) received a matched treatment. Median PFS in the matched treatment group was 61.5 days [interquartile range (IQR) 49.8-71.0] compared with 81.5 days (IQR 68.5-117.8) for the last evidence-based treatment, resulting in a median PFS ratio of 0.7 (IQR 0.6-0.9). Hence, as no patient experienced a PFS ratio ⩾1.2, the study was terminated. Except for one case, the CureMatch analysis identified either a two-drug or three-drug combination option., Conclusions: Our study employed a histotype-agnostic approach to harness molecular profiling data from both ctDNA and metastatic tumor tissue. The outcome results indicate that more innovative approaches to study design and matching algorithms are necessary to achieve improved patient outcomes. EU Clinical Trials Registry (https://www.clinicaltrialsregister.eu): EudraCT: 2014-005341-44., Competing Interests: Conflict of interest statement: EH and MRS have an unrelated sponsored research agreement with Servier within CANCER-ID, a project funded by the Innovative Medicines Joint Undertaking (IMI JU), EH receives funding from Freenome, South San Francisco, CA, and PreAnalytiX, Hombrechtikon, Switzerland. EH received honoraria from Roche for advisory boards., (© The Author(s), 2021.)

We addressed a significant unknown feature of circulating tumor DNA (ctDNA), i.e., how ctDNA levels change during chemotherapy, by serially monitoring ctDNA in patients with colorectal cancer during the 48-h application of FOLFOX. Surprisingly, we did not observe a spike in ctDNA as a sign of a responsive tumor, but instead ctDNA levels initially decreased and remained low in patients with stable disease or partial response. Our observations reveal further insights into cell destruction during chemotherapy with important implications for the management of patients.

Functional studies giving insight into the biology of circulating tumor cells (CTCs) remain scarce due to the low frequency of CTCs and lack of appropriate models. Here, we describe the characterization of a novel CTC-derived breast cancer cell line, designated CTC-ITB-01, established from a patient with metastatic estrogen receptor-positive (ER + ) breast cancer, resistant to endocrine therapy. CTC-ITB-01 remained ER + in culture, and copy number alteration (CNA) profiling showed high concordance between CTC-ITB-01 and CTCs originally present in the patient with cancer at the time point of blood draw. RNA-sequencing data indicate that CTC-ITB-01 has a predominantly epithelial expression signature. Primary tumor and metastasis formation in an intraductal PDX mouse model mirrored the clinical progression of ER + breast cancer. Downstream ER signaling was constitutively active in CTC-ITB-01 independent of ligand availability, and the CDK4/6 inhibitor Palbociclib strongly inhibited CTC-ITB-01 growth. Thus, we established a functional model that opens a new avenue to study CTC biology., (© 2020 The Authors. Published under the terms of the CC BY 4.0 license.)

Objective: Precision oncology depends on translating molecular data into therapy recommendations. However, with the growing complexity of next-generation sequencing-based tests, clinical interpretation of somatic genomic mutations has evolved into a formidable task. Here, we compared the performance of three commercial clinical decision support tools, that is, NAVIFY Mutation Profiler (NAVIFY; Roche), QIAGEN Clinical Insight (QCI) Interpret (QIAGEN) and CureMatch Bionov (CureMatch)., Methods: In order to obtain the current status of the respective tumour genome, we analysed cell-free DNA from patients with metastatic breast, colorectal or non-small cell lung cancer. We evaluated somatic copy number alterations and in parallel applied a 77-gene panel (AVENIO ctDNA Expanded Panel). We then assessed the concordance of tier classification approaches between NAVIFY and QCI and compared the strategies to determine actionability among all three platforms. Finally, we quantified the alignment of treatment suggestions across all decision tools., Results: Each platform varied in its mode of variant classification and strategy for identifying druggable targets and clinical trials, which resulted in major discrepancies. Even the frequency of concordant actionable events for tier I-A or tier I-B classifications was only 4.3%, 9.5% and 28.4% when comparing NAVIFY with QCI, NAVIFY with CureMatch and CureMatch with QCI, respectively, and the obtained treatment recommendations differed drastically., Conclusions: Treatment decisions based on molecular markers appear at present to be arbitrary and dependent on the chosen strategy. As a consequence, tumours with identical molecular profiles would be differently treated, which challenges the promising concepts of genome-informed medicine., Competing Interests: Competing interests: EH and MRS have an unrelated sponsored research agreement with Servier within CANCER-ID, a project funded by the Innovative Medicines Joint Undertaking (IMI JU). EH receives funding from Freenome, South San Francisco, CA and PreAnalytiX, Hombrechtikon, Switzerland. Roche Diagnostics and QIAGEN provided the authors with free access to their respective platforms for a restricted time period to facilitate this study. EH has received honoraria for advisory boards from Roche. ES has served as consultant or on the advisory board for AstraZeneca, Roche, Pfizer, Novartis, MSD/Merck, Bayer and Janssen Cilag (Johnson&Johnson). The other authors have no competing interests to declare., (© Author (s) (or their employer(s)) 2020. Re-use permitted under CC BY-NC. No commercial re-use. Published by BMJ on behalf of the European Society for Medical Oncology.)

Background: The transition from American Osteopathic Association (AOA) and Accreditation Council for Graduate Medical Education (ACGME) residency matches to a single graduate medical education accreditation system culminated in a single match in 2020. Without AOA-accredited residency programs, which were open only to osteopathic medical (DO) graduates, it is not clear how desirable DO candidates will be in the unified match. To avoid increased costs and inefficiencies from overapplying to programs, DO applicants could benefit from knowing which specialties and ACGME-accredited programs have historically trained DO graduates., Objective: This study explores the characteristics of residency programs that report accepting DO students., Methods: Data from the American Medical Association's Fellowship and Residency Electronic Interactive Database Access were analyzed for percentage of DO residents in each program. Descriptive statistics and a logit link generalized linear model for a gamma distribution were performed., Results: Characteristics associated with graduate medical education programs that reported a lower percentage of DO graduates as residents were surgical subspecialties, longer training, and higher US Medical Licensing Examination Step 1 scores of their residents compared with specialty average. Characteristics associated with a higher percentage of DO graduates included interviewing more candidates for first-year positions and reporting a higher percentage of female residents., Conclusions: Wide variation exists in the percentage of DO graduates accepted as residents among specialties and programs. This study provides valuable information about the single Match for DO graduates and their advisers and outlines education opportunities for the osteopathic profession among the specialties with low percentages of DO students as residents., Competing Interests: Conflict of interest: The authors declare they have no competing interests., (Accreditation Council for Graduate Medical Education 2020.)

Molecular profiling from liquid biopsy, in particular cell-free DNA (cfDNA), represents an attractive alternative to tissue biopsies for the detection of actionable targets and tumor monitoring. In addition to PCR-based assays, Next Generation Sequencing (NGS)-based cfDNA assays are now commercially available and are being increasingly adopted in clinical practice. However, the validity of these products as well as the clinical utility of cfDNA in the management of patients with cancer has yet to be proven. Within framework of the Innovative Medicines Initiative (IMI) program CANCER-ID we evaluated the use of commercially available reference materials designed for ctDNA testing and cfDNA derived from Diagnostic Leukaphereses (DLA) for inter- and intra-assay as well as intra- and inter-laboratory comparisons. In three experimental setups, a broad range of assays including ddPCR, MassARRAY and various NGS-based assays were tested. We demonstrate that both reference materials with predetermined VAFs and DLA samples are extremely useful for the performance assessment of mutation analysis platforms. Moreover, our data indicate a substantial variability of NGS assays with respect to sensitivity and specificity highlighting the importance of extensive validation of the test performance before offering these tests in clinical routine practice.

Background: Focal amplification of fibroblast growth factor receptor 1 ( FGFR1 ) defines a subgroup of breast cancers with poor prognosis and high risk of recurrence. We sought to demonstrate the potential of circulating cell-free DNA (cfDNA) analysis to evaluate FGFR1 copy numbers from a cohort of 100 metastatic breast cancer (mBC) patients. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples were screened for FGFR1 amplification by FISH, and positive cases were confirmed with a microarray platform (Oncoscan TM ). Subsequently, cfDNA was evaluated by two approaches, i.e., mFAST-SeqS and shallow whole-genome sequencing (sWGS), to estimate the circulating tumor DNA (ctDNA) allele fraction (AF) and to evaluate the FGFR1 status. Results: Tissue-based analyses identified FGFR1 amplifications in 20/100 tumors. All cases with a ctDNA AF above 3% ( n = 12) showed concordance for FGFR1 status between tissue and cfDNA. In one case, we were able to detect a high-level FGFR1 amplification, although the ctDNA AF was below 1%. Furthermore, high levels of ctDNA indicated an association with unfavorable prognosis based on overall survival. Conclusions: Screening for FGFR1 amplification in ctDNA might represent a viable strategy to identify patients eligible for treatment by FGFR inhibition, and mBC ctDNA levels might be used for the evaluation of prognosis in clinical drug trials.

Background. The phenotypes of patients with the recently discovered, dominant, ETV6 -linked leukaemia predisposition and familial thrombocytopenia syndrome are variable, and the exact mechanism of leukaemogenesis remains unclear. Patients and Methods. Here, we present novel clinical and laboratory phenotypes of seven individuals from three families with ETV6 germline mutations and a refined genetic analysis of one child with additional high-hyperdiploid acute lymphoblastic leukaemia (HD-ALL), aiming to elucidate second oncogenic hits. Results. Four individuals from two pedigrees harboured one novel or one previously described variant in the central domain of ETV6 (c.592C>T, p.Gln198* or c.641C>T, p.Pro241Leu, respectively). Neutropenia was an accompanying feature in one of these families that also harboured a variant in RUNX1 (c.1098&#95;1103dup, p.Ile366&#95;Gly367dup), while in the other, an autism-spectrum disorder was observed. In the third family, the index patient suffered from HD-ALL and life-threatening pulmonary mucor mycosis, and had a positive family history of 'immune' thrombocytopenia. Genetic analyses revealed a novel heterozygous mutation in the ETS domain of ETV6 (c.1136T>C, p.Leu379Pro) along with absence of heterozygosity of chromosome (10)(q21.2q21.3), yielding a biallelic leukaemia risk allele in ARID5B (rs7090445-C). The neutrophil function was normal in all individuals tested, and the platelet immune histochemistry of all three pedigrees showed delta-storage-pool defect-like features and cytoskeletal defects. Conclusions. Our clinical observations and results of high-resolution genetic analyses extend the spectrum of possible phenotypes cosegregating with ETV6 germline mutations. Further, we propose ARID5B as potential leukaemogenic cofactor in patients with ETV6 -linked leukaemia predisposition and familial thrombocytopenia syndrome., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2020. No commercial re-use. See rights and permissions. Published by BMJ.)

Context: Research on associations between medical student empathy and demographics, academic background and career interest is limited, lacks representative samples and suffers from single institutional features. This study was designed to fill the gap by examining associations between empathy in patient care, and gender, age, race and ethnicity, academic background and career interest in nationwide, multi-institutional samples of medical students in the United States and to provide more definitive answers regarding the aforementioned associations, with more confidence in the internal and external validity of the findings., Methods: Four nationwide samples participated in this study (n = 10 751). Samples 1, 2, 3 and 4 included 3616 first-year, 2764 second-year, 2413 third-year and 1958 fourth-year students who completed a web-based survey at the end of the 2017-2018 academic year. The survey included questions on demographics, academic background and career interest, the Jefferson Scale of Empathy, and the Infrequency Scale of the Zuckerman-Kuhlman Personality Questionnaire to control for the effect of 'good impression' response bias., Results: Statistically significant and practically important associations were found between empathy scores and gender (in favour of women), race and ethnicity (in favour of African-American and Hispanic/Latino/Spanish), academic background (in favour of 'Social and Behavioural Sciences' and 'Arts and Humanities' in Samples 1 and 2) and career interest (in favour of 'People-Oriented' and 'Psychiatry' specialties)., Conclusions: Special features of this study (eg, nationwide representative samples, use of a validated instrument for measuring empathy in patient care, statistical control for the effect of 'good impression' response bias, and consistency of findings in different samples from multiple institutions) provide more definitive answers to the issue of correlates of empathy in medical students and increase our confidence in the validity, reliability and generalisability of the results. Findings have implications for career counselling and targeting students who need more guidance to enhance their empathic orientation., (© 2020 The Authors. Medical Education published by Association for the Study of Medical Education and John Wiley & Sons Ltd.)

Purpose: To examine differences in students' empathy in different years of medical school in a nationwide study of students of U.S. DO-granting medical schools., Method: Participants in this cross-sectional study included 10,751 students enrolled in 41 of 48 campuses of DO-granting medical schools in the United States (3,616 first-year, 2,764 second-year, 2,413 third-year, and 1,958 fourth-year students). They completed a web-based survey at the end of the 2017-2018 academic year that included the Jefferson Scale of Empathy and the Infrequency Scale of the Zuckerman-Kuhlman Personality Questionnaire for measuring "good impression" response bias. Comparisons were made on empathy scores among students in different years of medical school using analysis of covariance, controlling for the effect of "good impression" response bias. Also, comparisons were made with preexisting data from students of U.S. MD-granting medical schools., Results: A statistically significant decline in empathy scores was observed when comparing students in the preclinical (years 1 and 2) and the clinical (years 3 and 4) phases of medical school (P < .001); however, the magnitude of the decline was negligible (effect size =0.13). Comparison of findings with MD students showed that while the pattern of empathy decline was similar, the magnitude of the decline was less pronounced in DO students., Conclusions: Differences in DO-granting and MD-granting medical education systems, such as emphasis on provision of holistic care, hands-on approaches to diagnosis and treatment, and patient-centered care, provide plausible explanations for disparity in the magnitude of empathy decline in DO compared with MD students. More research is needed to examine changes in empathy in longitudinal study and explore reasons for changes to avert erosion of empathy in medical school.

Cell-free DNA (cfDNA) is evolving into a widely used prognostic and predictive biomarker, particularly in oncology. However, its versatile clinical use precedes a profound understanding of the underlying biology of cfDNA release. There is much evidence to suggest that cfDNA is mainly derived from dying (i.e., apoptotic) cells. However, numerous cancer studies have shown that cfDNA is informative about acquired resistance to given therapies, which is present in living, proliferating tumor subclones. To explain this contradiction, we review current insights regarding cfDNA release, in particular the interplay between apoptosis and proliferation. We describe how improved knowledge about cfDNA biology could be used for novel therapeutic strategies and how this may affect patient management., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Background: Bevacizumab, a monoclonal antibody against soluble VEGFA, is an approved and commonly administered anti-angiogenic drug in patients with metastasized colorectal cancer (mCRC). The survival benefit of anti-VEGF therapy in mCRC patients is limited to a few months, and acquired resistance mechanisms are largely unknown. Here, we employed whole-genome sequencing of plasma DNA to evaluate the tumor genome of patients undergoing treatment with bevacizumab to determine novel aberrations associated with resistance., Methods: Using longitudinal plasma analyses, we studied the evolution of tumor genomes in a mCRC cohort (n = 150) and conducted analyses of CRC cases from The Cancer Genome Atlas (TCGA) database (n = 619) to identify associations between genomic aberrations and clinical features. We employed whole-genome sequencing to identify the most frequently occurring focal somatic copy number alterations (SCNAs). Using the TCGA data as a comparative and supporting dataset, we defined the minimally amplified overlapping region and studied the mechanistic consequences of copy number gain of the involved genes in this segment. In addition, we established an in vitro cell model and conducted downstream gene expression and cell viability assays to confirm our findings from the patient dataset., Results: We observed a recurrent focal amplification (8.7% of cases) on chromosome 13q12.2. Analysis of CRC cases from the TCGA database suggested that this amplicon is associated with more advanced stages. We confirmed that this 13q12.2 amplicon frequently emerges later during the clinical course of disease. After defining the minimally amplified region, we observed that the amplification and expression of one gene, POLR1D, impacted cell proliferation and resulted in upregulation of VEGFA, an important regulator of angiogenesis which has been implicated in the resistance to bevacizumab treatment. In fact, in several patients, we observed the emergence of this 13q12.2 amplicon under bevacizumab treatment, which was invariably associated with therapy resistance., Conclusions: Non-invasive analyses of cell-free DNA from patients undergoing treatment with bevacizumab enabled the tracking of evolving tumor genomes and helped identify a recurrent focal SCNA of clinical relevance. Here, we describe a novel resistance mechanism against a widely applied treatment in patients with mCRC which will impact the clinical management of patients.

Background: In cancer patients, circulating cell-free DNA (ccfDNA) can contain tumor-derived DNA (ctDNA), which enables noninvasive diagnosis, real-time monitoring, and treatment susceptibility testing. However, ctDNA fractions are highly variable, which challenges downstream applications. Therefore, established preanalytical work flows in combination with cost-efficient and reproducible reference materials for ccfDNA analyses are crucial for analytical validity and subsequently for clinical decision-making., Methods: We describe the efforts of the Innovative Medicines Initiative consortium CANCER-ID (http://www.cancer-id.eu) for comparing different technologies for ccfDNA purification, quantification, and characterization in a multicenter setting. To this end, in-house generated mononucleosomal DNA (mnDNA) from lung cancer cell lines carrying known TP53 mutations was spiked in pools of plasma from healthy donors generated from 2 different blood collection tubes (BCTs). ccfDNA extraction was performed at 15 partner sites according to their respective routine practice. Downstream analysis of ccfDNA with respect to recovery, integrity, and mutation analysis was performed centralized at 4 different sites., Results: We demonstrate suitability of mnDNA as a surrogate for ccfDNA as a process quality control from nucleic acid extraction to mutation detection. Although automated extraction protocols and quantitative PCR-based quantification methods yielded the most consistent and precise results, some kits preferentially recovered spiked mnDNA over endogenous ccfDNA. Mutated TP53 fragments derived from mnDNA were consistently detected using both next-generation sequencing-based deep sequencing and droplet digital PCR independently of BCT., Conclusions: This comprehensive multicenter comparison of ccfDNA preanalytical and analytical work flows is an important contribution to establishing evidence-based guidelines for clinically feasible (pre)analytical work flows., (© 2019 American Association for Clinical Chemistry.)

Deregulation of transcription factors (TFs) is an important driver of tumorigenesis, but non-invasive assays for assessing transcription factor activity are lacking. Here we develop and validate a minimally invasive method for assessing TF activity based on cell-free DNA sequencing and nucleosome footprint analysis. We analyze whole genome sequencing data for >1,000 cell-free DNA samples from cancer patients and healthy controls using a bioinformatics pipeline developed by us that infers accessibility of TF binding sites from cell-free DNA fragmentation patterns. We observe patient-specific as well as tumor-specific patterns, including accurate prediction of tumor subtypes in prostate cancer, with important clinical implications for the management of patients. Furthermore, we show that cell-free DNA TF profiling is capable of detection of early-stage colorectal carcinomas. Our approach for mapping tumor-specific transcription factor binding in vivo based on blood samples makes a key part of the noncoding genome amenable to clinical analysis.

Context: National norms are necessary to assess individual scores from validated instruments. Before undertaking this study, no national norms were available on empathy scores. The Project in Osteopathic Medical Education and Empathy (POMEE) provided a unique opportunity to develop the first national norms for medical students., Objective: To develop national norms for the assessments of osteopathic medical students' empathy scores on the broadly used and well-validated Jefferson Scale of Empathy (JSE) at all levels of osteopathic medical school education., Methods: Participants were students from 41 of 48 participating campuses of osteopathic medical schools. Students were invited to complete a web-based survey, which included the JSE, in the 2017-2018 academic year., Results: A total of 16,149 completed surveys were used to create national norm tables. Three national norm tables were developed for first-year matriculants and for students in preclinical (years 1 and 2) and clinical (years 3 and 4) phases of medical school. The norm tables allow any raw score on the JSE for male and female osteopathic medical students from matriculation to graduation to be converted to a percentile rank to assess an individual's score against national data., Conclusions: National norms developed in this project, for men and women and at different levels of medical school education, can not only be used for the assessment of student's individual scores on the JSE, but can also serve as a supplementary measure for admissions to medical school and postgraduate medical education programs.

The need for a liquid biopsy in non-small cell lung cancer (NSCLC) patients is rapidly increasing. We studied the relation between overall survival (OS) and the presence of four cancer biomarkers from a single blood draw in advanced NSCLC patients: EpCAM high circulating tumor cells (CTC), EpCAM low CTC, tumor-derived extracellular vesicles (tdEV) and cell-free circulating tumor DNA (ctDNA). EpCAM high CTC were detected with CellSearch, tdEV in the CellSearch images and EpCAM low CTC with filtration after CellSearch. ctDNA was isolated from plasma and mutations present in the primary tumor were tracked with deep sequencing methods. In 97 patients, 21% had ≥2 EpCAM high CTC, 15% had ≥2 EpCAM low CTC, 27% had ≥18 tdEV and 19% had ctDNA with ≥10% mutant allele frequency. Either one of these four biomarkers could be detected in 45% of the patients and all biomarkers were present in 2%. In 11 out of 16 patients (69%) mutations were detected in the ctDNA. Two or more unfavorable biomarkers were associated with poor OS. The presence of EpCAM high CTC and elevated levels of tdEV and ctDNA was associated with a poor OS; however, the presence of EpCAM low CTC was not. This single tube approach enables simultaneous analysis of multiple biomarkers to explore their potential as a liquid biopsy., (© 2018 UICC.)

Background: Merkel cell carcinoma (MCC) is a rare, aggressive skin cancer with increasing incidence and high mortality rates. MCC has recently become the subject of immune checkpoint therapy, but reliable biomarkers for estimating prognosis, risk stratification, and prediction of response are missing., Methods: Circulating tumor cells (CTCs) were detected in peripheral blood from patients with MCC by use of the CellSearch ® system. Moreover, CTCs of selected cases were characterized for Merkel cell polyomavirus (MCPyV), chromosomal aberrations, and programed death ligand 1 (PD-L1) production., Results: Fifty-one patients were tested at first blood draw (baseline), and 16 patients had 2 or 3 consecutive measurements to detect CTCs. At baseline, ≥1 CTC (range, 1-790), >1, or ≥5 CTCs/7.5 mL were detected in 21 (41%), 17 (33%), and 6 (12%) patients, respectively. After a median follow-up of 21.1 months for 50 patients, detection of CTCs correlated with overall survival (≥1, P = 0.030; >1, P < 0.020; and ≥5 CTCs/7.5 mL, P < 0.0001). In multivariate Cox regression analysis, the detection of ≥5 CTCs/7.5 mL adjusted to age and sex compared to that of <5 was associated with a reduced overall survival ( P = 0.001, hazard ratio = 17.8; 95% CI, 4.0-93.0). MCPyV DNA and genomic aberrations frequently found in MCC tissues could also be detected in single CTCs. Analyzed CTCs were PD-L1 negative or only weakly positive., Conclusions: The presence of CTCs is a prognostic factor of impaired clinical outcome, with the potential to monitor the progression of the disease in real time. Molecular characterization of CTCs might provide new insights into the biology of MCC., (© 2018 American Association for Clinical Chemistry.)

Precision oncology seeks to leverage molecular information about cancer to improve patient outcomes. Tissue biopsy samples are widely used to characterize tumours but are limited by constraints on sampling frequency and their incomplete representation of the entire tumour bulk. Now, attention is turning to minimally invasive liquid biopsies, which enable analysis of tumour components (including circulating tumour cells and circulating tumour DNA) in bodily fluids such as blood. The potential of liquid biopsies is highlighted by studies that show they can track the evolutionary dynamics and heterogeneity of tumours and can detect very early emergence of therapy resistance, residual disease and recurrence. However, the analytical validity and clinical utility of liquid biopsies must be rigorously demonstrated before this potential can be realized.

The switch/sucrose non-fermenting (SWI/SNF) complex is an ATP-dependent chromatin remodeller that regulates the spacing of nucleosomes and thereby controls gene expression. Heterozygous mutations in genes encoding subunits of the SWI/SNF complex have been reported in individuals with Coffin-Siris syndrome (CSS), with the majority of the mutations in ARID1B. CSS is a rare congenital disorder characterized by facial dysmorphisms, digital anomalies, and variable intellectual disability. We hypothesized that mutations in genes encoding subunits of the ubiquitously expressed SWI/SNF complex may lead to alterations of the nucleosome profiles in different cell types. We performed the first study on CSS-patient samples and investigated the nucleosome landscapes of cell-free DNA (cfDNA) isolated from blood plasma by whole-genome sequencing. In addition, we studied the nucleosome landscapes of CD14+ monocytes from CSS-affected individuals by nucleosome occupancy and methylome-sequencing (NOMe-seq) as well as their expression profiles. In cfDNA of CSS-affected individuals with heterozygous ARID1B mutations, we did not observe major changes in the nucleosome profile around transcription start sites. In CD14+ monocytes, we found few genomic regions with different nucleosome occupancy when compared to controls. RNA-seq analysis of CD14+ monocytes of these individuals detected only few differentially expressed genes, which were not in proximity to any of the identified differential nucleosome-depleted regions. In conclusion, we show that heterozygous mutations in the human SWI/SNF subunit ARID1B do not have a major impact on the nucleosome landscape or gene expression in blood cells. This might be due to functional redundancy, cell-type specificity, or alternative functions of ARID1B., (© 2019 S. Karger AG, Basel.)

The Jefferson Scale of Empathy (JSE) is a broadly used instrument developed to measure empathy in the context of health professions education and patient care. Evidence in support of psychometrics of the JSE has been reported in health professions students and practitioners with the exception of osteopathic medical students. This study was designed to examine measurement properties, underlying components, and latent variable structure of the JSE in a nationwide sample of first-year matriculants at U.S. colleges of osteopathic medicine, and to develop a national norm table for the assessment of JSE scores. A web-based survey was administered at the beginning of the 2017-2018 academic year which included the JSE, a scale to detect "good impression" responses, and demographic/background information. Usable surveys were received from 6009 students enrolled in 41 college campuses (median response rate = 92%). The JSE mean score and standard deviation for the sample were 116.54 and 10.85, respectively. Item-total score correlations were positive and statistically significant (p < 0.01), and Cronbach α = 0.82. Significant gender differences were observed on the JSE scores in favor of women. Also, significant differences were found on item scores between top and bottom third scorers on the JSE. Three factors of Perspective Taking, Compassionate Care, and Walking in Patient's Shoes emerged in an exploratory factor analysis by using half of the sample. Results of confirmatory factor analysis with another half of the sample confirmed the 3-factor model. We also developed a national norm table which is the first to assess students' JSE scores against national data.

Background: The BRCA1-associated protein-1 (BAP1) tumor predisposition syndrome (BAP1-TPDS) is a hereditary tumor syndrome caused by germline pathogenic variants in BAP1 encoding a tumor suppressor associated with uveal melanoma, mesothelioma, cutaneous melanoma, renal cell carcinoma, and cutaneous BAP1-inactivated melanocytic tumors. However, the full spectrum of tumors associated with the syndrome is yet to be determined. Improved understanding of the BAP1-TPDS is crucial for appropriate clinical management of BAP1 germline variant carriers and their families, including genetic counseling and surveillance for new tumors., Methods: We collated germline variant status, tumor diagnoses, and information on BAP1 immunohistochemistry or loss of somatic heterozygosity on 106 published and 75 unpublished BAP1 germline variant-positive families worldwide to better characterize the genotypes and phenotypes associated with the BAP1-TPDS. Tumor spectrum and ages of onset were compared between missense and null variants. All statistical tests were two-sided., Results: The 181 families carried 140 unique BAP1 germline variants. The collated data confirmed the core tumor spectrum associated with the BAP1-TPDS and showed that some families carrying missense variants can exhibit this phenotype. A variety of noncore BAP1-TPDS -associated tumors were found in families of variant carriers. Median ages of onset of core tumor types were lower in null than missense variant carriers for all tumors combined (P < .001), mesothelioma (P < .001), cutaneous melanoma (P < .001), and nonmelanoma skin cancer (P < .001)., Conclusions: This analysis substantially increases the number of pathogenic BAP1 germline variants and refines the phenotype. It highlights the need for a curated registry of germline variant carriers for proper assessment of the clinical phenotype of the BAP1-TPDS and pathogenicity of new variants, thus guiding management of patients and informing areas requiring further research.

Understanding the biological properties of plasma cell-free DNA may expand its applications in oncology (Mouliere et al , this issue)., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)