Interfaces of Malignant and Immunologic Clonal Dynamics in Ovarian Cancer.

High-grade serous ovarian cancer (HGSC) exhibits extensive malignant clonal diversity with widespread but non-random patterns of disease dissemination. We investigated whether local immune microenvironment factors shape tumor progression properties at the interface of tumor-infiltrating lymphocytes (TILs) and cancer cells. Through multi-region study of 212 samples from 38 patients with whole-genome sequencing, immunohistochemistry, histologic image analysis, gene expression profiling, and T and B cell receptor sequencing, we identified three immunologic subtypes across samples and extensive within-patient diversity. Epithelial CD8+ TILs negatively associated with malignant diversity, reflecting immunological pruning of tumor clones inferred by neoantigen depletion, HLA I loss of heterozygosity, and spatial tracking between T cell and tumor clones. In addition, combinatorial prognostic effects of mutational processes and immune properties were observed, illuminating how specific genomic aberration types associate with immune response and impact survival. We conclude that within-patient spatial immune microenvironment variation shapes intraperitoneal malignant spread, provoking new evolutionary perspectives on HGSC clonal dispersion.

Ovarian cancer mutational processes drive site-specific immune evasion.

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability1-4 patterned by distinct mutational processes5,6, tumour heterogeneity7-9 and intraperitoneal spread7,8,10. Immunotherapies have had limited efficacy in HGSOC11-13, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumour sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumours harboured inflammatory signalling and ongoing immunoediting, reflected in loss of HLA diversity and tumour infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback-inversion-bearing tumours exhibited elevated immunosuppressive TGFß signalling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumours and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.

Single-cell genomic variation induced by mutational processes in cancer.

How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.

Clonal fitness inferred from time-series modelling of single-cell cancer genomes.

Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models1-7. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model8,9 to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours.

Maternal, Infant, and Child Health Outcomes Associated With the Special Supplemental Nutrition Program for Women, Infants, and Children : A Systematic Review.

BACKGROUND: The Special Supplemental Nutrition Program for Women, Infants, and Children (WIC) is intended to improve maternal and child health outcomes. In 2009, the WIC food package changed to better align with national nutrition recommendations. PURPOSE: To determine whether WIC participation was associated with improved maternal, neonatal-birth, and infant-child health outcomes or differences in outcomes by subgroups and WIC enrollment duration. DATA SOURCES: Search (January 2009 to April 2022) included PubMed, Embase, CINAHL, ERIC, Scopus, PsycInfo, and the Cochrane Central Register of Controlled Trials. STUDY SELECTION: Included studies had a comparator of WIC-eligible nonparticipants or comparison before and after the 2009 food package change. DATA EXTRACTION: Paired team members independently screened articles for inclusion and evaluated risk of bias. DATA SYNTHESIS: We identified 20 observational studies. We found: moderate strength of evidence (SOE) that maternal WIC participation during pregnancy is likely associated with lower risk for preterm birth, low birthweight infants, and infant mortality; low SOE that maternal WIC participation may be associated with a lower likelihood of inadequate gestational weight gain, as well as increased well-child visits and childhood immunizations; and low SOE that child WIC participation may be associated with increased childhood immunizations. We found low SOE for differences in some outcomes by race and ethnicity but insufficient evidence for differences by WIC enrollment duration. We found insufficient evidence related to maternal morbidity and mortality outcomes. LIMITATION: Data are from observational studies with high potential for selection bias related to the choice to participate in WIC, and participation status was self-reported in most studies. CONCLUSION: Participation in WIC was likely associated with improved birth outcomes and lower infant mortality, and also may be associated with increased child preventive service receipt. PRIMARY FUNDING SOURCE: Agency for Healthcare Research and Quality. (PROSPERO: CRD42020222452).

The Effect of Neutropenia and Filgrastim (G-CSF) on Cancer Patients With Coronavirus Disease 2019 (COVID-19) Infection.

BACKGROUND: Neutropenia is commonly encountered in cancer patients. Recombinant human granulocyte colony-stimulating factor (G-CSF, filgrastim), a cytokine that initiates proliferation and differentiation of mature granulocytes, is widely given to oncology patients to counteract neutropenia, reducing susceptibility to infection. However, the clinical impact of neutropenia and G-CSF use in cancer patients with coronavirus disease 2019 (COVID-19) remains unknown. METHODS: An observational cohort of 379 actively treated cancer patients with COVID-19 was assembled to investigate links between concurrent neutropenia and G-CSF administration on COVID-19-associated respiratory failure and death. These factors were encoded as time-dependent predictors in an extended Cox model, controlling for age and underlying cancer diagnosis. To determine whether the degree of granulocyte response to G-CSF affected outcomes, the degree of response to G-CSF, based on rise in absolute neutrophil count (ANC) 24 hours after growth factor administration, was also incorporated into a similar Cox model. RESULTS: In the setting of active COVID-19 infection, outpatient receipt of G-CSF led to an increased number of hospitalizations (hazard ratio [HR]: 3.54, 95% confidence interval [CI]: 1.25-10.0, P value: .017). Furthermore, among inpatients, G-CSF administration was associated with increased need for high levels of oxygen supplementation and death (HR: 3.56, 95% CI: 1.19-10.2, P value: .024). This effect was predominantly seen in patients that exhibited a high response to G-CSF based on their ANC increase post-G-CSF administration (HR: 7.78, 95% CI: 2.05-27.9, P value: .004). CONCLUSIONS: The potential risks versus benefits of G-CSF administration should be considered in neutropenic cancer patients with COVID-19, because G-CSF administration may lead to worsening clinical and respiratory status.

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling.

Single-cell RNA sequencing has enabled the decomposition of complex tissues into functionally distinct cell types. Often, investigators wish to assign cells to cell types through unsupervised clustering followed by manual annotation or via 'mapping' to existing data. However, manual interpretation scales poorly to large datasets, mapping approaches require purified or pre-annotated data and both are prone to batch effects. To overcome these issues, we present CellAssign, a probabilistic model that leverages prior knowledge of cell-type marker genes to annotate single-cell RNA sequencing data into predefined or de novo cell types. CellAssign automates the process of assigning cells in a highly scalable manner across large datasets while controlling for batch and sample effects. We demonstrate the advantages of CellAssign through extensive simulations and analysis of tumor microenvironment composition in high-grade serous ovarian cancer and follicular lymphoma.

Deep learning-based histotype diagnosis of ovarian carcinoma whole-slide pathology images.

Ovarian carcinoma has the highest mortality of all female reproductive cancers and current treatment has become histotype-specific. Pathologists diagnose five common histotypes by microscopic examination, however, histotype determination is not straightforward, with only moderate interobserver agreement between general pathologists (Cohen's kappa 0.54-0.67). We hypothesized that machine learning (ML)-based image classification models may be able to recognize ovarian carcinoma histotype sufficiently well that they could aid pathologists in diagnosis. We trained four different artificial intelligence (AI) algorithms based on deep convolutional neural networks to automatically classify hematoxylin and eosin-stained whole slide images. Performance was assessed through cross-validation on the training set (948 slides corresponding to 485 patients), and on an independent test set of 60 patients from another institution. The best-performing model achieved a diagnostic concordance of 81.38% (Cohen's kappa of 0.7378) in our training set, and 80.97% concordance (Cohen's kappa 0.7547) on the external dataset. Eight cases misclassified by ML in the external set were reviewed by two subspecialty pathologists blinded to the diagnoses, molecular and immunophenotype data, and ML-based predictions. Interestingly, in 4 of 8 cases from the external dataset, the expert review pathologists rendered diagnoses, based on blind review of the whole section slides classified by AI, that were in agreement with AI rather than the integrated reference diagnosis. The performance characteristics of our classifiers indicate potential for improved diagnostic performance if used as an adjunct to conventional histopathology.

Implementation and Effectiveness of Integrating Palliative Care Into Ambulatory Care of Noncancer Serious Chronic Illness: Mixed Methods Review and Meta-Analysis.

PURPOSE: To perform a mixed methods review to evaluate the effectiveness and implementation of models for integrating palliative care into ambulatory care for US adults with noncancer serious chronic illness. METHODS: We searched 3 electronic databases from January 2000 to May 2020 and included qualitative, mixed methods studies and randomized and nonrandomized controlled trials. For each study, 2 reviewers abstracted data and independently assessed for quality. We conducted meta-analyses as appropriate and graded strength of evidence (SOE) for quantitative outcomes. RESULTS: Quantitative analysis included 14 studies of 2,934 patients. Compared to usual care, models evaluated were not more effective for improving patient health-related quality of life (HRQOL) (standardized mean difference [SMD] of 4 of 8 studies, 0.19; 95% CI, ‒0.03 to 0.41) (SOE: moderate) or for patient depressive symptom scores (SMD of 3 of 9 studies, ‒0.09; 95% CI, ‒0.35 to 0.16) (SOE: moderate). Models might have little to no effect on patient satisfaction (SOE: low) but were more effective for increasing advance directive (AD) documentation (relative risk, 1.62; 95% CI, 1.35 to 1.94) (SOE: moderate). Qualitative analysis included 5 studies of 146 patients. Patient preferences for appropriate timing of palliative care varied; costs, additional visits, and travel were considered barriers to implementation. CONCLUSION: Models might have little to no effect on decreasing overall symptom burden and were not more effective than usual care for improving HRQOL or depressive symptom scores but were more effective for increasing AD documentation. Additional research should focus on identifying and addressing characteristics and implementation factors critical to integrating models to improve ambulatory, patient-centered outcomes.

Cancer stemness, intratumoral heterogeneity, and immune response across cancers.

Regulatory programs that control the function of stem cells are active in cancer and confer properties that promote progression and therapy resistance. However, the impact of a stem cell-like tumor phenotype ("stemness") on the immunological properties of cancer has not been systematically explored. Using gene-expression-based metrics, we evaluated the association of stemness with immune cell infiltration and genomic, transcriptomic, and clinical parameters across 21 solid cancers. We found pervasive negative associations between cancer stemness and anticancer immunity. This occurred despite high stemness cancers exhibiting increased mutation load, cancer-testis antigen expression, and intratumoral heterogeneity. Stemness was also strongly associated with cell-intrinsic suppression of endogenous retroviruses and type I IFN signaling, and increased expression of multiple therapeutically accessible immunosuppressive pathways. Thus, stemness is not only a fundamental process in cancer progression but may provide a mechanistic link between antigenicity, intratumoral heterogeneity, and immune suppression across cancers.

Comparative Effectiveness of Surveillance, Primary Chemotherapy, Radiotherapy and Retroperitoneal Lymph Node Dissection for the Management of Early Stage Testicular Germ Cell Tumors: A Systematic Review.

PURPOSE: Cancer specific survival for men with early stage (I to IIB) testicular germ cell tumors is greater than 90% with any management strategy. The data regarding the comparative effectiveness of surveillance, primary chemotherapy, radiotherapy and retroperitoneal lymph node dissection were synthesized with a focus on oncologic outcomes, patient reported outcomes, and short and long-term toxicities. MATERIALS AND METHODS: PubMed®, Embase® and the Cochrane Central Register of Controlled Trials were searched from 1980 to 2018 for studies addressing the effectiveness of surveillance, chemotherapy, radiotherapy and retroperitoneal lymph node dissection, according to pathology and clinical stage, for men with an early stage testicular germ cell tumor. RESULTS: Cancer specific survival ranged from 94% to 100% for patients with early stage testicular germ cell tumors regardless of tumor histology and initial management strategy. For men with seminoma the median cancer specific survival was 99.7% (range 97% to 100%), 99.5% (96.8% to 100%) and 100% (100% to 100%) among those managed by surveillance, radiotherapy and chemotherapy, respectively. Median cancer specific survival for men with nonseminomatous testicular germ cell tumors was 100% (range 98.6% to 100%), 100% (96.9% to 100%) and 100% (94% to 100%) when managed by surveillance, retroperitoneal lymph node dissection and chemotherapy, respectively. Recurrence rates and toxicities varied by management strategy. For men with seminoma surveillance, chemotherapy and radiotherapy were associated with median recurrence rates of 15%, 2% and 3.7%, respectively. For men with nonseminomatous testicular germ cell tumors the median recurrence rates were 20.5%, 3.3% and 11.1% for surveillance, chemotherapy and retroperitoneal lymph node dissection, respectively. Surveillance was associated with minimal toxicities compared to other approaches. Primary chemotherapy had the highest rate of short-term toxicities and was associated with long-term risks of metabolic syndrome, hypogonadism, renal impairment, neuropathy, infertility and secondary malignancies. Toxicities with radiotherapy included acute dermatitis and long-term gastrointestinal complications, infertility and high rates of secondary malignancies (2% to 3%). Patients undergoing retroperitoneal lymph node dissection had significant risk of toxicity perioperatively and long-term infertility in men with anejaculation. Transient detriments in patient reported outcomes and quality of life were noted with all management options. CONCLUSIONS: Men with early stage testicular germ cell tumors experience excellent cancer specific survival regardless of management strategy. Management options, however, differ in terms of associated recurrence rates, short and long-term toxicities, and patient reported outcomes. The profile for each approach should be clearly communicated to patients and matched with patient preferences to offer the best individual outcome.

Projecting COVID-19 disease severity in cancer patients using purposefully-designed machine learning.

BACKGROUND: Accurately predicting outcomes for cancer patients with COVID-19 has been clinically challenging. Numerous clinical variables have been retrospectively associated with disease severity, but the predictive value of these variables, and how multiple variables interact to increase risk, remains unclear. METHODS: We used machine learning algorithms to predict COVID-19 severity in 348 cancer patients at Memorial Sloan Kettering Cancer Center in New York City. Using only clinical variables collected on or before a patient's COVID-19 positive date (time zero), we sought to classify patients into one of three possible future outcomes: Severe-early (the patient required high levels of oxygen support within 3 days of being tested positive for COVID-19), Severe-late (the patient required high levels of oxygen after 3 days), and Non-severe (the patient never required oxygen support). RESULTS: Our algorithm classified patients into these classes with an area under the receiver operating characteristic curve (AUROC) ranging from 70 to 85%, significantly outperforming prior methods and univariate analyses. Critically, classification accuracy is highest when using a potpourri of clinical variables - including basic patient information, pre-existing diagnoses, laboratory and radiological work, and underlying cancer type - suggesting that COVID-19 in cancer patients comes with numerous, combinatorial risk factors. CONCLUSIONS: Overall, we provide a computational tool that can identify high-risk patients early in their disease progression, which could aid in clinical decision-making and selecting treatment options.

Performance Characteristics of Clinical Staging Modalities for Early Stage Testicular Germ Cell Tumors: A Systematic Review.

PURPOSE: We synthesized evidence on the comparative performance characteristics, benefits and harms of diagnostic imaging modalities used in combination with serum tumor markers for clinical staging of testicular germ cell tumors. The diagnostic imaging modalities included computerized tomography, magnetic resonance imaging, positron emission tomography and chest radiographs. MATERIALS AND METHODS: Paired reviewers independently searched PubMed, Embase® and the Cochrane Central Register of Controlled Trials from 1980 to 2018 using title-abstract and full-text screening to identify original studies of the use of computerized tomography, magnetic resonance imaging, positron emission tomography, chest radiographs and serum tumor markers for the clinical staging of early stage testicular germ cell tumors. RESULTS: We found 21 studies of a total of 1,702 patients. With significant bias and limitations to the data, the performance characteristics of computerized tomography, magnetic resonance imaging and positron emission tomography for staging of the retroperitoneum were similar, with median sensitivity ranging from 67% to 80% and median specificity ranging from 95% to 100%. Computerized tomography of the chest (median sensitivity 100%) was more sensitive than a chest radiograph (median sensitivity 76%), especially in men with nonseminomatous germ cell tumors. The addition of serum tumor markers to diagnostic imaging improved staging sensitivity from 38% to 41% to 59% to 60%. No study specifically reported on harms of the imaging modalities. CONCLUSIONS: The combination of axial imaging with computerized tomography or magnetic resonance imaging and serum tumor markers demonstrates optimal performance characteristics for staging early stage testicular germ cell tumors. There is little use for chest computerized tomography in men with seminoma, negative abdominal imaging and negative serum tumor markers.

Diagnosis and Management of Intratubular Germ Cell Neoplasia In Situ: A Systematic Review.

PURPOSE: We performed a systematic review of studies assessing the diagnosis and effectiveness of management strategies for germ cell neoplasia in situ. MATERIALS AND METHODS: Paired investigators independently searched for studies on the diagnosis and management of testicular germ cell neoplasia in situ using PubMed®, Embase® and the Cochrane Central Register of Controlled Trials from January 1, 1980 through August 2018. The reviewers then extracted data and assessed quality. RESULTS: Eighteen studies met inclusion criteria. Among patients with a testicular germ cell tumor the prevalence of contralateral germ cell neoplasia in situ was 4.0% to 8.1%. No significant difference in the risk of metachronous malignancy was identified between unscreened groups vs those with routine contralateral testicular screening (cumulative incidence 1.9% vs 3.1%, p=0.097, respectively). Patients who presented with a history of testicular atrophy, age less than 40 years or cryptorchidism had an elevated risk of germ cell neoplasia in situ. In patients with germ cell neoplasia in situ the use of 18 to 20 Gy radiation therapy demonstrated the lowest rate of disease on followup biopsies (0% to 2.5%), compared to a median of 30% on biopsies in patients treated with cisplatin based chemotherapy. Carboplatin based treatment regimens demonstrated positive disease in 66% to 75% on repeat biopsies. Rates of treatment related hypogonadism were 30.8% to 38.5% and 13% to 20% for patients treated with 18 to 20 Gy and cisplatin based chemotherapy, respectively. CONCLUSIONS: In patients with a testicular germ cell tumor the risk of having contralateral germ cell neoplasia in situ is 4% to 8%, with a greater risk in patients with testicular atrophy, cryptorchidism or age less than 40 years. The risk is high enough to support use of contralateral testicular biopsy in patients with these risk factors for germ cell neoplasia in situ. However, routine screening is not advised. Radiation therapy with 18 to 20 Gy was associated with much better eradication of germ cell neoplasia in situ than chemotherapy. Chemotherapy may eradicate germ cell neoplasia in situ in up to two-thirds of patients undergoing chemotherapy as adjuvant treatment for a primary germ cell tumor. Further research and data are needed to strengthen many aspects of the evidence base.

Computational modelling in single-cell cancer genomics: methods and future directions.

Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, proteome, and epigenome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays offer new insights into tumour heterogeneity, which underlies cancer initiation, progression, and relapse. However, the large quantities of high-dimensional, noisy data produced by single-cell assays can complicate data analysis, obscuring biological signals with technical artifacts. In this review article, we outline the major challenges in analyzing single-cell cancer genomics data and survey the current computational tools available to tackle these. We further outline unsolved problems that we consider major opportunities for future methods development to help interpret the vast quantities of data being generated.

Rethinking the need for a platelet transfusion threshold of 50 × 109 /L for lumbar puncture in cancer patients.

BACKGROUND: Lumbar puncture (LP) is a frequently performed diagnostic and therapeutic procedure in oncology patients. Transfusing to a minimum preprocedural platelet threshold of 50 × 109 /L is widely upheld without good quality evidence. The objective was to compare the outcomes of LPs performed with platelets above and below this threshold. An increased risk of adverse events in patients with lower platelet counts was not expected. As a corollary, transfusion reaction rates incurred by transfusing to this recommended threshold are also reported. METHODS: A total of 2259 LPs performed on 1137 oncology patients (adult, n = 871, and pediatric, n = 266) were retrospectively analyzed between February 2011 and December 2017. The incidence of LP-related complications for groups above and below the minimum platelet threshold was compared. Traumatic tap was defined as 500 or more red blood cells per high-power field in the cerebral spinal fluid. Groups were compared using the 2-Proportion Z-test and Fisher exact test. RESULTS: At time of LP, the total number of events with platelets less than 50 × 109 /L and 50 × 109 /L or greater were 110 and 2149, respectively. There were no significant differences in LP-associated complications between patients with platelet counts above or below 50 × 109 /L (P = .29). Patients with a pre-LP platelet count of less than 50 × 109 /L had a higher proportion of traumatic taps (P < .001). Three patients developed transfusion-related adverse events. CONCLUSION: Patients with platelet counts less than 50 × 109 /L did not have a higher incidence of clinically significant post-lumbar puncture complications (P = .29).

CuboCube: Student creation of a cancer genetics e-textbook using open-access software for social learning.

Student creation of educational materials has the capacity both to enhance learning and to decrease costs. Three successive honors-style classes of undergraduate students in a cancer genetics class worked with a new software system, CuboCube, to create an e-textbook. CuboCube is an open-source learning materials creation system designed to facilitate e-textbook development, with an ultimate goal of improving the social learning experience for students. Equipped with crowdsourcing capabilities, CuboCube provides intuitive tools for nontechnical and technical authors alike to create content together in a structured manner. The process of e-textbook development revealed both strengths and challenges of the approach, which can inform future efforts. Both the CuboCube platform and the Cancer Genetics E-textbook are freely available to the community.

Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models.

Mutation signatures in cancer genomes reflect endogenous and exogenous mutational processes, offering insights into tumour etiology, features for prognostic and biologic stratification and vulnerabilities to be exploited therapeutically. We present a novel machine learning formalism for improved signature inference, based on multi-modal correlated topic models (MMCTM) which can at once infer signatures from both single nucleotide and structural variation counts derived from cancer genome sequencing data. We exemplify the utility of our approach on two hormone driven, DNA repair deficient cancers: breast and ovary (n = 755 samples total). We show how introducing correlated structure both within and between modes of mutation can increase accuracy of signature discovery, particularly in the context of sparse data. Our study emphasizes the importance of integrating multiple mutation modes for signature discovery and patient stratification, and provides a statistical modeling framework to incorporate additional features of interest for future studies.

Antipsychotics for Treating Delirium in Hospitalized Adults: A Systematic Review.

Background: Delirium is common in hospitalized patients and is associated with worse outcomes. Antipsychotics are commonly used; however, the associated benefits and harms are unclear. Purpose: To conduct a systematic review evaluating the benefits and harms of antipsychotics to treat delirium in adults. Data Sources: PubMed, Embase, CENTRAL, CINAHL, and PsycINFO from inception to July 2019 without language restrictions. Study Selection: Randomized controlled trials (RCTs) of antipsychotic versus placebo or another antipsychotic, and prospective observational studies reporting harms. Data Extraction: One reviewer extracted data and assessed strength of evidence (SOE) for critical outcomes, with confirmation by another reviewer. Risk of bias was assessed independently by 2 reviewers. Data Synthesis: Across 16 RCTs and 10 observational studies of hospitalized adults, there was no difference in sedation status (low and moderate SOE), delirium duration, hospital length of stay (moderate SOE), or mortality between haloperidol and second-generation antipsychotics versus placebo. There was no difference in delirium severity (moderate SOE) and cognitive functioning (low SOE) for haloperidol versus second-generation antipsychotics, with insufficient or no evidence for antipsychotics versus placebo. For direct comparisons of different second-generation antipsychotics, there was no difference in mortality and insufficient or no evidence for multiple other outcomes. There was little evidence demonstrating neurologic harms associated with short-term use of antipsychotics for treating delirium in adult inpatients, but potentially harmful cardiac effects tended to occur more frequently. Limitations: Heterogeneity was present in terms of dose and administration route of antipsychotics, outcomes, and measurement instruments. There was insufficient or no evidence regarding multiple clinically important outcomes. Conclusion: Current evidence does not support routine use of haloperidol or second-generation antipsychotics to treat delirium in adult inpatients. Primary Funding Source: Agency for Healthcare Research and Quality. (PROSPERO: CRD42018109552).

Antipsychotics for Preventing Delirium in Hospitalized Adults: A Systematic Review.

Background: Delirium is an acute disorder marked by impairments in attention and cognition, caused by an underlying medical problem. Antipsychotics are used to prevent delirium, but their benefits and harms are unclear. Purpose: To conduct a systematic review evaluating the benefits and harms of antipsychotics for prevention of delirium in adults. Data Sources: PubMed, Embase, CENTRAL, CINAHL, and PsycINFO from inception through July 2019, without restrictions based on study setting, language of publication, or length of follow-up. Study Selection: Randomized, controlled trials (RCTs) that compared an antipsychotic with placebo or another antipsychotic, and prospective observational studies with a comparison group. Data Extraction: One reviewer extracted data and graded the strength of the evidence, and a second reviewer confirmed the data. Two reviewers independently assessed the risk of bias. Data Synthesis: A total of 14 RCTs were included. There were no differences in delirium incidence or duration, hospital length of stay (high strength of evidence [SOE]), and mortality between haloperidol and placebo used for delirium prevention. Little to no evidence was found to determine the effect of haloperidol on cognitive function, delirium severity (insufficient SOE), inappropriate continuation, and sedation (insufficient SOE). There is limited evidence that second-generation antipsychotics may lower delirium incidence in the postoperative setting. There is little evidence that short-term use of antipsychotics was associated with neurologic harms. In some of the trials, potentially harmful cardiac effects occurred more frequently with antipsychotic use. Limitations: There was significant heterogeneity in antipsychotic dosing, route of antipsychotic administration, assessment of outcomes, and adverse events. There were insufficient or no data available to draw conclusions for many of the outcomes. Conclusion: Current evidence does not support routine use of haloperidol or second-generation antipsychotics for prevention of delirium. There is limited evidence that second-generation antipsychotics may lower the incidence of delirium in postoperative patients, but more research is needed. Future trials should use standardized outcome measures. Primary Funding Source: Agency for Healthcare Research and Quality. (PROSPERO: CRD42018109552).