Gene Therapy Versus Common Care for Eligible Individuals With Sickle Cell Disease in the United States : A Cost-Effectiveness Analysis.

BACKGROUND: Sickle cell disease (SCD) and its complications contribute to high rates of morbidity and early mortality and high cost in the United States and African heritage community. OBJECTIVE: To evaluate the cost-effectiveness of gene therapy for SCD and its value-based prices (VBPs). DESIGN: Comparative modeling analysis across 2 independently developed simulation models (University of Washington Model for Economic Analysis of Sickle Cell Cure [UW-MEASURE] and Fred Hutchinson Institute Sickle Cell Disease Outcomes Research and Economics Model [FH-HISCORE]) using the same databases. DATA SOURCES: Centers for Medicare & Medicaid Services claims data, 2008 to 2016; published literature. TARGET POPULATION: Persons eligible for gene therapy. TIME HORIZON: Lifetime. PERSPECTIVE: U.S. health care sector and societal. INTERVENTION: Gene therapy versus common care. OUTCOME MEASURES: Incremental cost-effectiveness ratios (ICERs), equity-informed VBPs, and price acceptability curves. RESULTS OF BASE-CASE ANALYSIS: At an assumed $2 million price for gene therapy, UW-MEASURE and FH-HISCORE estimated ICERs of $193 000 per QALY and $427 000 per QALY, respectively, under the health care sector perspective. Corresponding estimates from the societal perspective were $126 000 per QALY and $281 000 per QALY. The difference in results between models stemmed primarily from considering a slightly different target population and incorporating the quality-of-life (QOL) effects of splenic sequestration, priapism, and acute chest syndrome in the UW model. From a societal perspective, acceptable (>90% confidence) VBPs ranged from $1 million to $2.5 million depending on the use of alternative effective metrics or equity-informed threshold values. RESULTS OF SENSITIVITY ANALYSIS: Results were sensitive to the costs of myeloablative conditioning before gene therapy, effect on caregiver QOL, and effect of gene therapy on long-term survival. LIMITATION: The short-term effects of gene therapy on vaso-occlusive events were extrapolated from 1 study. CONCLUSION: Gene therapy for SCD below a $2 million price tag is likely to be cost-effective when applying a societal perspective at an equity-informed threshold for cost-effectiveness analysis. PRIMARY FUNDING SOURCE: National Heart, Lung, and Blood Institute.

Long-term survival with sickle cell disease: a nationwide cohort study of Medicare and Medicaid beneficiaries.

To our knowledge, we report the first population-based period life table, the expected lifetime survival for Medicare and Medicaid beneficiaries with sickle cell disease (SCD), and the disparities in survival by insurance types in the United States. We constructed a retrospective cohort of individuals with diagnosed SCD receiving common care (any real-world patterns of care except transplant) based on nationwide Medicare and Medicaid claim data (2008-2016), covering beneficiaries in all 50 states. We analyzed lifetime survival probabilities using Kaplan-Meier curves and projected life expectancies at various ages for all, stratified by sex and insurance types. Our analysis included 94 616 individuals with SCD that have not undergone any transplant. Life expectancy at birth was 52.6 years (95% confidence interval: 51.9-53.4). Compared with the adults covered by Medicaid only, those covered by Medicare for disabilities or end-stage renal disease and those dually insured by Medicare and Medicaid had significantly worse life expectancy. Similarly, for beneficiaries aged ≥65 years, these 2 insurance types were associated with significantly shorter life expectancy than those enrolled in Medicare old age and survivor's insurance. Our study underscores the persistent life expectancy shortfall for patients with SCD, the burden of premature mortality during adulthood, and survival disparities by insurance status.

Lifetime medical costs attributable to sickle cell disease among nonelderly individuals with commercial insurance.

Sickle cell disease (SCD) is a severe monogenic disease associated with high morbidity, mortality, and a disproportionate burden on Black and Hispanic communities. Our objective was to estimate the total healthcare costs and out-of-pocket (OOP) costs attributable to SCD among commercially insured individuals over their nonelderly lifetimes (0 to 64 years of age). We constructed a retrospective cohort of individuals with diagnosed SCD using Truven Health Marketscan commercial claims data from 2007 through 2018, compared with matched control subjects from the Medical Expenditure Panel Survey. We estimated Kaplan-Meier sample average costs using previously reported survival curves for SCD and control subjects. Individuals with SCD (20 891) and control subjects (33 588) were included in our analysis. The SCD sample had a mean age of 25.7 (standard deviation, 17.4) years; 58.0% were female. Survival-adjusted costs of SCD peaked at age 13 to 24 years and declined at older ages. There was no significant difference in total medical costs or OOP costs between the sexes. SCD-attributable costs over 0 to 64 years of age were estimated to be $1.6 million (95% confidence interval [CI], $1.3M-$1.9M) and $1.7 million (95% CI, $1.4M-$2.1M) for females and males with SCD, respectively. The corresponding OOP estimates were $42 395 (95% CI, $34 756-$50 033) for females and $45 091 (95% CI, $36 491-$53 691) for males. These represent a 907% and 285% increase in total medical and OOP costs over control subjects, respectively. Although limited to the commercially insured population, these results indicate that the direct economic burden of SCD is substantial and peaks at younger ages, suggesting the need for curative and new medical therapies.

Prevalence of comorbidities associated with sickle cell disease among non-elderly individuals with commercial insurance-A retrospective cohort study.

Sickle cell disease (SCD) is a severe monogenic disease associated with high morbidity and mortality and a disproportionate burden on Black communities. Few population-based studies have examined the prevalence of comorbidities among persons with SCD. We estimated the prevalence of comorbidities experienced by individuals with SCD enrolled in employer-based health insurance plans in the US over their non-elderly lifetimes (0-64 years of age) with a retrospective cohort design using Truven Health MarketScan commercial claims data from 2007-2018. ICD-9/10 codes were used to identify individuals with SCD using a previously published algorithm. For this cohort, comorbidities associated with SCD were identified across 3 age categories (<18, 18-45, 46-64 years-old), based on the CMS Chronic Comorbidities Warehouse or SCD-specific diagnosis codes, when applicable. The total number of SCD patients available for analysis in each age category was 7,502 (<18 years), 10,183 (18-45 years) and 4,459 (46-64 years). Across all ages, vaso-occlusive pain, infections (non-specific), and fever were the most common comorbidities. Vaso-occlusive pain and infection were the most prevalent conditions for persons age <18- and 18-45-year-olds, while in the 46-54-year-old age group, infection and cardiovascular including pulmonary hypertension were most prevalent. Compared to persons <18 years old, the prevalence of vaso-occlusive pain, fever, and acute chest syndrome claims declined in older populations. The comorbidity burden of SCD is significant across all age groups. SCD patients experience comorbidities of age such as chronic pain, cardio-vascular conditions including pulmonary hypertension and renal disease at far higher rates than the general population. Novel disease modifying therapies in development have the potential to significantly reduce the comorbidity burden of SCD.

Bond-specific fragmentation of oligopeptides via electronic stopping of swift heavy ions in molecular films.

Highly bond-specific fragmentation of oligopeptides induced by swift heavy ion (SHI) irradiation was investigated by means of mass spectrometry. In pronounced contrast to measurements of samples irradiated with keV ions, oligopeptides which were exposed to 946 MeV Au ions show a high abundance of specific fragments. The highly bond-specific nature of SHI-induced fragmentation is attributed to electronic stopping as the most relevant energy loss mechanism for SHI in the oligopeptide samples in combination with the subsequent coupling between the excited electronic and the atomic subsystem. Fragmentation induced by SHI is observed to be further influenced by the structure of the oligopeptides, suggesting that electronic excitation and/or the electronic-vibrational coupling depend on the details of the molecular structure.

Barriers to hydroxyurea use from the perspectives of providers, individuals with sickle cell disease, and families: Report from a U.S. regional collaborative.

Sickle cell disease (SCD) is an inherited blood disorder that affects about 100,000 people in the U.S., primarily Blacks/African-Americans. A multitude of complications negatively impacts quality of life. Hydroxyurea has been FDA approved since 1998 as a disease-modifying therapy for SCD, but is underutilized. Negative and uninformed perceptions of hydroxyurea and barriers to its use hinder adherence and promotion of the medication. As the largest real-world study to date that assessed hydroxyurea use for children and adults with SCD, we gathered and analyzed perspectives of providers, individuals with SCD, and families. Participants provided information about socio-demographics, hospital and emergency admissions for pain, number of severe pain episodes interfering with daily activities, medication adherence, and barriers to hydroxyurea. Providers reported on indications for hydroxyurea, reasons not prescribed, and current laboratory values. We found that hydroxyurea use was reported in over half of eligible patients from this large geographic region in the U.S., representing a range of sickle cell specialty clinical settings and practices. Provider and patient/caregiver reports about hydroxyurea use were consistent with one another; adults 26 years and older were least likely to be on hydroxyurea; and the likelihood of being on hydroxyurea decreased with one or more barriers. Using the intentional and unintentional medication nonadherence framework, we found that, even for patients on hydroxyurea, challenges to taking the medicine at the right time and forgetting were crucial unintentional barriers to adherence. Intentional barriers such as worry about side effects and "tried and it did not work" were important barriers for young adults and adults. For providers, diagnoses other than HgbSS or HgbS-ß0 thalassemia were associated with lower odds of prescribing, consistent with evidence-based guidelines. Our results support strengthening provider understanding and confidence in implementing existing SCD guidelines, and the importance of shared decision making. Our findings can assist providers in understanding choices and decisions of families; guide individualized clinical discussions regarding hydroxyurea therapy; and help with developing tailored interventions to address barriers. Addressing barriers to hydroxyurea use can inform strategies to minimize similar barriers in the use of emerging and combination therapies for SCD.

Simulating the restoration of normal gene expression from different thyroid cancer stages using deep learning.

BACKGROUND: Thyroid cancer (THCA) is the most common endocrine malignancy and incidence is increasing. There is an urgent need to better understand the molecular differences between THCA tumors at different pathologic stages so appropriate diagnostic, prognostic, and treatment strategies can be applied. Transcriptome State Perturbation Generator (TSPG) is a tool created to identify the changes in gene expression necessary to transform the transcriptional state of a source sample to mimic that of a target. METHODS: We used TSPG to perturb the bulk RNA expression data from various THCA tumor samples at progressive stages towards the transcriptional pattern of normal thyroid tissue. The perturbations produced were analyzed to determine if there are consistently up- or down-regulated genes or functions in certain stages of tumors. RESULTS: Some genes of particular interest were investigated further in previous research. SLC6A15 was found to be down-regulated in all stage 1-3 samples. This gene has previously been identified as a tumor suppressor. The up-regulation of PLA2G12B in all samples was notable because the protein encoded by this gene belongs to the PLA2 superfamily, which is involved in metabolism, a major function of the thyroid gland. REN was up-regulated in all stage 3 and 4 samples. The enzyme renin encoded by this gene, has a role in the renin-angiotensin system; this system regulates angiogenesis and may have a role in cancer development and progression. This is supported by the consistent up-regulation of REN only in later stage tumor samples. Functional enrichment analysis showed that olfactory receptor activities and similar terms were enriched for the up-regulated genes which supports previous research concluding that abundance and stimulation of olfactory receptors is linked to cancer. CONCLUSIONS: TSPG can be a useful tool in exploring large gene expression datasets and extracting the meaningful differences between distinct classes of data. We identified genes that were characteristically perturbed in certain sample types, including only late-stage THCA tumors. Additionally, we provided evidence for potential transcriptional signatures of each stage of thyroid cancer. These are potentially relevant targets for future investigation into THCA tumorigenesis.

Application of validated mapping algorithms between generic PedsQL scores and utility values to individuals with sickle cell disease.

PURPOSE: There is a paucity of empirically estimated health state utility (HSU) values to estimate health-related quality of life among individuals with sickle cell disease (SCD). This study aims to map the Pediatric Quality of Life Inventory generic core scales (PedsQL GCS) to HSUs for children and adolescents with SCD in the United States, using published algorithms, and to assess the construct validity of these HSUs against SCD-specific PedsQL scores. METHODS: We used the published mapping algorithms identified in four published articles, in which the PedsQL GCS was mapped to either the EuroQol-5 Dimension 3-Level, Youth Version or the Child Health Utility 9-Dimension to obtain HSUs. We employed the algorithms to calculate HSUs for a sample of children and adolescents from the Sickle Cell Clinical Research and Intervention Program. To assess the construct validity of the mapped HSUs in SCD patients, we computed Spearman's correlation coefficient comparing the HSUs with the PedsQL SCD total score and separately with each PedsQL SCD dimension-specific score. RESULTS: The mean mapped HSU across published algorithms was 0.792 (95% CI: 0.782-0.801). It was significantly higher among children aged 5-12 years than children aged 13-17 years. The Spearman's correlation coefficient for HSUs versus PedsQL SCD total scores was 0.64 (95% CI: 0.57-0.71). Correlations ranged from 0.40 (95% CI: 0.32-0.48) to 0.60 (95% CI: 0.54-0.66) for HSUs versus PedsQL SCD dimension-specific scores. CONCLUSIONS: The existing mapping algorithms show acceptable construct validity in children and adolescents with SCD. Additional algorithms are needed for adults and for specific SCD comorbidities.

GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure.

BACKGROUND: Quantification of gene expression from RNA-seq data is a prerequisite for transcriptome analysis such as differential gene expression analysis and gene co-expression network construction. Individual RNA-seq experiments are larger and combining multiple experiments from sequence repositories can result in datasets with thousands of samples. Processing hundreds to thousands of RNA-seq data can result in challenges related to data management, access to sufficient computational resources, navigation of high-performance computing (HPC) systems, installation of required software dependencies, and reproducibility. Processing of larger and deeper RNA-seq experiments will become more common as sequencing technology matures. RESULTS: GEMmaker, is a nf-core compliant, Nextflow workflow, that quantifies gene expression from small to massive RNA-seq datasets. GEMmaker ensures results are highly reproducible through the use of versioned containerized software that can be executed on a single workstation, institutional compute cluster, Kubernetes platform or the cloud. GEMmaker supports popular alignment and quantification tools providing results in raw and normalized formats. GEMmaker is unique in that it can scale to process thousands of local or remote stored samples without exceeding available data storage. CONCLUSIONS: Workflows that quantify gene expression are not new, and many already address issues of portability, reusability, and scale in terms of access to CPUs. GEMmaker provides these benefits and adds the ability to scale despite low data storage infrastructure. This allows users to process hundreds to thousands of RNA-seq samples even when data storage resources are limited. GEMmaker is freely available and fully documented with step-by-step setup and execution instructions.

Development of a conceptual model for evaluating new non-curative and curative therapies for sickle cell disease.

BACKGROUND: Sickle cell disease (SCD) is a clinically heterogeneous disease with many acute and chronic complications driven by ongoing vaso-occlusion and hemolysis. It causes a disproportionate burden on Black and Hispanic communities. Our objective was to follow the SMDM/ISPOR Task Force recommendations for good practices and create a conceptual model of the progression of SCD under current clinical practice to inform cost-effectiveness analyses (CEA) of promising curative therapies in the pipeline over a lifetime horizon. METHODS: We used consultations with experts, providers, and patients to identify acute events and chronic conditions in the conceptual model. We compared our model structure to previous CEA models of interventions for SCD, assessed the prevalence of the identified disease attributes in Medicaid and Medicare claims databases, and identified relevant outcomes following the 2nd Panel in CEA. We determined an appropriate modeling technique and relevant data sources for parameterizing the model. RESULTS: The conceptual model structure included four dimensions of disease: chronic pain, acute events, chronic conditions, and treatment complications, spanning 26 disease attributes with significant impacts on health-related quality of life and resource. We modeled chronic pain separately to reflect its importance to patients and interaction with all other disease attributes. We identified additional data sources for health state utilities and non-medical costs and benefits of SCD. We will use a microsimulation model with age- and sex-specific transitions between health states predicted by patient demographic characteristics and disease history. CONCLUSION: Developing the model structure through an explicit process of model conceptualization can increase the transparency and accuracy of results. We will populate the conceptual model with the data sources described and evaluate the cost-effectiveness of curative therapies.

Medical and Non-medical Costs of Sickle Cell Disease and Treatments from a US Perspective: A Systematic Review and Landscape Analysis.

BACKGROUND: Sickle cell disease (SCD) is a complex genetic disorder that manifests in infancy and progresses throughout life in the form of acute and chronic complications. As the upfront costs of potentially curative, genetic therapies will likely be high, an assessment and comprehensive characterization of the medical and non-medical cost burden will inform future decision making. OBJECTIVE: We sought to systematically summarize the existing literature surrounding SCD medical and non-medical costs. METHODS: We searched MEDLINE and EMBASE (2008-2020) and identified US-based studies that detailed medical or non-medical costs. Eligible studies provided empirical estimates about any aspect of cost or SCD individuals of all ages and their caregivers. Study quality was assessed using the Newcastle-Ottawa Scale, and costs were adjusted to 2019 US$. RESULTS: Search queries returned 479 studies, with 342 from medical burden searches and 137 from non-medical burden searches, respectively. Herein, we report the results of the 40 studies that contained relevant cost information: 39 detailed medical costs and 1 detailed non-medical costs. Costs were higher for SCD patients when compared with non-SCD individuals (cost difference range: $6636-$63,436 annually). The highest medical cost component for SCD patients was inpatient ($11,978-$59,851 annually), followed by outpatient and then pharmacy. No studies characterized the cost burden throughout the lifetime disease trajectory of an SCD individual, and no studies captured caregiver or productivity costs. CONCLUSION: Our results reveal an incomplete characterization of medical and non-medical costs within SCD. A deeper understanding of the medical and non-medical cost burden requires completion of additional studies that capture the burden across the patient's lifetime, in addition to expression of the impact of existing and emergent health technologies on disease trajectory.

A landscape analysis and discussion of value of gene therapies for sickle cell disease.

INTRODUCTION: Sickle cell disease (SCD) is a rare genetic disease with limited therapeutic options. Gene-based therapies are being investigated in clinical trials to evaluate their curative potential. The expected life-long benefits of one-time administration of genetically corrected stem cells present uncharted challenges in estimating value of these treatments. Our objective is to conduct a landscape analysis of clinical trials and prompt a discussion estimating the value of gene therapy as a therapeutic option for SCD. AREAS COVERED: We searched Clinicaltrials.gov to identify and characterize clinical trials in gene therapies for SCD. We report available results and discuss current concerns and elements of value necessary to consider as these products come to market. EXPERT OPINION: Gene therapies could represent a major advance in SCD treatment. Although clinical trials are ongoing, reports of serious adverse events have led to pause of these trials, emphasizing the need to prove long-term tolerability. Measured using the methods of health economic evaluation, we anticipate high up-front costs may be offset by potential life-long benefits of these treatments. During development and after treatment approval, attention should be focused on ensuring adequate availability and equitable access to emerging therapies in underserved areas and low-middle-income countries (LMIC).

A Meta-analysis of Combined Aspiration Catheter and Stent Retriever versus Stent Retriever Alone for Large-Vessel Occlusion Ischemic Stroke.

BACKGROUND: The efficacy of combined aspiration catheter and stent retriever compared with stent retriever alone for the treatment of large-vessel occlusion acute ischemic stroke is unclear. PURPOSE: Our aim was to conduct a systematic literature review and meta-analysis on several metrics of efficacy comparing aspiration catheter and stent retriever with stent retriever alone. DATA SOURCES: MEDLINE and the Cochrane Library Databases were searched. Randomized controlled trials and case-control and cohort studies were included. STUDY SELECTION: Ten comparative studies were included detailing a combined 1495 patients with aspiration catheter and stent retriever and 1864 with stent retrievers alone. DATA ANALYSIS: Data on first pass effect (TICI 2b/2c/3 after first pass), final successful reperfusion (modified TICI ≥2b), and 90-day functional independence (mRS ≤ 2) were collected. Meta-analysis was performed using a random-effects model. DATA SYNTHESIS: There was a pooled composite first pass effect of 40.8% (611/1495) versus 32.6% (608/1864) for aspiration catheter and stent retriever and stent retriever alone, respectively (P < .0001). Similarly, on a meta-analysis, aspiration catheter and stent retriever were associated with a higher first pass effect compared with stent retriever alone (OR = 1.63; 95% CI, 1.20-2.21; P = .002; I2 = 72%). There was no significant difference in composite rates of successful reperfusion between aspiration catheter and stent retriever (72.8%, 867/1190) and stent retriever alone (70.8%, 931/1314) (P = .27) or on meta-analysis (OR = 1.31; CI, 0.81-2.12; P = .27; I2 = 82%). No difference was found between aspiration catheter and stent retriever and stent retriever alone on 90-day functional independence (OR = 1.02; 95% CI, 0.77-1.36; P = .88; I2 = 40%). LIMITATIONS: This study is limited by high interstudy heterogeneity. CONCLUSIONS: On meta-analysis, aspiration catheter and stent retriever are associated with a superior first pass effect compared with stent retriever alone, but they are not associated with statistically different final reperfusion or functional independence.

Health State Utilities for Sickle Cell Disease: A Catalog Prepared From a Systematic Review.

OBJECTIVES: Sickle cell disease (SCD) is a complex, chronic condition that impairs health-related quality of life of affected individuals and their caregivers. As curative therapies emerge, comprehensive cost-effectiveness models will inform their value. These models will require descriptions of health states and their corresponding utility values that accurately reflect health-related quality of life over the disease trajectory. The objectives of this systematic review were to develop a catalog of health state utility (HSU) values for SCD, identify research gaps, and provide future directions for preference elicitation. METHODS: Records were identified through searches of PubMed and Embase, Tufts Medical Center Cost-Effectiveness Analysis Registry, reference lists of relevant articles, and consultation with SCD experts (2008-2020). We removed duplicate records and excluded ineligible studies. For included studies, we summarized the study characteristics, methods used for eliciting HSUs, and HSU values. RESULTS: Five studies empirically elicited utilities using indirect methods (EQ-5D) (n = 3) and Short Form-6 Dimension (n = 2); these represent health states associated with general SCD (n = 1), SCD complications (n = 2), and SCD treatments (n = 3). Additionally, we extracted HSUs from 7 quality-adjusted life-years-based outcome research studies. The HSU among patients with general SCD without specifying complications ranged from 0.64 to 0.887. Only 36% of the HSUs used in the quality-adjusted life-year-based outcomes research studies were derived from individuals with SCD. No study estimated HSUs in caregivers. CONCLUSIONS: There is a dearth of literature of HSUs for use in SCD models. Future empirical studies should elicit a comprehensive set of HSUs from individuals with SCD and their caregivers.

Coral reef fishes reveal strong divergence in the prevalence of traits along the global diversity gradient.

Coral reefs are experiencing declines due to climate change and local human impacts. While at a local scale these impacts induce biodiversity loss and shifts in community structure, previous biogeographical analyses recorded consistent taxonomic structure of fish communities across global coral reefs. This suggests that regional communities represent a random subset of the global species and traits pool, whatever their species richness. Using distributional data on 3586 fish species and latest advances in species distribution models, we show marked gradients in the prevalence of size classes and diet categories across the biodiversity gradient. This divergence in trait structure is best explained by reef isolation during past unfavourable climatic conditions, with large and piscivore fishes better represented in isolated areas. These results suggest the risk of a global community re-organization if the ongoing climate-induced reef fragmentation is not halted.

The Use of Cost-Effectiveness Analysis in Sickle Cell Disease: A Critical Review of the Literature.

Novel interventions for sickle cell disease (SCD) bring hope to patients, yet concern about the associated economic costs exists. Cost-effectiveness analysis (CEA) uses standardized methods, with robust underpinnings in health economics, to estimate the value of these interventions compared with usual care. However, because of the complexity and lifetime trajectory of SCD, CEAs are challenging to conduct. The objectives of this rapid review were to summarize the main characteristics, components, and results of published CEAs of existing interventions for SCD, identify research gaps, and provide directions for future analyses. We identified records through searches of bibliographic databases, from reference lists of relevant review articles, and through consultation with experts. A total of 13 CEAs met our inclusion criteria and were qualitatively synthesized. These evaluated blood transfusions (n = 2), hematopoietic stem cell transplantation (n = 1), pharmaceuticals (n = 2), hypothetical cell or genetic therapy (n = 1), screening programs (n = 4), and interventions for SCD treatment complications (n = 3). A limited number of potential SCD and treatment complications were evaluated. No study adopted a societal perspective in the base case, six studies examined lifetime cost-effectiveness, seven studies employed a Markov or discrete-event simulation model, and eight studies used an outcome metric that captured both quality and length of life. To better compare the value of emerging and current therapies, future CEAs should adopt a societal perspective incorporating both medical and nonmedical costs, comprehensively model SCD complexity using robust health economic simulation models over the patient's entire lifespan, and capture the intervention's effect on both survival and quality of life.

Tissue context determines the penetrance of regulatory DNA variation.

Functional assessment of disease-associated sequence variation at non-coding regulatory elements is complicated by their high degree of context sensitivity to both the local chromatin and nuclear environments. Allelic profiling of DNA accessibility across individuals has shown that only a select minority of sequence variation affects transcription factor (TF) occupancy, yet low sequence diversity in human populations means that no experimental assessment is available for the majority of disease-associated variants. Here we describe high-resolution in vivo maps of allelic DNA accessibility in liver, kidney, lung and B cells from 5 increasingly diverged strains of F1 hybrid mice. The high density of heterozygous sites in these hybrids enables precise quantification of effect size and cell-type specificity for hundreds of thousands of variants throughout the mouse genome. We show that chromatin-altering variants delineate characteristic sensitivity profiles for hundreds of TF motifs. We develop a compendium of TF-specific sensitivity profiles accounting for genomic context effects. Finally, we link maps of allelic accessibility to allelic transcript levels in the same samples. This work provides a foundation for quantitative prediction of cell-type specific effects of non-coding variation on TF activity, which will facilitate both fine-mapping and systems-level analyses of common disease-associated variation in human genomes.

Enhancers predominantly regulate gene expression during differentiation via transcription initiation.

Gene transcription occurs via a cycle of linked events, including initiation, promoter-proximal pausing, and elongation of RNA polymerase II (Pol II). A key question is how transcriptional enhancers influence these events to control gene expression. Here, we present an approach that evaluates the level and change in promoter-proximal transcription (initiation and pausing) in the context of differential gene expression, genome-wide. This combinatorial approach shows that in primary cells, control of gene expression during differentiation is achieved predominantly via changes in transcription initiation rather than via release of Pol II pausing. Using genetically engineered mouse models, deleted for functionally validated enhancers of the α- and ß-globin loci, we confirm that these elements regulate Pol II recruitment and/or initiation to modulate gene expression. Together, our data show that gene expression during differentiation is regulated predominantly at the level of initiation and that enhancers are key effectors of this process.

Improving Preventive Care for Children With Sickle Cell Anemia: A Quality Improvement Initiative.

Sickle cell disease is a complex chronic disorder associated with increased morbidity and early mortality. The Pediatric Quality Measures Program has developed new sickle cell-specific quality measures focused on hydroxyurea (HU) counseling and annual transcranial Doppler (TCD) screening; however, these measures have not been used in a clinical setting to inform quality improvement (QI) efforts. METHODS: From 2017 to 2018, 9 sickle cell subspecialty clinics from the Pacific Sickle Cell Regional Collaborative conducted a year-long QI collaborative focused on improving the percentage of patients with HU counseling and TCD screening based on the new quality measures. After an initial kick-off meeting, the 9 sites participated in monthly conference calls. We used run charts annotated with plan-do-study-act cycle activities to track each site's monthly progress and the overall mean percentage for the entire collaborative. RESULTS: There was an overall improvement in the aggregate HU counseling from 85% to 98% (P < 0.01). For TCD screening, referral frequency changed from 85% to 90% (P = 0.76). For both measures, the variation in frequencies decreased over the year. CONCLUSION: Over 1 year, we found that a regional QI collaborative increased HU counseling. Although referral for TCD screening increased, there was no overall change in TCD completion. Overall, this QI report's findings can help clinicians adopt and implement these quality measures to improve outcomes in children.