Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models.

Alignment is the cornerstone of many long-read pipelines and plays an essential role in resolving structural variants (SVs). However, forced alignments of SVs embedded in long reads, inflexibility of integrating novel SVs models and computational inefficiency remain problems. Here, we investigate the feasibility of resolving long-read SVs with alignment-free algorithms. We ask: (1) Is it possible to resolve long-read SVs with alignment-free approaches? and (2) Does it provide an advantage over existing approaches? To this end, we implemented the framework named Linear, which can flexibly integrate alignment-free algorithms such as the generative model for long-read SV detection. Furthermore, Linear addresses the problem of compatibility of alignment-free approaches with existing software. It takes as input long reads and outputs standardized results existing software can directly process. We conducted large-scale assessments in this work and the results show that the sensitivity, and flexibility of Linear outperform alignment-based pipelines. Moreover, the computational efficiency is orders of magnitude faster.

Bringing Generalists to Global Health: a Missed Opportunity and Call to Action.

The credo of the generalist physician has always been the promotion of health for all, in every aspect: not just multiple vulnerable organ systems, but multiple social, cultural, and political factors that contribute to poor health and exacerbate health inequity. In recent years, the field of global health has also adopted this same mission: working across both national and clinical specialty borders to improve health for all and end health disparities worldwide. Yet within the Society for General Internal Medicine, and among American generalists, engagement in global health, both within and outside the USA, remains uncommon. We see this gap as an opportunity, because in fact generalists in America already have the skills and experience that global health badly needs. SGIM could promote generalists to global health's vanguard, with three core steps. First, we generalists must continue to integrate health for the vulnerable into our domestic work, generating care models applicable in low-resource settings around the globe. Conversely, we must also engage with and implement international ideas and solutions for universal access to primary care for vulnerable patients in the USA. And lastly, we must build platforms to connect ourselves with colleagues worldwide to exchange these learnings.

Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis.

OBJECTIVE: Chronic pancreatitis (CP) is a potentially fatal disease of the exocrine pancreas, with no specific or effective approved therapies. Due to difficulty in accessing pancreas tissues, little is known about local immune responses or pathogenesis in human CP. We sought to characterise pancreatic immune responses using tissues derived from patients with different aetiologies of CP and non-CP organ donors in order to identify key signalling molecules associated with human CP. DESIGN: We performed single-cell level cellular indexing of transcriptomes and epitopes by sequencing and T-cell receptor (TCR) sequencing of pancreatic immune cells isolated from organ donors, hereditary and idiopathic patients with CP who underwent total pancreatectomy. We validated gene expression data by performing flow cytometry and functional assays in a second patient with CP cohort. RESULTS: Deep single-cell sequencing revealed distinct immune characteristics and significantly enriched CCR6+ CD4+ T cells in hereditary compared with idiopathic CP. In hereditary CP, a reduction in T-cell clonality was observed due to the increased CD4+ T (Th) cells that replaced tissue-resident CD8+ T cells. Shared TCR clonotype analysis among T-cell lineages also unveiled unique interactions between CCR6+ Th and Th1 subsets, and TCR clustering analysis showed unique common antigen binding motifs in hereditary CP. In addition, we observed a significant upregulation of the CCR6 ligand (CCL20) expression among monocytes in hereditary CP as compared with those in idiopathic CP. The functional significance of CCR6 expression in CD4+ T cells was confirmed by flow cytometry and chemotaxis assay. CONCLUSION: Single-cell sequencing with pancreatic immune cells in human CP highlights pancreas-specific immune crosstalk through the CCR6-CCL20 axis, a signalling pathway that might be leveraged as a potential future target in human hereditary CP.

SVIM-asm: structural variant detection from haploid and diploid genome assemblies.

MOTIVATION: With the availability of new sequencing technologies, the generation of haplotype-resolved genome assemblies up to chromosome scale has become feasible. These assemblies capture the complete genetic information of both parental haplotypes, increase structural variant (SV) calling sensitivity and enable direct genotyping and phasing of SVs. Yet, existing SV callers are designed for haploid genome assemblies only, do not support genotyping or detect only a limited set of SV classes. RESULTS: We introduce our method SVIM-asm for the detection and genotyping of six common classes of SVs from haploid and diploid genome assemblies. Compared against the only other existing SV caller for diploid assemblies, DipCall, SVIM-asm detects more SV classes and reached higher F1 scores for the detection of insertions and deletions on two recently published assemblies of the HG002 individual. AVAILABILITY AND IMPLEMENTATION: SVIM-asm has been implemented in Python and can be easily installed via bioconda. Its source code is available at github.com/eldariont/svim-asm. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Ranbow: A fast and accurate method for polyploid haplotype reconstruction.

Reconstructing haplotypes from sequencing data is one of the major challenges in genetics. Haplotypes play a crucial role in many analyses, including genome-wide association studies and population genetics. Haplotype reconstruction becomes more difficult for higher numbers of homologous chromosomes, as it is often the case for polyploid plants. This complexity is compounded further by higher heterozygosity, which denotes the frequent presence of variants between haplotypes. We have designed Ranbow, a new tool for haplotype reconstruction of polyploid genome from short read sequencing data. Ranbow integrates all types of small variants in bi- and multi-allelic sites to reconstruct haplotypes. To evaluate Ranbow and currently available competing methods on real data, we have created and released a real gold standard dataset from sweet potato sequencing data. Our evaluations on real and simulated data clearly show Ranbow's superior performance in terms of accuracy, haplotype length, memory usage, and running time. Specifically, Ranbow is one order of magnitude faster than the next best method. The efficiency and accuracy of Ranbow makes whole genome haplotype reconstruction of complex genome with higher ploidy feasible.

SVIM: structural variant identification using mapped long reads.

MOTIVATION: Structural variants are defined as genomic variants larger than 50 bp. They have been shown to affect more bases in any given genome than single-nucleotide polymorphisms or small insertions and deletions. Additionally, they have great impact on human phenotype and diversity and have been linked to numerous diseases. Due to their size and association with repeats, they are difficult to detect by shotgun sequencing, especially when based on short reads. Long read, single-molecule sequencing technologies like those offered by Pacific Biosciences or Oxford Nanopore Technologies produce reads with a length of several thousand base pairs. Despite the higher error rate and sequencing cost, long-read sequencing offers many advantages for the detection of structural variants. Yet, available software tools still do not fully exploit the possibilities. RESULTS: We present SVIM, a tool for the sensitive detection and precise characterization of structural variants from long-read data. SVIM consists of three components for the collection, clustering and combination of structural variant signatures from read alignments. It discriminates five different variant classes including similar types, such as tandem and interspersed duplications and novel element insertions. SVIM is unique in its capability of extracting both the genomic origin and destination of duplications. It compares favorably with existing tools in evaluations on simulated data and real datasets from Pacific Biosciences and Nanopore sequencing machines. AVAILABILITY AND IMPLEMENTATION: The source code and executables of SVIM are available on Github: github.com/eldariont/svim. SVIM has been implemented in Python 3 and published on bioconda and the Python Package Index. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Combination of pancreas volume and HbA1c level predicts islet yield in patients undergoing total pancreatectomy and islet autotransplantation.

Islet yield is an important predictor of acceptable glucose control after total pancreatectomy with islet autotransplantation (TP-IAT). We assessed if pancreas volume calculated with preoperative MRI could assess islet yield and postoperative outcomes. We reviewed dynamic MRI studies from 154 adult TP-IAT patients (2009-2016), and associations between calculated volumes and digest islet equivalents (IEQs) were tested. In multivariate regression analysis, pancreas volume (P < .001) and preoperative HbA1c levels (P = .009) were independently associated with digest IEQs. The IEQ prediction formula was calculated according to each preoperative HbA1c level, (a) pancreas volume × 5800 for HbA1c ≥ 6.5, (b) pancreas volume × 10 000 for HbA1c ≥5.7/<6.5 and (iii) pancreas volume × 11 400 for HbA1c < 5.7. The formula was internally validated with 28 TP-IAT patients between 2017 and 2018 (r2  = .657 and r2  = .710 when restricted to 24 patients without prior pancreatectomy). An estimated IEQs/Body Weight (kg) ≥3700 predicted HbA1c ≤6.5 and insulin independence at 1 year after TP-IAT with 77% and 88% sensitivity and 55% and 43% specificity, respectively. The combination of pancreas volume and preoperative HbA1c levels may be useful to estimate islet yield. Estimated IEQs were reasonably sensitive to predict acceptable glucose control at 1 year.

Adapting a nurse-led primary care initiative to cardiovascular disease control in Ghana: a qualitative study.

BACKGROUND: Cardiovascular Disease (CVD) is a growing cause of morbidity and mortality in Ghana, where rural primary health care is provided mainly by the Community-based Health Planning and Services (CHPS) initiative. CHPS locates nurses in community-level clinics for basic curative and preventive health services and provides home and outreach services. But CHPS currently lacks capacity to screen for or treat CVD and its risk factors. METHODS: In two rural districts, we conducted in-depth interviews with 21 nurses and 10 nurse supervisors to identify factors constraining or facilitating CVD screening and treatment. Audio recordings were transcribed, coded for content, and analyzed for key themes. RESULTS: Respondents emphasized three themes: community demand for CVD care; community access to CVD care; and provider capacity to render CVD care. Nurses and supervisors noted that community members were often unaware of CVD, despite high reported prevalence of risk factors. Community members were unable to travel for care or afford treatment once diagnosed. Nurses lacked relevant training and medications for treating conditions such as hypertension. Respondents recognized the importance of CVD care, expressed interest in acquiring further training, and emphasized the need to improve ancillary support for primary care operations. CONCLUSIONS: CHPS staff expressed multiple constraints to CVD care, but also cited actions to address them: CVD-focused training, provision of essential equipment and pharmaceuticals, community education campaigns, and referral and outreach transportation equipment. Results attest to the need for trial of these interventions to assess their impact on CVD risk factors such as hypertension, depression, and alcohol abuse.

Exploring patient experiences with and attitudes towards hypertension at a private hospital in Uganda: a qualitative study.

BACKGROUND: Hypertension is the leading risk factor for mortality worldwide and is more common in sub-Saharan Africa than any other region. Work to date confirms that a lack of human and material resources for healthcare access contributes to this gap. The ways in which patients' knowledge and attitudes toward hypertension determine their engagement with and adherence to available care, however, remains unclear. METHODS: We conducted an exploratory, qualitative descriptive study to assess awareness, knowledge, and attitudes towards hypertension and its management at a large private hospital in Kampala. We interviewed 64 participants (29 with hypertension and 34 without, 1 excluded) in English. General thematic analysis using the Integrated Conceptual Health Literacy Model was used to iteratively generate themes and categories. RESULTS: We identified three main themes: Timing of Hypertension Diagnosis, Aiming for Health Literacy, and the Influence of Knowledge on Behavior. Most participants with hypertension learned of their condition incidentally, speaking to the lack of awareness of hypertension as an asymptomatic condition. Drove nearly all participants to desire more information. However, many struggled to translate knowledge into self-management behaviors due to incomplete information and conflicting desires of participants regarding lifestyle and treatment. CONCLUSIONS: Internal patient factors had a substantial impact on adherence, calling attention to the need for educational interventions. Systemic barriers such as cost still existed even for those with insurance and need to be recognized by treating providers.

ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data.

RNA-binding proteins (RBPs) play an important role in RNA post-transcriptional regulation and recognize target RNAs via sequence-structure motifs. The extent to which RNA structure influences protein binding in the presence or absence of a sequence motif is still poorly understood. Existing RNA motif finders either take the structure of the RNA only partially into account, or employ models which are not directly interpretable as sequence-structure motifs. We developed ssHMM, an RNA motif finder based on a hidden Markov model (HMM) and Gibbs sampling which fully captures the relationship between RNA sequence and secondary structure preference of a given RBP. Compared to previous methods which output separate logos for sequence and structure, it directly produces a combined sequence-structure motif when trained on a large set of sequences. ssHMM's model is visualized intuitively as a graph and facilitates biological interpretation. ssHMM can be used to find novel bona fide sequence-structure motifs of uncharacterized RBPs, such as the one presented here for the YY1 protein. ssHMM reaches a high motif recovery rate on synthetic data, it recovers known RBP motifs from CLIP-Seq data, and scales linearly on the input size, being considerably faster than MEMERIS and RNAcontext on large datasets while being on par with GraphProt. It is freely available on Github and as a Docker image.

Evaluating the Impact and Cost-Effectiveness of Statin Use Guidelines for Primary Prevention of Coronary Heart Disease and Stroke.

BACKGROUND: Statins are effective in the primary prevention of atherosclerotic cardiovascular disease. The 2013 American College of Cardiology/American Heart Association (ACC/AHA) guideline expands recommended statin use, but its cost-effectiveness has not been compared with other guidelines. METHODS: We used the Cardiovascular Disease Policy Model to estimate the cost-effectiveness of the ACC/AHA guideline relative to current use, Adult Treatment Panel III guidelines, and universal statin use in all men 45 to 74 years of age and women 55 to 74 years of age over a 10-year horizon from 2016 to 2025. Sensitivity analyses varied costs, risks, and benefits. Main outcomes were incremental cost-effectiveness ratios and numbers needed to treat for 10 years per quality-adjusted life-year gained. RESULTS: Each approach produces substantial benefits and net cost savings relative to the status quo. Full adherence to the Adult Treatment Panel III guideline would result in 8.8 million more statin users than the status quo, at a number needed to treat for 10 years per quality-adjusted life-year gained of 35. The ACC/AHA guideline would potentially result in up to 12.3 million more statin users than the Adult Treatment Panel III guideline, with a marginal number needed to treat for 10 years per quality-adjusted life-year gained of 68. Moderate-intensity statin use in all men 45 to 74 years of age and women 55 to 74 years of age would result in 28.9 million more statin users than the ACC/AHA guideline, with a marginal number needed to treat for 10 years per quality-adjusted life-year gained of 108. In all cases, benefits would be greater in men than women. Results vary moderately with different risk thresholds for instituting statins and statin toxicity estimates but depend greatly on the disutility caused by daily medication use (pill burden). CONCLUSIONS: At a population level, the ACC/AHA guideline for expanded statin use for primary prevention is projected to treat more people, to save more lives, and to cost less compared with Adult Treatment Panel III in both men and women. Whether individuals benefit from long-term statin use for primary prevention depends more on the disutility associated with pill burden than their degree of cardiovascular risk.

Comparing Strategies for Lipid Lowering in Argentina: An Analysis from the CVD Policy Model-Argentina.

INTRODUCTION: In Argentina, the national guidelines for lipid control emphasize the use of relatively inexpensive low- or moderate-potency statins by patients at high risk (>20 %) of a cardiovascular event. The objective of this study was to compare the impact and costs of the current national CVD prevention guidelines with regard to morbidity and mortality in Argentina with the impact and costs of three strategies that incorporate high-potency statins. METHODS: We used the CVD Policy Model-Argentina to model the proposed interventions. This model is a national-scale, state-transition (Markov) computer simulation model of the CVD incidence, prevalence, mortality, and costs in adults 35-84 years of age. We modeled three scenarios: scenario 1 lowers the risk threshold for treatment to >10 % according the Framingham Risk Score (FRS); scenario 2 intensifies statin potency under current treatment thresholds; and scenario 3 combines both scenarios by lowering the treatment threshold to ≥10 % FRS and intensifying statin potency. RESULTS: Scenario 1 would translate into 1400 fewer MIs and 500 fewer CHD deaths every year, a 3 % and 2 % reduction, respectively. Scenario 2 would lead to 2000 fewer MIs and 1000 fewer CHD deaths every year. Scenario 3 would result in the greatest reduction in MIs and CHD deaths, with 3400 fewer MIs and 1400 fewer CHD deaths every year, which translates to a 7 % and 6 % reduction, respectively. All scenarios were cost-effective if the cost of a high-potency statin pill was under US$0.25. CONCLUSION: Incorporating those individuals with greater than 10 % cardiovascular risk and the use of high-potency statins into Argentina's national lipid guidelines could result in fewer CHD deaths and events at a reasonable cost.

Cost-effectiveness and population impact of statins for primary prevention in adults aged 75 years or older in the United States.

BACKGROUND: Evidence to guide primary prevention in adults aged 75 years or older is limited. OBJECTIVE: To project the population impact and cost-effectiveness of statin therapy in adults aged 75 years or older. DESIGN: Forecasting study using the Cardiovascular Disease Policy Model, a Markov model. DATA SOURCES: Trial, cohort, and nationally representative data sources. TARGET POPULATION: U.S. adults aged 75 to 94 years. TIME HORIZON: 10 years. PERSPECTIVE: Health care system. INTERVENTION: Statins for primary prevention based on low-density lipoprotein cholesterol threshold of 4.91 mmol/L (190 mg/dL), 4.14 mmol/L (160 mg/dL), or 3.36 mmol/L (130 mg/dL); presence of diabetes; or 10-year risk score of at least 7.5%. OUTCOME MEASURES: Myocardial infarction (MI), coronary heart disease (CHD) death, disability-adjusted life-years, and costs. RESULTS OF BASE-CASE ANALYSIS: All adults aged 75 years or older in the National Health and Nutrition Examination Survey have a 10-year risk score greater than 7.5%. If statins had no effect on functional limitation or cognitive impairment, all primary prevention strategies would prevent MIs and CHD deaths and be cost-effective. Treatment of all adults aged 75 to 94 years would result in 8 million additional users and prevent 105 000 (4.3%) incident MIs and 68 000 (2.3%) CHD deaths at an incremental cost per disability-adjusted life-year of $25 200. RESULTS OF SENSITIVITY ANALYSIS: An increased relative risk for functional limitation or mild cognitive impairment of 1.10 to 1.29 could offset the cardiovascular benefits. LIMITATION: Limited trial evidence targeting primary prevention in adults aged 75 years or older. CONCLUSION: At effectiveness similar to that in trials, statins are projected to be cost-effective for primary prevention; however, even a small increase in geriatric-specific adverse effects could offset the cardiovascular benefit. Improved data on the potential benefits and harms of statins are needed to inform decision making. PRIMARY FUNDING SOURCE: American Heart Association Western States Affiliate, National Institute on Aging, and the National Institute for Diabetes on Digestive and Kidney Diseases.

Is gold a hedge against inflation? New evidence from a nonlinear ARDL approach.

This paper aims to study the role of gold as a hedge against inflation based on local monthly gold prices in China, India, Japan, France, the United Kingdom and the United States of America in periods ranging from 1955 to 2015. We extend the literature by using a novel approach with the nonlinear autoregressive distributed lags (NARDL) model (Shin et al., 2014). The main advantage of this model relies on its ability to simultaneously capture the short- and long-run asymmetries through positive and negative partial sum decompositions of changes in the independent variable(s). Moreover, we rely on local gold prices instead of those from London converted into local currencies like in most of previous studies. The results show that gold is not a hedge against inflation in the long run in all cases. In the short run, gold is an inflation hedge only in the UK, USA, and India. Furthermore, there is no long-run equilibrium between gold prices and the CPI in China, India and France. This difference may be due to traditional aspects of gold and custom controls for gold trade in these countries. Our robustness check suggests that the data time-frequency does not change the specification of the NARDL model but can change conclusions regarding the role of gold as a hedge against inflation in certain countries.

Emergency and trauma care in Pakistan: a cross-sectional study of healthcare levels.

BACKGROUND: The importance of emergency medical care for the successful functioning of health systems has been increasingly recognised. This study aimed to evaluate emergency and trauma care facilities in four districts of the province of Sindh, Pakistan. METHOD: We conducted a cross-sectional health facility survey in four districts of the province of Sindh in Pakistan using a modified version of WHO's Guidelines for essential trauma care. 93 public health facilities (81 primary care facilities, nine secondary care hospitals, three tertiary hospitals) and 12 large private hospitals were surveyed. Interviews of healthcare providers and visual inspections of essential equipment and supplies as per guidelines were performed. A total of 141 physicians providing various levels of care were tested for their knowledge of basic emergency care using a validated instrument. RESULTS: Only 4 (44%) public secondary, 3 (25%) private secondary hospitals and all three tertiary care hospitals had designated emergency rooms. The majority of primary care health facilities had less than 60% of all essential equipments overall. Most of the secondary level public hospitals (78%) had less than 60% of essential equipments, and none had 80% or more. A fourth of private secondary care facilities and all tertiary care hospitals (n=3; 100%) had 80% or more essential equipments. The average percentage score on the physician knowledge test was 30%. None of the physicians scored above 60% correct responses. CONCLUSIONS: The study findings demonstrated a gap in both essential equipment and provider knowledge necessary for effective emergency and trauma care.

Supporting the needs of state health policy makers through university partnerships.

State Medicaid programs and other state health agencies need to monitor and evaluate changes in health insurance coverage, access to care, financing, and the quality of health care delivery. The availability of new financial resources through the Patient Protection and Affordable Care Act is accompanied by raised expectations for such accountability. While state agencies often contract with universities on an ad hoc basis for specific policy projects, fourteen states have established formal state-university partnerships so that their analytic and technical needs can be addressed more readily. After a brief overview of these partnerships, this article provides examples of their projects, which most often affect Medicaid policy, including work on program eligibility, provider payments, and optional benefits. State-university partnerships are working on policy-relevant projects that influence decision making. Like the variation in Medicaid programs across the country, no two partnerships are alike. They thrive in a mix of structures, using different means of contracting, and with varied degrees of data access. All partnerships are interested in building a national network to share innovative practices and projects, spawn comparative policy studies across states, and support the development of new state-university partnerships.

Sociodemographic and Behavioral Factors Associated With Hypertension and Depression in 4 Rural Communities in Northern Ghana: A Cross-Sectional Study.

OBJECTIVES: The prevalences of hypertension and depression in sub-Saharan Africa are substantial and rising, despite limited data on their sociodemographic and behavioral risk factors and their interactions. We undertook a cross-sectional study in 4 communities in the Upper East Region of Ghana to identify persons with hypertension and depression in the setting of a pilot intervention training local nurses and health volunteers to manage these conditions. METHODS: We quantified hypertension and depression prevalence across key sociodemographic factors (age, sex, occupation, education, religion, ethnicity, and community) and behavioral factors (tobacco use, alcohol use, and physical activity) and tested for association by multivariable logistic regression. RESULTS: Hypertension prevalence was higher in older persons (7.6% among 35- to 50-year-olds vs 16.4% among 51- to 70-year-olds) and among those reporting alcohol use (18.9% vs 8.5% between users and nonusers). In multivariable models, only older age (AOR 2.39 [1.02, 5.85]) and residence in the community of Wuru (AOR 7.60 [1.81, 32.96]) were independently associated with hypertension, and residence in Wuru (AOR 23.58 [7.75-78.25]) or Navio (AOR 7.41 [2.30-24.74]) was the only factor independently associated with depression. CONCLUSIONS: We report a high prevalence of both diseases overall and in select communities, a trend that requires further research to inform targeted chronic disease interventions.

Emotional and Financial Stressors in New York City During the COVID-19 Pandemic: A Consecutive Cross-Sectional Analysis.

Mental and financial hardship during the COVID-19 pandemic in New York City was severe, but how vulnerable groups have been disproportionately impacted is incompletely understood. In partnership with community stakeholders, we administered a web-based survey to a convenience sample of New York City residents (18 + years) from May 2020 to April 2021 to evaluate their financial and emotional stressors. We analyzed outcomes by race, ethnicity, and education level. A total of 1854 adults completed the survey across three consecutive non-overlapping samples. Fifty-five percent identified other than non-Latinx White. Sixty-four percent reported emotional stress; 38%, 32%, and 32% reported symptoms of anxiety, depression, and post-traumatic stress disorder respectively; and 21% reported a large adverse financial impact. The leading unmet needs were mental health and food services (both 19%), and health services (18%). Need for both resources grew over time. Adverse financial impact directly correlated with presence of all four adverse mental health outcomes above. In multivariate analysis, non-White race and lack of college degree were associated with adverse financial impact, whereas LGBT identity and lack of college degree were associated with mental health impact. Throughout the COVID-19 pandemic, participants in this research demonstrated a large and growing mental and financial strain, disproportionately associated with lower education level, non-White race, and LGBT status. Our findings suggest an urgent need to differentially target COVID-19 mental health and resource support in New York City to persons in these vulnerable communities.

Understanding research methods, limitations, and applications of drug data collected by the National Forensic Laboratory Information System (NFLIS-Drug).

The National Forensic Laboratory Information System (NFLIS) is a drug surveillance program of the US Drug Enforcement Administration that systematically collects data on drugs that are seized by law enforcement and submitted to and analyzed by the Nation's forensic laboratories (NFLIS-Drug). NFLIS-Drug data are increasingly used in predictive modeling and drug surveillance to examine drug availability patterns. Given the complexity of the data and data collection, there are some common methodological pitfalls that we highlight with the aim of helping researchers avoid these concerns. The analysis done for this Technical Note is based on a review of the scientific literature that includes 428 unique, refereed article citations in 182 distinct journals published between January 1, 2005, and April 30, 2021. Each article was analyzed according to how NFLIS-Drug data were mentioned and whether NFLIS-Drug data were included. A sample of 37 articles was studied in-depth, and data issues were summarized. Using examples from the literature, this Technical Note highlights eight broad concerns that have important implications for the proper applications, interpretations, and limitations of NFLIS-Drug data with suggestions for improving research methods and accurate reporting of forensic drug data. NFLIS-Drug data are timely and provide key information to inform drug use trends across the United States; however, our present analysis shows that NFLIS-Drug data are misunderstood and represented in the literature. In addition to highlighting these issues, DEA has created several resources to assist NFLIS data users and researchers, which are summarized in the discussion.