Epidemiological research on rare diseases using large-scale online search queries and reported case data

BACKGROUND

Rare diseases have become a major public health concern worldwide. However, detailed epidemiological data are lacking. With the development of the Internet, search queries have played an important role in disease surveillance. In this study, we explored a new method for the epidemiological research on rare diseases, using large-scale online search queries and reported case data. We distilled search logs related to rare diseases nationwide from 2016 to 2019. The case data were obtained from China's national database of rare diseases during the same period.

RESULTS

A total of 120 rare diseases were included in this study. From 2016 to 2019, the number of patients with rare diseases estimated using search data and those obtained from the case database showed an increasing trend. Rare diseases can be ranked by the number of search estimated patients and reported patients, and the rankings of each disease in both search and reported case data were generally stable. Furthermore, the disease rankings in the search data were relatively consistent with the reported case data in each year, with more than 50% of rare diseases having a ranking difference of -20 to 20 between the two systems. In addition, the relationship between the disease rankings in the two systems was generally stable over time. Based on the relationship between the disease rankings in the search and reported case data, rare diseases can be classified into two categories.

CONCLUSION

Online search queries may provide an important new resource for detecting rare diseases. Rare diseases can be classified into two categories to guide different epidemiological research strategies.

Deduplicating records in systematic reviews: there are free, accurate automated ways to do so

OBJECTIVE

Here, we examined the accuracy measures of a set of automated deduplication tools to identify duplicate in the eligibility process of systematic reviews.

STUDY DESIGN AND SETTING

A planned search strategy was carried out on seven electronic databases until May 31, 2021. Using manual search as the reference standard, we assessed sensibility, specificity, negative predictive value, and positive predictive value (PPV).

RESULTS

Specificity ranged from 0.96 to 1.00. Rayyan, Mendeley, and Systematic Review Accelerator (SRA) presented high sensibility (0.98 [95% CI = 0.94-1.00]; 0.93 [95% CI = 0.88-0.97] and 0.90 [95% CI = 0.84-0.95], respectively), whereas EndNote X9 and Zotero had only fair sensitivity (0.73 [95% CI = 0.65-0.80] and 0.74 [95% CI = 0.66-0.81], respectively). Negative predictive value ranged from 0.99 to 1.00. Mendeley and SRA had good PPV (0.93 [95% CI = 0.88-0.97] and 0.99 [95% CI = 0.96-1.00], respectively). PPV was fair for EndNote X9 (0.61 [95% CI = 0.54-0.69]) and Zotero (0.62 [95% CI = 0.54-0.69]) and poor for Rayyan (0.41 [95% CI = 0.36-0.47]).

CONCLUSION

Choosing the most suitable tool depends on its interface's characteristics, the algorithm to identify and exclude duplicates, and the transparency of the process. Therefore, Rayyan, Mendeley, and SRA proved to be accurate enough for the systematic reviews' deduplication step.

Factors associated with 5- and 10-year survival among a recent cohort of childhood cancer survivors (France, 2000-2015)

BACKGROUND

Childhood cancer survival currently exceeds 80 % five years after diagnosis in high-income countries. In this study, we aimed to describe long-term trends and to investigate socioeconomic and spatial disparities in childhood cancer survival.

METHODS

The study included 28,073 cases recorded in the French National Registry of Childhood Cancers from 2000 to 2015. Contextual census data (deprivation indices, population density, spatial accessibility to general practitioners) were allocated to each case based on the residence at diagnosis. Overall survival (OS) and conditional 10-year OS for 5-year survivors were estimated for all cancers combined and by diagnostic group and subgroup. Comparisons were conducted by sex, age at diagnosis, period of diagnosis, and contextual indicators. Hazard ratios for death were estimated using Cox models.

RESULTS

All cancers combined, the OS reached 82.8 % [95 % CI: 82.4-83.3] at 5 years and 80.8 % [95 % CI: 80.3-81.3] at 10 years. Conditional 10-year OS of 5-year survivors reached 97.5 % [95 % CI: 97.3-97.7] and was higher than 95 % for all subgroups except osteosarcomas and most subgroups of the central nervous system. In addition to disparities by sex, age at diagnosis, and period of diagnosis, we observed a slight decrease in survival for cases living in the most deprived areas at diagnosis, not consistent across diagnostic groups.

CONCLUSION

Our results confirm the high 5-year survival for childhood cancer and show an excellent 10-year conditional survival of 5-year survivors. Additional individual data are needed to clarify the factors underlying the slight decrease in childhood cancer survival observed in the most deprived areas.

Adapting World Health Organization Disability Assessment Schedule 2.0 for Nepal

Background

Disability is a vital public health issue for health care programs. Affluent countries usually prioritize disability-related research, while often it remains neglected in resource-poor countries like Nepal. The aim of this study was to make available a translated and culturally adapted version of the World Health Organization Disability Assessment Schedule 2.0 (WHODAS 2.0) for measuring disability in the Nepalese population.

Methods

WHODAS 2.0 (12-items version) was translated into Nepali using a standard forward–backward translation protocol. Purposive and convenience recruitment of participants with psychiatric disabilities was done at the Psychiatry services in a tertiary care hospital. Age and gender-matched participants with physical disabilities were selected from the Internal Medicine department, and participants with no disability were recruited from their accompanying persons. A structured interview in Nepali including the translated WHODAS 2.0 was administered to all participants. Exploratory factor analysis and parallel analysis assessed the construct validity. Content validity was explored, and a quality of life instrument was used for establishing criterion validity. Reliability was measured via Cronbach alpha. Mann–Whitney test explored score differences between the disabled and non-disabled.

Results

In total, 149 persons [mean age: 40.6 (12.8); 43.6% males, 56.4% females; 61.7% disabled, 38.3% non-disabled] consented to participate. Parallel analysis indicated that a single factor was adequate for the Nepali WHODAS version that captured 45.4% of the total variance. The translated scale got a good Cronbach alpha (= 0.89). Satisfactory construct, content and criterion validity was found. The WHODAS total scores showed a significant difference between the disabled and non-disabled (U = 2002.5; p = 0.015). However, the difference between psychiatric and physical disabilities was not significant, which underscores that the scale is rating disability in general.

Conclusion

The one-factor structure of the translated and culturally adapted Nepali-version of WHODAS 2.0 showed acceptable validity and an adequate reliability. For epidemiological research purposes, this version of WHODAS 2.0 is now available for measuring global disability in Nepal.

The Mediterranean diet from past to future: Key concepts from the second "Ancel Keys" International Seminar

The year 2020 celebrated the tenth anniversary of the recognition of the Mediterranean Diet as Intangible Cultural Heritage of Humanity by the UNESCO Intergovernmental Committee. This event represented a milestone in the history of nutrition, as the Mediterranean diet was the first traditional food practice to receive such award. Since then, a lot has been discussed not only on the beneficial aspects of the Mediterranean diet, but also on its complex role as a lifestyle model that includes a set of skills, knowledge and intercultural dialogue. This process ended up with the recognition in 2019 of Mediterranean diet as a possibly universal model of healthy diet from the EAT-Lancet Commission. These concepts were widely debated at the 2019 "Ancel Keys" International Seminar, held in Ascea (Italy) (for more information see: www.mediterraneandietseminar.org) with the aim to stimulate interest and awareness of a young group of participants on the current problems inherent to the effective implementation of the Mediterranean diet. The present article collects the contributions of several lecturers at the Seminar on key issues such as methodological and experimental approach, sustainability, molecular aspects in disease prevention, future exploitation, without neglecting a historical view of the Seven Countries Study. From the Seminar conclusions emerged a still vibrant and modern role of Mediterranean diet. The years to come will see national and international efforts to reduce the barriers that limit adherence to Mediterranean diet in order to plan for multi-factorial and targeted interventions that would guide our populations to a sustainable healthy living.

CRISPR 2 PCR and high resolution melting profiling for identification and characterization of clinically-relevant Salmonella enterica subsp. enterica

Background

Nontyphoidal Salmonella spp. constitute a major bacterial cause of food poisoning. Each Salmonella serotype causes distinct virulence to humans.

Method

A small cohort study was conducted to characterize several aspects of Salmonella isolates obtained from stool of diarrheal patients (n = 26) admitted to Phayao Ram Hospital, Phayao province, Thailand. A simple CRISPR 2 molecular analysis was developed to rapidly type Salmonella isolates employing both uniplex and high resolution melting (HRM) curve analysis.

Results

CRISPR 2 monoplex PCR generated a single Salmonella serotype-specific amplicon, showing S. 4,[5],12:i:- with highest frequency (42%), S. Enteritidis (15%) and S. Stanley (11%); S. Typhimurium was not detected. CRISPR 2 HRM-PCR allowed further classification of S. 4,[5],12:i:- isolates based on their specific CRISPR 2 signature sequences. The highest prevalence of Salmonella infection was during the summer season (April to August). Additional studies were conducted using standard multiplex HRM-PCR typing, which confirmed CRISPR 2 PCR results and, using a machine-learning algorithm, clustered the majority of Salmonella serotypes into six clades; repetitive element-based (ERIC) PCR, which clustered the serotypes into three clades only; antibiogram profiling, which revealed the majority resistant to ampicillin (69%); and test for extended spectrum β-lactamase production (two isolates) and PCR-based detection of bla alleles.

Conclusion

CRISPR 2 PCR provided a simple assay for detection and identification of clinically-relevant Salmonella serotypes. In conjunction with antibiogram profiling and rapid assay for β-lactamase producers, this approach should facilitate detection and appropriate treatment of Salmonellosis in a local hospital setting. In addition, CRISPR 2 HRM-PCR profiling enabled clustering of S. 4,[5],12:i:-isolates according to CRISPR 2 locus signature sequences, indicative of their different evolutionary trajectories, thereby providing a powerful tool for future epidemiological studies of virulent Salmonella serotypes.

[Risk of bias assessment: (1) overview]

This paper reviews the concept of risk of bias, followed by demonstrating why assessment of risk of bias in systematic reviews should be different from that of quality of evidence, methodological quality, reporting quality, precision, and external validity. We also discuss the recent development of tools for risk of bias assessment, the problems with the tools themselves, and the challenges in using these tools. This review may help systematic reviewers understand risk of bias assessment and the use of assessment tools.

[Risk of bias assessment: (9) Application of the risk of bias assessment results]

In this last paper of the series about risk of bias assessment, we introduce the application of risk of bias assessment results. Risk of bias assessment is one of the key steps in the assessment of quality of evidence. The risk of bias assessment results could be the "diagnosis" of individual studies, which helps decision making related to the inclusion and exclusion of individual studies, as well as the data analysis in the systematic review process. This paper focuses on how to incorporate risk of bias assessment results in the GRADE assessment for quality of evidence, including the principles and the tips for the application.

Theory and methodology: essential tools that can become dangerous belief systems

We thank Dr. Karp for his interest [1 ] in our paper [2 ]. We agree on some points, but our theoretical description differs from his in ways leading to important divergences for teaching and practice. We also see a danger of overextending abstract theory (with its inevitable and extensive simplifications) into practice [3 ], especially when the practical questions are causal but the theory applied lacks an explicit, sound longitudinal causal model to address these questions. As we will explain, a defect in the “study base” theory Dr. Karp adopts as a foundational belief system is that it takes as a foundation a parameter affected by baseline risk factors—including exposure when that has effects on follow-up or disease. It consequently leads to biases and misconceptions of the sort documented elsewhere [4 , 5 ] and below, which require a coherent theory of longitudinal causality to address. Our divergence from Dr. Karp thus raises the issue of the role of theory and methods in research, although matching serves to illustrate our points in a familiar epidemiologic context.

Epidemiology in wonderland: Big Data and precision medicine

Big Data and precision medicine, two major contemporary challenges for epidemiology, are critically examined from two different angles. In Part 1 Big Data collected for research purposes (Big research Data) and Big Data used for research although collected for other primary purposes (Big secondary Data) are discussed in the light of the fundamental common requirement of data validity, prevailing over "bigness". Precision medicine is treated developing the key point that high relative risks are as a rule required to make a variable or combination of variables suitable for prediction of disease occurrence, outcome or response to treatment; the commercial proliferation of allegedly predictive tests of unknown or poor validity is commented. Part 2 proposes a "wise epidemiology" approach to: (a) choosing in a context imprinted by Big Data and precision medicine-epidemiological research projects actually relevant to population health, (b) training epidemiologists,

Toolbox for Research, or how to facilitate a central data management in small-scale research projects

Background

In most research projects budget, staff and IT infrastructures are limiting resources. Especially for small-scale registries and cohort studies professional IT support and commercial electronic data capture systems are too expensive. Consequently, these projects use simple local approaches (e.g. Excel) for data capture instead of a central data management including web-based data capture and proper research databases. This leads to manual processes to merge, analyze and, if possible, pseudonymize research data of different study sites.

Results

To support multi-site data capture, storage and analyses in small-scall research projects, corresponding requirements were analyzed within the MOSAIC project. Based on the identified requirements, the Toolbox for Research was developed as a flexible software solution for various research scenarios. Additionally, the Toolbox facilitates data integration of research data as well as metadata by performing necessary procedures automatically. Also, Toolbox modules allow the integration of device data. Moreover, separation of personally identifiable information and medical data by using only pseudonyms for storing medical data ensures the compliance to data protection regulations. This pseudonymized data can then be exported in SPSS format in order to enable scientists to prepare reports and analyses.

Conclusions

The Toolbox for Research was successfully piloted in the German Burn Registry in 2016 facilitating the documentation of 4350 burn cases at 54 study sites. The Toolbox for Research can be downloaded free of charge from the project website and automatically installed due to the use of Docker technology.

The Performance Scales disability measure for multiple sclerosis: use and sensitivity to clinically important differences

BACKGROUND

In 1993, the Performance Scales© was created to assess multi-dimensional disability in multiple sclerosis (MS). This tool has been used in a variety of settings and study designs internationally. The present work provides an overview of the history and psychometric characteristics of the Performance Scales©, reviews its use over the past two decades, and summarizes its responsiveness to subgroup differences.

METHODS

A Google Scholar and Ovid search yielded 230 articles citing the Performance Scales©, of which 82 studies used the tool in empirical research. Twelve articles provided sufficient information to enable computation of effect sizes. Forest plots were used to show effect sizes for the overall summary score and by domain by patient demographics, MS disease trajectory, and treatment adherence.

RESULTS

The Performance Scales© evidenced sensitivity to clinically important differences by disease trajectory and age (for selected domains). In contrast, groups distinguished by patient adherence to disease-modifying therapies and ethnicity were relatively small.

CONCLUSIONS

The Performance Scales© has been used in a large number of studies since its development, suggesting that this psychometrically sound tool is acknowledged to be a useful tool for MS clinical research. It is recommended that future work include the entire measure, so that the whole-person impact of MS can be characterized and considered in MS outcome research.