A Systematic Overview of Single-Cell Transcriptomics Databases, their Use cases, and Limitations

Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we systematically examined large-scale scRNA-seq databases, categorizing them based on their scope and purpose such as general, tissue-specific databases, disease-specific databases, cancer-focused databases, and cell type-focused databases. Next, we discuss the technical and methodological challenges associated with curating large-scale scRNA-seq databases, along with current computational solutions. We argue that understanding scRNA-seq databases, including their limitations and assumptions, is crucial for effectively utilizing this data to make robust discoveries and identify novel biological insights. Furthermore, we propose that bridging the gap between computational and wet lab scientists through user-friendly web-based platforms is needed for democratizing access to single-cell data. These platforms would facilitate interdisciplinary research, enabling researchers from various disciplines to collaborate effectively. This review underscores the importance of leveraging computational approaches to unravel the complexities of single-cell data and offers a promising direction for future research in the field.

iCare - a self-directed, interactive online program to improve health and wellbeing for people living with upper gastrointestinal or hepato-pancreato-biliary cancers, and their informal carers: the study protocol for a Phase II randomised controlled trial

BACKGROUND

Up to 70% of people diagnosed with upper gastrointestinal (GI) tract or hepato-pancreato-biliary (HPB) cancers experience substantial reductions in quality of life (QoL), including high distress levels, pain, fatigue, sleep disturbances, weight loss and difficulty swallowing. With few advocacy groups and support systems for adults with upper GI or HPB cancers (i.e. pancreas, liver, stomach, bile duct and oesophageal) and their carers, online supportive care programs may represent an alternate cost-effective mechanism to support this patient group and carers. iCare is a self-directed, interactive, online program that provides information, resources, and psychological packages to patients and their carers from the treatment phase of their condition. The inception and development of iCare has been driven by consumers, advocacy groups, government and health professionals. The aims of this study are to determine the feasibility and acceptability of iCare, examine preliminary efficacy on health-related QoL and carer burden at 3- and 6-months post enrolment, and the potential cost-effectiveness of iCare, from health and societal perspectives, for both patients and carers.

METHODS AND ANALYSIS

A Phase II randomised controlled trial. Overall, 162 people with newly diagnosed upper GI or HPB cancers and 162 carers will be recruited via the Upper GI Cancer Registry, online advertisements, or hospital clinics. Patients and carers will be randomly allocated (1:1) to the iCare program or usual care. Participant assessments will be at enrolment, 3- and 6-months later. The primary outcomes are i) feasibility, measured by eligibility, recruitment, response and attrition rates, and ii) acceptability, measured by engagement with iCare (frequency of logins, time spent using iCare, and use of features over the intervention period). Secondary outcomes are patient changes in QoL and unmet needs, and carer burden, unmet needs and QoL. Linear mixed models will be fitted to obtain preliminary estimates of efficacy and variability for secondary outcomes. The economic analysis will include a cost-consequences analysis where all outcomes will be compared with costs.

DISCUSSION

iCare provides a potential model of supportive care to improve QoL, unmet needs and burden of disease among people living with upper GI or HPB cancers and their carers.

AUSTRALIAN AND NEW ZEALAND CLINICAL TRIALS REGISTRY

ACTRN12623001185651. This protocol reflects Version #1 26 April 2023.

The association between perioperative frailty and ability to complete a web-based geriatric assessment among older adults with cancer

INTRODUCTION

The aim of this study was to assess the degree to which patient frailty is associated with both need for assistance and time required to complete the eRFA, a web-based GA tool.

MATERIALS AND METHODS

We retrospectively identified patients who underwent surgery for cancer from 2015 to 2020, had a hospital length of stay ≥1 day, and completed the eRFA before surgery. Frailty was assessed using two methods: the MSK-FI (score 0-11) and the AGD (score 0-13). Time to complete the eRFA was automatically recorded by a web-based tool; assistance with eRFA completion was self-reported by the patient.

RESULTS

In total, 3456 patients were included (median age, 78 years). Overall, 58% of surveys were completed without assistance, 30% were completed with assistance, and 12% were completed by someone other than the patient. Younger age (median age: without assistance, 77 years; with assistance, 80 years; completed by someone else, 80 years) and lower frailty score (median AGD: 4, 6, and 8, respectively; median MSK-FI: 2, 3, and 3, respectively) were associated with independency (all p < 0.001). Higher frailty score was associated with longer time to complete the eRFA (all nonlinear association p < 0.001).

CONCLUSION

Frail patients are more likely to benefit from completion of GA to determine appropriate treatment. Given that not all cancer patients have a caregiver who can assist completing a digital questionnaire, innovative solutions are needed to help frail patients complete the eRFA without assistance.

The road to successful people-centric research in rare diseases: the web-based case study of the Immunology and Congenital Disorders of Glycosylation questionnaire (ImmunoCDGQ)

Background

Congenital Disorders of Glycosylation (CDG) are a complex family of rare metabolic diseases. Robust clinical data collection faces many hurdles, preventing full CDG biological and clinical comprehension. Web-based platforms offer privileged opportunities for biomedical data gathering, and participant recruitment, particularly in rare diseases. The immunology and CDG electronic (e-) questionnaire (ImmunoCDGQ) explores this paradigm, proposing a people-centric framework to advance health research and participant empowerment.

Objective

The objectives of this study were to: (1) Describe and characterize the ImmunoCDGQ development, engagement, recruitment, participation, and result dissemination strategies; (2) To critically compare this framework with published literature and making recommendations.

Methods

An international, multistakeholder people-centric approach was initiated to develop and distribute the ImmunoCDGQ, a multi-lingual e-questionnaire able to collect immune-related data directly from patients and family caregivers. An adapted version was produced and distributed among the general “healthy” population (ImmunoHealthyQ), serving as the control group. Literature screening was performed to identify and analyze comparable studies.

Results

The ImmunoCDGQ attained high participation and inclusion rates (94.6%, 209 out of 221). Comparatively to the control, CDG participants also showed higher and more variable questionnaire completion times as well as increased English version representativeness. Additionally, 20% of the CDG group (42 out of 209) chose not to complete the entire questionnaire in one go. Conditional logic structuring guided participant data provision and accurate data analysis assignment. Multi-channel recruitment created sustained engagement with Facebook emerging as the most followed social media outlet. Still, most included ImmunoCDGQ questionnaires (50.7%, 106 out of 209) were submitted within the first month of the project’s launch. Literature search and analysis showed that most e-questionnaire-based studies in rare diseases are author-built (56.8%, 25 out of 44), simultaneously addressing medical and health-related quality of life (HRQoL) and/or information needs (79.5%, 35 out of 44). Also, over 68% of the studies adopt multi-platform recruitment (30 out of 44) actively supported by patient organizations (52.3%, 23 out of 44).

Conclusions

The ImmunoCDGQ, its methodology and the CDG Community served as models for health research, hence paving a successful and reproducible road to people-centricity in biomedical research.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13023-022-02286-w.