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Data standards for single-cell RNA-sequencing of paediatric cancer
Xiaohan Xu1, John Saxon1, Megan Sioe Fei Soon1
1Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Health, Medicine and Behavioural Sciences The University of Queensland Brisbane QLD Australia.
Insights
Publicly available single-cell RNA sequencing (scRNA-seq) data for pediatric cancers lack standards, hindering research. This study proposes recommendations to improve data deposition for better reproducibility and accelerated discoveries.
Area of Science:
- Genomics
- Oncology
- Bioinformatics
Background:
- Single-cell RNA sequencing (scRNA-seq) offers deep insights into pediatric cancers.
- Public data repositories are crucial for reproducibility and cost-effective research.
- Challenges exist in accessing and utilizing pediatric cancer scRNA-seq data due to inconsistent deposition standards.
Purpose of the Study:
- To systematically review publicly available scRNA-seq datasets in pediatric cancer research.
- To identify inconsistencies in data deposition and their impact on downstream analyses.
- To propose a framework for standardized data deposition to enhance data usability and reproducibility.
Main Methods:
- Systematic review of public scRNA-seq datasets from pediatric cancer studies.
- Analysis of data availability and study design across 488 clinical samples (over 1.3 million cells).
- Identification of inconsistencies hindering data validation and utilization.
Main Results:
- Significant inconsistencies found in study design and data availability across reviewed datasets.
- Lack of standardized data deposition practices impedes data validation and tailored analyses.
- Current practices limit the full potential of public scRNA-seq data in pediatric cancer research.
Conclusions:
- Standardized data deposition practices are essential for pediatric cancer research.
- A proposed recommendations framework aims to improve the quality and accessibility of deposited scRNA-seq data.
- Enforcement of data standards by repositories like GEO and EGA is urged to accelerate scientific discovery.
Abstract:
Single-cell RNA sequencing (scRNA-seq) is a powerful tool for investigating paediatric cancers, but individual studies often profile a small number of individuals. It is now the standard practice to upload the scRNA-seq data to data repositories to support scientific reproducibility. Public data deposition is a cost-effective and sustainability-conscious solution that allows any researcher to download and analyse existing scRNA-seq data to develop new ideas. This is incredibly valuable, especially in the context of paediatric cancer research, where access to funding and to patient cohorts may be prohibitive. However, standards for data deposition are absent, leading to significant issues that may slow progress. As a consequence, it is difficult, even impossible, for other researchers to validate findings or utilise these data for tailored analyses. Here, we systematically accessed and reviewed publicly available scRNA-seq data sets from various paediatric cancer studies, covering over 1.3 million cells across 488 clinical samples. We highlight striking inconsistencies with study design and data availability across several levels, which hinder downstream analyses and data reproducibility. To address these challenges, we propose a recommendations framework to improve data deposition practices that promote more effective use of scRNA-seq data sets deposited on public repositories and accelerate discoveries in paediatric cancer research and beyond. We urge data standards institutes and repositories, such as NCBI Gene Expression Omnibus (GEO) and European Genome-Phenome Archive (EGA), to strictly enforce these standardised data practices.
