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Your domain: Human pathogen genomics

Introduction

The human pathogen genomics domain focuses on studying the genetic code of organisms that cause disease in humans. Studies to identify and understand pathogens are conducted across different types of organisations ranging from research institutes to regional public health authorities. The aims can include urgent outbreak response, prevention measures, and developing remedies such as treatments and vaccines.

Data management challenges in this domain include the potential urgency of data sharing and secondary use of data across initiatives emerging from research, public health and policymakers. While pathogenic organisms are the object of interest, there are many considerations to take into account when dealing with samples collected from patients, pathogen surveillance, and human research subjects.

The genomic data can represent anything from the genetic sequence of a single pathogen isolate to various fragments of genetic materials from a flora of pathogens in a larger population. Other data can represent a wide range of contextual information about the human host, the disease, and various environmental factors.

Planning a study with pathogen genomic data

Description

While the objects of interest in this domain are pathogens, the data is usually derived from samples originating from human research subjects. This means that you must plan to either remove or handle human data during your study.

Considerations

  • What legal and ethical aspects do you need to consider?
    • Can you separate pathogen and human host material and data?
    • What data protection measures should be implemented in contracts and procedures dealing with suppliers and collaborators?
    • What is the appropriate scope for the legal and ethical agreements necessary for the study?
    • How should statements related to data processing be phrased to allow timely and efficient data sharing?
    • How much time would be required to negotiate access to the samples and data for the study?
  • What public health and research initiatives should you consider aligning with?
    • What data could be shared with or reused from other initiatives during the project?
    • How will you align your practices with these initiatives to maximise the impact of the data and insight generated by the project?
    • How will you share data with your collaborators and other initiatives?
  • What conventions will you adopt when planning your study?
    • What existing protocols should you consider adopting for sample preparation, sequencing, variant calling and other operations?
    • What conventions should you adopt for documenting your research?

Solutions

Working with human data

Isolate pathogen from host information

  • Depending on the pathogen and how it interacts with the host or the methods applied, it can be possible to generate clean isolates that do not contain host-related material. Data produced from a clean isolate could potentially be handled with fewer restrictions, while other data will be considered to be sensitive and will need protection.

Public health initiatives

Sequencing experiments

Collecting and processing pathogen genomic data

Considerations

  • What information should you consider recording when collecting data?
    • What should you note when collecting, storing, and preparing the samples?
    • How will you capture information about the configuration and quality of the sequencing results?
    • How will you ensure that the captured information is complete and correct?
  • What data and file formats should you consider for your project?
    • What are the de-facto standards used for the experiment type and downstream analysis pipelines?
    • Where are the instrument-specific aspects of the data and file formats documented?
  • What existing data will you integrate or use as a reference in your project?
    • What reference genome(s) will you need access to?
    • What is the recommended citation for the data and their versions?

Solutions

Filtering genomic reads corresponding to human DNA fragments

  • Data files with reads produced by sequencing experiments sometimes contain fragments of the host organism’s DNA. When the host is a human research subject, these fragments can be masked or removed to produce files that could potentially be handled with fewer restrictions. The approach chosen to mask the host-associated reads leads to different trade-offs. Make sure to include this as a factor in your risk assessment.

Contextual information about the sample

Generating genomic data

Sharing and preserving pathogen genomic data

Considerations

  • What data needs to be preserved by the project and for how long?
  • What is preserved by others and how would someone find and access the data?
  • What databases should I use to share human pathogen genomics data?
  • What other research information (such as protocols, computational tools, and samples) can the project share?

Solutions

  • Some host-related information can be personal and/or sensitive and care should be taken when storing and sharing it. Apply data masking and aggregation techniques to pseudonymise or anonymise the contextual information and take measures to separate personal and sensitive information from the pathogen data when possible.
  • Adopt solutions for federated analysis to support distributed analyses on information that could otherwise not be shared, such as establishing contractual agreements with suitable regional or international data infrastructures.
  • GA4GH is a global organisation that frames policy and builds standards to meet the real-world needs of the genomics and health community. Its GDPR & International Health Data Sharing Forum shares GDPR Briefs that represent a consensus position among its Forum Members (not legal advice) regarding the current understanding of the GDPR and its implications for genomic and health-related research, such as

Sharing pathogen genomic data

Bibliography

  1. Stevens, I. et al. Ten Simple Rules for Annotating Sequencing Experiments. PLOS Computational Biology 16, (2020).
  2. Bush, S. J., Connor, T. R., Peto, T. E. A., Crook, D. W. & Walker, A. S. Evaluation of Methods for Detecting Human Reads in Microbial Sequencing Datasets. Microbial Genomics 6, (2020).
  3. Gut, I. et al. B1MG D3.1 - Quality Metrics for Sequencing. (2021) doi:10.5281/ZENODO.5018495.

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