Can I upload my Next-Generation Sequencing (NGS) results?

Uploading NGS Results: Recommendations and Best Practices

Yes, you can upload your Next-Generation Sequencing (NGS) results, but this should be done through secure, standardized platforms that ensure data privacy and proper interpretation of the complex genomic data. 1

Data Upload Considerations

Technical Requirements

• Use standardized file formats (typically compressed FASTQ files) along with quality control reports and basic processing results 1
• Include provenance information (software versions, parameters used, workflows) to ensure reproducibility 1
• For large datasets, use specialized file transfer tools like Aspera or GRIDftp for efficient data movement 1

Data Security and Privacy

• NGS data contains sensitive genetic information requiring robust privacy protections 2
• Upload through secure channels with appropriate encryption and authentication 1
• Ensure the platform complies with relevant healthcare data privacy regulations 2

Sample Quality Documentation

When uploading NGS results, include critical metadata:

• Sample type and identifier (including date of collection) 1
• Sample quality metrics:
  • Percentage of tumor cells (if applicable)
  • DNA quality score
  • Any tumor cell enrichment techniques used
  • Extent of necrosis (for tumor samples) 1
• DNA/RNA concentration and amount 1
• For liquid biopsies: plasma volume, total cfDNA amount, cfDNA concentration, and ctDNA tumor fraction 1

Recommended Upload Platforms

Cloud-Based Solutions

• Cloud platforms provide scalable computing resources for NGS data analysis 1
• Ensure the cloud service provider meets healthcare data security standards 1
• Be aware of potential bandwidth limitations, especially in regions with unreliable internet connectivity 1

Institutional Systems

• Many healthcare institutions have dedicated secure servers for genomic data 1
• These typically include standardized workflows for data processing 1
• May offer integration with electronic health records for clinical applications 1

Common Pitfalls and How to Avoid Them

Connectivity Issues

• For large NGS datasets, intermittent connectivity can disrupt uploads 1
• Use fault-tolerant mechanisms that divide data into smaller chunks and can resume after interruptions 1
• Consider persistent upload workflows that automatically restart if internet connection is interrupted 1

Data Quality Concerns

• Poor quality sequencing data can lead to erroneous interpretations 3
• Always include quality control metrics with your upload 1
• Use quality control tools like NGS QC Toolkit before uploading to filter low-quality data 3

Interpretation Challenges

• NGS generates massive amounts of data with varying clinical relevance 2
• Include contact information for the responsible molecular pathologist who can help interpret the report 1
• Consider including relevant clinical information to aid in interpretation 1

Future Directions

• Integration of complementary tests (tissue and liquid biopsy data) in unified reports 1
• Development of standardized electronic pathology reports with links to genomic databases 1
• Improved fault-tolerant mechanisms for data upload in regions with limited connectivity 1
• Enhanced privacy protections as NGS becomes more widespread in clinical practice 2

By following these guidelines when uploading NGS results, you can ensure data integrity, maintain privacy, and facilitate proper interpretation of the complex genomic information for optimal clinical decision-making.