Human sample requirements for omics-based... | Science Exchange
Human sample requirements for omics-based preclinical research
Omics-based research is important for preclinical research and provides a comprehensive understanding of biological systems. Many areas of research fall under omics, such as proteomics, transcriptomics, genomics, metabolomics, lipidomics, and epigenomics. These areas correspond to the global analysis of proteins, RNA, genes, metabolites, lipids, and methylated DNA or modified histone proteins in chromosomes. Human biospecimen requirements for omics research studies vary. Omics-based research and discovery studies require biological molecules extracted from various human biospecimen types:
- Blood: Frequently used due to its accessibility and the wealth of information it provides. Blood can be collected in various blood collection tube types and fractionated into plasma, serum, and cellular components.
- Tissue Biopsies: Used for more specific studies, such as cancer research, where tissue-specific omics data is needed. Tissue samples can be preserved as fresh-frozen (FF, snap-frozen in liquid nitrogen and stored at -80C) and as formalin-fixed paraffin-embedded (FFPE) tissue blocks.
- Saliva, Urine, and Feces: Non-invasive samples that can provide valuable information for certain types of studies, such as microbiome analysis and metabolic profiling. These samples can be collected in a variety of specimen-collection kits and used as fresh or frozen.
- Cerebrospinal Fluid (CSF): Used for studies related to neurological conditions.
- Synovial fluid.
Key considerations and requirements for human biospecimen collection and handling in omics-based research.
- Inclusion/Exclusion Criteria: Factors such as treatment status, disease stage, and demographics can impact biomolecules in biospecimens.
- Timing: Sample collection and processing time can affect biomolecule levels. Record warm and cold ischemia times for surgical tissue collection. Postmortem tissue collection should occur within a defined interval.
- Collection Method: Use proper techniques to avoid contamination and degradation. Consider blood draw techniques, collection tube types, and stabilizing reagents for preserving RNA, DNA, and proteins.
- Biospecimen Handling and Processing:
- Sample Processing: Standard protocols for sample processing are crucial to ensure consistency and reproducibility. Delays in processing can impact sample integrity. At room temperature, tissue fixation using neutral-buffered formalin should be done within 16-24 hours. Proper sample preparation for fresh-frozen tissues and blood components is also essential to preserve biomarkers and ensure reliable results.
- Biomolecule Extraction: Implement standardized protocols for biomolecule extraction to maintain high integrity, yield, and consistency, especially with fresh-frozen tissues. Cureline Molecular Services has developed proprietary NO-THAW (TM) protocols for tissue cryo pulverization, aliquoting, and biomolecule extraction, as well as unique RNA isolation protocols that preserve RNA integrity, improve extraction efficiency, and require smaller tissue weights.
- Transportation: Conditions during transportation (temperature fluctuations, delays) can degrade samples. Proper packaging, temperature tracking technology, and verified courier service are essential.
- Storage Conditions: Temperature, storage duration, and freeze-thaw cycles can affect the stability of proteins and nucleic acids. To prevent degradation of RNA, proteins, and metabolites, immediate freezing and storage at -80°C for long-term preservation are necessary.
The specific requirements depend on multiple factors, such as the technology, downstream application, and equipment. The general considerations are:
- Genomics: High-quality un-sheared DNA, typically requiring 20-50 ng/µl concentration, A260 / A280 ratio close to ~1.8. Whole-genome sequencing or targeted sequencing may need different quantities and qualities of DNA.
- Transcriptomics: High-quality RNA with an RNA Integrity Number (RIN) > 7.0 (for RNA from frozen specimens) and DV200 > 30% (for RNA from FFPE). RNA sequencing (RNA-Seq) often requires RNA free from DNA contamination and an A260 / A280 ratio close to ~2.0 reading.
- Proteomics: Proteins should be free from inhibitors and other contaminants. Sample preparation might involve protein extraction, purification, and quantification. Protein digestion and peptide enrichment are used for mass spectrometry-based analyses.
- Metabolomics: Requires samples with minimal metabolite degradation. Proper quenching and extraction methods are essential for accurate metabolite profiling.
Why use Cureline services for your omics projects?
Cureline, Inc is a global precision and translational medicine CRO providing preclinical and laboratory services to the biopharmaceutical industry since 2003. Cureline Group offers a full range of ISO-certified, CAP-compliant clinical research services (Biobanking, Histo/Digital and molecular pathology, small animal and POC validation) for biopharma researchers conducting preclinical and biomarker/companion diagnostics development projects. Cureline headquarters, based in California (USA), oversees global clinical operations and regulatory affairs in 20+ countries (US, EU, Eastern Europe, China, India, and South America). A preclinical studies center is in Vilnius, Lithuania.
- Our Quality Management system follows the College of American Pathologists (CAP) guidelines, is ISO 20387:2018 compliant, and is ISO 9001:2015 certified.
- Rigorous Quality control program at the collection sites.
- Clinical Network participants are major clinics, research centers, or central laboratories that undergo audits, receive training on Cureline SOPs, and are supported in professional development.
- Shipments are temperature-controlled.
- Storage is temperature-controlled with appropriate thresholds.
- Biospecimens are diagnosis-verified and validated for morphology quality by a US board-certified MD pathologist.