1. Introduction
1.1. Objectives of the Guideline
The main objective of this guideline is to provide harmonised principles of genomic sampling and management of genomic data in clinical studies. This guideline will facilitate the implementation of genomic studies by enabling a common understanding of critical parameters for the unbiased collection, storage, and optimal use of genomic samples and data. This guideline also intends to increase awareness and provide a reminder regarding subjects’ privacy, protection of the data generated, the need to obtain suitable informed consent, and the need to consider transparency of findings in line with local legislation and regulations. This guideline is intended to foster interactions amongst stakeholders, including drug developers, investigators and regulators, and to encourage genomic research within clinical studies.
- Background
Increased awareness and interest in genomic data from clinical studies are evident, with potential applications in drug development, including assessing genomic correlates of drug response and understanding disease mechanisms. Identifying genomic biomarkers can optimize patient therapy, enhance study designs, and aid in drug labelling. Regulatory agencies in the ICH regions promote genomic sample collection throughout drug life cycles, yet the absence of a unified ICH guideline on genomic sampling hampers consistent research in global clinical studies. Genomic samples can facilitate various analyses, impacting study objectives and outcomes.
1.3. Scope of the Guideline
The scope of this guideline pertains to genomic sampling and management of genomic data obtained from interventional and non-interventional clinical studies. Genomic research can be conducted during or after a clinical study. It may or may not be pre-specified in the clinical protocol. This document addresses use of genomic samples and data irrespective of the timing of analyses and both pre-specified and non-pre-specified use. Genomic samples and data described in this guideline are consistent with the deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) characteristics defined in ICH E151. The focus of this guideline is on the general principles of collection, processing, transport, storage, and disposition of genomic samples or data, within the scope of an informed consent. Technical aspects are also discussed when appropriate, recognizing the rapidly evolving technological advances in genomic sampling and data generation.
No detailed guidance is included on biobanking regulations or ethical aspects, as these are
governed by the principles of the Declaration of Helsinki and national rules and regulations.
The same applies to issues related to privacy/data protection. The principles in this guideline may apply to any genomic research utilizing human-derived materials.
The recommendations in this guideline are principles and they should be interpreted in
accordance with legislations, regulations as well as policies in each jurisdiction where
genomic research is undertaken.
1.4. General Principles
With advances in science and increased awareness of the impact of genomics, there is a need and an opportunity to maximize the value of the collected samples and the data generated from them. Therefore, genomic sample acquisition is strongly encouraged in all phases and studies of clinical development. Moreover, the quality of genomic research is dependent upon unbiased systematic collection and analysis of samples, ideally from all subjects participating in the trial, in order to fully represent the study population. Maintaining sample integrity is important and has a major impact on the scientific utility of genomic samples. The quality and amount of samples, and technical performance of the assay (e.g., accuracy, precision, sensitivity, specificity, reproducibility) will determine the reliability of genomic data. Establishing standardized practice for handling and processing of genomic samples will foster integration of data from different analytical platforms and facilitate decision making. Genomic samples and data should be securely stored, maintained, and access-controlled similar to non-genomic samples and health information.
- GENOMIC SAMPLING
Genomic research encompasses a wide variety of methods and applications. These may include, but are not limited to, nucleic acid sequencing and genotyping, analysis of various types of RNA, gene expression or regulation, and detection of epigenetic modifications. Ever evolving technological advancements are expected to yield novel applications. The scope of the research will determine the specimen type and the analyte(s) to be assessed, and the methodologies used to extract analytes and to stabilize and store well-annotated samples for genomic testing. Sample quality and amount can influence the accuracy and reliability of the generated data. Therefore, collection, handling, and preparation of the biological samples are critical steps in the research process.
To minimize pre-analytical variation in genomic sample handling, standardized procedures for sample collection, processing, transport, and storage must be developed and documented. These procedures should be tailored to specimen types, analytes, and tests conducted. It is crucial to define, document, and verify handling processes across study sites and record the timing, method, location, and conditions of sample collection. Any deviations from established procedures should be well-documented throughout the sample’s lifecycle. The chain of custody and timing for all steps in sample collection, handling, and analysis must be recorded. Implementing quality control programs is recommended to ensure biological sample stability from acquisition to testing.
2.1. Collection and Processing of Samples
A strategy for sample collection and processing for genomic testing must consider several pre-analytical variables to ensure sample suitability. Variations in procedures across different clinical study sites can influence test performance, affecting data interpretability and reliability. Thus, all staff must be adequately trained in standardized procedures, and specimens should be collected and labeled following biosafety practices, privacy regulations, and informed consent guidelines.
2.1.1. Specimen Type
Nucleic acids may be extracted from a variety of clinical specimen types and matrices (e.g., blood cells, tissue, buccal swab, saliva, bone marrow aspirate, urine, feces). Novel sources of tissue-derived nucleic acids (e.g., cell-free DNA, circulating tumor cells) are emerging and might require distinct isolation methods. The principles detailed herein also apply to these sources. The type of specimens to be collected should be compatible with the intended use. For example, some types of specimens could be used for both DNA and RNA studies while other specimen types may not be suitable for RNA analysis due to the lack of analyte stability.
In pediatric subjects, only limited amounts of blood or other tissues may be available and therefore non-invasive alternatives, such as saliva, dried blood spot or skin scrapings could be considered. For certain types of sample (e.g., blood, muscle biopsy) attention should be paid to aseptic collection. Care should be taken when biological materials that may bear the risk for contamination with other than host DNA and RNA are used (e.g., buccal swabs, saliva).
2.1.2. Timing of Specimen Collection
Inter- and intra-subject variability should be considered in the context of the clinical study objectives when defining the sample collection strategy. For example, diurnal variation or administered treatments can influence gene expression and should be considered when selecting sampling time points. Epigenetics such as DNA methylation may also change over time (e.g., subject age). While the sequence of germline DNA is relatively stable over time, information obtained from tumor DNA and RNA can be affected by the source, method and/or timing of the sample collection.
2.1.3. Specimen Preservation Conditions
The type of specimen, the quantity or volume of sample needed, the prospective test and technology, the nucleic acid target, and the type and necessity of an additive, stabilising agent, or preservative will all influence the collection container. For instance, tubes with anticoagulants or additives suitable for the intended nucleic acid type are used to collect blood or bone marrow aspirate specimens. Tissue samples can be put in a suitable preservative or snap-frozen in liquid nitrogen.
Tissues are often fixed for long-term storage. Parameters that should be carefully considered for tissue fixation are the type of fixative, fixation time, humidity, oxygenation, and temperature, as well as the compatibility with the downstream nucleic acid extraction method. It is recommended to evaluate the impact of fixation and additives on the analytes of interest and the types of tests to be carried out prior to sample collection in a clinical study. In addition, the specimen tissue type and volume may affect the optimal duration of fixation and therefore should be taken into account. Sample handling methods subsequent to initial fixation could also impact the integrity of the specimens.
2.1.4. Sample Stability and Degradation
Appropriate handling measures should be taken to prevent nucleic acid degradation and
genomic profile alterations during sample collection and processing. Nucleic acid
fragmentation and apparent changes in gene expression can occur and are dependent on
conditions related to pH, hypoxia, the presence of endonucleases, and/or other tissue specific
parameters. In addition, the time from specimen collection to freezing, fixation, or processing,
as well as the storage time, should be optimized as needed.
The parameters for sample collection and handling should be documented in relevant instructions, training materials, and sample reports. It is advisable to monitor storage and processing conditions, such as temperature, to ensure consistency across samples.
2.1.5. Specimen Volume and Composition
Collection volume for samples is an issue that requires careful consideration. Consideration should be given to the minimum tissue or cell content needed for the intended purposes (e.g., analytical methodology) to minimize burden on subjects. The optimal amount of tissue may be dependent upon the cellularity of the tissue (e.g., smaller amounts may be sufficient for highly cellular tissue types) and the relative proportion of particular cell types in the entire specimen (e.g., tumor area and/or other aspects of a disease as represented in a biopsy). In the event that only a limited amount of tissue is available, alternative biological material may be considered for collection (see also section 2.1.1). As tumor tissue may exhibit molecular heterogeneity (mosaicism) and tumor biopsies often consist in part of normal tissue, a documented pathological evaluation of the sample prior to genomic analysis may be helpful. When paired samples are collected (e.g., tumor versus normal tissue, pre- versus post-treatment samples, prenatal versus maternal specimens), additional considerations (e.g., matched samples, cell types) may be needed to allow comparison.
2.1.6. Parameters Influencing Genomic Sample Quality and Quantity
The quality and yield of the extracted nucleic acids are affected by the quality of the source
specimens amongst other factors (see also section 2.1.5). As a result, the extraction
procedures should be defined and validated for the handling conditions and the specimen type
to be used. Specimen types have diverse characteristics and components that can affect the
recovery of nucleic acids, and these should be considered when selecting a methodology for
nucleic acid extraction. For example, the procedures for cell lysis may vary for different
tissue and body fluid specimens. The process for removing specific cell constituents may also
differ depending on the composition of the specimens. It should be noted that such processes
may affect gene expression and lead to unintended spurious results. If both DNA and RNA
will be extracted from the same specimen it should be determined whether extraction is best
performed simultaneously or if the tissue specimen should be divided at the time of collection.
Due to the labile nature of RNA compared to DNA, additional precautions are needed when
isolating RNA, such as the use of RNase-free equipment and reagents. Repeated freezing and
thawing of specimens prior to nucleic acid extraction can affect genomic sample integrity and
should be avoided when possible or otherwise evaluated. To determine if the quality and
quantity of the extracted nucleic acid targets are adequate for the intended downstream
genomic testing, appropriate quality control methods should be applied relative to the analyte
being measured.
The entire text of ICH E18 could not be presented in this article due to space constraints. To properly grasp,GUIDELINE ON GENOMIC SAMPLING AND MANAGEMENT OF GENOMIC DATA E18it is advised that you read the entire guideline. The link is provided below
Reference:
https://database.ich.org/sites/default/files/E18_Guideline.pdf
Dr Subramanian S Iyer
