Identification of genetic variants demands high quality genomic DNA (gDNA). Pre-analytical variations in (i) sample collection, (ii) stability, (iii) sample labelling, (iv) transport to the site of analysis, (v) tissue/sample processing and (vi) storage, should be minimized throughout the workflow to guarantee the highest possible sample quality (see guideline ICH E18 cited in section 3).
Procedures to ensure sample adequacy and quality must be in place in any genomic study particularly where multiple centres are involved. There is published advice regarding pre-analytical workflows encompassing e.g. isolation of DNA from snap frozen tissue as well as for isolation of gDNA, cell-free DNA (cfDNA) and circulating tumour DNA (ctDNA) from whole venous blood.
Barcode or radio frequency identification (RFID) labelling of samples has several advantages and the same label should follow the sample throughout all analyses. Coding and anonymization of stored samples should follow established protocols and quality management systems allowing for (i) the destruction of the samples if the patient withdraws the consent or (ii) further follow-up analyses if the patient consent is still valid (see ISO15189).
Sample quality is usually retained during long term storage of DNA samples in water at + 4°C and – 20°C with attention to avoid sample dry-out or repeated freeze- thaw cycles. The reader is here also referred to the guideline on genomic sampling and management of genomic data (as well as ICH E18).
Retrospective PGx (Pharmacogenomics) related studies using DNA analyses, including NGS, are often performed on stored samples. It is important that these biosamples are not limited by their quality and/or quantity.
Increasingly, sophisticated genomic techniques for PGx analysis require the establishment of dedicated PGx sample repositories that employ scrupulous standards governing sample quality and usage.
Read also: Specific Issues for HLA Alleles