e because they can meet the sensitivity expectation.
SAMPLE PRETREATMENT
Analysis of residual DNA requires accurate quantication of picogram levels of DNA in mg (or larger) quantities of product, which may be in a variety of matrices. In certain circumstances, the sample can be analyzed neat in the analytical procedure with acceptable recovery and precision. When the product or other sample components interfere with the assay sample, dilution may be all that is required to overcome the interference, so long as the specied DNA content of the sample remains within the useful range of the analytical procedure. When sample dilution is not effective in reducing assay interference, it may be necessary to use more extensive sample pretreatment procedures, such as proteolytic digestion, chemical dissociation, or extractions. It may be necessary to use a combination of different pretreatment steps to remove interference to an acceptable level. Extensive sample manipulation can lead to losses of DNA or introduction of environmental DNA, and should be a consideration when using one or more sample pretreatment steps. Contamination with environmental DNA may only be a concern when using a residual DNA procedure that is not sequence specic.
Protein samples may only require digestion with proteinase (e.g., Proteinase K, Pronase) to allow the analytical method to quantitatively recover the residual DNA. It may also be possible that the DNA is bound to the sample components, and chemical dissociation (e.g., detergents) may disrupt the binding, allowing sucient recovery in the residual DNA assay. Residual DNA test procedures often use protein reagents and the use of a chemical dissociation reagent. These materials must be used at a suciently low level or removed so that the analysis is not compromised.
It may be necessary to extract the DNA from the sample to remove the inhibitory substances that are causing the reduced DNA recovery. Extraction procedures are typically based on precipitating the DNA from the sample or DNA-specic binding to a matrix
https://online.uspnf.com/uspnf/document/1_GUID-373A1D1F-60DD-40E4-A922-1BDCC0C1AAF9_1_en-US?source=TOC 2/8
OF OFFICIAL
2021/8/25 USP-NF 〈1130〉 Nucleic Acid-Based Techniques—Approaches for Detecting Trace Nucleic Acids (Residual Dna Testing)
(e.g., magnetic beads). Historically, extraction methods based on phenol and chloroform, followed by ethanol precipitation, have been applied to the purication of DNA in molecular biology research. The phenol/chloroform extraction technique may be a useful pretreatment for residual DNA samples before analysis, but the phenol/chloroform extraction technique might not be the best choice for the low levels of DNA typically found in biopharmaceutical samples. Because of these low levels, quantitative DNA recovery with ethanol precipitation may be dicult. For this reason, a carrier molecule (e.g., glycogen) may be necessary to aid in DNA recovery if the phenol/chloroform extraction technique is used. Commercial kits are available and have been used successfully for pretreatment of residual DNA samples for improved recovery in the residual DNA assay. For example, some kits use a chaotrope (sodium iodide) and a detergent (sodium N-lauroyl sarcosinate) to disrupt the association of the DNA with the sample. The DNA is then co- precipitated using glycogen as the carrier molecule in the presence of isopropanol. Extraction of DNA from the sample, based on binding to a solid matrix, can be found in various formats. One of the most popular formats uses magnetic beads, where the beads are added to a sample with a binding solution to capture the sample DNA on the beads. The beads are then captured and held in the sample tube using a magnetic stand while the supernatant containing the interfering substances is removed and discarded. The beads are washed repeatedly using a magnetic stand and a wash solution. Finally, the DNA is eluted from the beads for the assay using an elution buffer, with the beads being removed from the sample preparation using the magnetic stand.
The sample manipulation involved with pretreatment may reduce the recovery of the residual DNA or introduce environmental DNA into the sample. Great care must be taken during any sample manipulations to avoid DNA losses or contamination. The addition of target DNA-spiked samples in the residual DNA assay is a common practice. The target DNA-spiked sample should not be confused with the internal positive control (IPC), which is typically a nontarget DNA added after the sample pretreatment step to detect the presence of PCR inhibitors and to evaluate DNA amplication during the analysis. The IPC may also be introduced before the extraction to improve the control of this step. A recovery of 50%–150% of the spiked target DNA is often applied to residual DNA assays to ensure that the assay yields acceptable results. When sample characteristics (e.g., matrix effects or sample preparation method) make achieving a recovery acceptance criterion of 50%–150% impractical, then correcting the observed DNA concentration by using the load recovery percentage is also an acceptable approach.
HYBRIDIZATION-BASED RESIDUAL DNA ASSAY
The rst residual DNA assays were based on DNA hybridization, wherein a DNA probe created from host cell DNA detects and quanties the amount of complementary DNA present in the product under assay. Double-stranded host cell DNA consists of two complementary strands of DNA that are held together by hydrogen bonding. The double-stranded DNA in the test sample is denatured to single strands and immobilized to a membrane, typically a nitrocellulose or nylon membrane. The sample is probed using host cell
https://online.uspnf.com/uspnf/document/1_GUID-373A1D1F-60DD-40E4-A922-1BDCC0C1AAF9_1_en-US?source=TOC 3/8