Before beginning library preparation for next-generation sequencing, it is highly recommended to perform sample quality control (QC) to check the nucleic acid quantity, purity and integrity. The starting material for NGS library construction might be any type of nucleic acid that is or can be converted into double-stranded DNA (dsDNA). These materials, often gDNA, RNA, PCR amplicons, and ChIP samples, must have high purity and integrity and sufficient concentration for the sequencing reaction.
1. Nucleic Acid Quantification
Measuring the concentration of nucleic acid samples is a key QC step to determine the fit and amount of nucleic acid available for further processing.
A UV-Vis spectrophotometer can be used to analyze spectral absorbance to measure the whole nucleic acid profile and can differentiate between DNA, RNA and other absorbing contaminants. Different molecules such as nucleic acids, proteins, and chemical contaminants absorb light in their own pattern. By measuring the amount of light absorbed at a defined wavelength, the concentration of the molecules of interest can be calculated. Most laboratories are equipped with a US-Vis spectrophotometer to quantify nucleic acids or proteins for their day-to-day experiments. Customers can choose from several spectrophotometers currently available such as Thermo Scientific™ NanoDrop™ UV-Vis spectrophotometer, Qiagen QIAExpert System, Shimadzu Biospec-nano etc.
Fluorescence methods are more sensitive than absorbance, particularly for low-concentration samples, and the use of DNA-binding dyes allows more specific measurement of DNA than spectrophotometric methods. Fluorescence measurements are set at excitation and emission values that vary depending on the dye chosen (Hoechst bis-benzimidazole dyes, PicoGreen® or QuantiFluor™ dsDNA dyes). The concentration of unknown samples is calculated based on comparison to a standard curve generated from samples of known DNA concentration.
The availability of single-tube and microplate fluorometers gives flexibility for reading samples in PCR tubes, cuvettes or multiwell plates and makes fluorescence measurement a convenient modern alternative to the more traditional absorbance methods. Thermo Scientific (Invitrogen) Qubit™ Fluorometer is one of the most commonly used fluorometers that accurately measure low concentration DNA, RNA, and protein.
2. Nucleic Acid Purity
Nucleic acid samples can become contaminated by other molecules with which they were co-extracted and eluted during the purification process or by chemicals from upstream applications. Purification methods involving phenol extraction, ethanol precipitation or salting-out may not completely remove all contaminants or chemicals from the final eluates. The resulting impurities can significantly decrease the sensitivity and efficiency of your downstream enzymatic reactions.
- UV spectrophotometry measurements enable calculation of nucleic acid concentrations based on the sample’s absorbance at 260 nm. The absorbance at 280 nm and 230 nm can be used to assess the level of contaminating proteins or chemicals, respectively. The absorbance ratio of nucleic acids to contaminants provides an estimation of the sample purity, and this number can be used as acceptance criteria for inclusion or exclusion of samples in downstream applications.
- Contaminants such as RNA, proteins or chemicals can interfere with library preparation and the sequencing reactions. When sequencing DNA, an RNA removal step is highly recommended, and when sequencing RNA, a gDNA removal step is recommended. Sample purity can be assessed following nucleic acid extraction and throughout the library preparation workflow using UV/Vis spectrophotometry. For DNA and RNA samples the relative abundance of proteins in the sample can be assessed by determining the A260/A280ratio, which should be between 1.8–2.0. Contamination by organic compounds can be assessed using the A260/A230 ratio, which should be higher than 2.0 for DNA and higher than 1.5 for RNA. Next-generation spectrophotometry with the Qiagen QIAxpert system enables spectral content profiling, which can discriminate DNA and RNA from sample contaminants without using a dye.
Quantitative PCR, or real-time PCR, (qPCR) uses the linearity of DNA amplification to determine absolute or relative quantities of a known sequence in a sample. By using a fluorescent reporter in the reaction, it is possible to measure DNA generation in the qPCR assay. In qPCR, DNA amplification is monitored at each cycle of PCR. When the DNA is in the log-linear phase of amplification, the amount of fluorescence increases above the background. The point at which the fluorescence becomes measurable is called the threshold cycle (CT) or crossing point. By using multiple dilutions of a known amount of standard DNA, a standard curve can be generated of log concentration against CT. The amount of DNA or cDNA in an unknown sample can then be calculated from its CT value.
qPCR-based assays can accurately qualify and quantify amplifiable DNA in challenging samples. For example, DNA derived from Formalin-fixed paraffin-embedded tissue samples, is oftentimes highly fragmented, cross-linked with protein and has a high proportion of single-stranded DNA making it challenging to perform library preparation steps. For FFPE samples, the Agilent NGS FFPE QC kit enables functional DNA quality assessment of input DNA.
3. Nucleic Acid Integrity (Size distribution)
Along with quantity and purity, size distribution is a critical QC parameter that provides valuable insight into sample quality. Analyzing nucleic acid size informs you about your sample’s integrity and indicates whether the samples are fragmented or contaminated by other DNA or RNA products. Various electrophoretic methods can be used to assess the size distribution of your sample.
- Agarose Gel Electrophoresis
In this method, a horizontal gel electrophoresis tank with an external power supply, analytical-grade agarose, an appropriate running buffer (e.g., 1X TAE) and an intercalating DNA dye along with appropriately sized DNA standards are required. A sample of the isolated DNA is loaded into a well of the agarose gel and then exposed to an electric field. The negatively charged DNA backbone migrates toward the anode. Since small DNA fragments migrate faster, the DNA is separated by size. The percentage of agarose in the gel will determine what size range of DNA will be resolved with the greatest clarity. Any RNA, nucleotides, and protein in the sample migrate at different rates compared to the DNA so the band(s) containing the DNA will be distinct.
Analyzing PCR amplicons or RFLP fragments confirms the presence of the expected size fragments and alerts you to the presence of any non-specific amplicons. Electrophoresis also helps you assess the ligation efficiency yield for plasmid cloning procedures as well as the efficiency of removal of primer–dimers or other unspecific fragments during sample cleanup.
For complex samples such as genomic DNA (gDNA) or total RNA, the shape and position of the smear from electrophoresis analysis directly correlates with the integrity of the samples. Nucleic acid species of larger size tend to be degraded first and provide degradation products of lower molecular weight. Samples of poor integrity generally have a higher abundance of shorter fragments, while high-quality samples contain intact nucleic acid molecules with higher molecular size.
Eukaryotic RNA samples have unique electrophoretic signatures, which consist of a smear with major fragments corresponding to 28S, 18S and 5S ribosomal RNA (rRNA). These electrophoretic patterns correlate with the integrity of the RNA samples. The RNA integrity can either be assessed manually or with automation that employs a dedicated algorithm such as the RNA Integrity Number (RIN) that gives an objective integrity grade to RNA samples ranging from 1–10. RNA samples of highest quality usually have a score of 8 or above.
- Capillary Electrophoresis
In this method, charged DNA or RNA molecules are injected into a capillary and are resolved during migration through a gel-like matrix. Nucleic acids are detected as they pass by a detector that captures signals of specific absorbance. Results are presented in the form of an electropherogram, which is a plot of signal intensity against migration time. The fragment sizes are precisely determined using a size marker consisting of fragments of known size. This method provides highly resolving and sensitive nucleic acid analysis that is faster and safer.