Published: July 17th, 2021
Here we describe a simple protocol to generate DNA fingerprinting profiles by amplifying the VNTR locus D1S80 from epithelial cell DNA.
In biological sciences, DNA fingerprinting has been widely used for paternity testing, forensic applications and phylogenetic studies. Here, we describe a reliable and robust method for genotyping individuals by Variable Number of Tandem Repeat (VNTR) analysis in the context of undergraduate laboratory classes. The human D1S80 VNTR locus is used in this protocol as a highly polymorphic marker based on variation in the number of repetitive sequences.
This simple protocol conveys useful information for teachers and the implementation of DNA fingerprinting in practical laboratory classes. In the presented laboratory exercise, DNA extraction followed by PCR amplification is used to determine genetic variation at the D1S80 VNTR locus. Differences in the fragment size of PCR products are visualized by agarose gel electrophoresis. The fragment sizes and repeat numbers are calculated based on a linear regression of the size and migration distance of a DNA size standard.
Following this guide, students should be able to:
• Harvest and extract DNA from buccal mucosa epithelial cells
• Perform a PCR experiment and understand the function of various reaction components
• Analyze the amplicons by agarose gel electrophoresis and interpret the results
• Understand the use of VNTRs in DNA fingerprinting and its application in biological sciences
Molecular fingerprinting, also referred to as DNA fingerprinting, was introduced by Sir Alec Jeffreys while working in the Department of Genetics at the University of Leicester in 19841. It is based on the 0.1% of the human genome that differs between individuals and is comprised of approximately three million variants. These unique differences in the genotype allow for the differentiation between individuals and can therefore function as a genetic fingerprint except for monozygotic twins. Consequently, DNA fingerprinting is used for the estimation of relatedness of different individuals that is applied for example in paternity testing or in population diversity studies. In our laboratory classes we aimed to convey the concept of DNA fingerprinting and allele frequencies. The method described here demonstrates a reliable and robust method for genetic fingerprinting by analyzing the Variable Number of Tandem Repeats (VNTR) at the D1S80 locus. The method comprises the extraction of DNA from buccal mucosa epithelial cells and subsequent Polymerase Chain Reaction (PCR) to amplify the D1S80 locus, followed by visualization of fragment length differences on an agarose gel.
The D1S80 VNTR minisatellite locus is highly variable and located at the telomeric region of chromosome 1 (1p36-p35). It was identified and described by Karsai and co-workers in 1990 as a locus with a core repeat unit of 16 bp, allowing for the separation of alleles differing by just one unit2. Furthermore, D1S80 shows a high degree of variation with a mutation rate of approximately 7.77 x 10-5 3. D1S80 has a high degree of heterozygosity4,5 (e.g., 80.8% heterozygosity for Caucasians6 and up to 87% heterozygosity for African-Americans7). Additionally, the D1S80 locus is polymorphic in most populations, with typically over 15 different alleles carrying 14 to 41 repeats each. The frequency of D1S80 alleles varies between populations. The allele with 24 repeat units (allele 24) is most frequent in European and Asian populations, whereas allele 21 is most common in African populations4,7,8,9,10. Consequently, the allele frequency distributions are diagnostic for different human populations and need to be taken into account for the estimation of relatedness (e.g., in paternity tests).
PCR based amplification of the D1S80 VNTR locus has been a very useful method in forensic science, paternity tests, disease analysis and population diversity studies11,12,13,14. While in forensics today the use of VNTRs has been replaced by short tandem repeats, the D1S80 VNTR locus is widely used in the determination of origins and genetic relations among and between populations4,8,9,11. Furthermore, it is often used to teach DNA fingerprinting in practical laboratory classes15,16. The method described here represents a robust, cost-effective and easy-to-use method with a very high success rate in undergraduate laboratory classes. The purpose of this article is to provide an overview of the workflow for the molecular analysis of the human D1S80 minisatellite locus from buccal mucosa epithelial cells. It includes demonstration of techniques, simplified protocols and practical suggestions described in previously published works2,17.
NOTE: This protocol is only to be used if students or respective legal guardians agreed to the conductance of this protocol as genotypic profiles give insights into genetic relationships. DNA fingerprinting is a common molecular biology method mainly applied to population studies and forensic matters. Therefore, attention should be devoted to keep contamination risks as low as possible. To avoid contamination of the sample with DNA from an outside source or DNases, gloves should be worn, instruments should be thoroughly cleaned or sterilized and solutions should be filter-sterilized or autoclaved before usage.
1. Harvesting of buccal mucosa epithelial cells
CAUTION: Work with saliva and epithelial cells can lead to a transmission of infectious diseases. Therefore, standard and transmission-based precautions should be applied (e.g., the use of appropriate personal protective equipment).
NOTE: Include a positive control, which is provided by the instructor (e.g., DNA extracted by the instructor) and included in the downstream processing steps.
2. Extraction of genomic DNA from human cells
3. Amplifying the D1S80 VNTR locus using PCR
NOTE: Record the number of samples that will be used and prepare a worksheet with the required reagents and their volumes before collecting the necessary plastics and other materials. Label the sterile tubes/strips/plates to be used for the PCR with sample numbers. Remember to include a negative control using H2O instead of DNA and a positive control (e.g., using the DNA provided by the instructor) to validate the PCR.
4. Agarose gel electrophoresis of PCR products
5. Analysis of fragment length results
NOTE: Use linear regression analysis to estimate the lengths of the fragments.
6. Estimation of the number of repeat units in the alleles of the tested individuals
NOTE: The D1S80 repeat unit is 16 bp in length. The smallest known allele for D1S80 has 14 repeats. The amplicon scheme described here produces amplicons with flanking regions adding up an extra 145 bp to the final size.
Using the described protocol, D1S80 VNTR marker analysis was performed on human genomic DNA extracted from buccal mucosa epithelial cells harvested by swab sampling (Figure 6). Following the amplification using PCR, a typical representation of an agarose gel containing the D1S80 amplicons is shown in Figure 1. Lane 1 shows the 50 bp molecular weight standard. Next to the molecular weight standard, PCR products from eight student samples are visualized. Lane 10 shows the NTC in which water was used instead of template DNA. Most of the analyzed samples clearly display two bands, representing individuals heterozygous for the D1S80 locus. Lane 2 and Lane 9 show a single band representing individuals homozygous for the D1S80 locus. Lane 5 is showing an ambiguous single band which is much wider compared to the other bands. This could be a result of two D1S80 alleles differing in only one repeat unit. For further analysis, the sample in lane 5 will be considered as a single band, representing a homozygous individual.
Downstream gel electrophoresis fragment analysis performed on verified PCR products was used for size calling of the D1S80 VNTR locus of different student samples. Interpretation of the amplicon sizes obtained by PCR analysis relies on the molecular weight standard used. The distance from the well for each band of the molecular weight standard was measured (Figure 1) and recorded (Figure 2). Based on the size and migration distance the size of the individual bands can be calculated using a linear regression analysis. The log (base 10) was determined for each band in the student samples (Figure 5) and the respective antilog represents the number of bp for each amplicon. The number of repeat units can be calculated according to the amplicon size obtained (Table 2).
For each student sample the amplicon sizes were calculated by linear regression and each band could be easily assigned to a particular allele as shown in Table 2. The information on the D1S80 allele sizes can then be used to determine allele frequencies amongst the small population subset of undergraduate students. The 28-repeat allele is the most frequent among the students due to two homozygous individuals for this repeat allele (individuals 1 and 4). The second most frequent allele is the 18-repeat allele, which is carried by the homozygous individual 8 and by the heterozygous individual 6. Low frequency alleles are the 21-, 26- and 30-repeat alleles found only once in individuals 6, 5 and 3, respectively. The allele frequency patterns of the D1S80 VNTR locus of the small student population can further be compared to the allele frequency of larger human populations, for example populations originating from different continents4,7,8,9,10.
Among the students, individuals 2 and 3 share the 24-repeat allele, individuals 2 and 7 share the 20-repeat allele and individuals 5 and 7 share the 23-repeat allele. Interestingly, the two D1S80 homozygous individuals (individual 1 and 4) share the 28-repeat allele. Matching alleles between two individuals can indicate a potential relatedness. However, shared alleles can also occur by chance. Thus, it is crucial to determine the likelihood of an allele match between two individuals. The likelihood depends on the allele frequency of individual alleles in the general population and statistical approaches should be employed to attach a statistical weight to VNTR marker analysis such as the Bayesian approach. In summary, the presented fingerprinting method can be utilized in hands-on class practicals to teach the use of VNTRs in DNA fingerprinting and its application in biological science.
Figure 1: Representation of an agarose gel after electrophoresis of D1S80 amplification products with a ruler placed beside the 50 bp molecular weight standard lane. Lane 1 contains the 50 bp molecular weight standard, while lanes 2-9 contain PCR reaction products. Lane 10 contains the no template control (NTC). Please click here to view a larger version of this figure.
Figure 2: Determination of DNA fragment migration distance and log of each fragment size of the 50 bp molecular weight standard. The distance from the well (in cm) for each band of the 50 bp molecular weight standard is recorded and the log (base 10) for each fragment is determined. Values are entered into a table using a spreadsheet program. Please click here to view a larger version of this figure.
Figure 3: Scatter plot generated by plotting DNA fragment migration distance of the molecular weight standard on the x-axis against the log (base 10) of the size of each fragment on the y-axis. Please click here to view a larger version of this figure.
Figure 4: Exploitation of the linear regression line and regression equation as well as the R2 value for the data. Please click here to view a larger version of this figure.
Figure 5: Determination of the size of the D1S80 amplicons. The distance from the well for each fragment is entered into the regression equation. The antilog of the y-value represents the fragment size in bp. Please click here to view a larger version of this figure.
Figure 6: Suggested timeline and workflow for D1S80 VNTR analysis. The entire D1S80 VNTR analysis procedure presented here, from buccal epithelial cell harvesting to fragment length evaluation, may be completed within a single working day. Please click here to view a larger version of this figure.
|Allele size (in bp)
|Number of repeats
Table 1: Amplicon size for each D1S80 VNTR locus.
|Distance (in cm)
|Size (in bp)
|Number of repeat units
|5.2 ; 5.5
|4.9 ; 5.2
|5.1 ; 5.3
|5.4 ; 5.6
|5.3 ; 5.5
Table 2: Allele composition of the different individuals tested. The number of repeat units can be approximated according to the amplicon size obtained by linear regression analysis.
Here we described a simple and cost-efficient method for implementing molecular fingerprinting in undergraduate practical classes.
To screen for genetic variation at the D1S80 locus, human biological sample collection along with DNA extraction and analysis is required. It is essential that the ethical use of human biological specimens is ensured throughout the whole process. Sample management is controlled within a comprehensive regulatory framework which ensures the correct use of samples and associated data18 (e.g., consent for the use of human biological material). Participants must be properly informed about the use of their samples, the risk of discovery of anomalies in genetic relations (e.g., for related individuals), privacy protection and intentions for future storage of the biological specimens and data. All donors (students or colleagues) must give consent freely and understand the right to withdraw without giving reason. In general, it is indispensable to make oneself familiar with the respective guidelines and regulations for human sample management before conducting this lab class.
For the collection of buccal mucosa epithelial cells in undergraduate laboratory courses, care must be taken to avoid contamination of the DNA samples with DNA from the operator or with DNases. It is recommended that lab coats, gloves and protective glasses are always used as well as sterile swabs and microcentrifuge tubes. Buccal swab-based cell harvesting is considered a convenient and cost-effective method for the collection of genetic material suitable for PCR-based VNTR analysis, as it is relatively inexpensive and noninvasive. Beside buccal swabs, saliva is the most common oral sampling method for medical research. It has been shown that buccal swabs contain a higher proportion of epithelial cells than saliva, making them more reliable in providing sufficient quantity and quality of DNA for PCR-based D1S80 VNTR analysis19,20. Additionally, buccal swabs can be mailed out after self-collection overcoming geographical impediments when used, for example, in population diversity studies21.
DNA extraction has become relatively easy due to the development of extraction kits from different companies. Nevertheless, the use of those kits may not be suitable in laboratory classes due to limited financial resources. Here, we presented an easy, fast and cost-efficient method for DNA extraction from human samples without the need of a commercially available DNA extraction kit. The DNA extraction method described does not use organic solvents, instead cellular proteins are removed by increasing the salt concentration using an 8 M potassium acetate solution. This method also allows for handling of several samples at once and yields in sufficient DNA for several genotype analyses for each sample.
PCR is a common technique in many molecular laboratories. While generally trouble-free, there are pitfalls that may complicate the reaction producing spurious results, which have been discussed elsewhere22. PCR conditions presented here have appeared very robust in the face of poor template DNA quality, but lack of PCR amplification was nevertheless occasionally observed when using templates with extremely low DNA concentrations due to poor buccal epithelial cell harvesting. The DNA primers used in this study can be ordered from different companies, such as those cited in the table of materials at the end of this paper. Special care must be taken when working with DNA primers in order to avoid contamination with DNases or DNA from the operator. PCR products should also be kept cold when not in use.
Another critical step is the agarose gel electrophoresis. Fragments differing by only one repeat unit of 16 bp may not be separated in the gel electrophoresis and thus appear as a single band. In this case, a proper determination of the number of repeat units of the D1S80 alleles tested cannot be assured. Therefore, the run time of the gel should be increased while the voltage must be reduced and the gel concentration may be increased to provide a better resolution and separation of the single bands.
It is worth mentioning that not all alleles for an VNTR locus contain complete repeat units. Non-consensus alleles (microvariants) that contain incomplete repeat units are common at most VNTR loci and their sizes fall in between sizes of alleles with full repeat units. These microvariants are barely detectable by agarose gel electrophoresis. In contrast, techniques like polyacrylamide gels or capillary electrophoresis can resolve alleles that differ by one to a few repeat units or microvariants12,23,24,25,26. However, the latter techniques are less suitable for undergraduate laboratory classes as they have many disadvantages including use of hazardous compounds, complex preparation and lack of equipment. For the fragment size determination, special care must be taken when measuring the distance of the migrated DNA fragments. If the bands are too diffuse to be measured precisely, the calculation of the D1S80 allele fragment size by linear regression may be incorrect resulting in the wrong estimation of repeat unit numbers. In that case a re-run of the agarose gel electrophoresis after optimizing the gel conditions is advisable as previously described by Lorenz and co-workers22.
The entire D1S80 VNTR analysis procedure presented here, from buccal epithelial cell harvesting to fragment length evaluation, may be completed in a single working day. This protocol is a robust, cost-efficient and easy-to-use method suitable for undergraduate practical laboratory classes.
The authors have no conflict of interest to disclose.
The authors would like to thank Kevin Graham for his voice-over and all participants who donated samples for this work.
|1.5 mL microcentrifuge tube
|2 mL microcentrifuge tube
|5x PCR buffer
|dNTPs (10 mM)
|Gel Doc XR+
|GeneRuler 50 bp DNA Ladder
|1.5 mL and 2 mL
|1000 µL, 200 µL, 20 µL, 2 µL
|PowerPac power supply
|PCB 2.5 kg
|IKA RH basic
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