The following genetic testing techniques are commonly used to test for specific SNPs (single nucleotide polymorphisms). These methods are useful for identifying the location of SNPs and genetic variants.
1. PCR (polymerase chain reaction) and RFLP (restriction enzyme fragment length polymorphism) analysis
- Description: PCR is used to amplify a target DNA region, followed by cleavage of the DNA using a specific restriction enzyme; if SNPs are present, differences in cleavage patterns can be observed, thus confirming the presence of genetic polymorphisms.
- Characteristics: This is a relatively inexpensive and commonly used basic method. However, the disadvantage is that the process is complicated and the throughput is low because it is specific to a particular SNP. 2.
2. Real-time PCR (qPCR) and allele-specific probes
- Description: This method uses allele-specific probes (e.g., TaqMan probes) to detect specific SNPs. The probe binds specifically to the variant of the SNP, allowing real-time quantification of which allele is present.
- Features: High sensitivity and accuracy, and results are obtained in a relatively short time. Especially efficient when the target SNP is known.
3. DNA sequencing (Sanger sequencing)
- Description: The Sanger sequencing method is used to read specific DNA regions to directly confirm the position and mutation of SNPs.
- Features: Highly accurate and reliable method, but expensive and inefficient for large numbers of targets. Suitable for single or small number of SNP detection. 4.
4. Next Generation Sequencing (NGS)
- Description: NGS is a highly accurate and high-throughput method for sequencing whole DNA or specific regions. It can detect not only specific SNPs but also other genetic variants simultaneously.
- Features: Because it can analyze a large number of SNPs at once, it is suitable for obtaining comprehensive genetic information. However, it is expensive and may provide an excessive amount of information when targeting only specific SNPs.
5. SNP array (DNA microarray)
- Description: Pre-designed probes are placed on an array and sample DNA binds to these probes to detect specific SNPs; depending on the position of the SNP, the signal on the array changes, resulting in confirmation of the SNP type.
- Features: The ability to rapidly screen for many SNPs at once allows for a wide range of genetic information. However, there is a limitation that SNPs not on the array cannot be detected.
6. Digital PCR (dPCR)
- Description: dPCR divides DNA into many small partitions and performs PCR on each partition to detect specific SNPs. This allows quantification of specific alleles with high accuracy.
- Characteristics: It allows absolute quantification of specific SNPs and is excellent for low-frequency SNP detection, but is not suitable for simultaneous detection of other SNPs or polymorphisms.
Points to consider when performing a specific SNP test
- Purpose and cost of the test: Depending on the amount of information and accuracy needed, it is important to choose the most appropriate method, taking into account cost and time.
- Use of a laboratory: Because genetic testing requires specialized equipment and knowledge, it is usually performed by a genetic testing service or medical facility.
