Do I need SNP in addition to STR for paternity test?

In paternity testing, Short Tandem Repeats (STRs) are a very effective and common method, but Single Nucleotide Polymorphisms (SNPs) may also be used as an adjunct. Below we describe the characteristics of STRs and SNPs and how each can be useful in paternity testing.

Difference between STR and SNP

STR（Short Tandem Repeats）

• Characteristics: STRs are short sequences of 2-6 base pairs that are repeated, and the number of repeats varies from individual to individual, making them highly diverse.
• Use: Due to its high mutation rate and diversity, it is widely used in forensic science, paternity testing, and personal identification. By using multiple STR markers, the accuracy of determining parent-child relationships exceeds 99.99%.

For example.)

D1S1656 is a sequence of four bases called TAGA on the first chromosome.
A person has two chromosomes.One chromosome comes from the person’s father and the other from the mother.

XXXXXXXXTAGA-TAGA-TAGA-TAGA-TAGA-TAGA-TAGAXXXXXXXXXXXXXXXXXXXXXXXX 6 pieces XXXXXXXXTAGA-TAGA-TAGA-TAGA-TAGA-TAGAXXXXXXXXXXXXXX 4 pieces
There is a combination of the two.
In that case, it displays D1S1656 6, 4.
X indicates a random sequence.

SNP（Single Nucleotide Polymorphisms）

• Characteristics: SNPs are points at which single bases in the genome differ, while mutations are differences at the single nucleotide level. In general, SNPs are not as diverse as STRs, but are widely distributed throughout the genome.
• Use: SNPs are used in evolutionary studies, population genetics, and disease association studies due to their low mutation rates and wide distribution.

For example.)
rs1490413 SNP on chromosome 1 at position 4307263.
The base in the Tsujo position can be either A (adenine) or G (guanine).

Role of STRs and SNPs in paternity testing

Role of STR

STR is used as the primary method in parent-child appraisals. The following are the main reasons

1. High diversity: the number of STR repeats varies from individual to individual and has many different alleles, making it very useful for individual identification.
2. Rapid analysis: PCR (polymerase chain reaction) can be used for rapid amplification and analysis.
3. High accuracy: By combining many STR markers, the accuracy of determining parent-child relationships is very high.

Role of SNPs

SNPs may be used as an adjunct in paternity testing. Here is why

1. Widespread distribution: Widespread distribution throughout the genome allows for the use of this information as a complement to specific genetic traits and relationships.
2. Additional Accuracy Improvement: If the STR analysis yields ambiguous results, the accuracy can be improved by adding SNP analysis.
3. Disease association analysis: Simultaneously with paternity testing, it is possible to provide risk assessments for genetic diseases and other genetic information.

Conclusion.

STRs are very effective as the primary method of parent-child identification and can determine parent-child relationships with a very high degree of accuracy due to their high diversity and rapid analysis capabilities. SNPs play a major ancillary role and may be used especially when STRs alone cannot resolve the issue. SNPs can further improve accuracy by providing additional information. At HIROCLICK, we also use this concept to perform prenatal paternity DNA testing.

Therefore, while STR is primarily used in normal paternity testing, it is beneficial to also use SNP when more detailed analysis or additional information is needed. Both methods provide a high degree of reliability in determining parent-child relationships by taking advantage of their respective characteristics.

参考文献

Supervisor of the article

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Dr. Hiroshi Oka

Director of CAP Laboratory

Graduated from Keio University, Faculty of Medicine

Doctor of Medicine

Medical Doctor