What are the limitations of Sanger sequencing?
Posted May 2, 2023
Answer
Limitations of Sanger sequencing include:
- Inability to detect large deletions or duplications of sequences
- Can only sequence short DNA fragments of about 300 to 1000 base pairs
- Sequence quality is not very good in the first 15 to 40 bases as that is where the primer binds
- Sequence quality degrades after 700 to 900 bases
- Not suitable for parallel testing
- Not suitable for sequencing large genomes
- High infrastructure costs and high cost per test
Despite its limitations, Sanger sequencing is still a good choice when sequencing single genes or amplicon targets up to 100 base pairs, analyzing fragments or short tandem repeats, or identifying microbes.
Additional resources