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Sanger Sequencing vs. Next-Generation Sequencing (NGS)
2024-11-27
DNA SequencingProtein
DNA sequencing is the process of determining the sequence of nucleic acids containing four nucleotides (adenine, guanine, cytosine, and thymine). Early DNA sequencing methods included using chain termination inhibitors for DNA sequencing and chemical degradation for DNA sequencing. Subsequently, in the 1990s, several sequencing methods were developed, collectively known as next-generation sequencing (NGS sequencing), including Sanger sequencing (Chain termination), Large scale sequencing and de novo sequencing, basic methods of Shotgun sequencing, and high-throughput methods such as Single molecule real time (SMRT) sequencing and Illumina (Solexa) sequencing. DNA sequencing has become an important foundational technology in fields such as the Human Genome Project and basic biological research.

Fig 1: History of sequencing technology. (Wikipedia)
Sanger Sequencing Workflow and PrincipleProtein
Sanger sequencing is a DNA sequencing method based on the random insertion of double deoxyribonucleotides (ddNTP) terminated by DNA polymerase during the DNA replication process. The chain termination nucleotide lacks the 3 '- OH group necessary for the formation of the phosphodiester bond. When ddNTP is incorporated, DNA polymerase will stop DNA extension, and ddNTP can be radiolabeled or fluorescent labeled for detection, and then separated by gel electrophoresis to read the sequence from the gel image. Although it has been replaced by next-generation sequencing with technological development, it can meet the requirements of small-scale and deep sequencing results with low error rates.
Material requirements
Single stranded DNA template, primers, DNA polymerase, normal deoxyribonucleotide triphosphate, and labeled deoxyribonucleotide triphosphate.
Process
1. The required DNA serves as a template for PCR reaction.
2. In the reaction, the normal base dNTP originally used as a raw material is mixed with the chain terminating base (ddNTP). If normal bases are added during the reaction process, DNA extension proceeds normally. If chain terminating bases are added, the chain stops extending. Random addition of chain terminating bases will result in DNA ending at the end of the chain terminating base and forming fragments of different sizes.
3. Use capillary electrophoresis to separate DNA fragments of different sizes.
4. Use laser excitation to fluorescently label the deoxyribonucleotides located at the end of the chain.
5. Create a chromatogram by comparing and recording the arrangement of bases on DNA to obtain the DNA sequence.

Figure 2: The Sanger (chain-termination) method for DNA sequencing. (Wikipedia)
Next-Generation Sequencing Workflow and PrincipleProtein
Next generation sequencing is a set of sequencing technologies, specifically the term next-generation sequencing is broader and includes a series of sequencing methods such as short read sequencing, large-scale sequencing, and long read sequencing. It can be applied to whole genome sequencing, whole exome sequencing, single gene sequencing, etc. The commonly used NGS sequencing platform is Illumina HiSeq.
Process
1. DNA fragmentation. Use mechanical methods, enzymatic digestion, ultrasound treatment, and other techniques to break DNA into fragments of 100-300 bp.
2. Library preparation. DNA fragments can be used for library preparation by adding sequencing adapters to the DNA fragments.
3. Sequencing. Upload the library to the sequencing platform and analyze it using bioinformatics methods.
4. Data analysis. Using bioinformatics methods to align with reference gene sequences and concatenate them into full-length DNA results.

Figure 3: Generic workflow for NGS. (J.F. Hess,2020)
Sanger Sequencing vs Next-Generation SequencingProtein
Sanger Sequencing | Next-Generation Sequencing | |
---|---|---|
Read Length | 500-1000bp | 50-300bp |
Degree of Dependence on Computing Tools | Low | High |
Input DNA Quantity | More | Less |
Cost Per Base | High | Low |
Time | Long | Short |
Accuracy | High | High, with errors corrected by coverage |
Throughput | Low | High |
Application | Targeted sequencing, validate results, small-scale sequencing | Whole-genome sequencing, large-scale sequencing |
ReferenceProtein
[1] Qin D. Next-generation sequencing and its clinical application. Cancer Biol Med. 2019 Feb;16(1):4-10. doi: 10.20892/j.issn.2095-3941.2018.0055. PMID: 31119042; PMCID: PMC6528456.
[2] J.F. Hess, T.A. Kohl, M. Kotrová, et al. Library preparation for next generation sequencing: A review of automation strategies, Biotechnology Advances, Volume 41, 2020, https://doi.org/10.1016/j.biotechadv.2020.107537.
[3] Crossley, Beate M.; Bai, Jianfa; Glaser, Amy; Maes, Roger; Porter, Elizabeth; Killian, Mary Lea; Clement, Travis; Toohey-Kurth, Kathy (November 2020). "Guidelines for Sanger sequencing and molecular assay monitoring". Journal of Veterinary Diagnostic Investigation. 32 (6): 767–775. doi:10.1177/1040638720905833.