Sanger Sequencing

Introduction And Definition

Sanger sequencing is the historical gold standard method for DNA sequencing and mutation screening.
It is classified as a first-generation sequencing technology.
The technique evaluates the specific sequence of a patient's DNA.
The resulting DNA sequence is then compared to a normal reference population.
This comparison allows for the precise detection of genetic alterations.

The technique is based on chain-termination methodology.
It relies on the selective incorporation of chain-terminating dideoxynucleotides.
This incorporation is catalyzed by the enzyme DNA polymerase.
The entire sequencing process occurs during in vitro DNA replication.

Sanger sequencing can only evaluate a part of a single gene at a given time.
The technique is designed to sequence only one DNA fragment at a time.
The final results of the sequencing are typically visualized on an electropherogram.

The technique accurately detects single nucleotide variants (SNVs).
It is also utilized to detect small insertions and deletions, commonly known as indels.
It provides an exceptionally high diagnostic sensitivity of greater than 99% for point mutations.

It is the ideal testing modality when a distinct clinical phenotype points clearly to a single specific gene.
It is highly recommended for conditions that exhibit minimal locus heterogeneity.
It serves as the gold standard for analyzing small genes that contain fewer than 20 exons.
It is highly useful for investigating known mutation hotspots within a gene.

It is utilized for the cascade screening of specific, known mutations in family members.
It remains the gold standard for confirming variants that are initially identified by next-generation sequencing.

Disease Category	Specific Condition	Target Gene For Sanger Sequencing
Inborn Errors Of Metabolism	Phenylketonuria (PKU)	PAH gene sequencing.
Monogenic Disorders	Cystic fibrosis	CFTR gene sequencing.
Neuromuscular Disorders	Duchenne muscular dystrophy	DMD gene sequencing for point mutations after deletions are ruled out.
Skeletal Dysplasias	Achondroplasia	Targeted testing for precise known mutations.

Feature	Description
Key Advantages	It is highly accurate for targeted genetic testing.
	It remains the definitive gold standard for point mutation detection and confirmation.
Major Limitations	It provides very low overall throughput.
	It is highly time-consuming for large-scale genome analysis.
	The method is not easily scalable for comprehensive diagnostics.
	It is exceptionally expensive when analyzing multiple genes sequentially, potentially costing lakhs of rupees compared to broader sequencing methods.

Feature	Sanger Sequencing	Next-Generation Sequencing (NGS)
Throughput	Low throughput (analyzes one fragment at a time).	High throughput (massively parallel sequencing).
Target Scope	Small genes or specific mutation hotspots.	Entire exome or whole genome.
Locus Heterogeneity	Best for minimal locus heterogeneity.	Best for extreme locus heterogeneity.
Cost-Effectiveness	Expensive for large-scale or multiple gene analysis.	Highly cost-effective for analyzing multiple targets simultaneously.