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Targeted Sequencing – Method & Clinical Use

Targeted sequencing is a molecular genetic method in which specific gene regions are selectively analyzed to identify disease-causing mutations with high precision.

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Things worth knowing about "Targeted sequencing"

Targeted sequencing is a molecular genetic method in which specific gene regions are selectively analyzed to identify disease-causing mutations with high precision.

What is targeted sequencing?

Targeted sequencing is a modern molecular diagnostic technique in which not the entire genome, but specifically selected regions of DNA or RNA are analyzed. These regions are chosen because of their relevance to particular diseases or genetic conditions. Compared to whole genome sequencing (WGS), targeted sequencing is more cost-effective, faster, and delivers focused, clinically actionable results.

How does it work?

The process begins with the extraction and preparation of genetic material – typically from blood, tissue, or other body fluids. Specific DNA regions of interest are then selectively enriched using probes or primers. These enriched sequences are subsequently read out using Next-Generation Sequencing (NGS) or other high-throughput technologies and analyzed with bioinformatics tools.

Key sub-methods

Panel sequencing: Simultaneous analysis of a defined set of genes associated with a specific disease or disease group (e.g., cancer gene panels, cardiac gene panels).
Exome sequencing: Analysis of all protein-coding regions of the genome (exome), representing approximately 1–2% of the total genome.
Amplicon sequencing: Specific gene regions are amplified by PCR and subsequently sequenced.
Capture-based enrichment: Hybridization of specific probes to target DNA for selective enrichment prior to sequencing.

Clinical applications

Targeted sequencing is applied across many areas of modern medicine:

Oncology: Identification of somatic mutations in cancer genes (e.g., BRCA1/2, KRAS, EGFR, TP53) to guide selection of targeted therapies.
Medical genetics: Diagnosis of hereditary diseases such as cystic fibrosis, muscular dystrophy, or congenital heart defects.
Infectious diseases: Detection and typing of pathogens as well as resistance profiling (e.g., antibiotic resistance in bacteria, viral variants).
Prenatal diagnostics: Detection of chromosomal or genetic anomalies in the unborn child.
Pharmacogenetics: Analysis of genetic variants that influence the efficacy or tolerability of medications.

Advantages of targeted sequencing

High sensitivity and specificity for the detection of rare variants
Lower costs compared to whole genome sequencing
Faster turnaround time and simpler bioinformatic analysis
High sequencing depth at target regions is achievable
Clinically focused results with direct therapeutic relevance

Limitations and challenges

Despite its many advantages, targeted sequencing also has limitations. Because only pre-defined regions are analyzed, mutations outside these areas cannot be detected. The quality of results depends strongly on the design of the panel used and the quality of the sample material. Furthermore, the interpretation of genetic findings and their clinical significance requires specialized expertise.

Relevance in personalized medicine

Targeted sequencing is a cornerstone of personalized medicine (also known as precision medicine). It enables therapies to be tailored to the individual genetic profile of a patient or tumor. In oncology in particular, the method has become well established for identifying so-called driver mutations – mutations that drive tumor growth – and for selecting appropriate targeted therapeutics.

References

Metzker ML. Sequencing technologies – the next generation. Nature Reviews Genetics, 2010; 11(1):31–46. DOI: 10.1038/nrg2626
Roychowdhury S, Chinnaiyan AM. Translating genomics for precision cancer medicine. Annual Review of Medicine, 2016; 67:437–452. DOI: 10.1146/annurev-med-090814-120548
Mardis ER. A decade's perspective on DNA sequencing technology. Nature, 2011; 470:198–203. DOI: 10.1038/nature09796

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