The human genome, an expansive blueprint of our biological makeup, contains billions of DNA building blocks. Understanding this vast genetic information is fundamental to modern biology and medicine. Scientists have developed methods to study DNA, allowing them to pinpoint specific instructions that govern health and traits.
What is Targeted Sequencing?
Targeted sequencing is a genetic analysis technique that focuses on pre-selected genes or specific regions of interest within a genome. This method concentrates sequencing efforts on particular areas, rather than analyzing the entire genetic code. This approach is useful for investigating diseases and disorders caused by changes in a limited set of genes.
It is considered a next-generation DNA sequencing (NGS) technique, also known as target amplicon sequencing or panel sequencing. This technique allows scientists to study specific genes, groups of genes, or small segments of chromosomes.
How Targeted Sequencing Works
The process of targeted sequencing begins with selecting specific DNA regions to be studied. These “targets” can include particular genes, protein-coding segments, or other areas of interest within the human genome. Once identified, DNA samples are prepared for sequencing through target enrichment.
Target enrichment is a step in sample preparation that ensures only the desired regions are sequenced. There are two main approaches: amplicon-based sequencing and hybridization capture. Amplicon-based sequencing uses polymerase chain reaction (PCR) to create many copies of the targeted DNA segments, effectively amplifying them.
Alternatively, hybridization capture employs specialized probes, small pieces of DNA or RNA designed to bind to the specific target regions. These probes “capture” the desired DNA fragments, separating them from the rest of the genome. After enrichment, the isolated target regions are sequenced using NGS platforms, which generate millions of short DNA reads. Finally, the data is analyzed to align these reads to a reference genome and identify genetic variations within the targeted areas.
Why Targeted Sequencing is Used
Targeted sequencing is used for its ability to analyze specific genomic regions. It is useful for identifying genetic variants, such as mutations or single nucleotide polymorphisms (SNPs), linked to diseases or particular traits. This method offers a cost-effective way to investigate genetic variations associated with different conditions.
For instance, in cancer research, targeted sequencing can identify specific tumor mutations, guiding diagnostic and therapeutic decisions. It is also valuable in screening for inherited diseases, monitoring infectious diseases like SARS-CoV-2, and in pharmacogenomics, where it helps predict an individual’s response to certain medications. The ability to achieve high sequencing depth on specific areas means it can detect rare genetic changes with greater sensitivity.
Targeted Sequencing Compared to Other Methods
Targeted sequencing stands in contrast to broader DNA sequencing methods like Whole-Genome Sequencing (WGS) and Whole-Exome Sequencing (WES). WGS involves sequencing nearly the entire human genome, providing the most comprehensive view of an individual’s genetic makeup. WES focuses on sequencing all protein-coding regions, which make up approximately 1.5% of the genome and are known as the exome.
Compared to WGS, targeted sequencing offers several advantages, including lower cost per sample, higher sequencing depth for specific regions, and simpler data analysis. Because it focuses on a smaller, pre-selected set of genes, targeted sequencing requires less sequencing data and computational resources, making it more efficient. This allows for a higher number of samples to be processed simultaneously in a single sequencing run, leading to faster results.
However, targeted sequencing also has limitations; it only provides information on the pre-selected regions and cannot discover novel genetic variants outside of these targets. WGS and WES are suited for discovery-based research where unknown genomic variants are sought. Targeted sequencing is ideal when specific genes or regions are already suspected of being involved in a condition, offering an efficient way to investigate known or highly probable genetic causes.