Next Generation Sequencing Offers Several Clinical Benefits

Next-generation sequencing (NGS) is one of several names for a technology that has made it possible to sequence an entire human genome in just one day. Meanwhile, it took the prior Sanger sequencing technology an entire decade to do the same thing. Needless to say, next generation sequencing is far more useful for genetic research and the development of gene-based therapies.

One of the keys to NGS’s ability to sequence genes so quickly is its ability to process data in parallel. This gives the technology alternative names like “massively parallel sequencing” and “deep sequencing.” However, the term “next generation sequencing” has overtaken the others in most circles.

At their roots, the various NGS platforms use the same basic process. They sequence millions of small bits of DNA in parallel, and then bioinformatics analyses are used to put the information from the fragments together. A human reference genome is used to provide the map for this assembly.

Each of the three billion base pairs in the genome is sequenced several times during a next generation sequencing run. This not only provides high accuracy, but also highlights unexpected variations.

With this technology, researchers do not have to sequence the entire genome of a subject every time. Sequencing can also be directed to small sections of the genome, or to genes of specific interest like the coding genes. This makes it a useful tool for looking for mutations suspected of causing specific diseases.

Potential Uses of Next Generation Sequencing

There are many potential uses of next-generation sequencing, so it is likely to be seen in an expanding number of places as the years go by. An article in the National Library of Medicine reports that as of 2013, this technology was shining in three key areas.

Clinical Genetics

This technology exceeds Sanger sequencing not only in speed, but in capabilities. It can detect small base changes, substitutions, deletions and insertions, large deletions of exons or entire genes, inversions, and translocations. Meanwhile, Sanger sequencing is limited to detecting substitutions and small insertions or deletions.

While other technologies can be used to detect other genetic abnormalities, this requires the use of dedicated assays. Next-generation sequencing can detect them directly, and can do so as part of a single examination. Therefore, it eliminates the need for special assays.

There are some limitations to NGS, such as difficulty decoding in the presence of a large amount of guanine/cytosine pairs or extreme numbers of repeated sequences such as those found in Fragile X Syndrome. However, its expanded capabilities make it ideal for sequencing the genomes of the majority of patients.

Thanks to NGS’s ability to sequence full genomes or exomes, there is no need for clinicians to try to pre-guess which genes to examine. This makes it useful for diagnosing unexplained syndromes, which is especially useful in pediatric medicine.

The newer technology can also be used to detect mosaic mutations. Since these mutations do not present uniformly throughout the body, they are especially challenging for older methods to detect.

Microbiology

In microbiology, the main use of next generation sequencing is to provide a genomic definition of pathogens. It can spot genetic similarities that identify pathogens as related even when conventional methods do not detect the similarities. NGS can also help researchers determine which drugs will work best against a specific pathogen.

Oncology

Cancer is believed to be caused by defects in the genes. Attempts to sequence these genes have been hampered by the need for specific candidate genes for examination and by low sample numbers. With NGS, cancer genomes can be studied completely, hopefully leading to new treatments.

Currently, next-generation sequencing is used mostly in research. In the future, it is likely to take on a direct role in the care of individual patients.