A Game-Changer in Clinical Genomics
In recent years, the emergence of long-read sequencing (LRS) has enabled a more comprehensive and accurate view of the genome. This technology has overcome some of the limitations of short-read sequencing, including PCR bias, identification of structural variants, repetitive elements, and haplotyping.
This has contributed to the use of LRS in fields like immunology, oncology, and infectious diseases. LRS has also impacted the clinical setting, being used for diagnosis, prognosis, and therapy selection for rare disorders.
Understanding Long-Read Sequencing
Long-read sequencing, also known as third-generation sequencing, can generate reads tens of thousands of bases in length. The leading long-read sequencing technologies currently in use are PacBio's Single Molecule Real-Time (SMRT) sequencing and Oxford Nanopore Technologies' nanopore sequencing.
One key advantage of LRS is that it occurs in real time, without the need for PCR amplification during the entire process. This means that LRS can directly detect modification to DNA bases.
PacBio's SMRT sequencing uses circular consensus sequencing. This results in longer reads, reduced error rates, and the ability to span repetitive and complex regions of the genome. Nanopore sequencing, on the other hand, relies on the measurement of changes in electrical current as DNA molecules pass through nanopores. This produces continuous, long reads.
Clinical Applications of LRS
Diagnosis of rare disease
The first reported use of long-read sequencing in a clinical setting dates back to 2018. Researchers investigated the genome of a single patient for whom clinical testing and short-read sequencing had not uncovered a cause for their symptoms. Long-read sequencing detected a 2,184 bp pathogenic deletion in the PRKAR1 gene.
This gene is a major genetic mechanism behind Carney complex disease. Carney complex is a rare genetic disorder where patients develop multiple benign tumors that can affect the heart, skin, and endocrine system. This demonstrates the ability of LRS to detect and uncover the causal mechanisms behind certain rare diseases. This variation was not detected by short-read sequencing, where DNA is separated into segments of a few hundred base pairs.
In breast cancer, ERBB2 (also called HER2) is one of the most important genes for tumorigenesis and diagnosis. HER2 impacts one fifth of all breast cancer patients. PacBio SMRT technology was used to investigate structural variants (SVs) on a cell line of breast cancer (SK-BR-3) important to HER2 research.
These results were used to develop one of the most detailed cancer genome structural variant maps ever created. This research identified many translocations and duplications around the ERBB2 gene.
These SVs could explain why some drugs targeting the protein codified by ERBB2 are not effective in some patients with breast cancer. Results like these could help to stratify patients into responder and non-responders, making cancer treatment more effective.
Quick identification of viral variants and lineage is critical for an appropriate public health response. Thanks to LRS, researchers from France were able to detect mutations in a region responsible for coding the spike protein (S1) of the SARS-CoV-2 virus. S1 variations can make SARS-CoV-2 resistant to monoclonal antibodies and allow the virus to escape the vaccine-induced immune response.
Traditional sequencing methods did not identify these mutations. Investigating the entirety of S1 is important for detecting key viral changes.
Long-read sequencing technology has emerged as a powerful tool in clinical genomics, offering unprecedented insights into genetic variations and structural complexities. Its applications range from disease diagnosis and personalized medicine to unraveling the mysteries of the human genome.
As technology continues to advance and costs decrease, long-read sequencing is set to play an increasingly pivotal role in shaping the future of clinical healthcare.