Next-Generation Sequencing (NGS) Overview
Next-generation sequencing is a massive parallel sequencing technology. Genomic DNA is extracted, fragmented, and linked to adapters and primers for the amplification reaction (PCR) to generate a library. DNA fragments in the library are simultaneously sequenced. This provides a massive set of sequence data in a matter of days. The data obtained is processed with bioinformatics software and interpreted. In addition to rapidly obtaining sequence data of whole genomes, NGS can help with the characterization of DNA-protein interactions, DNA methylation analysis, and more.
The medical advantages of obtaining comprehensive genomic sequence information are many. Disease-associated mutations can be identified for more accurate diagnoses. Also, genomic sequencing information can be utilized to determine the presence of drug resistance (antibiotic and chemotherapeutic) and predicting response to medical interventions. It can also be used to drive and direct the development of new pharmaceutical agents that affect biological targets associated with disease progression.
Drug Discovery and Development Concepts
One of the most important steps in the drug discovery process is target identification. Various methods are used to validate the targets identified. This involves conducting clinical trials to know if there is actually a therapeutic benefit associated with modifying or focusing on the proposed target. Screening assays are then conducted to find the best drug candidate out of numerous that are tested. Synthesis reactions and other laboratory endeavors are used to modify candidates to achieve the most effective compound with the least adverse effects.
Once a promising drug lead is identified, preclinical (in animals) and phases of clinical studies (in humans after the preclinical phase) are conducted to determine if the drug functions as intended and without undue side effects. This entails gathering information on the effects on the body and how the body processes the drug. Other efforts in the development phase are conducted to determine the best dosing and administration, any drug interactions, toxicity, the best patient group characteristics, and more.
Integrating NGS into Drug Development Efforts
Single nucleotide polymorphisms (SNPs) are extensively used to analyze individual characteristics, including how one can respond to a therapeutic agent. NGS technology can be used for large-scale screening of SNPs to ultimately determine if a drug candidate will be effective and safe. With the genomic sequence data obtained rapidly by NGS, it is quite feasible to obtain data that will allow the development of novel therapeutic agents addressing specific disease mechanisms1. RNA can also be sequenced and studied using NGS technology. In addition, NGS can aid in identifying gene expression levels and alternative splicing2.
Knowing the mechanism and molecular basis of a disease is a key to determining possible drug targets. This is important particularly for genetic disorders that are difficult to diagnose or treat with current knowledge. The power of massive parallel sequencing allows the simultaneous screening of mutations in a large number of genes. For example, for a one-year-old girl with symptoms suggestive of Leigh syndrome, exome sequencing was performed to identify candidate gene variants. With further analysis and the use of bioinformatics tools to interpret the sequencing data, the specific gene associated with the girl´s clinical condition was identified3. This type of clinically valuable information allows the design of specific therapies and design of new drugs for rare syndromes that have no specific drug treatment.
DNA-encoded chemical libraries are utilized in drug discovery research. These libraries consist of small molecules bound to DNA tags with unique sequences. These sequences serve as DNA barcodes. The DNA barcode/tag facilitates the identification of binding molecules after immobilization on a specific target protein. Sequencing a tag allows the identification of the molecule to which it was bound. This is a way to know which small molecule bound to the target of interest.
Next-generation sequencing can rapidly and accurately provide the means to sequence a massive number of DNA barcodes. High-throughput screening is, therefore, possible allowing a faster lead generation process at lower costs. An example of the use of DNA-encoded chemical libraries is the use by Ding et al4. A DNA-encoded triazine library was used to discover a therapeutic target (ADAMTS-4) for osteoarthritis. Using the DNA-encoded library, ADAMTS-4 inhibitors were identified.
Next-generation sequencing supports molecular profiling efforts given the lower costs and higher speeds to obtain whole genome sequences. Unique biomarkers are identified so that drug targets can be discovered. As previously discussed, high-throughput sequencing technology, such as NGS, has much utility in identifying potential drug targets. An area where this is used more extensively is in cancer therapeutic research. The goal is to identify targeted cancer therapies that can stop tumor growth and progression. This approach has the potential to provide drug choices that are alternatives to chemotherapy, spare healthy cells, and increase survival rates.
Limitations in current drug development are being resolved due to the advent of NGS. The identification of novel molecular targets, biomarkers, and mechanistic information at record rates bolsters the drug discovery process. Next-generation sequencing provides an enormous database of information that is interpreted and then used to make decisions regarding drug leads. As in the case of DNA-encoded libraries, this allows the screening of the many initial potential candidates to narrow down to one or a few strong drug candidates.
Although there are challenges that exist with the application of NGS at the clinical level, it is rapidly bringing us to an era when genomic testing in the doctor´s office or clinical laboratory will be routine. The role of NGS in the translation of research findings to the bedside is ever increasing and demands the development of bioinformatics tools to manage the massive sequence data that appears to grow exponentially. Next-generation sequencing offers unmatched opportunities for new diagnostic approaches, drug target discovery, and further development of the personalized medicine arena.
- Voisey J, Morris CP. SNP technologies for drug discovery: a current review. Current drug discovery technologies. 2008;5(3):230-5.
- Sultan M, Schulz MH, Richard H, Magen A, Klingenhoff A, Scherf M, et al. A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (New York, NY). 2008;321(5891):956-60.
- Kirby DM, Thorburn DR. Approaches to finding the molecular basis of mitochondrial oxidative phosphorylation disorders. Twin research and human genetics : the official journal of the International Society for Twin Studies. 2008;11(4):395-411.
- Ding Y, O’Keefe H, DeLorey JL, Israel DI, Messer JA, Chiu CH, et al. Discovery of Potent and Selective Inhibitors for ADAMTS-4 through DNA-Encoded Library Technology (ELT). ACS medicinal chemistry letters. 2015;6(8):888-93.