Exome sequencing

Research Activities for Next Generation Sequencing Accelerate, New Studies Outline Efficacy on Treating Fatal Conditions

By Pratik Kirve
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Exome sequencing

Research and development activities to find potential treatments using next generation sequencing for various fatal conditions including melanoma, epilepsy, antibody deficiency, and other diseases have gained traction. In April, FDA finalized two guidance documents to speed up development of NGS-based tests.

Next generation sequencing (NGS) has become a medical sensation, as it can help to determine genomic variations that convey whether a person is on the verge of developing a disease. Based on the analysis, further treatment decisions can be taken. Millions of changes in DNA can be detected with a single test and the cause of the disease can be determined. Research activities for NGS are in full swing and innovative technologies have been evolving rapidly. These activities are one of the crucial reasons are behind the growth of the global NGS industry. According to the research firm Allied Market Research, if R&D activities continue to bring innovative technologies forward, the global NGS industry will reach $12.801 billion by 2022.1 The development of the industry is dependent majorly on the rise in R&D investment activities.

Moreover, supportive government initiatives could supplement the growth in next few years. The availability of NGS tests is important in the medical sector to find treatments for fatal diseases and conditions such as melanoma, epilepsy and antibody conditions. The current research activities show that there is a huge potential for the market growth and further advancements would make a significant difference in coming years in the NGS industry.

Next generation sequencing
Next generation sequencing testing

Detection of More Mutations in Melanoma

According to a research published in Virchows Archive, targeted NGS used for detection of BRAF mutations detected more mutations that were potentially actionable as compared to mutations detected by allele-specific polymerase chain reaction (PCR) in samples from patients with advanced metastatic melanoma.2 As molecular characterization is a crucial part of a selection of appropriate treatment method. BRAF V600K is a biomarker used in various therapies. Before the emergence of NGS, allele-specific PCR was used for detection of mutations such as BRAF mutations that resulted in variants of V600K. Navid Sadri, M.D., Ph.D., at Case Western Reserve University School of Medicine in Cleveland, Ohio, and a researcher of the study, told Cancer Therapy Advisor, allele-specific PCR has limitations as it detects only a few specific mutations. Other technologies such as Sanger sequencing has low sensitivity. As NGS emerged, it offered high sensitivity as it was not restricted to certain mutations only.

The research was aimed at analysis of the DNA extracted from metastatic melanoma tumor tissue using allele-specific PCR and NGS. Results of both technologies were compared. In the research, specimens were collected for detection of BRAF variants, V600K and V600E, using allele-specific PCR. Across 46 samples, the V600K mutation was detected in 9% of the samples and a V600E mutation in 30% of samples for the period, October 2016 to December 2017. The NGS technique was carried out on 62 metastatic melanoma samples. The common mutations resulting in BRAF variants, such as V600E, V600K, and V600R, were found in 37% of samples. Moreover, NGS detected mutations in NRAS that results in variations at Q61 in 23% of samples. It also detected some of the rare mutations including non-V600 BRAF and mutations in GNA11, GNAQ, and KIT. The study found that nearly 47% of the potentially actionable mutations identified by NGS might not have been identified by allele-specific PCR for BRAF mutations.

Improvement in Pediatric Epilepsy Tx using NGS

A study published in CNS Neuroscience & Therapeutics outlined that NGS has capabilities to improve the effectiveness of treatment and reduce hospital stay in children with drug-resistant epilepsy (DRE).3 Researchers at Central South University, China carried out genetic testing on 273 pediatric DRE patients. These patients did not have acquired etiology. Out of 273, 74 went through whole-exome sequencing (WES), 141 underwent epilepsy-related gene panel testing, and 58 went through clinical WES gene panel testing. In addition, researchers observed the frequency of outpatient visits, seizures and hospitalization.

The detection rate for WES was 17.3%, epilepsy-related gene panel testing was 32.6%, and clinical WES gene panel was 44.8%. Moreover, 34 patients underwent the therapy as per their mutant genes. After the therapy, 52.9% of them became seizure-free and 38.2% had a reduction in the seizure. Incidents of hospitalization lowered after testing. Researchers concluded, “These results offer further proof that NGS approaches represent powerful tools for establishing a definitive diagnosis.”

Exome sequencing
Exome sequencing

Exome Sequencing to Diagnose Primary Antibody Deficiency

The NGS could become a useful tool in the diagnosis of patients with primary antibody deficiency (PAD), according to the new study published by Genetics in Medicine.4 Researchers from Karolinska Institute, Sweden utilized exome sequencing technique to determine mutations related to the disease in nearly 68% of their 126 PAD patients. “We suggest that NGS could replace a conventional multi-step genetic approach because it can be expanded to cover all known PID-associated genes and potentially detect CNVs and new genes associated with PID,” wrote Lennart Hammarström and other researchers in the paper.

PAD is one of the common forms of primary immunodeficiency (PID). The researchers conducted a study on 126 individuals, mostly children and adolescents, with undefined PAD to the study. Out of 126 subjects, 81 had common variable immunodeficiency, 11 had an unsolved agammaglobulinemia, 11 were suffering from an IgAD deficiency, 14 had an unsolved hyper IgM syndrome, and remaining nine were suffering from a type of PAD. Nearly 83% of the subjects had parents who were biologically related. The genetic diagnosis was carried out in 86 patients with the help of exome sequencing technique. The remaining patients had no diagnosis.

The researchers found that the patients with agammaglobulinemia had the lowest diagnostic yield. Although parents of many patients were biologically related, researchers discovered that nearly two-thirds of genes could be inherited recessively. They noted that a genetic diagnosis could affect the clinical treatment and management of around 50% proband if they could find a pathogenic variant. They concluded that exome sequencing can be the first step of screening for PAD patients. “[E]mploying next-generation sequencing as a preliminary step of molecular diagnostic approach to patients with PAD is crucial for management and treatment of the patients and their family members,” wrote researchers.

NGS in the Diagnosis of Cerebral Palsy

The study conducted by researchers from the University of Delaware outlined that patients suffering from spastic cerebral palsy (CP) can be detected with the help of DNA methylation patterns found in circulating blood cells. The study was published in BMC Bioinformatics.5 Blood samples of subjects aged between 9 and 19 were studied as a part of a blinded study. The objective was to determine if DNA methylation patterns are different in patients with spastic CP who will undergo surgery and regular orthopedic patients.

DNA methylation
DNA methylation

Researchers detected distinct variations in DNA methylation patterns. This finding suggested that the genome of children suffering from spastic CP were different than regular orthopedic patients. In the second phase of the study, the researchers tried to validate their findings. They collected samples from another group in which patients were aged between 2 and 5 years. They predicted the blood samples belonging to children with spastic CP with 73% accuracy. Having detailed insights on methylation patterns could enable gaining more insights into various cellular processes that speed up CP. This would help in obtaining improved treatments for the condition. The researchers also outlined that this test would help in the treatment of other disorders including infant leukemia.

FDA’s Crucial Decision to Change Review Capabilities

Identifying the rapid gain in research & development activities in NSG, the FDA realized the need to change in its approach to review innovations. According to the press release announcing the final guidance documents, FDA Commissioner Scott Gottlieb, M.D., said, “The new policies issued today provide a modern and flexible framework to generate data needed to support the FDA’s review of NGS-based tests, and give developers new tools to support the efficient development and validation of these technologies.”

FDA released the final guidances based on comprehensive feedback received from citizens as well as stakeholders who have been working on the development of innovative NGS technologies. This approach and release of new guidance from FDA are appreciable as it encourages the development of new and accurate testing technologies by adapting its review capabilities. Such initiatives from various food and drug governing bodies would encourage researchers and stakeholders to bring new technologies and help the global industry grow significantly in the next few years.

References

  1. Sumant, O. and Shaikh, S. (April 2017), Next Generation Sequencing (NGS) Market by Product (Consumables, Platforms and Services), By Application (Diagnostics, Biomarkers and Cancer, Reproductive Health), Technology (Sequencing by Synthesis, Ion Semiconductor Sequencing, Sequencing by Ligation, Pyrosequencing, Single Molecule Real Time Sequencing, Other Technologies) – Global Opportunity Analysis and Industry Forecast, 2014-2022.
    Retrieved from https://www.alliedmarketresearch.com/next-generation-sequencing-market
  2. Zhu M-L, Zhou L, Sadri N. (June 21, 2018), Comparison of targeted next generation sequencing (NGS) versus isolated BRAF V600E analysis in patients with metastatic melanoma. Virchows Archiv. doi: 10.1007/s00428-018-2393-2
    Retrieved from https://link.springer.com/article/10.1007%2Fs00428-018-2393-2
  3. Peng, J., et. al. (June 22, 2018). Next‐generation sequencing improves treatment efficacy and reduces hospitalization in children with drug‐resistant epilepsy. Retrieved from
    Retrieved from – https://onlinelibrary.wiley.com/doi/full/10.1111/cns.12869
  4. Hammarström, L., et. al., (June 19, 2018), Clinical implications of systematic phenotyping and exome sequencing in patients with primary antibody deficiency. Genetics in Medicine. Retrieved from https://doi.org/10.1038/s41436-018-0012-x
  5. Crowgey, E., et. al. (June 21, 2018), Epigenetic machine learning: utilizing DNA methylation patterns to predict spastic cerebral palsy. BMC Bioinformatics. Retrieved from
    https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2224-0

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