Targeted DNA sequencing

Abstract

Targeted DNA sequencing is function technology advancement and it has made significant impact on the health care sector. The technology helps medical researchers to understand the root causes of diseases faster and accurately. The traditional approaches of diagnoses for diseases are based on the assumption that causative pathogens for infectious diseases can be cultured. DNA targeted sequencing is highly effective in terms of time saving as it does not need the culturing steps. The mobile phone based targeted DNA sequencing may be the best option in settings of limited laboratory resources as it allows for remote diagnostic testing of infectious diseases[i]. This paper focuses on the option I would consider regarding Targeted DNA sequencing as a diagnostic approach in a situation where I would be in a remote area in Africa with no access to a laboratory.

 

Introduction

Targeted DNA sequencing is part of the Next- Generation sequencing technology that has made significant impact on the health care sector. The technology helps medical researchers to understand the root causes of diseases. However, the technology has several challenges such as time consuming and costly. Targeted gene sequencing is beneficial for analysis of specific gene mutations. Focused gene sequencing panels have a particular gene regions or set of genes that are associated with specific diseases under investigation. The gene panels can be custom made to include the genomic regions and purchased for particular interest. Targeted gene sequencing results into small datasets that are easily manageable compared to whole-genome sequencing[ii].

In the global health sector, there is great need for a rapid and accurate identification of causative agents for infectious diseases. Time limitation in identification of the infectious agents can be devastating. Target gene sequencing allows for effective and specific identification of the agents hence providing direct and accurate options of treatment. Treatment is based on the symptoms and diagnosis. It can also be based on tentative diagnosis that is yet to be confirmed[iii].

Comparison of Targeted DNA sequencing with traditional diagnostic approaches

The traditional approach of diagnose of diseases is based on the assumption that causative pathogens for infectious diseases can be cultured. In case they cannot be cultured, the causative pathogen may not be accurately identified hence may result into wrong diagnosis. It is common for pathogen identification errors to occur. This increases the chances of progression and spread of disease. Enzyme immune-essays have the ability to use antibodies to detect proteins that are associated with particular pathogens. The approach of enzymes immunoassays produces quick results. The limitation with this approach is that there may be variations in results depending on the test sensitivity and timing depending on the onset of symptoms. Real-time PCR is commonly used in microbiology laboratories. The approach is effective in detecting pathogens rapidly and at early stage. The approach is less likely to produce false positives because of its high sensitivity level. However, false positives may occur because of the presence of PCR inhibitors in the test specimens. Pulsed-field gel electrophoresis is another diagnosis approach that is capable of generating specific DNA patterns for a variety of pathogen strains. The multi-locus sequencing typing depends on DNA sequence nucleotide polymorphism analysis. This approach is convenient in terms of portability .However; it has high level of ambiguity such that sometimes it may fail in differentiating between different strains[iv].

Advantages of DNA targeted sequencing in diagnosis for infectious diseases

DNA targeted sequencing is highly effective in terms of time saving. The approach does not require the time consuming steps for pathogen culture as in other traditional diagnosis approaches.DNA target sequencing can identify microorganisms direct from specimen samples inclusive of the cerebrospinal and blood specimen. This approach has proved to be advantageous compared to the conventional approaches of genotyping in epidemic investigation. The information on genomic sequencing using this approach can be obtained in a matter of days because identification of the causative pathogen can take place in the initial stages of disease outbreak. Target gene sequencing has the capability to identify the pathogens that are un-culturable at laboratory settings .This approach can distinguish between a variety of pathogen strains, discover new pathogens and identify co-infections. This approach is also effective in discovering the emerging viruses. Target DNA sequencing has the genotyping capability for infectious diseases as well as molecular detection for disease causing pathogens[v].

As much as urgent laboratory testing for potential infectious diseases is important, modern high technology laboratories are well established in developed countries such as those in the Western world. The economy of these countries has the capacity to establish and develop laboratories for time effective and accurate diagnosis procedures for potential infectious diseases In developing countries, particularly those in Africa, there is a major challenge of accessing laboratories that can perform DNA analysis of specimen to identify the infectious pathogens.DNA analysis procedures are extremely expensive to conduct not considering that construction of the facility is also an expensive cost. Most remote areas are breeding grounds of different parasites and pathogens .Some exists in so many strains that some of the strains are still unknown.  Sometimes, an individual may contract a serious bacterial infection while in a remote area far from a well equipped lab facility which they can obtain immediate and accurate diagnosis of the infection[vi].

My options

However, with technological advancement in the health sector, outsourcing of molecular diagnostics has been made possible such that a patent can be diagnosed remotely far from the laboratory. Research had allowed for the development of portable optical imaging devises and molecular assays. This equipment allows on-site diagnostics to be performed on a multimodal microscope based on a mobile phone. Research has proved that DNA sequencing reactions can be imaged and examined remotely through cell phone-based microscopy. This kind of molecular diagnostics makes it possible to diagnose unknown infections in a setting that is characterised by resource limitation. However, this diagnostic technique is outsourced in specialised DNA sequencing laboratories. Digital pathology is another medical development that allows pathologists to examine specimens and analyse their associated molecular data in a remote setting. This approach is the best in utilisation of the limited resources available for pathological expertise. Mobile phones contributes to the effectiveness of the approach because it is portable, affordable and it provides cost-effective infrastructure for technology, connectivity, imaging and sensing capability that allows for efficient diagnostic analysis of an individual in a remote setting. In an event where I am in a remote area such as in Africa with no access to a DNA sequencing facility, I would use my mobile phone to connect to a DNA sequencing facility for quick and accurate diagnosis for my bacterial infection[vii]. The challenge that would arise would be in a case where I have no link to such a facility at all. For this approach to work, I need to have a CMOS imager chip installed in my mobile phone before I leave for Africa. The chips are linked with the phone camera to allow for remote diagnosis using high quality images and spatial resolutions that are compatible with those of the DNA sequencing microscopes in the laboratory. Research has demonstrated that mobile phone-based remote diagnosis can transfer targeted DNA sequencing information from an individual in a remote location. This is made possible by the integration of the multimodal microscope with mobile phones[viii]..

Conclusion

Technological advancement has resulted into tremendous transformation of the medical sector especially in diagnostics and drug research. Africa, being a third world country needs expatriates from different parts of the world to relocate there in order to assist in meeting their needs. In many cases, the expatriates are sent to deliver their services to remote area. Such services may include; food and nutrition aid, medical aid, peace keeping and enlightenment of populations among others. During such situations, foreigners may contract bacterial infections that may need urgent laboratory attention. This means that diagnostic testing and commencement of treatment should be made as soon as possible. Unfortunately most areas in African lack efficient diagnostic laboratories. The mobile phone based targeted DNA sequencing may be the best option in this case as it allows for remote diagnostic testing of infectious diseases. The approach also allows for determination of the pathogen load, pathogen identity and markers for antibiotic markers. Upon receiving fast and accurate diagnosis result, the platform can recommend the appropriate anti-biotic which I can access from a local drug store and take as prescribed.

[i] Beroukhim, R. and Ligon, K.L.,. Clinical targeted exome-based sequencing in            combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors.(2017)

 

[ii] Mellmann, A., Bletz, S., Böking, T., Kipp, F., Becker, K., Schultes, A., Prior, K. and Harmsen, D., 2016. Real-time genome sequencing of resistant bacteria provides precision infection control in an institutional setting. Journal of clinical microbiology, 54(12), pp.2874-2881.

 

[iii] Leung, M.L., Wang, Y., Kim, C., Gao, R., Jiang, J., Sei, E. and Navin, N.E., . Highly multiplexed targeted DNA sequencing from single nuclei. Nature protocols, 11(2), pp.214-235.(2016)

 

[iv] Langelier, C., Christenson, S., O’Donovan, B., Nerella, S., Sontag, M.K., Harris, K., Mourani, P.M. and DeRisi, J.,. Next Generation Sequencing Of Respiratory Fluids Accurately Distinguishes Bacterial From Viral Lower Respiratory Tract Infection By Both Microbial And Host Transcriptional Profiling. In B106. CELLULAR/MOLECULAR MECHANISMS AND TRANSLATIONAL ASPECTS OF RESPIRATORY TRACT INFECTIONS (pp. A4452-A4452). American Thoracic Society.(2016)

 

[v] Maxson, T. and Mitchell, D.A., 2016. Targeted treatment for bacterial infections: prospects for pathogen-specific antibiotics coupled with rapid diagnostics. Tetrahedron, 72(25), pp.3609-3624.

 

[vi] Kühnemund, M., Wei, Q., Darai, E., Wang, Y., Hernández-Neuta, I., Yang, Z., Tseng, D., Ahlford, A., Mathot, L., Sjöblom, T. and Ozcan, A.,. Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy. Nature     Communications, 8.Retrieved from    http://www.nature.com/articles/ncomms13913.(2017)

 

[vii] Heyduk, K., Stephens, J.D., Faircloth, B.C. and Glenn, T.C.,. Targeted DNA region re-sequencing. In Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing (pp. 43-68). Springer International Publishing.(2016)

 

[viii] Didelot, X., Walker, A.S., Peto, T.E., Crook, D.W. and Wilson, D.J., 2016. Within-host evolution of bacterial pathogens. Nature Reviews Microbiology, 14(3), pp.150-162.

 

Beroukhim, R. and Ligon, K.L.,. Clinical targeted exome-based sequencing in             combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors.(2017)

 

[1] Mellmann, A., Bletz, S., Böking, T., Kipp, F., Becker, K., Schultes, A., Prior, K. and Harmsen, D., 2016. Real-time genome sequencing of resistant bacteria provides precision infection control in an institutional setting. Journal of clinical microbiology, 54(12), pp.2874-2881.

 

[1] Leung, M.L., Wang, Y., Kim, C., Gao, R., Jiang, J., Sei, E. and Navin, N.E., . Highly multiplexed targeted DNA sequencing from single nuclei. Nature protocols, 11(2), pp.214-235.(2016)

 

[1] Langelier, C., Christenson, S., O’Donovan, B., Nerella, S., Sontag, M.K., Harris, K., Mourani, P.M. and DeRisi, J.,. Next Generation Sequencing Of Respiratory Fluids Accurately Distinguishes Bacterial From Viral Lower Respiratory Tract Infection By Both Microbial And Host Transcriptional Profiling. In B106. CELLULAR/MOLECULAR MECHANISMS AND TRANSLATIONAL ASPECTS OF RESPIRATORY TRACT INFECTIONS (pp. A4452-A4452). American Thoracic Society.(2016)

 

[1] Maxson, T. and Mitchell, D.A., 2016. Targeted treatment for bacterial infections: prospects for pathogen-specific antibiotics coupled with rapid diagnostics. Tetrahedron, 72(25), pp.3609-3624.

 

[1] Kühnemund, M., Wei, Q., Darai, E., Wang, Y., Hernández-Neuta, I., Yang, Z., Tseng, D., Ahlford, A., Mathot, L., Sjöblom, T. and Ozcan, A.,. Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy. Nature     Communications, 8.Retrieved from    http://www.nature.com/articles/ncomms13913.(2017)

 

[1] Heyduk, K., Stephens, J.D., Faircloth, B.C. and Glenn, T.C.,. Targeted DNA region re-sequencing. In Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing (pp. 43-68). Springer International Publishing.(2016)

 

[1] Didelot, X., Walker, A.S., Peto, T.E., Crook, D.W. and Wilson, D.J., 2016. Within-host evolution of bacterial pathogens. Nature Reviews Microbiology, 14(3), pp.150-162.