Utility Of Next-Generation Sequencing Assignment Sample

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Introduction: Utility Of Next-Generation Sequencing

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Background of research

Rett Syndrome (RTT) is recognised as a neurodevelopment disorder, which mainly affects girls. In 1960, Andreas Rett first discovered the disease Rett Syndrome. It has been identified that this syndrome completely affects an individual and makes an individual disabled. According to Vidal et al. (2017), RTT creates a loss of speech, alexia, and motor syndrome disease among individuals. This literature also stated that MECP2, CDKL5 and FOXG1 are common genes that are responsible for this disorder. On other hand, Ip et al. (2018) reported that RTT is a common neurological disorder, which is developed due to mutation of genes encoding the “Methyl CPG binding protein 2”.

By focusing on the above discussion, it can be stated that RTT is a common neurological syndrome, which is developed due to the mutation of the methyl CPG binding protein 2 gene. This literature also stated that RTT is associated with multiple symptoms including hypotonic, limb movement issues. Further, Kyle et al. (2018) reported that RTT is a common neurological disorder that creates a significant effect on girls around 1:10000 ratio. It has been identified that the disease is associated with multiple stages and it develops severe symptoms including motor skill issues, speech issues, and repetitive hand movement issues. 

Now, this section is going to discuss the aim of the search. The aim of this research paper is to evaluate usefulness of the NGS in context of genetic diagnosis. This research paper has been undertaken the RTT genomic study to evaluate usefulness of NGS(Next generation Sequencing)in terms of genetic diagnosis. 

The chosen research paper aim is to identify importance of NGS in identifying genetic diagnosis of RTT. By focusing on multiple previous literatures, it has been identified that the concept of RTT, its prevalence and symptoms. However, the reason behind the disease or role of NGS in this disease for diagnosis has not been identified from a previous paper. In this aspect, the research paper is essential to identify the role of NGS in the genetic diagnosis of RTT. 

Genomics methods used

In order to identify the usefulness of NGS in RTT genetic diagnosis, this study has chosen multiple genetic sequencing methods. This literature has chosen a Sanger sequencing method to determine the usefulness of the NGS. This research paper has utilized four different types of genetic diagnosis processes to determine the usefulness of NGS. Before discussing each of the genetic diagnosis methods, this section is going to discuss the basic concept of genetic diagnosis. In context of methods, this research paper has been undertaken the Whole Exome Sequencing (WES) method to analyse utility of this method to diagnoses the RTT disorder. Further, this literature identified that molecular analysis has been performed. In addition, the literature stated that HPC and TSO data analysis has been conducted at Genycell Biotech S.L. Further, this literature stated that both panel sequencing trimmed form the three prime end and up to the first base. In the basis of protein coding genes, Whole Exome sequencing (WES) target around 3% of total genome (Suwinskiet al. 2019). Purpose of WES is to identifying genetic cause of particular sign and symptom that are genetically connected. However, the WES is failed to provide the information regarding the variant of gene that is linked with the particular disorder. WES process is associated with some follow-up stages those are discussed as follows.

At the initiation of the method is recognised as sample preparation, next step is target enrichment and the final step is sequencing process. In context of sample preparation, DNA extraction, purification and quality control are three common steps. Further, the target enrichment is also associated with three basic steps including DNA fragmentation, exome capture and washing. It has to be mentioned here that exome capture and washing steps are performed whenever it was required. The DNA fragmentation process can be implemented by two different ways including physical fragmentation and enzymatic fragmentation. In context of physical fragmentation, DNA can be differentiated into multiple pieces due to ultrasound including acoustic cavitation and hydrodynamic shearing. In context of enzymatic method, DNA broke through enzyme including nuclease and protease. In final stage sequencing process sequencing and data analysis are key stages for conduct the WES. 

According to García& Bustos, (2018), genetic diagnosis of genetic testing is a process, which helps to determine alteration or mutation of genes to determine cause or region of the specific disease. It has to be mentioned here that the genetic diagnosis allows an organization to determine the current or future condition of an individual regarding genetic disorder. Now this section is going to discuss four different types of genetic diagnosis. This research paper has undertaken Sanger sequencing, Haloplex Custom Panel, TruSight One panel and whole genome sequencing. 

Sanger sequencing or first generation sequencing is one of the traditional processes of DNA sequencing which allow determining nucleotide sequencing (Bruijnset al. 2018). The Sanger sequencing method is also known as chain termination sequencing. On other hand, Vidal et al. (2017) reported that this is one of traditional methods of genetic sequencing which have minimal chances to provide false results. It has been identified that Sanger sequencing produces longer reads compared to coin generation sequencing. However, the sequencing method has poor efficiency, which may create a negative effect on the result. 

This research paper has utilized the Haloplex Custom Panel (HCP) method to determine the usefulness of NGS in genetic diagnosis. This is one of rare DNA sequencing methods, which help to determine gene alteration. However, it has to be mentioned here that efficiency of DNA sequencing is relatively low in this method. Further, this search paper has undertaken the Trusight One Panel sequencing method to continue the process. According to Deleye et al. (2018), this is one of common DNA sequencing processes, which helps to sequence genes and determine the genetic disorder condition. It has been identified that this is one of the common and low cost methods, which successfully identified genetic position. However, this method can only be applicable for single gene disorders. 

In the final stage, this research paper has performed a whole genome sequencing method. Whole genome sequencing method is a next generation sequencing method, which helps to determine more than 3 billion DNA nucleotides. It has been identified that this whole exome sequencing is a process that helps to identify all protein coding regions of genes form a whole genome (Nakagawa & Fujita, 2018). This literature also stated that whole exome sequencing also helps in complete gene analysis and it determines the health conditions and future possible disorders. Therefore, by focusing on the above discussion, it has been identified that whole genome sequencing and NGS is one significant steps to determine a genetic diagnosis. 

Aim of this research is to determine the usefulness of NGS in RETT syndrome for genetic diagnosis. In this regard, this research paper has been chosen multiple DNA sequencing methods from first generation to next generation sequencing to determine usefulness of next generation process. This research paper chose multiple methods, which allow this paper to successfully compare next generation methods with others. This comparison ensures why people should follow the NGS and it is directly linked with the aim of the research paper. Therefore, by focusing on the above analysis, it can be stated that this research paper has undertaken an accurate method to continue the research. 

Explanation of one figure

Now, this section is going to choose one figure from the result section of the chosen research paper to analyse that figure and determine the research results and its linked with research aim. 

In the above figure SS indicates Sanger Sequencing, HCP indicates Halopex Custom panel, TSO define TruSight One Panel and WES indicates Whole Exome Sequencing (Vidal et al. 2017).Above figure indicates the percentage of total families and unsolved families based on four different types of sequencing techniques for the RTT syndrome. By keeping an eye on the above figure, it has been identified that 353 patients among 1341 patients have RTT mutated genes. It has to be mentioned here that the result has been identified from the Sanger sequencing or first generation sequencing techniques. Further, Sanger sequencing processindicates that around 26.3% of patients have positive RTT mutated genes disorder (Vidal et al. 2017). `

Further, above figure indicates that 47 among 242 patients have been diagnosed with the techniques of HCP. In this case, around 19% of patients have RTT mutated genes. In terms of trust, one panel around 15 patients among 51 patients have been faced with RTT mutated genes. T has to be mentioned here that around 29.4% of patients have been diagnosed by the TSO method for determining genetic diagnosis of RTT. In the final section, the above figure denotes that 10 patients among 25 patients have RTT mutated genes. This section indicates that 40% of patients have RTT mutated genes (Vidal et al. 2017). Therefore, by keeping an eye on the above discussion, it can be stated that whole genome sequencing or next generations sequence process shows the most reliable and significant result regarding a genetic diagnosis of RTT. 

Conclusion

This research paper has concluded that next generation sequencing or NGS is one of the significant methods, which helps to determine a genetic diagnosis of RTT more efficiently compared to other approaches. This research paper chose multiple methods, which allow this paper to compare next generation methods with others successfully. Further, this research paper also stated that the NHS allows this paper to cover a wide range of DNA compared to other three approaches. This literature also summarized that the detected variant by NGS helps to prevent future disease by implementing pharmacological therapy(Vidal et al. 2017). In addition, this research paper has concluded that based on the cost efficient aspect the TSO is the most crucial and effective method to analyse genes of RTT and continue the process. Therefore, this literature has been concluded that NGS is one of the crucial and most significant methods to analyse genetic diagnosis of the RETT syndrome. 

By keeping an eye on research aim, this assignment has identified that the chosen research papers have successfully discussed the importance of next generation sequencing in genetic diagnosis of RTT syndrome. It has to be mentioned here that this research paper also discussed advantages of NGS over the other approaches. Therefore, by focusing on the above discussion, it can be concluded that the chosen research paper has successfully met the research aims and objectives. In addition, it can be stated that this is an accurate way to meet the search aim, therefore no further search or other approaches are required. The chosen data collections and statistical analysis method play a significant role. 

Reference list

Bruijns, B., Tiggelaar, R., &Gardeniers, H. (2018). Massively parallel sequencing techniques for forensics: A review. Electrophoresis, 39(21), 2642-2654.https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/pdf/10.1002/elps.201800082

Deleye, L., Gansemans, Y., De Coninck, D., Van Nieuwerburgh, F., &Deforce, D. (2018). Massively parallel sequencing of micro-manipulated cells targeting a comprehensive panel of disease-causing genes: A comparative evaluation of upstream whole-genome amplification methods. PLoS One, 13(4), e0196334.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0196334&type=printable

García, J. C., & Bustos, R. H. (2018). The genetic diagnosis of neurodegenerative diseases and therapeutic perspectives. Brain sciences, 8(12), 222.https://www.nejm.org/doi/full/10.1056/NEJMoa1714458

Ip, J. P., Mellios, N., & Sur, M. (2018). Rett syndrome: insights into genetic, molecular and circuit mechanisms. Nature Reviews Neuroscience, 19(6), 368-382.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402579/

Kyle, S. M., Vashi, N., & Justice, M. J. (2018). Rett syndrome: a neurological disorder with metabolic components. Open biology, 8(2), 170216.https://royalsocietypublishing.org/doi/full/10.1098/rsob.170216?rss%3D1%26ssource%3Dmfr=

Nakagawa, H., & Fujita, M. (2018). Whole genome sequencing analysis for cancer genomics and precision medicine. Cancer science, 109(3), 513-522.https://onlinelibrary.wiley.com/doi/pdfdirect/10.1111/cas.13505

Suwinski, P., Ong, C., Ling, M.H., Poh, Y.M., Khan, A.M. & Ong, H.S., (2019). Advancing personalized medicine through the application of whole exome sequencing and big data analytics. Frontiers in genetics, 10, p.49. https://www.frontiersin.org/articles/10.3389/fgene.2019.00049/full

Vidal, S., Brandi, N., Pacheco, P., Gerotina, E., Blasco, L., Trotta, J. R., ...& Armstrong, J. (2017). The utility of Next Generation Sequencing for molecular diagnostics in Rett syndrome. Scientific reports, 7(1), 1-11.https://www.nature.com/articles/s41598-017-11620-3