What is The History of Genetic Sequencing?
It was only a little more than 50 years ago that Hershey and Chase proved that DNA carries genetic information from one generation to the next. In the next 30 years, research on the human genome progressed tremendously. In 1977 Frederick Sanger developed the very first DNA sequencing technique that we now refer to as the first-generation sequencing. It would change the future of genomic studies, clinical diagnosis, and lead to the development of personalized medicine. The more significant part of sequencing the transcriptome and capturing the cellular RNA seq data depends considerably on the first-generation DNA sequencing technique.
What are the contributions of first-generation sequencing techniques?
In 1990, the Human Genome Project, a 13-year long research project, was launched. It aimed at determining the entire DNA sequence of the human genome. The US Department of Energy and the NIH formally founded the project in 1990 with a $3 billion budget. Although the project did not sequence the entire human genome, only the euchromatic regions, it was completed in 2003.
Over the last 16 years, it has served as one of the most important references for researches in the fields of genomics, molecular medicine, virology, disease progression, pathogenesis, and even human evolution. It has contributed to the understanding of different types of mutations linked to various forms of cancer and tumor progression. Since the DNA sequence is stored in an openly accessible database, it continues to help thousands of research institutes across the world by providing updated and correct information necessary to corroborate their finds.
What changed the pace of genome sequencing studies in the early 2000s?
The techniques used by researchers in the 90s and early 2000s to sequence human euchromatic DNA were slow and labor-intensive. Although they relied upon software programs and automation considerably, a significant part of the data analysis was still manual. The artifacts in the result and the challenges of replicability further slowed the progress of DNA sequencing techniques down. The high-throughput genome sequencing needs for studies on mutations linked to cancer, diagnosis of fast progressing chronic diseases, and viral pathogenesis demanded more rapid techniques that promised quick and accurate results.
Then came the Next-generation sequencing (NGS) techniques. These are high-throughput methods that enable parallel DNA sequencing and analysis. While the Sanger method is quite expensive, the NGS is a much cheaper alternative that supports bulk sample analysis at significantly higher rates with fewer artifacts. NGS generates digital read types that allow straightforward quantitative comparisons between sequences.
Why are NGS technologies so highly valued among research teams?
NGS reduces the need for fragment-cloning as is necessary in case of Sanger Sequencing methods. Over the next few years, the time required to analyze more than gigabase-sized sequences was reduced to a few hours or days at the most. It was a significant advancement from the older methods that took more than a week to analyze the same volume of sequences. One can never forget that JC Venter needed more than 13 years and $1 million to complete the Human Genome Project. The JD Watson genome used NGS and only required 2 months for complete sequencing at a one-one hundredth of the cost.
The tremendous progress of NGS technology allows the complete genome sequencing of prokaryotes (bacteria) within a day at around $1000. It is a hallmark of success. The advancement of whole genome sequencing (WGS) of 2,636 residents of Iceland has made it possible to meet the stipulated schedule of the 1000 Genome Project. The use of NGS for WGS has now made it possible for research groups to analyze genomes of any organisms of interest on a tight budget.
How has sequencing evolved since the discovery of NGS?
Apart from WGS, NGS can be used for whole transcriptome shotgun sequencing or RNA sequencing, whole exome sequencing (WES), post-transcriptional modifications, epigenetic modifications, methylation sequencing, and targeted exome sequencing. The RNA Seq data gives an insight into the entire repertoire of known and unknown regulation pathways, and transcriptional activities in vitro. Before the genesis of completely automated software-based analysis of RNA sequencing data, WES was considered a cost-effective technique for the study of human genetics and diagnosis of genetic diseases.
What was the next development in the world of genomics and transcriptomics?
In 2008, RNA-sequencing came to existence. This new technique allowed the biologists to focus on the link between DNA and proteins. They could take a look at the dynamic factor within the cells that control the protein expression within. RNA sequencing focuses on the messenger RNAs that are the products of DNA transcription. It enabled the researchers to take an in-depth look into the protein machinery, upregulation, and downregulation of protein profiles within a cell.
What’s the latest challenge posed by NGS, and how have research teams overcome it?
The only challenge was the analysis of massive volumes of data that each RNA-seq cycle generated. The introduction of fully automated software with cloud-based tools provided the answer to all RNA Seq data analysis challenges. Now, research teams can have reports from the analysis of their samples within a couple of hours. Earlier, people had to wait for an entire day to get comprehensive reports after the analysis of data from their RNA samples. For more information on RNA sequencing data analysis, visit the official Basepair website.
The ease of RNA Seq data analysis has opened new avenues for scientists, doctors, pathologists, pharmaceutical companies, and molecular biologists. The sequencing process not only involves the RNA from the host cells but also biomarkers from the potential pathogen. That makes studies on viral infections at the molecular level much more comfortable than before.
How can you complete NGS RNA seq data analysis on a budget?
Today, it is possible for small and large teams of researchers to access NGS technologies from third-party service providers. Although NGS is not cost-intensive, the setup is quite expensive and preventative for smaller research institutes. They can outsource not only their NGS technology needs but also request accurate and fast analysis of the RNA seq data from the professional NGS service providers.
If the teams already have the sequences or the NGS setup, they can request third-party analysis services. These services typically have dedicated cloud-native and automated analytics software that can capture and analyze RNA Seq datawithin record time. While looking for a similar service, always ensure that the service provider offers replicable results in publication-ready formats. The kind of technology, experience, and knowledge of the analytics company plays a significant role in the quality of the results you can expect from them.