Advances in Long-Read Sequencing with Short-Read Next-Generation Sequencers

The Ascent of Short-Read Next-Generation Sequencing

During the past two decades, short-read next-generation sequencing (srNGS) has expanded the science of genetics far beyond what became possible using Fred Sanger’s first-ever sequencing technology (AKA Sanger sequencing), developed in 1977. The impact of srNGS has been so far-reaching that “genetics” was renamed to “genomics” to account for the vast increase in genetic information the new technology generated compared to its predecessor.

Since its early deployment twenty years ago, srNGS has been on a steady trajectory of generating more data for fewer resources. Genomes that took years to sequence can now be sequenced in hours, revolutionizing genomics research and development, with widespread impact on everyday life.

srNGS now permeates every domain of the life sciences and healthcare, enabling advancements in vaccine and drug development, better monitoring and early detection of disease, as well as numerous other contributions on a broad application spectrum ranging from increasing crop productivity to pushing the boundaries of pre-natal diagnostics, to name a few.

Challenges and Limitations of Short-Read NGS

Two decades of srNGS have also revealed many genomics challenges that short reads cannot fully resolve. Domains such as genome, transcriptome, microbiome, and immune repertoire sequencing are a few areas where short-read lengths have limitations. The wide availability of inexpensive and accurate short-read sequencing has provided a foundation to appreciate that the true complexities of the genome and transcriptome will benefit from higher and higher resolution. Improvements in resolution are most recognized in higher accuracy sequencing, longer read lengths, or ideally, both.

Many biological questions cannot be fully resolved with short reads, regardless of how many of them we throw at the problem. Genomics will increasingly require alternative technologies that push the boundaries of existing srNGS. Making this trend even more severe are two decades of short-read thinking (see the Law of the Instrument), conditioning scientists to view problems through the lens of the short-read sequencer. This trend results in biases in how scientists think about experiments in genomics, primarily seeking to address questions that can be answered with short reads and neglecting questions that short reads cannot answer.

In other words, we are devising scientific questions that fit the existing sequencing technology instead of devising sequencing technologies to fit the scientific questions we want to ask.

Advancements in Long-Read Technologies

Fortunately, genomic technologies are diversifying in technology platforms that allow native long-read sequencing and applications that leverage short-read output to develop long-read resolution through creative molecular biology and bioinformatics.

Native long-read platforms offer unparalleled opportunities to sequence tens of thousands to millions of bases in a single read. Tradeoffs for the longer reads can be lower per-base accuracy or higher cost per read compared to short-read technologies. Application-based methods that leverage short read platforms’ accuracy and cost advantages are also advancing.

Multiple new sequencing technologies are emerging in the long-read and synthetic long sequencing space, enabling scientists to uncover previously inaccessible genetic information. The opportunities these technologies present are everywhere and are positioned to accelerate advancements in antibody development through the sequencing of full-length antibodies, drug target identification through the sequencing of disease-specific transcription isoforms, and the development of more effective viral vaccines through the characterization of viral quasi-species, to name a few examples.

Learn More About Long-Read Sequencing with Loop Genomics

To learn how you can get a head start in your research by integrating advanced sequencing technologies like synthetic long-read sequencing, visit us at the Loop Genomics’ website's Learn section to read peer-reviewed publications, listen to webinars, and read tech notes about Loopseq™, our emerging synthetic long-read sequencing technology.

Join us and the ever-growing community of scientists embracing new long-read sequencing technologies and participate in bringing about the future!

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