High-Molecular Weight DNA for Long-Read Sequencing

Imagine that you’re putting together a large, complex jigsaw puzzle, comprising thousands of exceptionally small pieces. You lay them all out and attempt to make sense of them. It would be far easier to assemble this puzzle were the pieces larger, containing more of the image advertised on the box. The same can be said when sequencing a genome.

high-molecular weight DNA  Depiction of a DNA helix

Traditional short-read or next-generation sequencing relies on DNA spliced into small fragments (≤300 base pairs) and then amplified. While useful for detecting small genetic variants like single-base changes to the DNA, this type of sequencing can fail to illuminate larger variations (typically over 50 base pairs) in the genome. Long-read sequencing, or third generation sequencing, allows more accurate genome assemblies, facilitating better detection of structural variants like copy number variations, duplications, translocations and inversions that are too large to identify with short-read sequencing. Long-read sequencing has the capability to fill in “dark regions” of a genome that are unfinished and can be used to assemble larger, more complex genomes using longer fragments of DNA, or high-molecular weight (HMW) DNA.

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An Ambitious Endeavor: The Human Proteoform Project

On November 15, 2021, Science Advances announced the launch of The Human Proteoform Project. The ambitious project, led by the Consortium for Top-Down Proteomics, aims to address a critical next step in disease research. This means developing new technologies to outline a complete set of protein forms based on the ~20,000 genes in the human genome.

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Deep in the Jungle Something Is Happening: DNA Sequencing

This blog was written by guest blogger and 2018 Promega Social Media Intern Logan Godfrey.

Only 30 years ago, the polymerase chain reaction (PCR) was used for the first time, allowing the exponential amplification of a specific DNA segment. A small amount of DNA could now be replicated until there was enough of it to study accurately, even allowing sequencing of the amplified DNA. This was a massive breakthrough that produced immediate effects in the fields of forensics and life science research. Since these technologies were first introduced however, the molecular biology research laboratory has been the sole domain of PCR and DNA sequencing.

While an amazing revolution, application of a technology such as DNA sequencing is limited by the size and cost of DNA sequencers, which in turn restricts accessibility. However, recent breakthroughs are allowing DNA sequencing to take place in jungles, the arctic, and even space—giving science the opportunity to reach further, faster than ever before. 

Gideon Erkenswick begins extractions on fecal samples collected from wild tamarins in 2017. Location: The GreenLab, Inkaterra.

Gideon Erkenswick begins extractions on fecal samples collected from wild tamarins in 2017. Location: The GreenLab, Inkaterra. Photo credit: Field Projects International.

The newfound accessibility of DNA sequencing means a marriage between fields of science that were previously largely unacquainted. The disciplines of genomics and wildlife biology/ecology have largely progressed independently. Wildlife biology is practiced in the field through observations and macro-level assessments, and genomics, largely, has developed in a lab setting. Leading the charge in the convergence of wildlife biology and genomics is Field Projects International. 

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The Ongoing Legacy of the Human Genome Sequence

When the first draft sequence of the human genome was announced, I was a research assistant for a lab that was part of the Genome Center of Wisconsin where I created shotgun libraries of bacterial genomes for sequencing. Of course, the local news organizations were all abuzz with the news and sought opinions on what this meant for the future, including that of the lab’s PI and oddly enough, my own. While I do not recall the exact words I offered on camera, I believe they were something along the lines of this is only the first step toward the future of human genetics. Ten years later, we have not fulfilled the potential of the grandiose words used to report the first draft sequence but have gained enough knowledge of what our genome holds to only intrigue scientists even more.

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