Sequencing Human Genome with Pocket-Sized “Nanopore” Device

MinION sequencing device

Caption: MinION sequencing device plugged into a laptop/Oxford Nanopore Technologies

It’s hard to believe, but it’s been almost 15 years since we successfully completed the Human Genome Project, ahead of schedule and under budget. I was proud to stand with my international colleagues in a celebration at the Library of Congress on April 14, 2003 (which happens to be my birthday), to announce that we had stitched together the very first reference sequence of the human genome at a total cost of about $400 million. As remarkable as that achievement was, it was just the beginning of our ongoing effort to understand the human genome, and to use that understanding to improve human health.

That first reference human genome was sequenced using automated machines that were the size of small phone booths.  Since then, breathtaking progress has been made in developing innovative technologies that have made DNA sequencing far easier, faster, and more affordable. Now, a report in Nature Biotechnology highlights the latest advance: the sequencing and assembly of a human genome using a pocket-sized device [1]. It was generated using several “nanopore” devices that can be purchased online with a “starter kit” for just $1,000. In fact, this new genome sequence—completed in a matter of weeks—includes some notoriously hard-to-sequence stretches of DNA, filling several key gaps in our original reference genome.

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Creative Minds: Bacteria, Gene Swaps, and Human Cancer

Julie Dunning Hotopp

Julie Dunning Hotopp

When Julie Dunning Hotopp was a post-doctoral fellow in the early 2000s, bacteria were known for swapping bits of their DNA with other bacteria, a strategy known as lateral gene transfer. But the offloading of genes from bacteria into multicellular organisms was thought to be rare, with limited evidence that a bacterial genus called Wolbachia, which invades the cells of other organisms and takes up permanent residence, had passed off some of its DNA onto a species of beetle and a parasitic worm. Dunning Hotopp wondered whether lateral gene transfer might be a more common phenomenon than the evidence showed.

She and her colleagues soon discovered that Wolbachia had engaged in widespread lateral gene transfer with eight species of insects and nematode worms, possibly passing on genes and traits to their invertebrate hosts [1]. This important discovery put Dunning Hotopp on a research trail that now has taken a sharp turn toward human cancer and earned her a 2015 NIH Director’s Transformative Research Award. This NIH award supports exceptionally innovative research projects that are inherently risky and untested but have the potential to change fundamental research paradigms in areas such as cancer and throughout the biomedical sciences.

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Genome Exhibit Opens at Smithsonian

Photo of one of the interacive touch screen exhibits

Credit: Sasan Azami-Soheily, National Human Genome Research Institute, NIH

To celebrate the 10th anniversary of the completion of the Human Genome Project—a 13-year endeavor that I had the privilege of leading—the Smithsonian’s National Museum of Natural History in Washington, DC is launching an absolutely fantastic exhibit called “Genome: Unlocking Life’s Code.”

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DNA’s Double Anniversary

Images of the first publication of DNA's structure adjacent to the image on the cover of the published human genome

April 25 is a very special day. In 2003, Congress declared April 25th DNA Day to mark the date that James Watson and Francis Crick published their seminal one-page paper in Nature [1] describing the helical structure of DNA. That was 60 years ago. In that single page, they revealed how organisms elegantly store biological information and pass it from generation to generation; they discovered the molecular basis of evolution; and they effectively launched the era of modern biology.

But that’s not all that’s special about this date. It was ten years ago this month that we celebrated the completion of all of the original goals of the Human Genome Project (HGP), which produced a reference sequence of the 3 billion DNA letters that make up the instruction book for building and maintaining a human being. The $3 billion, 13-year project involved more than 2,000 scientists from six countries. As the scientist tasked with leading that effort, I remain immensely proud of the team. They worked tirelessly and creatively to do something once thought impossible, never worrying about who got the credit, and giving all of the data away immediately so that anyone who had a good idea about how to use it for human benefit could proceed immediately. Biology will never be the same. Medical research will never be the same. Continue reading