Milestones in genomics and laser diodes

Nov. 1, 2012
The 1000 Genomes Project has reached the goal implied by its name: As of October 2012, the international public-private effort to create the world's largest, most detailed catalog of human genetic variation had sequenced the genomes of 1,092 humans from 14 distinct populations in Europe, East Asia, sub-Saharan Africa, and the Americas.
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The 1000 Genomes Project has reached the goal implied by its name: As of October 2012, the international public-private effort to create the world's largest, most detailed catalog of human genetic variation had sequenced the genomes of 1,092 humans from 14 distinct populations in Europe, East Asia, sub-Saharan Africa, and the Americas (see doi:10.1038/nature11632).

This exciting milestone was made possible by optics and photonics-based technologies, as even casual observers—for instance, those who learn about the project through Wikipedia—may know. The Wikipedia reference to "newly developed technologies which are faster and less expensive" means the "massively parallel" systems described by Elaine Mardis of The Genome Institute at Washington University in St. Louis, in her article beginning on page 27. (By the way, The Genome Institute is one of the key organizations participating in 1000 Genomes.)

But there's another generation of systems on its way, as Mardis also describes—and there is a large unmet need to effectively analyze the massive collection of data that the project is generating. Meantime, all project data is freely available on the Internet through public databases such as those at the National Center for Biotechnology Information (NCBI; Bethesda, MD) and the European Bioinformatics Institute (Hinxton, England), and through the cloud via Amazon Web Services (AWS).

The impact of the advanced technologies could hardly be more dramatic. "I view this project as a Lewis and Clark expedition to the interior of the human genome," said Stephen Sherry, Chief of the Reference Collections Section, Information Engineering Branch, NCBI. "We knew the outlines and contours. Now, we're trying to document all the fine details such as the rivers and tributaries."

To that end, the project aims to identify and compile variants in the human genome that occur in at least 1 in 50 people. Although most of these genetic variants have negligible effect, some contribute to disease while others protect against it. For example, one rare variant blocks the human immunodeficiency virus from infecting white blood cells and thereby can protect people exposed to HIV. Ultimately, 1000 Genomes will study more than 2,500 individuals from 26 populations.

Another technology covered in this issue, the laser diode, was also in the news recently—and not just because of its 50th anniversary. The highest award (the "Future Prize") of the 2012 Berthold Leibinger Zukunftpreis—which recognizes outstanding research in the generation of laser light, particularly those that concern healthcare and other important sectors—went to Dr. Osamu Kumagi of Sony Tokyo. Kumagi was instrumental in facilitating mass production of laser diodes, which continue to evolve in their impact on life sciences. In her article on page 39, Marion Lang offers insight into that.

About the Author

Barbara Gefvert | Editor-in-Chief, BioOptics World (2008-2020)

Barbara G. Gefvert has been a science and technology editor and writer since 1987, and served as editor in chief on multiple publications, including Sensors magazine for nearly a decade.

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