Category Archives: Genetics

Genome Sequencing Technology Advancing at an Astounding Rate

Background

On 14 April 2003 the National Human Genome Research Institute (NHGRI), the Department of Energy (DOE) and their partners in the International Human Genome Sequencing Consortium declared the successful completion of the Human Genome Project. Under this project, a “working draft” of the human genome had been developed and published in 2000 – 2001. At $2.7 billion in FY 1991 dollars, this project ended up costing less than expected and was completed more than two years ahead of its original schedule. However, “finishing” work continued through 2006 when sequencing of the last chromosome was reported.

A parallel project was conducted by the Celera Corporation, which was founded by Craig Venter in 1998 in Rockville, MD. The Celera project had access to the public data from the Human Genome Project and was funded by about $300 million from private sources. Competitive pressure from Celera, coupled with Celera’s plans to seek “intellectual property protection” on “fully-characterized important structures” of the genome likely accelerated the public release of the genome sequencing work performed by the Human Genome Project team.

In 2006, XPRIZE announced the Archon Genomics XPRIZE, offering $10 million to the first team that could rapidly and accurately sequence 100 whole human genomes to a standard never before achieved at a cost of $10,000 or less per genome.

DNA helix Genomic XPRIZESource: genomics.xprize.com

This contest was cancelled in August 2013 (first-ever XPRIZE competition to be cancelled), when it became obvious that, independent of this XPRIZE competition, the cost of commercial genome sequencing was plummeting while the sequencing speed was rapidly increasing. At the time the XPRIZE was cancelled in 2013, the cost of sequencing had dropped to about $5,000 per genome. You can read more about the cancellation of this XPRIZE at the following link:

http://genomics.xprize.org/news/outpaced-innovation-canceling-xprize

Remarkable progress at Illumina

About six months after the XPRIZE was cancelled, the San Diego gene sequencing firm Illumina announced on 14 January 2014 that it could sequence a human genome for $1,000 with their HiSeqX Ten sequencing system. A 15 January 2014 BBC report on this achievement is at the following link:

http://www.bbc.com/news/science-environment-25751958

At the time, the HiSeqX Ten was the top-of-the-line gene sequencing system in the world. It was reported to be capable of sequencing five human genomes per day. That’s about 4.8 hours per genome for a cost of $1,000 in January 2014. The HiSeqX Ten system actually is a set of 10 machines that sold originally for about $10 million. The smaller HiSeqX Five system, comprised of five machines, sold for about $6 million. One of the early customers for the HiSeqX Ten system was San-Diego-based Human Longevity Inc. (HLI), which Craig Venter co-founded.

Illumina Hiseq-x-tenIllumina’s HiSeqX Ten sequencing system. Source: Illumina

You’ll find details on the HiSeqX Ten system on the Illumina website at the following link:

http://www.illumina.com/systems/hiseq-x-sequencing-system/system.html

About six months later, on 16 July 2014, Dr. Allison Hahn, Sr. Applications Scientist from Illumina, Inc. was the Lyncean Group’s 87th speaker, with her presentation entitled, “How Genomics is Changing the Way We Think About Health and Disease.” The focus of this presentation was on how next-generation sequencing technology was paving the way toward using genomics in medicine. While this presentation was fascinating, one thing missing was a sense of just how short a “generation” was in the gene sequencing machine business.

On 10 January 2016, San Diego Union-Tribune reporter Bradley Fikes (another Lyncean Group speaker, April 2016) broke the news on Illumina’s new top-of-the-line genome sequencer, the NovaSeqTM sequencing system, which claims the capability to sequence a human genome in an average time of about one hour.

Illumina NovaSeq

 NovaSeqTM 6000. Source: Illumina

The U-T report provided the following additional details:

  • Illumina will sell the NovaSeqTM sequencing systems individually, with the first units expected to ship in March 2017
  • Two models, NovaSeqTM 5000 and 6000, are priced at $850,000 and $985,000, respectively.
  • “And ‘one day,’ Illumina chief executive Francis DeSouza said, the company’s NovaSeq line is expected to reduce the cost of sequencing to $100 per human genome.”

You can read Bradley Fike’s complete U-T article at the following link:

http://www.sandiegouniontribune.com/business/biotech/sd-me-illumina-novaseq-20170109-story.html

You’ll find product details on the NovaSeqTM series of sequencing systems on the Illumina website at the following link:

http://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/novaseq-series-specification-sheet-770-2016-025.pdf

In less than two decades, human genome sequencing has gone from a massive research program to an extraordinarily efficient commercial process that now is on the brink of becoming a commodity for ever broadening applications.  The great speed and relatively low price of the new NovaSeqTM sequencing systems, and any other commercially competitive counterparts, are certain to transform the way genomic science is integrated into medical services.

What will Illumina do for an encore?

Just What are Those U.S. Scientists Doing in the Antarctic and the Southern Ocean?

The National Academies Press (NAP) recently published the report, “A Strategic Vision for NSF Investments in Antarctic and Southern Ocean Research”, which you can download for free at the following link if you have established a MyNAP account:

http://www.nap.edu/catalog/21741/a-strategic-vision-for-nsf-investments-in-antarctic-and-southern-ocean-research

Print Source: NAP

NSF states that research on the Southern Ocean and the Antarctic ice sheets is becoming increasingly urgent not only for understanding the future of the region but also its interconnections with and impacts on many other parts of the globe. The research priorities for the next decade, as recommended by the Committee on the Development of a Strategic Vision for the U.S. Antarctic Program; Polar Research Board; Division on Earth and Life Studies; National Academies of Sciences, Engineering, and Medicine, are summarized below:

  • Core Program: Investigator-driven basic research across a broad range of disciplines
    • NSF gives the following rationale: “…it is impossible to predict where the next major breakthroughs or advances will happen. Thus to ensure that the nation is well positioned to take advantage of such breakthroughs, it is important to be engaged in all core areas of scientific research.”
      • NSF notes, “…discoveries are often made by single or small groups of PIs thinking outside the box, or with a crazy new idea, or even just making the first observations from a new place.”
    • Examples of basic research that have led to important findings include:
      • Ross Sea food chain is affected by a high abundance of predator species (whales, penguins and toothfish) all competing for the same limited resource: krill. Decline or recovery of one predator population can be seen in an inverse effect on the other predator populations.  This food chain response is not seen in other areas of the Antarctic ice shelf where predator populations are lower, allowing a larger krill population that adequately supports all predators.
      • Basic research into “curious” very-low frequency (VLF) radio emissions produced by lightning discharges led to a larger program (with a 21.2-km-long VLF antenna) and ultimately to a better understanding of the behavior of plasma in the magnetosphere.
  • Strategic, Large Research Initiatives –  selection criteria:
    • Primary filter: compelling science – research that has the potential for important, transformative steps forward in understanding and discovery
    • Subsequent filters: potential for societal impact; time-sensitive in nature; readiness / feasibility; and key area for U.S. and NSF leadership.
    • Additional factors: partnership potential; impact on program balance; potential to help bridge existing disciplinary divides
  • Strategic, Large Research Initiative – recommendations::
    • Priority I: The Changing Antarctic Ice Sheets Initiative to determine how fast and by how much will sea level rise?
      • A multidisciplinary initiative to understand why the Antarctic ice sheets is changing now and how they will change in the future.
      • Will use multiple records of past ice sheet change to understand rates and processes.
    • Priority II: How do Antarctic biota evolve and adapt to the changing environment?
      • Decoding the genomic (DNA) and transcriptomic (messenger RNA molecules) bases of biological adaptation and response across Antarctic organisms and ecosystems.
    • Priority III: How did the universe begin and what are the underlying physical laws that govern its evolution and ultimate fate?
      • A next-generation cosmic microwave background (CBM) program that builds on the current successful CMB program using telescopes at the South Pole and the high Atacama Plateau in Chile and possibly will add a new site in the Northern Hemisphere to allow observations of the full sky

You will find detailed descriptions of the Priority I to III strategic programs in the Strategic Vision report.

 

How Close Are We to Cloning a Mammoth?

mammoth-cloning-840x420  Source: www.makeuseof.com

Mammoths lived from the Pliocene epoch, about 5 million years ago, into the current Holocene epoch; dying out about four thousand years ago.  Many lived in Arctic tundra regions in Siberia and northern Canada, where many frozen, relatively well-preserved mammoth “mummies” have been found in permafrost.   Scientists have been able to extract mammoth DNA from these remains.  Unfortunately, the mammoth DNA samples have been degraded by the long-term actions of water and oxygen and have been contaminated with DNA from other sources, such as: (1) bacteria that lived symbiotically in or on the mammoth, or (2) bacteria and fungi that existed in the environment where the mammoth was found.  Techniques exist to discriminate original mammoth DNA fragments from these other DNA sources.    Genetically, the mammoth is more closely related to the modern Asian elephant than the African elephant. Scientists are working to complete the mapping of the mammoth genome and identify all the differences with the Asian elephant genome.   In the not too distant future, it appears that it will be possible to splice mammoth DNA fragments into the complete DNA sequence of an Asian elephant.  If this work is successful, we may have the opportunity to visit a living mammoth in a “Pliocene Park” somewhere in the Arctic.

Read more details and see some very interesting embedded videos at the following link:

http://www.makeuseof.com/tag/far-cloning-mammoth/

 

 

The Svalbard Global Seed Vault Provides a Genetic Agricultural Safety Net

The Svalbard Global Seed Vault, which was opened in 2008 by the Norwegian government, is a secure seed bank on the Norwegian island of Spitsbergen in the remote Arctic Svalbard archipelago, about 1,300 kilometres from the North Pole. The mission of the Seed Vault is to provide a safety net against accidental loss of diversity in traditional agricultural genebanks.

svalbard-map

Svalbard Global Seed Vault

From all across the globe, crates of seeds are sent here for safe and secure long-term storage in cold and dry rock vaults.

Read more about the Svalbard Global Seed Vault at the following link:

https://www.regjeringen.no/en/topics/food-fisheries-and-agriculture/agriculture/svalbard-global-seed-vault/id462220/

A new documentary film, “Seeds of Time,” tracks the history and mission of the Svalbard Global Seed Vault, and its founder Cary Fowler. The film is due to be released on 22 May 2015. You can see the trailer for this movie at the following link:

http://earthsky.org/earth/seeds-of-time-to-hit-theaters-in-may?utm_source=EarthSky+News&utm_campaign=5c4858146d-EarthSky_News&utm_medium=email&utm_term=0_c643945d79-5c4858146d-394288401