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NHGRI's Green Surveys Genomic Landscape a Decade after Human Genome Release

NEW YORK (GenomeWeb News) - It was 10 years ago yesterday that the partners behind the Human Genome Project unveiled the first reference sequence of the human genome to the public, and although it has not yet revolutionized medical treatment, genomics is beginning to seep into the clinic and many advances have been made.

To mark the anniversary, the National Human Genome Research Institute has been hosting a seminar series and has a day-long symposium planned for Apr. 25, in which luminaries in genomics plan to discuss the breadth of human genome sciences today and mull over the past decade.

In a conference call on Friday, NHGRI Director Eric Green said that the anniversary, or this "genomic odometer moment," is a ripe opportunity to highlight some of the innovations that have occurred since those 3 billion or so letters of genetic code were made available to the global research, medical, and life science business communities.

"Since that milestone, the genomic era has reached a remarkably mature stage and the field has expanded in many productive ways, both anticipated and unanticipated," Green said. "When I look back at what has been done and how far we've come in genomics over the past 23 years, since the beginning of the genome project, and in particular in the past 10 years since the end of the genome project, I am simply amazed."

"I'm profoundly excited about these new frontiers that we at NHGRI will be pushing ourselves into as we explore the application of genomics in medical care. Day in and day out, I think about where genomics is going, and I continually conclude the field's future is really quite bright," he continued.

In the talk, Green focused on the major developments in technologies, the volumes of data that have been added to the base of genomic knowledge, discoveries about diseases, and businesses and projects that have started pulling genomics into the clinic.

Technology Developments and a Data Deluge

All that has happened in genomics since the HGP has been enabled by the advance of new technologies, which has led to the plummeting cost of gene sequencing, Green explained. He noted that when the project started, the HGP partners did not really know how to sequence a human genome, and the effort took "six to eight years of active sequencing and cost roughly $1 billion to complete the task."

But by the end of the project, the cost of sequencing had already dropped so much that if the researchers who had just finished the first human genome in 2003 decided to turn around and immediately sequence a second one, it would have taken only three or four months and cost between $30 million and $40 million, Green estimated.

"Fast forward to today, 10 years later, and DNA sequencing technologies have advanced tremendously, perhaps the most impressive technology development in the history of biomedical research," so much so that the cost of sequencing a human genome is now $4,000 or $5,000, he said.

"In 10 short years, we have knocked five zeroes from that $1 billion price tag, and will likely knock that last zero off within a year or two or three. So, today, sequencing the human genome is in the cost range of a sophisticated medical test, like an MRI," Green said.

As sequencing platforms have evolved and become extensively used in life sciences research over the past 10 years, seas of genomic data have been churned out. In 2003, there was just the one human genome sequence, and today there are thousands of genomes that have been sequenced.

When the HGP was completed there were around 3.4 million known human single-nucleotide polymporphisms, and in 2013 there are roughly 53.6 million, Green further noted.

In addition to the growth in human genome studies, comparative genome sequencing efforts and the many studies that have sprung from them over the past decade have enabled scientists to "essentially read evolution's notebook," said Green.

Ten years ago, there were a total of three vertebrate genome sequences, and today there are 112. There were 14 non-vertebrate eukaryote sequences, and now there are 455, Green noted, and there were 167 prokaryotic genomes sequences, and today 8,760 have been amassed, with most of those being bacterial pathogens.

"We looked at lab animals such as mice and rats and worms and flies, but also companion animals such as dogs and cats, agricultural animals such as cows and pigs, and weirdo animals along the way, such as the platypus and possum," Green said.

These comparative studies have enabled researchers to "see what parts of the genome nature thought was important enough to keep the same across mice and rats and dogs and other animals," he said.

Human Genomes: A 'Beehive of Activity'

The greatest gains from the HGP, the ones that will more likely be used to develop new treatments and therapies and understanding of disease, will be found in the realm of human genetics, and much has happened on this front as well, Green explained.

"Human genomics is a beehive of activity ... and our ENCODE data now suggest that upwards of 80 percent of the human genome is associated with computational or experimental evidence for being functional," and thus serving some purposes in development, health, or disease, he said.

A decade ago, there were 1,474 genes with a known phenotype or disease-causing mutation, and now there are nearly 3,000 such genes known; there were 2,264 phenotypes or disorders with a known molecular basis, and now there are almost 5,000; and there were zero published genome-wide association studies, and today there are more than 1,500.

"Reflecting back to a decade ago, we know a tremendous amount more, in terms of the functional parts of the human genome, while at the same time there is so much more to know and understand with respect to the complexity of the biological information encoded in our genome," Green said.

Green also pointed to the growth of the pharmacogenomics industry as a result of the HGP. In 2003, there were 46 drugs on the market that included pharmacogenomic information on the label, and today there are 106 such drugs, he said.

"It is true that we have not cured every disease since the human genome project ended, no one seriously thought that we would, but we can say today that genomics is beginning to have a meaningful impact on medicine," he added.

There have been the occasional critics in recent years who have suggested that the era of personalized medicine has been too slow to arrive and others who have wondered if the complexity of the human genome and epigenome will continue to hamper the rise of genomic medicine. Green said that such questions are common but that a little perspective is needed.

The history of biomedical research, including basic research and clinical innovations such as the development of drugs like statins or the germ theory of antibiotics that led to the discovery of penicillin, shows that clinically useful medical advances usually come decades after the initial discoveries in basic science were made, said Green.

"So, the notion that we would revolutionize medicine a decade after the first full human genome sequence was put in front of us was naive. ... It was unrealistic to think it was going to be game-changing in the first decade," he said.

But the innovations have been happening, Green argued. "I challenge anybody to come up with an example of better technical innovation in biomedical research than what has happened in the arena of DNA sequencing technologies over the last decade. ... If you look across the full landscape of what was going to be needed and what is going to be needed to advance genomics and eventually have it play a major role in improving the medical care of patients, I think we have major progress to report on every front."

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