The study of genes, called genetics, has been around for decades. But of late, it has been overshadowed by genomics, which studies all the DNA in an organism.

San Diego County’s large biotech industry has made this region a hotbed of genomics, as shown during the Biotechnology Innovation Organization’s recent national convention here and the Festival of Genomics, which took place this past week in the same city.

Genomics is a logical progression from the breakthrough discovery of the structure of DNA, announced in 1953 by James Watson and Francis Crick, a feat that won them a Nobel Prize. The structure gave evidence that DNA is the carrier of heredity and showed how the molecule replicates itself. This in turn explains how genes, whose existence had been deduced decades before, propagate and what they are made of.

Back then, the study of single genes was all that could be done with the era’s technology. Today it’s vastly different.


Human genomes can be sequenced and their meaning studied in days, all using technology produced in San Diego. These advancements are being used to better human and animal health, improve agriculture and inspire other advances in technology that Watson and Crick couldn’t have imagined when they made their momentous announcement.

Below are answers to some frequently asked questions about genomics.

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Question: What is genomics?


Answer: The study of the genome, which is the complete set of DNA in an organism.

Question: How is genomics different from genetics?

Answer: Genetics is the study of genes and what they do. Genomics is more inclusive. It looks at all DNA in an organism — not only genes, but also regions of DNA outside of genes that have some function for our bodies. Only a few percent of human DNA actually represent genes; the rest play either no function or other functions that scientists are still exploring.

Question: What is a gene?


A: It’s hard to be precise about just what a gene is, because the definition is a bit loose. In general, genes are usually thought of as sequences of DNA that contain instructions for making proteins, which are the building blocks of life. These sequences are defined by specific patterns that signal the stop and start of each gene. Moreover, genes may overlap, sharing parts of the same DNA sequence.

Human DNA contains about 20,000 to 25,000 protein-coding genes, scientists currently estimate.

Question: If genes are so important, why not just study that fraction of the genome and ignore the rest?

Answer: This is frequently done. It’s less expensive and difficult than sequencing the entire genome. The part containing protein-expressing genes is called the exome, and exome sequencing can find disease-causing genetic mutations.


However, some serious disease-causing mutations occur in the rest of the DNA. To detect them, you need to sequence the entire genome.

Question: What functions are performed by DNA sequences outside of genes?

A: In one very important example, these sequences protect chromosomes, the structures that DNA is packaged in. Certain sequences cap the ends of chromosomes, safeguarding the information from being worn away when cells divide and replicate their DNA. These are called telomeres.

Other non-genetic sequences of DNA regulate how genes function.


Still other sequences represent ancient viruses that have become integrated into human DNA. These are usually latent, but can become activated and cause infection. But they can also help us.

Research suggests that remnants of these viruses were co-opted by some ancestors of modern mammals, giving rise to the placenta. (Marsupial mammals, such as kangaroos, and egg-laying monotremes, including echidnas, have no placenta.)

NO PLACENTA FOR YOU -- Victor the echidna, who lived at the San Diego Zoo for 56 years before dying in 2012. Unlike nearly all mammals, female echidnas lay eggs. (K.C. Alfred)

Still, much of the non-genetic DNA appears to perform no function at all. It’s just along for the ride. What percentage of the genome belongs in this category isn’t clear.


A few years ago, a massive study called ENCODE put an upper limit of 80 percent on the amount of human DNA that produces a specific biochemical activity, meaning that it might do something necessary for life.

That figure has been misconstrued as meaning that at least 80 percent of the human genome is active and needed. However, just because a certain stretch of DNA causes something to happen doesn’t mean the activity performs a useful function.

Ewan Birney, a lead scientist for the ENCODE study, estimates that perhaps 20 percent of human DNA does something needed for life.

Question: Do all of these genes and non-genetic functional elements interact in complex ways?


A: Indeed they do, and that’s why the study of single genes in a vacuum is often misleading. Using big data tools, genomes can be scrutinized to detect combinations of variants that affect health. This requires access to many people’s genomes, along with the associated health information linked to these genomes. And the rarer the disease, the more genomes must be examined to find mutations and other patterns.

Questions: How many genomes are we talking about?

Answer: As many as feasible. Under a federal program administered by Dr. Eric Topol, a San Diego-based cardiologist and genomics expert, 1 million Americans are being recruited to have their genomes sequenced. Topol is conducting the program at The Scripps Research Institute; he is also affiliated with Scripps Health and with the Scripps Translational Science Institute.

Other researchers are also trying to do genomic sequencing on a large scale.


Question: Won’t this massive sharing of genomic and health information invade the privacy of the participants, and their families, if the health information becomes public?

A: The information will be anonymized. While each genome will be linked to the individual’s health information, personal identifying information will be removed.

Question: We’ve known about genes for many decades. Why has genomics become so popular only in this century?

Answer: The technology to sequence a human genome didn’t exist until nearly the end of the 20th century. A human genome contains about 3 billion letters of DNA’s four-letter alphabet. Better machines began appearing in the 1990s, and scientists found it feasible to try sequencing a human genome.


This feat was accomplished at the beginning of the 21st century. Two competing efforts, the government-supported Human Genome Project and a private one by Celera Genomics, ended in a draw.

Question: What role did San Diego play in this process?

A: Not much. The action took place mostly in the San Francisco Bay Area and near Washington, D.C.

Question: What changed to make San Diego so prominent as a center of genomics?


Answer: There are three main reasons.

One of the major makers of DNA-sequencing equipment was purchased by Carlsbad’s Invitrogen Corp., which resulted in a merged company called Life Technologies. Although Life Technologies was then purchased by Massachusetts-based Thermo Fisher Scientific, the Carlsbad location continues to create DNA sequencers.

Second, a tiny San Diego company called Illumina has grown like crazy, developing new sequencers and purchasing companies with attractive technology. Illumina has become the dominant maker of high-end sequencers. A few years ago, it crossed a milestone by bringing the price of sequencing human genomes to $1,000 when performed in bulk. By comparison, sequencing the first human genome cost hundreds of millions of dollars.

Third, J. Craig Venter, an early advocate of sequencing the human genome who led Celera’s effort, moved from the D.C. area to San Diego and began setting up an infrastructure to support genomic research and product commercialization in San Diego. The San Diego branch of his J. Craig Venter Institute resides on land provided by UC San Diego, where Venter got his Ph.D.


Question: Where can I read more about genomics?

A: Here are some Web resources: j.mp/ggenomics, j.mp/ggenomics1 and j.mp/ggenomics2.

For related stories, see:

San Diego 2nd in genomics, study finds


Genomics event moves to San Diego

Genome engineering shortcut from JCVI, Synthetic Genomics

Illumina’s Flatley on genomics, San Diego and the future


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