TR Editors' blog

The Human Genome, 10 Years Later

What have we learned about the genome and what hurdles still remain?

Emily Singer 02/08/2011

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It's been ten years since Science and Nature, the two most prestigious science journals in the world, published the first detailed look at the sequence of the human genome. Both journals are commemorating the event with special sections looking back at the progress the field has made over the last decade and the hurdles that still remain.(Check out our January issue for TR's take on the genome ten years later, our understanding of inheritance, and the implications for cancer .)

A series of short essays in Science, authored by Francis Collins, who oversaw the Human Genome Project and now runs the National Institutes of Health, Desmond Tutu, archbishop emeritus of South Africa, and many others, explore the facets of the genome.

Collins describes one of the field's successes: the case of a 6-year-old Wisconsin boy who had suffered for years with a severe form of inflammatory bowel disease.

Despite numerous tests and more than 100 surgeries, doctors remained at loss for a diagnosis and the little boy grew sicker. Then, researchers at the Medical College of Wisconsin carried out whole-exome sequencing, examining the protein-coding regions of every gene in Nic's genome. They identified a mutation in his XIAP gene. XIAP mutations were not previously associated with bowel symptoms, but had been linked to a severe blood disorder that is curable through bone marrow transplantation. The medical team raised the possibility of a transplant, which would not have been considered without a firm diagnosis. It was performed in July 2010, using stem cells from the cord blood of a matched, healthy donor. Seven months later, Nic appears to be on the road to recovery. While he is still on immunosuppressants, doctors report the new stem cells are stably engrafted, blood counts are good, and there's been no return of bowel disease (http://journals.lww.com/geneticsinmedicine/Documents/GIM200819_Revised.pdf). More important to Nic, he can finally eat solid foods!

Craig Venter, a genomics pioneer who ran the private arm of the genome race, outlines a major missing chunk of information that is necessary to interpret the meaning of the genome.

Among the many improvements that are needed in human genome research, the most important is the collection of human phenotypes (according to agreed-upon parameters and standards), in conjunction with tens of thousands of accurate human genome sequences. Such data sets will be the foundation for accurately predicting clinical outcomes from DNA sequence information. This is true not only for diagnosis but also in foreseeing and avoiding drug side effects, as well as monitoring stem cell genome mutations and/or variations before cell therapies.

Desmond Tutu, who had his genome sequenced as part of a study of human genetic diversity, writes about how important it is to understand the genomes of all the world's peoples.

As a nation, however, we need to continue to fight against racial inequalities and socioeconomic disparities on a daily basis. My participation in the Southern African Genome Project was a step in this direction, generating the first Southern African Genome to be sequenced—exactly 9 years after the publication of the human genomes.

My reasoning was simple. Southern Africans are victims of many devastating diseases whose eradication requires immediate attention and international resources. My hope is that my genetic code may provide a voice for the region and serve as the starting point for a map of DNA variation significant for Southern African peoples, to be used for medical research efforts and effective design of medicines. I implore the scientific community to continue what I hope was just a first step to further medical research within the region.

Kari Stefansson, chief executive officer of DeCode Genetics, a leader in the study of genomics and disease, points out that what we call a complete genome is not truly complete.

However, still today, we do not have "the complete sequence" of the reference human genome as parts (such as the centromeres or regions of copy number variation) are still incomplete. The suboptimal quality of the reference sequence is one of the limiting factors in the work of those who are using whole-genome sequencing to understand human biology. Hence, this is an anniversary of a moment in the history of our quest for an instrument (the reference sequence) to use in better understanding ourselves.

Eric Schadt, chief scientific officer of Pacific Biosciences of California, one of several companies racing to develop cheaper and faster sequencing technology, describes how complex the genome has revealed itself to be.

We have learned that the human genome is much more dynamic than previously thought. Elucidating its complexity will require a more systems-level approach, including comprehensive integration with other data dimensions, such as RNA, metabolite, protein, and clinical data. For me, although this past decade has exposed many amazing aspects of the genome, it has revealed the existence of a world about which we know very little. We will have to become masters of information if we ever hope to go from the big data sets coming to dominate biology to knowledge and to understanding.

On Thursday, Nature will feature a piece by Eric Green, current director of the National Human Genome Research Institute, outlining the institute's vision for the next ten to 20 years. Check back Thursday for a Q&A with Green.

Ozzy Osbourne's Genome

Genome sequencing makes its move into pop culture.

Emily Singer 10/25/2010

The "Godfather of heavy metal," "the Prince of Darkness," the man who made himself famous by biting the heads off small animals--Ozzy Osbourne--has had his genome sequenced.

The former frontman for Black Sabbath and reality show star recently became one of only a few hundred people in the world who have had their entire genetic code deciphered and analyzed. Osbourne, 61, wrote about his experience in a column in The Times of London on Sunday. He says he was initially skeptical of the idea--"The only Gene I know anything about is the one in Kiss"--but quickly came around when the originator of the project, identified only as Chris, convinced him the results could help explain how he survived 40 years of intense drug and alcohol abuse and all the ill-advised antics that go along with it. As Osbourne notes in his column;

"Look," said Chris, "you've said it yourself: you're a medical miracle. You went on a drink and-drugs bender for 40 years. You broke your neck on a quad bike. You died twice in a chemically induced coma. You walked away from your tour bus without a scratch after it was hit by a plane. Your immune system was so compromised by your lifestyle, you got a positive HIV test for 24 hours, until they proved it was wrong. Yet here you are, alive and well."

Osbourne's blood sample was collected in early July and sent to Cofactor Genomics, a company in St. Louis, Missouri, that sequences DNA. The DNA sequence results were then sent to Knome, a startup based in Cambridge that analyzes human genomes.

Researchers will present the research in more detail later this week at the TED Med conference in San Diego, where Osbourne and his wife, Sharon, will participate in a roundtable discussion. But Jorge Conde, Knome's chief executive officer and a former TR35 winner, shared some of the results with me this morning.

According to the analysis, Osbourne has about 300,000 novel variants, a figure similar to that of other newly sequenced genomes. (The number of novel variants discovered per genome will fall as more people are sequenced.) Analysis of his mitochondrial DNA, inherited from his mother, revealed that Osbourne shared a common ancestor with Stephen Colbert about 1,000 years ago.

The rocker also learned that, like most people of European descent, he has some some DNA segments inherited from Neandertals. "For fun, we did the same analysis for George Church," says Conde. Church, a pioneer in DNA sequencing, Harvard professor, and one of Knome's cofounders, "had three times as much Neandertal DNA."

Given his infamous history, researchers also analyzed a number of genes involved in drug metabolism and addiction. Knome's director of research, Nathan Pearson, aka Dr. Nathan, embarked to England earlier this month to explain the findings to Osbourne.

Bearing in mind what Dr. Nathan said about those odds being dodgy, here are some other interesting things he told me: I'm 6.13 times more likely than the average person to have alcohol dependency or alcohol cravings (er... yeah); 1.31 times more likely to have a cocaine addiction (this must be bollocks, because anyone who takes coke as much as I did gets hooked); and 2.6 times more likely to have hallucinations while taking cannabis (makes sense, although I was usually loaded on so many different things at the same time, it was hard to know what was doing what).

..."One of the unusual things we found in your genome was a spelling in the regulatory segment of your ADH4 gene, which metabolises alcohol," said Dr Nathan. "It could make you more able to break down alcohol than the average person. Or less able." I used to drink four bottles of cognac a day. I'm not sure I need a Harvard scientist to get to the bottom of that mystery.

In my mind, the findings best demonstrate how easy it is to create a narrative out of a genome, especially one belonging to someone with as colorful a personality as Ozzy's. But Dr. Nathan got it right when he explained his own theory for how the musician has survived thus far.

"Look, Mr. Osbourne, after studying your history, taking your blood, extracting your genes from the white cells, making them readable, sequencing them, analysing and interpreting the data using some of the most advanced technology available in the world today--and of course comparing your DNA against all the current research in the US National Library of Medicine, not to mention the 18th revision of the public human reference genome--I think I can say with a good deal of confidence why you're still alive."

I looked at him. He looked at me.

"Go on, then," I said. "Spit it out."

"Sharon," he replied.

One Day Only: A $99 Genetic Test

In honor of "DNA Day," personal genomics company 23andMe is offering a $99 test.

Erika Jonietz 04/23/2010

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In honor of National DNA Day (or in a blatant-yet-brilliant marketing move, depending on your perspective), personal genetic testing firm 23andMe is offering $99 genetic testing. The fee covers the company's "Complete Edition" testing. This doesn't mean full-genome sequencing, since 23andMe uses DNA microarrays to determine which version of 550,000 SNPs (single-letter changes in your genome) you carry. But it does include information on the following...

  • Ancestry
    • Relative Finder
    • Maternal Line
    • Paternal Line (for men only)
    • Ancestry Painting
    • Global Similarity
  • Health (148 reports)
    • Carrier Status (24)
    • Disease Risk (12)
    • Drug Response (9)
    • Traits (10)
    • Cutting-edge Research (93)

...as well as the ability to download raw data about the SNPs present in your mitochondrial and Y chromosome DNA, as well as data for nearly 600,000 other positions.

Pretty cool for $99--at least for a bio geek like me!


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