[Emapymosy]

http://www.nytimes.com/2007/05/31/sc...d-gene.html?hp
May 31, 2007
Genome of DNA Pioneer Is Deciphered
By NICHOLAS WADE

The full genome of James D. Watson, one of the discoverers of the structure of DNA in 1953, has been deciphered, marking what some scientists believe is the gateway to an impending era of personalized genomic medicine.

A copy of his genome, recorded on a pair of DVDs, is to be presented to Dr. Watson today in a ceremony in Houston by Richard Gibbs, director of the Human Genome Sequencing Center at the Baylor College of Medicine, and by Jonathan Rothberg, founder of the company 454 Life Sciences.

Dr. Rothberg’s company makes an innovative DNA sequencing machine, the latest version of which proved capable of decoding Dr. Watson’s genome in two months at a cost of less than $1 million, said Michael Egholm, 454’s vice president for research. The sequence was verified and analyzed by Dr. Gibbs’s center in Houston. It was Dr. Gibbs who proposed the idea of sequencing Dr. Watson’s genome.

Dr. Watson has said he will make his entire genome available for researchers to study, with the single exception of his apolipoprotein E gene, the status of which he does not wish to know because it predisposes a person toward Alzheimer’s disease.

Dr. Watson was “the right guy to do first” because of his discovery that DNA is the basis of heredity, Dr. Rothberg said in an e-mail. Dr. Watson was also the architect and first director of the government’s $3 billion human genome project, which completed the first human genome in 2003.

But that genome sequence, at present the standard reference for the human genome, belonged to a composite of anonymous donors from Buffalo, N.Y., and cannot be matched up with medical information from a whole person.

The first two genome sequences belonging to individuals are now being made available to researchers within a few days of each other. One is Dr. Watson’s and the other belongs to J. Craig Venter, who as president of the Celera Corporation started a human genome project in competition with the government.

Dr. Venter left Celera after producing only a draft version of a genome, his own, in 2001, on which the company did no further work. He has now brought his genome to completion at his own institute in Rockville, Md., and deposited it last week in GenBank, a public DNA database, he said.

Dr. Watson and Dr. Venter are both taking a considerable personal risk in making their genomes publicly available. As is probably true for everyone, their genomes are likely to contain mutations that could lead to disease, revealing possibly unfavorable information about themselves and their relatives. Even though the interpretation of the human genome sequence has only just begun, they are, in principle, exposing all their imperfections to public view for the sake of advancing research.

“The complexity of the analysis is such that I’m not worried about people making major discoveries that explain my idiosyncrasies,” Dr. Venter said.

Amy McGuire, a medical ethicist at the Baylor College of Medicine who was involved in the Watson sequencing project, said Dr. Watson and Dr. Venter were following the medical tradition of making oneself the first subject of a new experiment and would incur unknown risks. “I think that both have been motivated by their commitment to the science and genomic medicine and advancing the field,” she said.

Neither Dr. Venter nor 454 Life Sciences will talk in detail about the new individual genome sequences for fear of sanctions from the journals considering publications about them. But both genomes seem to be significantly better in many ways than the present reference standard.

Both are diploid genomes, meaning that they include the DNA sequence in the chromosomes inherited from both parents, whereas the reference genome completed by the Human Genome Project did not capture these differences.

Some 3.5 percent of Dr. Watson’s genome could not be matched to the reference genome. One reason may be that the project scientists had to amplify human DNA by growing it in bacteria and may have lost many regions of human DNA that are toxic to bacteria, said Michael Egholm, 454’s vice president for research. The 454 sequencer skips the bacteria stage entirely and is free of this source of bias.

Dr. Venter said 454 would have assembled Dr. Watson’s genome by comparing short lengths of analyzed DNA to the reference sequence, so the company might not have detected any structural errors present in the reference assembly.

Dr. Venter said his new genome has been assembled from scratch. There were many more differences than he had expected, including in single units of DNA that were extra or absent. “It’s clear we have grossly underestimated the extent of human variation,” Dr. Venter said.

Both he and Dr. Egholm said it would be valuable to compare the two new genomes, especially as they were generated by different methods. “We are looking forward to getting the data and layering it on my genome,” Dr. Venter said of his former rival’s genome sequence.

Dr. Venter’s new genome is “a real tour de force” and could become the new reference genome, said a researcher who heard him give a recent presentation on its technical details.

Some scientists believe that it will be medically useful to sequence patients’ genomes when the cost of sequencing falls to around $10,000 or less. Dr. Egholm said that with improvements already under way, the 454 sequencing machine will soon be able to sequence a human genome for $100,000. The cost of sequencing has been dropping so fast in the hands of groups like 454 Life Sciences and Solexa Inc. that some technologists predict the $10,000 genome will be attained in a few years.

At a news conference in Houston today, Dr. Watson urged that more human genomes should be sequenced, including those of successful people as well as those of medical interest. “I just want the information assessed as soon as possible,” he said.

Copyright 2007 The New York Times Company

[zithromaxlinks]

Anyone is sequencing their genome in 2010, when it's $10,000?

[LSDDSL]

I have been looking for a way to realize the harvesting of my clone's liver when I need it from him in the future. Will this help?

[cialesxtr]

It might MK....

Things like this are great tools, but just like atomic theory, you have to keep a watch on it to be used properly.

A knife can kill, but can also save someone's life (as well as julianne fries, but that is another subject....). This Genome mapping can be great for organ cloning, fertility treatments and elimination of known deleterious sequences (Altzheimers, etc). But it also has to be kept a close eye on. No using it in a fascist military means of ID, avoidance of genome specific biological weapons (the true magic bullet), limited or no engineering your kid to be "perfect" and eliminating the genetic diversity that helps our species survive things like plagues and other maladies.

So this is both great, and scary news. Lets see how the scientifically illeterate paranoid constituents of the world handle it.

[mGUuZRyA]

I think this article is really fascinating, because with so many advances in DNA, I think we will learn a lot about ourselves and hopefully cure some major diseases. However, if personal genomes started to become publicly available for everyone, say in 100 years or less, would you date someone knowing they have a gene that predisposes them to Alzheimers or another debilitating disease? Is this just another way that humans would be trying to push natural selection?

[Maribellin]

Would You Date Someone With Bad DNA? Prediction: we all have some sort of "bad DNA."

The question you'd ask your potential partner would not be "Do you have bad DNA?" It would be "Which bad DNA do you have?"

[Starichok]

http://www.nytimes.com/2007/11/16/science/17gene.html

November 16, 2007
Company Offers Genome Assessments
By NICHOLAS WADE

The revolution in human genomics, though barely understood by professionals, is about to hit the street, at least for those able to pay about $1,000 for a glance at their entire genome.

The Icelandic company Decode Genetics announced today that it is launching a service called deCODEme, which will assess a person’s genome for disease risk, bodily traits like hair and eye color, and ancestral origins. Subscribers have to send in a scraping of cells from inside the cheek and a check for $985.

A similar service, using a smaller but custom-made analytic device, is expected to be announced soon by 23andMe, a Google-financed company founded by Linda Avey, a biotechnology executive, and Anne Wojcicki, a health-care investor who is married to Sergey Brin, Google’s co-founder. The 23 in the company’s name refers to the 23 pairs of chromosomes in the human genome.

A third company, Navigenics, of Redwood Shores, Calif., is expected to focus on disease genes.

Unlike the present genetic testing and genetic genealogy companies, which look at a few specific genes, the three new services will sample the whole human genome.

Many people may welcome the rich new trove of data about their hereditary make-up and ancestry, but genetic counselors are concerned that some people may find the information hard to handle, given that much of the current genetic knowledge is related to a person’s risk of developing common and often untreatable diseases.

The new services will use devices known as SNP chips, which offer a cheap substitute for decoding the 3 billion units of the human genome, a task that would probably cost $1 million or so per person at present.

The chips, made by companies like Illumina of San Diego and Affymetrix of Santa Clara, Calif., are programmed to determine the DNA unit at sites along the genome which are known to vary from person to person. The chips thus capture the major points of difference — the single nucleotide polymorphism or “snip” — in an individual’s DNA while ignoring the many sites at which all people have the same DNA unit.

The deCODEme service will use a chip that tests a person’s DNA at one million sites along the genome. The company will then compare this set of data, known as a genotype, with the patients’ genotypes in its own and other databases that have been used in discovering disease-related SNPs. From this comparison the company will estimate a customer’s relative risk of developing the 20 or so common diseases for which disease-related SNPs have been identified.

Decode will also test for genetic variants, discovered by its own and other scientists, that influence the color of a person’s skin, hair and eyes, and whether or not they are prone to freckles.

Besides information about disease risk and normal physiology, Decode will also examine the Y chromosome and mitochondrial DNA, the only two elements of the genome that are always passed down essentially unchanged from one generation to the next. SNPs on the Y chromosome reflect the origin of a man’s ancestors back to 50,000 years ago when modern humans first left their ancestral homeland in northeast Africa. Those on the mitochondrial DNA reflect the wanderings of women throughout the globe.

The significance of most variation in the human genome is presently unknown. Most of the SNPs studied so far have been identified in the course of searching for the genetic roots of common diseases, such as cancer, diabetes and heart disease. Because the diseases are common, many people possess the underlying SNPs. So any interpretation of a person’s genome is at present heavily skewed toward generating ominous news.

This may alarm some customers, even though they will never get most or any of the diseases for which they simply have some genetic risk. There are undoubtedly genes that promote longevity and good health but far fewer of these have yet been spotted. And environmental factors, too, can affect whether certain genes are ever activated.

Genetic counselors have long been concerned that the growing availability of genomic information will outpace the ability to interpret it. Genetic information affects not only the person from whom it is obtained but also their family members. And it cannot ever be changed.

“If people can go into this testing knowing what its limits are, and can take it with a grain of salt, that’s fine,” said Angela Trepanier, incoming president of the National Society of Genetic Counselors. “But you have to be really careful about what you know and don’t know.”

Elizabeth Balkite, a genetic counselor in Durham, N.C., said that “I don’t believe in keeping information from people but I’d be curious as to how useful this would be to the average individual.” If the information is misunderstood, the field will be set back, she said.

Dr. Kari Stefansson, chief executive of Decode Genetics, said the genotyping information his company would provide was not the same as a genetic test. If customers felt they were at particular risk of a disease, they should get a proper test from their physician, he said.

“In our genomes is written the history of our family, the history of our nation and the history of our species,” he said. “People can look at their own genomes and find where your and your family fit into human population history, so I think this is terribly exciting.”

Dr. Stefansson said he genotyped himself and had found disease variants in his own genome, as would be expected since the variants are common.

Decode has genotyped thousands of patients in its search for genetic variants that lie at the roots of common diseases. Dr. Stefansson said this expertise gives the company an advantage over other genotyping services in terms of accuracy, safeguarding privacy, and the ability to interpret the information. 23andMe is using a smaller chip, one with only 650,000 SNPs, he said, although some of the test sites are tailored to generate information about population ancestry.

“They don’t have any track record in human genetics” and will be relying on others to do the genotyping, Dr. Stefansson said.

Ms. Wojcicki said in an email she could not comment on Decode’s announcement because she did not know the details of its service. She declined to elaborate on her own company’s plans.

Dr. Stefansson said that consent forms and other ethical rules drawn up to govern genetic testing in the wake of Nazi experiments were designed to prevent procedures being done on people against their will. But it would be wrongheaded, he said, to prevent people from obtaining information about themselves of their own free will. “The genetic counselors cannot deprive people of the right of genetic self determination,” he said.

In September this year, Craig Venter, the pioneer of decoding genomes, published the almost full sequence of his DNA. But because so little is known about the meaning of variation at each site on the genome, there was not much of interest he could say about himself. Companies like Decode hope that the more people have themselves genotyped, the better they will become at interpreting each DNA difference.

Looking to the day when genomes can be sequenced for just $1,000 or so, the National Society of Genetic Counselors has prepared consumer guidelines that apply to the new genotyping services. Family history is a good guide to disease “and often contains more useful information than full genome sequencing,” the guidelines say. Also, people may find they are at risk for diseases they had not expected, and should consider the impact such findings may have on themselves and their family.

[anaisdannyxys]

$985
http://www.decodeme.com/

[weaddercaps]

$999
https://www.23andme.com/

[blodwarttufla]

Good.

Finally in the future, after centuries of easy deception, a lot of husbands are going to know whether they really are the father. Thats just the reality.

[jdynwa]

Hey Edward and everyone,

I'm actually trying to decode my genome by Christmas. I'm raising donations on my blog for the $1000 cost of 23andMe's service. I will be blogging my entire experience (discovered genetic diseases and all).

Here is where I will be blogging: http://buzzyeah.com/2007/12/06/help-...e-by-christmas