CHAPTER 12

Genome

Clue to Chemistry of Heredity Found

A scientific partnership between an American and a British biochemist at the Cavendish Laboratory in Cambridge has led to the unraveling of the structural pattern of a substance as important to biologists as uranium is to nuclear physicists. The substance is nucleic acid, the vital constituent of cells, the carrier of inherited characters and the fluid that links organic life with inorganic matter.

The form of nucleic acid under investigation is called DNA (deoxyribonucleic acid) and has been known since 1869.

But what nobody understood before the Cavendish Laboratory men considered the problem was how the molecules were grooved into each other like the strands of a wire hawser so they were able to pull inherited characters over from one generation to another.

Further Tests Slated

The two biochemists, James Dewey Watson, a former graduate student of the University of Chicago, and his British partner, Francis H. C. Crick, believe that in DNA they have at last found the clue to the chemistry of heredity. If further X-ray tests prove what has largely been demonstrated on paper, Drs. Watson and Crick will have made biochemical history.

Dr. Watson has now returned to the United States, where he intends to join Dr. Linus Pauling, of California, who has done most of the pioneer work on the problem.

[In Pasadena, Calif., Dr. Pauling said that the new Crick-Watson solution appeared to be somewhat better than the proposal for the structure of the nucleic acids worked out by Dr. Pauling and associates at the California Institute of Technology. The California solution was published in the February, 1953, issue of the Proceedings of the National Academy of Sciences.]

Dr. Crick may leave Britain, too, when he has done some more work on the problem. Right now, he said, it “simply smells right” and confirms research in many institutions, particularly the Rockefeller Foundation in the United States and at King’s College in London.

The acid DNA, Dr. Crick explained is a “high polymer”—that is, its chemical components can be disentangled and rearranged in different ways.

DNA is the essential constituent of the microscopic life-threads called chromosomes that carry the genes of heredity like beads on a string.

In all life cells, including those of man, DNA is the substance that transmits inherited characters such as eye color, nose shape and certain types of blood and diseases. The transmission occurs at the vital moment of mitosis or cell division when a tangle of DNA containing chromosomes becomes thicker and the cell separates into two daughter cells.

Forming of Molecular Chain

Although DNA has never been synthesized, Drs. Watson and Crick knew it was composed of horizontal hook-ups of bases (sugars and phosphates) piled one above the other in chain-like formations. The problem was to find out how these giant molecules could be fitted together so they could duplicate themselves exactly.

By a method of scientific doodling with hand-drawn models of the molecules, Drs. Watson and Crick worked out which molecules could be joined together with regard to the fact that some molecules were more rigid than others and had critical angles of attachment. Some months ago they decided that the only possible interrelation of the molecules was in the form of two chains arranged in a double helix—like a spiral staircase, with the upper chain resembling the staircase handrail and the lower resembling the outside edge of the stairs.

New evidence for double DNA chains in helical form now has been obtained from the King’s College Biophysics Department in London, where a group of workers extracted crystalline DNA from the thymus gland of a calf and bombarded it with X-rays.

The resulting X-ray diffraction photographs showed a whirlpool of light and shade that could be analyzed as the components of a double helix.

Dr. Crick emphasized that years of work still must be applied to the helical carriers of life’s characteristics. But a working model to aid in the genetical studies of the future now has been laid out in blueprint form by Drs. Watson and Crick—or so most biochemists here believe.

Looks Good, Pauling Says

Reached by telephone in Pasadena, Dr. Pauling said last night that the Crick-Watson proposal for the structure of the nucleic acids “looks very good.” Dr. Pauling has just returned from London where he talked with Dr. Crick and with Dr. Watson, who was formerly a student at California Institute of Technology.

Dr. Pauling said that he did not believe the problem of understanding “molecular genetics” had been finally solved, and that the shape of the molecules was a complicated matter. Both the California and the Crick-Watson explanations of the structure of the substances that control heredity are highly speculative, he remarked.

June 13, 1953

After 10 Years’ Effort, Genome Mapping Team Achieves Sequence of a Human Chromosome

By NICHOLAS WADE

After a decade of preparation, scientists have for the first time decoded the information in a human chromosome, the unit in which the genetic information is packaged.

The achievement, by a public consortium of university centers in Britain, the United States and Japan, is a milestone in the human genome project, an initiative started in 1990 with the goal of deciphering all of human DNA by 2005.

The success in decoding the first chromosome, even though it is the second-smallest of the 23 pairs in every human cell, validates the approach chosen by the public consortium and bolsters the chance that it can complete the full human genome as planned. In the last 18 months the consortium’s strategy has been challenged by a private company, the Celera Corporation of Rockville, Md., which asserts it can sequence the genome faster by a different method.

“A new era has dawned—we have fulfilled the dreams of Mendel, Morgan, Watson and Crick, and Sanger, as we now have the essentially complete structure of the first human chromosome,” said Dr. Bruce Roe of the University of Oklahoma, a member of the decoding team, referring to the principal architects of today’s knowledge about genetics.

Understanding the human genome is expected to yield vast medical benefits, because almost every disease has a genetic component.

The central feature of each chromosome is an enormously long DNA molecule. The chromosome on which the latest work was done is called Chromosome 22, which, small as it is, contains 43 million units of DNA, of which researchers have now decoded 33.5 million. Though there is still much left to be done, the Chromosome 22 team believes that it has sequenced all regions of major interest to biomedical researchers—that is, the regions that contain the protein-making genes.

The fruit of the team’s labors is an eye-glazing march of A’s, C’s, G’s, and T’s, as the four chemical units are abbreviated, which would take up 949 pages of this newspaper if printed in ordinary type.

Techniques for analyzing such vast molecules have only recently been developed. Two industrial-scale laboratories, at the Sanger Centre in England and Washington University in St. Louis, are the principal powerhouses in the public consortium’s campaign. The team working on Chromosome 22 also included scientists at Keio University in Japan and the University of Oklahoma. The team’s leader is Dr. Ian Dunham of the Sanger Centre, where the bulk of the sequence was completed. The results are reported in today’s issue of Nature, and the genome sequence will be posted on the Internet at www.genome.ou.edu/Chr22.xhtmll.

Dr. Roe estimated the total cost of sequencing the chromosome at $15 million to $20 million. The human genome project as a whole is budgeted at $3 billion.

So far, the Dunham team has identified 545 genes—each of which is composed of thousands of chemical units—and altogether there are probably 1,000 or so genes strung out along the chromosome. The total number of human genes is still unknown and estimates vary widely, from 60,000 to 120,000.

If there is a pattern in the types of genes nature has chosen to store on Chromosome 22, it has escaped the researchers. The genes appear to be a random assortment, including a large set of genes involved in the immune system and more than 20 genes that cause known human diseases when defective, such as DiGeorge and cat eye syndromes. In addition, one of the genes suspected of contributing to schizophrenia is believed to lie on Chromosome 22 but has not yet been identified.

Besides the interest in specific genes, biologists can also see for the first time the full architecture of a human chromosome. Their immediate reaction is in some cases pure awe at the daunting complexity of the structure and the distance yet to travel before its features are understood.

“I don’t often pick up a scientific paper and find myself getting chills, as I did when I saw this whole chromosomal landscape,” said Dr. Francis Collins, director of the human genome project at the National Institutes of Health. “This is a phenomenal historical moment, to see a full chapter of the human instruction book.”

Although the goal of the human genome project is to sequence every one of the three billion letters in human DNA, the sequence of Chromosome 22 is not yet complete. There are 11 gaps, all of known length and fairly short. These are mostly regions that could not be cloned in bacteria, the standard way of amplifying long segments of human DNA for further analysis.

In addition, the team has not sequenced the DNA in two important features of the chromosome. One is the centromere, a region that helps the chromosome get copied correctly to each daughter cell when the cell divides. The other is the chromosome’s short arm—a length of DNA on the other side of the centromere—which in Chromosome 22’s case contains only multiple copies of genes involved in protein manufacture.

Dr. Collins said that completing every letter in the human genome was still the public consortium’s goal but that at a recent meeting participants agreed that chromosomes could be declared essentially complete provided that the researchers had done everything possible with available techniques and had defined the size of any remaining gaps.

But the intent is to close every gap when better techniques are developed, he said, as “one should not declare victory just because one got tired of the problem.”

December 2, 1999

Genetic Code of Human Life Is Cracked by Scientists

By NICHOLAS WADE

In an achievement that represents a pinnacle of human self-knowledge, two rival groups of scientists said today that they had deciphered the hereditary script, the set of instructions that defines the human organism.

“Today we are learning the language in which God created life,” President Clinton said at a White House ceremony attended by members of the two teams, Dr. James D. Watson, co-discoverer of the structure of DNA, and, via satellite, Prime Minister Tony Blair of Britain.

The teams’ leaders, Dr. J. Craig Venter, president of Celera Genomics, and Dr. Francis S. Collins, director of the National Human Genome Research Institute, praised each other’s contributions and signaled a spirit of cooperation from now on, even though the two efforts will remain firmly independent.

The human genome, the ancient script that has now been deciphered, consists of two sets of 23 giant DNA molecules, or chromosomes, with each set—one inherited from each parent—containing more than three billion chemical units.

The successful deciphering of this vast genetic archive attests to the extraordinary pace of biology’s advance since 1953, when the structure of DNA was first discovered and presages an era of even brisker progress.

Understanding the human genome is expected to revolutionize the practice of medicine. Biologists expect in time to develop an array of diagnostics and treatments based on it and tailored to individual patients, some of which will exploit the body’s own mechanisms of self-repair.

The knowledge in the genome could also be used in harmful ways, particularly in revealing patients’ disposition to disease if their privacy is not safeguarded, and in causing discrimination.

The joint announcement is something of a shotgun marriage because neither side’s version of the human genome is complete, nor do they agree on the genome’s size. Neither has sequenced—meaning to determine the order of the chemical subunits—the DNA of certain short structural regions of the genome, which cannot yet be analyzed.

With the rest of the genome, which contains the human genes and much else, both sides’ versions have many small gaps, although these are thought to contain few or no genes. Today’s versions are effectively complete representations of the genome but leave much more work to be done.

The two groups even differ on the size of the gene-coding part of the genome. Celera says it is 3.12 billion letters of DNA; the public consortium that it is 3.15 billion units, a letter difference of 30 million. Neither side can yet describe the genome’s full size or determine the number of human genes.

The public consortium has also fallen somewhat behind in its goal of attaining a working draft in which 90 percent of the gene-containing part of the genome was sequenced. Its version today has reached only 85 percent, suggesting it was marching to Celera’s timetable.

Today’s announcement heralded an unexpected truce between the two groups of scientists who have been racing to finish the genome. Veering away from the prospect of asserting rival claims of victory, the two chose to report simultaneously their attainment of different milestones in their quest.

Celera, a unit of the PE Corporation, has obtained its 3.12 billion letters of the genome in the form of long continuous sequences, mostly about 2 million letters each, but with many small gaps.

A less complete version has been reported by the Human Genome Project, a consortium of academic centers supported largely by the National Institutes of Health and the Wellcome Trust, a medical philanthropy in London. Dr. Collins, the consortium’s leader, said its scientists had sequenced 85 percent of the genome in a “working draft,” meaning its accuracy will be upgraded later.

Both versions of the human genome meet the important goal of allowing scientists to search them for desired genes, the genetic instructions encoded in the DNA. The consortium’s genome data is freely available now. Celera has said it will make a version of its genome sequence freely available at a later date.

In their remarks at the White House, Dr. Collins and Dr. Venter both sought to capture the wider meaning of their work in identifying the eye-glazing stream of A’s, G’s, C’s and T’s, the letters in the genome’s four-letter code.

“We have caught the first glimpses of our instruction book, previously known only to God,” Dr. Collins said. Dr. Venter spoke of his conviction from seeing people die in Vietnam, where he served as a medic, that the human spirit transcended the physiology that is controlled by the genome.

The two genome versions were obtained through prodigious efforts by each side, involving skilled management of teams of scientists working around the clock on a novel technological frontier.

Spurring their efforts was the glittering lure of the genome as a scientific prize, and a rivalry fueled by personal differences and conflicting agendas.

Dr. Venter, a genomics pioneer whose innovative methods have at times been scorned by experts in the consortium’s camp, has often cast himself, not without reason, as an outsider battling a hostile establishment.

The consortium scientists were halfway through a successful 15-year program to complete the human genome by 2005, when Dr. Venter announced in May 1998 that as head of a new company, later called Celera, he would beat them to their goal by 5 years.

His bombshell entry turned an academic pursuit into a fierce race. Dr. Collins responded by moving his completion date forward to 2003 and setting this month as the target for a 90 percent draft.

“These folks have pulled out all the stops,” he said of his staff in an interview last week. “They have achieved a ramp-up that is beyond anything one would have imagined possible.”

The 15-year cost of the Human Genome Project, which began in 1990, has been estimated at $3 billion, but includes many incidental expenses. The consortium has spent only $300 million on sequencing the human genome since January 1999, when its all-out production phase began. Celera has not released its costs, but Dr. Venter said a year ago that he expected Celera’s human genome to cost $200 million to $250 million.

The race opened with mutual predictions of defeat. The consortium’s senior scientists predicted in December 1998 that Dr. Venter’s method of reassembling the sequenced fragments of genomic DNA was bound to fail. In May 1999, Dr. Venter, confident of Celera’s impending success, observed that the National Institutes of Health and the Wellcome Trust were “putting good money after bad.”

The groups were divided by political as well as technical agendas. The consortium’s two principal scientists, Dr. John E. Sulston of the Sanger Center in England and Dr. Robert Waterston of Washington University in St. Louis, insisted that the genome data should be published nightly, an unusually generous policy because scientists generally harvest new data for their own discoveries before sharing it.

Both of the consortium’s administrative leaders, Dr. James D. Watson, and his successor, Dr. Collins, made a point of seeking out international partners so that the rest of the world would not feel excluded from the genome triumph. Thus even though centers in the United States and Britain have done most of the heavy lifting, important contributions to the consortium’s genome draft have been made by centers in Germany, France, Japan and China.

Academic scientists have felt some chagrin that an altruistic, open and technically successful venture like the Human Genome Project should be upstaged by a commercial rival financed by the company that made the consortium’s DNA sequencing machines.

But though Celera seeks to profit by operating a genomic database, Dr. Venter also believed that he could make the genome and its benefits available a lot sooner. He has succeeded in doing so, and in spurring the consortium to move faster.

Today’s truce between the two teams offers several advantages. For Celera to claim victory over the consortium would risk alienating customers in the academic community. For the consortium, the surety of opting into a draw now may have seemed better than the risks of claiming victory with a complete genome much later.

Celera’s version of the genome depends on the consortium’s data. And the many small gaps in Celera’s sequence will probably be filled by the consortium’s scientists, adding further to their claim on credit for the final product.

The present truce between the sides is limited to today’s announcement and an agreement to publish their reports in the same journal, although the details remain to be worked out. A joint workshop will be held to discuss the genome versions.

The versions of the human genome produced by the two teams are in different states of completion because of the different methods each used to determine the order of DNA units in the genome.

The consortium chose first to break the genome down into large chunks, called BAC’s, which are about 150,000 DNA letters long, and to sequence each BAC separately. This BAC by BAC strategy also required “mapping” the genome, or defining short sequences of milestone DNA that would help show where each BAC belonged on its parent chromosome, the giant DNA molecules of which the genome is composed.

BAC’s are assembled from thousands of snippets of DNA, each about 500 DNA letters in length. This is the longest run of DNA letters that the DNA sequencing machines can analyze. A computer pieces together the snippets by looking for matches in the DNA sequence where one snippet overlaps another.

But the BAC’s do not assemble cleanly from their component snippets. One reason is that human DNA is full of repetitive sequences—the same run of letters repeated over and over again—and these repetitions baffle the computer algorithms set to assemble the pieces.

The stage the consortium has now reached is that all its BAC’s are mapped, making the whole genome available in a nested set of smaller jigsaw puzzles. But the BAC’s are in varying stages of completion. The BAC’s covering the two smallest human chromosomes, numbers 21 and 22, are essentially complete. But many other BAC’s are in less immaculate states of assembly. Many consist of assembled pieces no more than 10,000 units long, and the order of these pieces within each BAC is not known.

The sum of the assembled pieces in each BAC now covers 85 percent of the genome. This working draft, as the consortium calls it, is maybe not a thing of beauty but is of great value to researchers looking for genes and represents a major accomplishment.

Celera’s genome has been assembled by a different method, called a whole genome shotgun strategy. Following a scheme proposed by Dr. Eugene Myers and Dr. J. L. Weber, Celera skips the time-consuming mapping stage and breaks the whole genome down into a set of fragments that are 2,000, 10,000 and 50,000 letters long. These fragments are analyzed separately and then assembled in a single mammoth computer run, with a handful of clever tricks to step across the repetitive sequence regions in the DNA.

The approach ideally required sequencing 30 billion units of DNA—10 times that in a single genome. Dr. Venter seems to have taken a considerable risk by starting his assembly at the end of March this year when he possessed only a threefold coverage of the genome. He has since raised his total to 4.6-fold coverage.

The decision may have been influenced by Celera’s rate of capital expenditure—the company’s electric bill alone is $100,000 a month—and by the need to sequence the mouse genome as well so as to offer database clients a two-genome package. The mouse genome is expected to be invaluable for interpreting the human genome, and Dr. Venter said today that Celera would finish sequencing it by the end of the year.

Because of having relatively little of its own data, Celera made use of the consortium’s publicly available sequence data and, indirectly, of the positional information contained in the consortium’s mapped set of BAC’s. The consortium can justifiably share in the credit for Celera’s version of the genome, another cogent factor in the logic of today’s truce.

Biotech Shares Rise and Fall

Stocks of biotechnology companies rose early yesterday after a White House announcement that the first survey of the human genome had been completed, but investors cashed in some of their profits before trading ended, causing several issues to fall.

Biotechnology shares peaked in March in a speculative frenzy, before backsliding sharply. In recent weeks, they again posted significant increases in anticipation of the genome announcement.

The Celera Genomics unit of the PE Corporation, which participated in the mapping project and has been one of the highest fliers, dropped $12.25, to $113 yesterday. The stock of the company, based in Rockville, Md., hit a record high of $252 a share on Feb. 25. Although well off its high, Celera shares are still up 1,400 percent from this time last year.

June 27, 2000

The Quest for the $1,000 Human Genome

By NICHOLAS WADE

As part of an intensive effort to develop a new generation of machines that will sequence DNA at a vastly reduced cost, scientists are decoding a new human genome—that of James D. Watson, the co-discoverer of the structure of DNA and the first director of the National Institutes of Health’s human genome project.

Decoding a person’s genome is at present far too costly to be a feasible medical procedure. But the goal now being pursued by the N.I.H. and by several manufacturers, including the company decoding Dr. Watson’s DNA, is to drive the costs of decoding a human genome down to as little as $1,000. At that price, it could be worth decoding people’s genomes in certain medical situations and, one day, even routinely at birth.

Low-cost decoding may bring the genomic age to the doctor’s office, but it will also raise quandaries about how to safeguard and interpret such a wealth of delicate and far-reaching personal information.

The first human genome decoding, completed by a public consortium of universities in 2003, cost more than $500 million. With the same technology, dependent on DNA sequencing machines made by Applied Biosystems, a human genome could probably now be decoded for $10 million to $15 million, experts say.

Much greater efficiency is expected from the new generation of DNA sequencing machines, based on different, highly miniaturized technologies. One machine, made by 454 Life Sciences, has been on the market since March 2005. Another, made by Solexa, will start shipping this summer. Applied Biosystems will start marketing its own next-generation machine next year.

Last month, at a training course organized by the Cold Spring Harbor Laboratory on Long Island, researchers were learning how to use the DNA decoding machines made by 454 Life Sciences. Looking like a hybrid between a washing machine and a giant iPod, the machines cost $500,000 each, not counting the computer software needed to analyze the results.

At their heart lies a plate of light-sensitive chips, the same as those used in telescopes for detecting faint light from distant stars. On top of the plate sits a glass slide pitted with thousands of tiny wells, each containing a fragment of the DNA to be decoded.

As each unit of DNA is analyzed in a well, a flash of light is generated by luciferase, the enzyme that fireflies use to make themselves glow. The telescope plate records the twinkling lights from each well and, at the end of the run, which lasts four or five hours, the sequence of units in each well’s DNA fragment has been recorded. The fragments are about 100 units in length, and from their overlaps a computer can then be set to piece together the entire genome they come from.

In the training course, the project was to analyze DNA from a Tasmanian devil, a marsupial afflicted with a mysterious malady called devil facial tumor disease. The researchers found that the genome was laden with a virus that had integrated its sequence into the devil’s DNA.

The 454 machine can assemble small genomes like those of bacteria, which perhaps accounted for the presence at the course of three scientists from the Department of Homeland Security. But the human genome is about 600 times larger than a bacterium’s and includes many repetitive sequences that, like identical pieces in a jigsaw puzzle, make the solution much harder.

At the Cold Spring Harbor course, researchers heard Dr. Watson, the laboratory’s chancellor, say that 454 Life Sciences had asked to sequence his genome with their new machine. Only two human genomes have been sequenced to date. The genome sequenced by the public consortium was a mosaic of DNA from several anonymous people. The consortium’s rival, Celera Genomics, prepared a draft sequence, most of it from the genome of its former president, Dr. J. Craig Venter.

Dr. Watson told the students that he had given the company permission to publish the sequence of his genome, “provided they didn’t release to the world that I have some disease I don’t want to know about.”

Genomic information can already reveal a lot and will reveal much more as the roles of new genes are discovered.

“I think that personal genetic information should ordinarily be kept secret,” Dr. Watson said. “But I have said that 454 can put mine out there, even though it’s saying something about my sons.”

So far, however, 454 Life Sciences has not published Dr. Watson’s genome, and it is not clear how much progress the company has made. Christopher K. McLeod, its chief executive, said, “Technically, we’ve done a lot of good work on it.” But, he added, “I don’t think we want to discuss where we are.”

Mr. McLeod expressed reservations about releasing personal genetic information, despite having Dr. Watson’s permission to do so. “Jim feels there are certain things he’d be comfortable releasing,” he said. “I’m not sure we would agree.”

Another factor may be that the company is developing a more powerful model of its machine that will be able to read DNA fragments that are 200 or even 400 units in length. These longer-read lengths should make it more feasible to decode large genomes, like those of people.

The 454 machine is at present being bought chiefly by researchers and by the large genome sequencing centers established by the public consortium. But it has begun to show promise for the clinic. One new use is in screening tumors for genes known to be mutated in cancer, a task that existing machines do not do well. Spotting which mutation has occurred in a patient’s tumor can help in the choice of chemotherapy.

Although the 454 model is the only next-generation DNA sequencing machine on the market, it will be joined this summer by the machine from Solexa. The Solexa instrument, which will cost $400,000, works on somewhat similar principles but uses fluorescent dyes to visualize the structure of DNA. And next year Applied Biosystems will introduce its next-generation machine, based on a technology developed by George Church of Harvard, said Dennis A. Gilbert, the company’s chief scientific officer.

Each of the manufacturers claims special advantages for its technology, ensuring that researchers will have a rich choice.

David Bentley, Solexa’s chief scientist, said that the company’s DNA sequencing machine had already decoded several bacterial genomes and that he was planning to sequence a human genome—that of an anonymous man from the Yoruba people of Nigeria. An African genome was chosen because there is greater genetic diversity in African populations, Dr. Bentley said.

The demand for whole genome sequencing is a long way off, in Dr. Bentley’s view, but not so distant that it is too early to think about the consequences of generating such information. He advocates that two people should control access to a person’s genome sequence—the patient and the physician.

Why not the patient alone? Dr. Bentley said genomes would be so difficult to analyze correctly that interpretation should stay within the medical profession. Otherwise, freelance services will spring up, offering to predict whether a person will get heart disease or their age of death. This potential for misinformation “would have a huge adverse impact on the medical use of genetic information,” Dr. Bentley said.

A recent example of genetic misinformation occurred last month when a DNA testing genealogy company, Oxford Ancestors, told Thomas R. Robinson, an accountant at the University of Miami, that he was a descendant of Genghis Khan. Only because Mr. Robinson sought a second opinion did he find that the information was incorrect.

Technology, not medicine, is the immediate force behind the quest for the $1,000 human genome. The new decoding machines are being developed because they are possible, not because hospitals are demanding them. But the makers expect that demand will grow as researchers develop new uses.

“As we drop the price and increase the capability, there are applications that couldn’t be done before,” like a researcher being able to screen a thousand patients for cancer mutations, Dr. Gilbert said.

At present, only a handful of genes are monitored by doctors in clinical practice, and specific tests for these genes make it unnecessary to decode a person’s entire genome. But at some point, the new machines or their successors may make genome decoding a routine medical test.

Already, every newborn baby endures its heel being pricked to draw a few drops of blood, which are tested for a handful of enzymic deficiencies. But when genomes can be decoded for $1,000, a baby may arrive home like a new computer, with its complete genetic operating instructions on a DVD.

July 18, 2006

In Good Health? Thank Your 100 Trillion Bacteria

By GINA KOLATA

For years, bacteria have had a bad name. They are the cause of infections, of diseases. They are something to be scrubbed away, things to be avoided.

But now researchers have taken a detailed look at another set of bacteria that may play even bigger roles in health and disease: the 100 trillion good bacteria that live in or on the human body.

No one really knew much about them. They are essential for human life, needed to digest food, to synthesize certain vitamins, to form a barricade against disease-causing bacteria. But what do they look like in healthy people, and how much do they vary from person to person?

In a new five-year federal endeavor, the Human Microbiome Project, which has been compared to the Human Genome Project, 200 scientists at 80 institutions sequenced the genetic material of bacteria taken from nearly 250 healthy people.

They discovered more strains than they had ever imagined—as many as a thousand bacterial strains on each person. And each person’s collection of microbes, the microbiome, was different from the next person’s. To the scientists’ surprise, they also found genetic signatures of disease-causing bacteria lurking in everyone’s microbiome. But instead of making people ill, or even infectious, these disease-causing microbes simply live peacefully among their neighbors.

The results, published on Wednesday in Nature and three PLoS journals, are expected to change the research landscape.

The work is “fantastic,” said Bonnie Bassler, a Princeton University microbiologist who was not involved with the project. “These papers represent significant steps in our understanding of bacteria in human health.”

Until recently, Dr. Bassler added, the bacteria in the microbiome were thought to be just “passive riders.” They were barely studied, microbiologists explained, because it was hard to know much about them. They are so adapted to living on body surfaces and in body cavities, surrounded by other bacteria, that many could not be cultured and grown in the lab. Even if they did survive in the lab, they often behaved differently in this alien environment. It was only with the advent of relatively cheap and fast gene sequencing methods that investigators were able to ask what bacteria were present.

Examinations of DNA sequences served as the equivalent of an old-time microscope, said Curtis Huttenhower of the Harvard School of Public Health, an investigator for the microbiome project. They allowed investigators to see—through their unique DNA sequences—footprints of otherwise elusive bacteria.

The work also helps establish criteria for a healthy microbiome, which can help in studies of how antibiotics perturb a person’s microbiome and how long it takes the microbiome to recover.

In recent years, as investigators began to probe the microbiome in small studies, they began to appreciate its importance. Not only do the bacteria help keep people healthy, but they also are thought to help explain why individuals react differently to various drugs and why some are susceptible to certain infectious diseases while others are impervious. When they go awry they are thought to contribute to chronic diseases and conditions like irritable bowel syndrome, asthma, even, possibly, obesity.

Humans, said Dr. David Relman, a Stanford microbiologist, are like coral, “an assemblage of life-forms living together.”

Dr. Barnett Kramer, director of the division of cancer prevention at the National Cancer Institute, who was not involved with the research project, had another image. Humans, he said, in some sense are made mostly of microbes. From the standpoint of our microbiome, he added, “we may just serve as packaging.”

The microbiome starts to grow at birth, said Lita Proctor, program director for the Human Microbiome Project. As babies pass through the birth canal, they pick up bacteria from the mother’s vaginal microbiome.

“Babies are microbe magnets,” Dr. Proctor said. Over the next two to three years, the babies’ microbiomes mature and grow while their immune systems develop in concert, learning not to attack the bacteria, recognizing them as friendly.

Babies born by Caesarean section, Dr. Proctor added, start out with different microbiomes, but it is not yet known whether their microbiomes remain different after they mature. In adults, the body carries two to five pounds of bacteria, even though these cells are minuscule—one-tenth to one-hundredth the size of a human cell. The gut, in particular, is stuffed with them.

“The gut is not jam-packed with food; it is jam-packed with microbes,” Dr. Proctor said. “Half of your stool is not leftover food. It is microbial biomass.” But bacteria multiply so quickly that they replenish their numbers as fast as they are excreted.

The bacteria also help the immune system, Dr. Huttenhower said. The best example is in the vagina, where they secrete chemicals that can kill other bacteria and make the environment slightly acidic, which is unappealing to other microbes.

Including the microbiome as part of an individual is, some researchers said, a new way to look at human beings.

It was a daunting task, though, to investigate the normal human microbiome. Previous studies of human microbiomes had been small and had looked mostly at fecal bacteria or bacteria in saliva in healthy people, or had examined things like fecal bacteria in individuals with certain diseases, like inflammatory bowel disease, in which bacteria are thought to play a role.

But, said Barbara B. Methé, an investigator for the microbiome study and a microbiologist at the J. Craig Venter Institute, it was hard to know what to make of those studies.

“We were stepping back and saying, ‘We don’t really have a population study. What does a normal microbiome look like?’” she said.

The first problem was finding completely healthy people for the study. The investigators recruited 600 subjects, ages 18 to 40, poking and prodding them. They brought in dentists to probe their gums, looking for gum disease, and pick at their teeth, looking for cavities. They brought in gynecologists to examine the women to see if they had yeast infections. They examined skin and tonsils and nasal cavities. They made sure the subjects were not too fat and not too thin. Even though those who volunteered thought they filled the bill, half were rejected because they were not completely healthy. And 80 percent of those who were eventually accepted first had to have gum disease or cavities treated by a dentist.

When they had their subjects—242 men and women deemed free of disease in the nose, skin, mouth, gastrointestinal tract and, for the women, vagina—the investigators collected stool samples and saliva, and scraped the subjects’ gums and teeth and nostrils and their palates and tonsils and throats. They took samples from the crook of the elbow and the folds of the ear. In all, women were sampled in 18 places, including three sites in the vagina, and men in 15. The investigators resampled subjects three times during the course of the study to see if the bacterial composition of their bodies was stable, generating 11,174 samples.

To catalog the body’s bacteria, researchers searched for DNA with a specific gene, 16S rRNA, that is a marker for bacteria and whose slight sequence variations can reveal different bacterial species. They sequenced the bacterial DNA to find the unique genes in the microbiome. They ended up with a deluge of data, much too much to study with any one computer, Dr. Huttenhower said, creating “a huge computational challenge.”

The next step, he said, is to better understand how the microbiome affects health and disease and to try to improve health by deliberately altering the microbiome.

But, Dr. Relman said, “we are scratching at the surface now.”

It is, he said, “humbling.”

June 13, 2012

In Treatment for Leukemia, Glimpses of the Future

By GINA KOLATA

Genetics researchers at Washington University, one of the world’s leading centers for work on the human genome, were devastated. Dr. Lukas Wartman, a young, talented and beloved colleague, had the very cancer he had devoted his career to studying. He was deteriorating fast. No known treatment could save him. And no one, to their knowledge, had ever investigated the complete genetic makeup of a cancer like his.

So one day last July, Dr. Timothy Ley, associate director of the university’s genome institute, summoned his team. Why not throw everything we have at seeing if we can find a rogue gene spurring Dr. Wartman’s cancer, adult acute lymphoblastic leukemia, he asked. “It’s now or never,” he recalled telling them. “We will only get one shot.”

Dr. Ley’s team tried a type of analysis that they had never done before. They fully sequenced the genes of both his cancer cells and healthy cells for comparison, and at the same time analyzed his RNA, a close chemical cousin to DNA, for clues to what his genes were doing.

The researchers on the project put other work aside for weeks, running one of the university’s 26 sequencing machines and supercomputer around the clock. And they found a culprit—a normal gene that was in overdrive, churning out huge amounts of a protein that appeared to be spurring the cancer’s growth.

Even better, there was a promising new drug that might shut down the malfunctioning gene—a drug that had been tested and approved only for advanced kidney cancer. Dr. Wartman became the first person ever to take it for leukemia.

And now, against all odds, his cancer is in remission and has been since last fall.

While no one can say that Dr. Wartman is cured, after facing certain death last fall, he is alive and doing well. Dr. Wartman is a pioneer in a new approach to stopping cancer. What is important, medical researchers say, is the genes that drive a cancer, not the tissue or organ—liver or brain, bone marrow, blood or colon—where the cancer originates.

One woman’s breast cancer may have different genetic drivers from another woman’s and, in fact, may have more in common with prostate cancer in a man or another patient’s lung cancer.

Under this new approach, researchers expect that treatment will be tailored to an individual tumor’s mutations, with drugs, eventually, that hit several key aberrant genes at once. The cocktails of medicines would be analogous to H.I.V. treatment, which uses several different drugs at once to strike the virus in a number of critical areas.

Researchers differ about how soon the method, known as whole genome sequencing, will be generally available and paid for by insurance—estimates range from a few years to a decade or so. But they believe that it has enormous promise, though it has not yet cured anyone.

With a steep drop in the costs of sequencing and an explosion of research on genes, medical experts expect that genetic analyses of cancers will become routine. Just as pathologists do blood cultures to decide which antibiotics will stop a patient’s bacterial infection, so will genome sequencing determine which drugs might stop a cancer.

“Until you know what is driving a patient’s cancer, you really don’t have any chance of getting it right,” Dr. Ley said. “For the past 40 years, we have been sending generals into battle without a map of the battlefield. What we are doing now is building the map.”

Large drug companies and small biotechs are jumping in, starting to test drugs that attack a gene rather than a tumor type.

Leading cancer researchers are starting companies to find genes that might be causing an individual’s cancer to grow, to analyze genetic data and to find and test new drugs directed against these genetic targets. Leading venture capital firms are involved.

For now, whole genome sequencing is in its infancy and dauntingly complex. The gene sequences are only the start—they come in billions of small pieces, like a huge jigsaw puzzle. The arduous job is to figure out which mutations are important, a task that requires skill, experience and instincts.

So far, most who have chosen this path are wealthy and well connected. When Steve Jobs had exhausted other options to combat pancreatic cancer, he consulted doctors who coordinated his genetic sequencing and analysis. It cost him $100,000, according to his biographer. The writer Christopher Hitchens went to the head of the National Institutes of Health, Dr. Francis Collins, who advised him on where to get a genetic analysis of his esophageal cancer.

Harvard Medical School expects eventually to offer whole genome sequencing to help cancer patients identify treatments, said Heidi L. Rehm, who heads the molecular medicine laboratory at Harvard’s Partners Healthcare Center for Personalized Genetic Medicine. But later this year, Partners will take a more modest step, offering whole genome sequencing to patients with a suspected hereditary disorder in hopes of identifying mutations that might be causing the disease.

Whole genome sequencing of the type that Dr. Wartman had, Dr. Rehm added, “is a whole other level of complexity.”

Dr. Wartman was included by his colleagues in a research study, and his genetic analysis was paid for by the university and research grants. Such opportunities are not available to most patients, but Dr. Ley noted that the group had done such an analysis for another patient the year before and that no patients were being neglected because of the urgent work to figure out Dr. Wartman’s cancer.

“The precedent for moving quickly on a sample to make a key decision was already established,” Dr. Ley said.

Ethicists ask whether those with money and connections should have options far out of reach for most patients before such treatments become a normal part of medicine. And will people of more limited means be tempted to bankrupt their families in pursuit of a cure at the far edges?

“If we say we need research because this is a new idea, then why is it that rich people can even access it?” asked Wylie Burke, professor and chairwoman of the department of bioethics at the University of Washington. The saving grace, she said, is that the method will become available to all if it works.

A Life in Medicine

It was pure happenstance that landed Dr. Wartman in a university at the forefront of cancer research. He grew up in small-town Indiana, aspiring to be a veterinarian like his grandfather. But in college, he worked summers in hospitals and became fascinated by cancer. He enrolled in medical school at Washington University in St. Louis, where he was drawn to research on genetic changes that occur in cancers of the blood. Dr. Wartman knew then what he wanted to do—become a physician researcher.

Those plans fell apart in the winter of 2002, his last year of medical school, when he went to California to be interviewed for a residency program at Stanford. On the morning of his visit, he was nearly paralyzed by an overwhelming fatigue.

“I could not get out of bed for an interview that was the most important of my life,” Dr. Wartman recalled. Somehow, he forced himself to drive to Palo Alto in a drenching rain. He rallied enough to get through the day.

When he returned to St. Louis, he gave up running, too exhausted for the sport he loved. He started having night sweats.

“I thought it might be mono,” he said. “And I thought I would ride it out.”

But then the long bones in his legs began to hurt. He was having fevers.

He was so young then—only 25—and had always been so healthy that his only doctor was a pediatrician. So he went to an urgent care center in February 2003. The doctor there thought his symptoms might come from depression, but noticed that his red and white blood cell counts were low. And Lukas Wartman, who had been fascinated by the biology of leukemia, began to suspect he had it.

“I was definitely scared,” he said. “It was so unreal.”

The next day, Mr. Wartman, who was about to graduate from Washington University’s medical school, went back there for more tests. A doctor slid a long needle into his hip bone and drew out marrow for analysis.

“We looked at the slide together,” Dr. Wartman said, recalling that terrible time. “It was packed with leukemia cells. I was in a state of shock.”

Dr. Wartman remained at the university for his residency and treatment: nine months of intensive chemotherapy, followed by 15 months of maintenance chemotherapy. Five years passed when the cancer seemed to be gone. But then it came back. Next came the most risky remedy—intensive chemotherapy to put the cancer into remission followed by a bone-marrow transplant from his younger brother.

Seven months after the transplant, feeling much stronger, he went to a major cancer meeting and sat in on a session on his type of leukemia. The speaker, a renowned researcher, reported that only 4 or 5 percent of those who relapsed survived.

“My stomach turned,” Dr. Wartman said. “I will never forget the shock of hearing that number.”

But his personal gauge of recovery—how far he could run—was encouraging.

By last spring, three years after his transplant, Dr. Wartman was running six to seven miles every other day and feeling good. “I thought maybe I would run a half marathon in the fall.”

Then the cancer came back. He remembered that number, 4 or 5 percent, for patients with one relapse. He had relapsed a second time.

This time, he said, “There is no number.”

His doctors put him on a clinical trial to try to beat the cancer with chemotherapy and hormones. It did not work.

They infused him with his brother’s healthy marrow cells, to no avail.

A Clue in RNA

Dr. Wartman’s doctors realized then that their last best hope for saving him was to use all the genetic know-how and technology at their disposal.

After their month of frantic work to beat cancer’s relentless clock, the group, led by Richard Wilson and Elaine Mardis, directors of the university’s genome institute, had the data. It was Aug. 31.

The cancer’s DNA had, as expected, many mutations, but there was nothing to be done about them. There were no drugs to attack them.

But the other analysis, of the cancer’s RNA, was different. There was something there, something unexpected.

The RNA sequencing showed that a normal gene, FLT3, was wildly active in the leukemia cells. Its normal role is to make cells grow and proliferate. An overactive FLT3 gene might be making Dr. Wartman’s cancer cells multiply so quickly.

Even better, there was a drug, sunitinib or Sutent, approved for treating advanced kidney cancer, that inhibits FLT3.

But it costs $330 a day, and Dr. Wartman’s insurance company would not pay for it. He appealed twice to his insurer and lost both times.

He also pleaded with the drug’s maker, Pfizer, to give him the drug under its compassionate use program, explaining that his entire salary was only enough to pay for 7½ months of Sutent. But Pfizer turned him down, too.

As September went by, Dr. Wartman was getting panicky.

“Every day is a roller coaster,” he said at the time, “and everything is up in the air.”

Desperate to try the drug, he scraped up the money to buy a week’s worth and began taking it on Sept. 16. Within days, his blood counts were looking more normal.

But over dinner at a trendy St. Louis restaurant, he picked at his chicken and said he was afraid to hope.

“Obviously it’s exciting,” he said. “But Sutent could have unanticipated effects on my bone marrow.” Maybe his rising red blood cell counts were just a side effect of the drug. Or maybe they were just a coincidence.

“It’s hard to say if I feel any different,” Dr. Wartman said.

And the cost of the drug nagged at him. If it worked, how long could he afford to keep taking it?

The next day, a nurse at the hospital pharmacy called with what seemed miraculous news: a month’s supply of Sutent was waiting for Dr. Wartman. He did not know at the time, but the doctors in his division had pitched in to buy the drug.

Two weeks later, his bone marrow, which had been full of leukemia cells, was clean, a biopsy showed.

Still, he was nervous. The test involved taking out just a small amount of marrow. Cancer cells could be lurking unseen.

The next test was flow cytometry, which used antibodies to label cancer cells. Again, there were no cancer cells.

But even flow cytometry could be misleading, Dr. Wartman told himself.

Finally, a yet more sensitive test, called FISH, was done. It labels cancer cells with fluorescent pieces of DNA to identify leukemia cells. Once again, there were none.

“I can’t believe it,” his awe-struck physician, Dr. John DiPersio, told him.

Dr. Wartman, alone in his apartment, waited for his partner, Damon Berardi, to come home from work. That evening, Mr. Berardi, a 31-year-old store manager, opened the door with no idea of Dr. Wartman’s momentous news. To his surprise, Dr. Wartman was home early, waiting in the kitchen with champagne and two flutes he had given Mr. Berardi for Christmas. He told Mr. Berardi he should sit down.

“My leukemia is in remission,” he said. The men embraced exultantly, and Dr. Wartman popped open the champagne.

“I felt an overwhelming sense of relief and a renewed vision of our future together,” Mr. Berardi said. “There were no tears at that moment. We had both had cried plenty. This was a moment of hope.”

Hunches and Decisions

Dr. Wartman and his doctors had fateful decisions to make, with nothing but hunches to guide them. Should he keep taking Sutent or have another bone-marrow transplant now that he was in remission again?

In the end, Dr. DiPersio decided Dr. Wartman should have the transplant because without it the cancer might mutate and escape the Sutent.

Meanwhile, Pfizer had decided to give him the drug. Dr. Wartman has no idea why. Perhaps the company was swayed by an impassioned plea from his nurse practitioner, Stephanie Bauer.

Dr. Wartman’s cancer is still gone, for now, but he has struggled with a common complication of bone-marrow transplants, in which the white blood cells of the transplanted marrow attack his cells as though they were foreign. He has had rashes and felt ill. But these complications are gradually lessening, and he is back at work in Dr. Ley’s lab.

His colleagues want to look for the same mutation in the cancer cells of other patients with his cancer. And they would like to start a clinical trial testing Sutent to discover whether the drug can help others with leukemia, or whether the solution they found was unique to Lukas Wartman.

Dr. Wartman himself is left with nagging uncertainties. He knows how lucky he is, but what does the future hold? Can he plan a life? Is he cured?

“It’s a hard feeling to describe,” he said. “I am in uncharted waters.”

July 7, 2012