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A Brief History of DNA Patents
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- The Cat’s Out of the Bag
A Brief History of DNA Patents The U.S. Patent Act, passed in 1790, defined a patentable invention as novel, useful, and non-obvious to an expert in the field. It’s easy to see how a patent might apply to a self-flushing toilet or an electronic gadget, but the picture gets murky on the matter of DNA. One can’t patent ideas, laws of nature, or products of nature. But it’s been okay to isolate a chemical from nature since Parke-Davis claimed adrenaline in 1911, deeming it different outside a body. U.S. patent law ventured into biology in 1980, with General Electric’s “oil eater” bacterium that combined DNA rings from four microbes. Nature hadn’t invented that. Then in 1990, the patent office added rules for claiming DNA sequences. Within a year, Amgen patented the first gene, erythropoietin (EPO), used to treat anemia. The European Union declared genes patentable in 1998. Isolating a gene supposedly renders it patentable, for it is no longer a “product of nature,” separate from its chromosome, its non-essential parts removed. The remaining DNA becomes a novel ‘composition of matter.’
An early gene patenting battle concerned Canavan disease, which strips brain cells of their insulating myelin coating beginning in infancy and usually lethal in childhood. The patent holders – four researchers and the University of Miami – developed a diagnostic test using the gene. Then families who had donated their children’s brains to the gene researchers found themselves having to pay to test their other children. Although that case was settled when the plaintiffs ran out of funds, with the cost of the test dropped and the gene made available to researchers, it set an informal precedent for the current BRCA controversy. Three years after the Canavan gene patent issued, in 2000, the first of Myriad Genetics’ BRCA patents issued. They’ve triggered outrage ever since. The American Civil Liberties Union and the Association for Molecular Pathology, representing 150,000 geneticists, cancer survivors, pathologists, and others, sued the U.S. Patent and Trademark Office (USPTO), Myriad, and the University of Utah in May 2009. On March 29, 2010, senior judge Robert W. Sweet for the Federal District Court for the Southern District of New York ruled the patents invalid. Said he at the International Congress of Human Genetics, “A human gene is not an invention. DNA’s existence in an isolated form alters neither this fundamental quality of DNA as it exists in the body nor the information it holds.” In August 2011 the U.S. Court of Appeals for the Federal Circuit overturned Judge Sweet’s decision, and now the March 26, 2012 Supreme Court’s setting aside of that ruling for further discussion is keeping the patent ball in play. The final result, whatever it is, will be important to many, because a fifth of the 20,325 or so human genes are patented. The Cat’s Out of the Bag It looks, at least this week, like DNA patents will become a thing of the past as consensus slowly builds that a product of nature isn’t an invention after all. But another reason why such patents are headed for extinction, I think, is that DNA testing has transcended the single-gene legacy of Gregor Mendel that peaked in a crescendo of discoveries in the 1990s, giving way to the age of genomics. Genes are no longer seen as islands. Even the three most common mutations in the much-discussed BRCA genes impart susceptibility, not certainty, with actual risk reflecting influences of other genes and the environment. Here are four ways that average people are encountering genes, without a thought to who or what entity “owns” them. Will gene patents interfere with whole exome and whole genome sequencing? Gavin Stevens' diagnosis of Leber congenital amaurosis, which causes his blindness, would not have been possible without the sequencing of his, his parents', and his grandparents' exomes. Photo: Jennifer Stevens Three-year-old Gavin Stevens, blind from birth, had been tested for more than a dozen genes known to cause Leber congenital amaurosis when his parents, Troy and Jennifer, met with John Chiang, PhD, director of the Molecular Diagnostic Laboratory at the Casey Eye Institute in Portland, Oregon, who sent the family’s DNA samples to the Beijing Genomics Institute to have their exomes sequenced. And within this protein-encoding portion of the genome lay the answer: Gavin’s mutant gene – the first stage in developing a gene therapy. Clients of direct-to-consumer genetic testing companies are providing the numbers to accelerate discovery of the many genes that contribute to common diseases. 23andMe has already found two new Parkinson’s disease, susceptibility genes, thanks to the DNA of 3,426 customers with the disease and nearly 30,000 controls. Forensic DNA databanks track some two dozen sites of short repeated sequences in the genome that collectively vary in more ways than there are people on the planet. DNA profiling has led to hundreds of exonerations and convictions. Several states have recently expanded their forensic DNA databases. Every few weeks, Family Tree DNA alerts me to the existence of a possible long-long-lost cousin among the many consumers sending in DNA samples. The power of tracing the deeper branches of the human family tree, of inferring when and from where and how many times some of our ancestors left Africa and spread around the globe, depends upon amassing DNA information from as many populations as possible. Could any of these potentially life-altering uses of DNA sequencing have happened if gene patent-holders charged prohibitively high licensing fees to the companies that package their discoveries into test panels and kits? Will our courts allow patented genes to impede progress at the genomic level, like tiny private stretches of sand interrupting an extensive public beach? Because so many applications of the information in our genomes are clearly already here, I think that the idea of owning a gene is already obsolete, and the courts need to catch up with the science. Summed up James Evans, “the human genome is a shared legacy.” I couldn’t agree more. http://www.sciencedaily.com/releases/2012/04/120403135516.htm Coral Links Ice Sheet Collapse to Ancient 'Mega Flood' Coral off Tahiti has linked the collapse of massive ice sheets 14,600 years ago to a dramatic and rapid rise in global sea-levels of around 14 metres. ScienceDaily - Previous research could not accurately date the sea-level rise but now an Aix-Marseille University-led team, including Oxford University scientists Alex Thomas and Gideon Henderson, has confirmed that the event occurred 14,650-14,310 years ago at the same time as a period of rapid climate change known as the Bølling warming. The finding will help scientists currently modelling future climate change scenarios to factor in the dynamic behaviour of major ice sheets. A report of the research is published in this week's Nature. 'It is vital that we look into Earth's geological past to understand rare but high impact events, such as the collapse of giant ice sheets that occurred 14,600 years ago,' said Dr Alex Thomas of Oxford University's Department of Earth Sciences, an author of the paper. 'Our work gives a window onto an extreme event in which deglaciation coincided with a dramatic and rapid rise in global sea levels -- an ancient 'mega flood'. Sea level rose more than ten times more quickly than it is rising now! This is an excellent test bed for climate models: if they can reproduce this extraordinary event, it will improve confidence that they can also predict future change accurately.' During the Bølling warming high latitudes of the Northern hemisphere warmed as much as 15 degrees Celsius in a few tens of decades. The team has used dating evidence from Tahitian corals to constrain the sea level rise to within a period of 350 years, although the actual rise may well have occurred much more quickly and would have been distributed unevenly around the world's shorelines. Dr Thomas said: 'The Tahitian coral is important because samples, thousands of years old, can be dated to within plus or minus 30 years. Because Tahiti is an ocean island, far away from major ice sheets, sea-level evidence from its coral reefs gives us close to the 'magic' average of sea levels across the globe, it is also subsiding into the ocean at a steady pace that we can easily adjust for.' The research is part of a large international consortium, the Integrated Ocean Drilling Program (IODP), and the coral samples were obtained by drilling down to the sea floor from a ship positioned off the coast of Tahiti. What exactly caused the Bølling warming is a matter of intense debate: a leading theory is that the ocean's circulation changed so that more heat was transported into Northern latitudes. The new sea-level evidence suggests that a considerable portion of the water causing the sea-level rise at this time must have come from melting of the ice sheets in Antarctica, which sent a 'pulse' of freshwater around the globe. However, whether the freshwater pulse helped to warm the climate or was a result of an already warming world remains unclear.
Bernard Buigues of the Mammuthus organisation acquired the frozen mammoth from tusk hunters in Siberia. Scientists completed an initial assessment of the animal, known as Yuka, in March this year. Wounds indicate that both lions and humans may have been involved in the ancient animal's death. "Already there is dramatic evidence of a life-and-death struggle between Yuka and some top predator, probably a lion," says leading mammoth expert, Daniel Fisher, professor of earth and environmental sciences at the University of Michigan. "Even more interesting, there are hints that humans may have taken over the kill at an early stage." If further investigation by Mr Buigues, Professor Fisher and fellow scientists at the Sakha Academy of Sciences in Yakutsk confirms this analysis, it will be the first carcass to show signs of interaction with ancient humans found in this part of the world. The Yuka mammoth was filmed as part of the BBC/Discovery Co-Production programme Woolly Mammoth: Secrets from the Ice. By analysing the teeth and tusks, the team estimate Yuka was about two and a half years old when it died. Teeth, tusks and bone are the most common ways extinct animals such as mammoths are studied, as these parts of the body take a relatively long time to decompose. Soft tissues such as muscle, skin and internal organs decompose far quicker, and are very rarely found on old carcasses. This means that vital information is usually lost. But much of Yuka's soft tissue as well as its woolly coat has remained intact, well-preserved in its icy tomb for possibly more than 10,000 years. Kevin Campbell, associate professor of environmental and evolutionary physiology at the University of Manitoba said: "These are remarkably rare finds and have huge significance." One of the most striking things about Yuka is its strawberry-blonde hair, he said. The possibility of mammoths having lighter coat colours was proposed in 2006 after scientists studied the genes extracted solely from a mammoth bone. Yuka provides direct evidence that mammoths did have lighter-coloured coats. Associate Professor Campbell said the find "will be a boon to researchers as it will help them link observed phenotypes (morphological features that we can see) with genotype (DNA sequences)". These links will allow scientists to determine how widespread physical traits such as eye and hair colour were "within and among mammoth populations" simply from studying genes from bone or hair samples in the future. Professor Fisher agreed the find was extraordinary: "It's like a diary or journal someone has just handed you - you just haven't had a chance to read it."
Healed scratches found on the skin indicate a lion attack that Yuka survived earlier in its relatively short life. However, similar deep cuts that had not healed suggest a subsequent lion attack that either caused or happened very near the time of Yuka's death. Also, when moving one of Yuka's legs, Professor Fisher recognised evidence of a freshly broken leg when it died and suggested this may have occurred as Yuka tried to flee from attackers. The lions in question (Panthera leo spelea) are an extinct subspecies of the African lion, known commonly as Eurasian cave lions but were present at the same time as the mammoths. "Did we know lions hunted mammoths? Well, we guessed they did. But could we ever have expected to see such graphic evidence? No - but here it is," explained Professor Fisher. In modern-day Africa, young elephants are attacked by lions, providing a means of comparing their injuries with Yuka's. Lions will usually enter the carcass through the belly, clamp their teeth over the mouth in order to suffocate their prey, and chew at an elephant's muscular trunk. However, Yuka's trunk is not damaged and there is only slight damage to the hide around the face. Instead of entering Yuka's body via the belly, there is what Professor Fisher describes as "a bizarre set of damage on the hide". This includes a "long, straight cut that stretches from the head to the centre of the back" as well as "very unusual patterned openings" into the skin and "scalloped margins" on the upper right-hand flank. The skull, spine, ribs and pelvis were all removed from Yuka's body, but the skull and pelvis were found nearby. However, most of the spine and three-quarters of the ribs are missing. Human interference Each scalloped mark on the skin is made up by 15-30 small, serrations that "could be the saw-like motion of a human tool" and there are "some quite striking cut marks" on the leg bones, according to Professor Fisher. Prof Fisher said they had questioned whether the cuts could have been made more recently. "We asked the people who found this mammoth multiple times if they had done this. They replied 'No! We did not get our knives out' which suggests we're looking at some sort of interaction of humans, mammoths and lions. "Were humans using the lions to catch mammoths and then moving the lions off their kill... was that what happened? I don't know but I wouldn't have thought about it without seeing it [the evidence]." Supporting this argument, the Dorobo tribe still practise the art of stealing kills from lions in Kenya. "Each new specimen has something to teach us, but Yuka provides some of the most dramatic evidence yet available for events surrounding the death of a woolly mammoth on the arctic steppes of Siberia." Professor Alice Roberts was part of the film crew that followed Yuka being recovered from the tusk hunters. She said: "There are some odd things. What we need to do is find out if this was human interference near the time of death or was it something that happened much later? "If it happened near the time of death then it means Yuka is a very important specimen as there are not many [mammoths] that show human interactions." She said seeing Yuka in the flesh was almost "poignant". "You feel it has only just died as it is so beautifully preserved." http://www.eurekalert.org/pub_releases/2012-04/ind-ang040412.php A new gene thought to be the cause in early-onset forms of Alzheimer's disease A new gene that causes early-onset of Alzheimer's disease has been discovered by the research team of Dominique Campion at the Insert unit 1079 "Genetics of cancer and neuropsychiatric diseases" in Rouen. The research scientists showed that in the families of 5 of 14 patients suffering from the disease, mutations were detected on the gene SORL1. This gene regulates the production of a peptide involved in Alzheimer's disease. The results of this study have been published in the review Molecular Psychiatry issued April 3rd. Precise genetic mutations have been seen to play a part in early-onset forms of Alzheimer's disease. However, there is a sub-population of patients in whom there is no mutation of these genes. So how can these patients, in whom there are no pre-established mutations, be suffering from early-onset Alzheimer's? To reply to this question, the research team working under the leadership of Dominique Campion and Didier Hannequin (Inserm unit 1079 and Centre national de référence malades Alzheimer jeunes, University hospital Rouen), studied the genes from 130 families suffering from early-onset forms of Alzheimer's disease. These families were identified by 23 French hospital teams within the framework of the "Alzheimer Plan". Of these families, 116 presented mutations on the already known genes. But in the 14 remaining families, there was no mutation at all observed on these genes. A study of the genome of the 14 families using new whole DNA sequencing techniques showed evidence of mutations on a new SORL1 gene. The SORL1 gene is a coding gene for a protein involved in the production of the beta-amyloid peptide. This protein is known to affect the functioning of the brain cells (see insert). Two of the identified mutations are responsible for an under-expression of SORL1, resulting in an increase in the production of the beta-amyloid peptide. "The mutations observed on SORL1 seem to contribute to the development of early-onset Alzheimer's disease. However, we still need to identify more clearly the way in which these mutations are transmitted on the SORL1 gene within families" states Dominique Campion. Alzheimer's disease is one of the main causes of dependency among the elderly. It results from neuron degradation in different areas of the brain. Its symptoms include increased alterations to memory, cognitive functions and behaviour disorders that lead to a progressive loss of independence. Alzheimer's disease is characterized by the development of two types of lesion in the brain: amyloid plaques and neurofibrillary degenerescence. Amyloid plaques are caused by extracellular accumulation of a peptide, beta-amyloid peptide (Aβ) in specific areas of the brain. Neurofibrillary degenerescences are intraneuronal lesions caused by abnormal filamentary aggregation of a protein known as a Tau protein.
The groundbreaking "Black Queen Hypothesis" got its name from the game of Hearts. In Hearts, the goal is to avoid "winning" the Queen of Spades (the Black Queen), which is worth a lot of points. Subsequently, players allow others to take the high-point card while they enjoy low-score tallies. This same premise applies in evolution, the scientists say. According to the hypothesis, evolution pushes microorganisms to lose essential functions when there is another species around to perform them. This idea counters popular evolutionary thinking that living organisms evolve by adding genes rather than discarding them. "A common assumption about evolution is that it is directed toward increasing complexity," said Erik Zinser, associate professor of microbiology. "But we know from analysis of microbial genomes that some lineages trend toward decreasing complexity, exhibiting a net loss of genes relative to their ancestor." Zinser's opinion piece is published in mBio, the online open-access journal of the American Society for Microbiology. Jeffrey Morris and Richard Lenski of Michigan State University are co-authors. Morris was Zinser's doctoral student at UT. The authors formed their theory after studying photosynthetic bacteria called Prochlorococcus. "This marine microorganism continued to mystify us because it is the most common photosynthetic organism on Earth, but it is extremely difficult to grow in pure culture," Zinser said. "A major reason for this difficulty is that Prochlorococcus is very sensitive to reactive oxygen species such as hydrogen peroxide and relies on other bacteria to protect them by breaking down these toxic substances for them." Prochlorococcus had once performed this function itself, but natural selection decided it was too costly, like carrying the Queen of Spades, and discarded this ability. Instead Prochlorococcus benefits from the hard work of others within its community allowing it to concentrate its energies elsewhere—such as multiplying. The hypothesis offers a new way of looking at complicated, interdependent communities of microorganisms. "We know that certain microbial activities, such as hydrogen peroxide scavenging, are 'leaky,' meaning their impacts extend beyond the cell and into the environment," Zinser said. "What the hypothesis suggests is that this leakiness can drive a community toward greater interdependence, even if some members are unwitting participants in this process." This interdependence could lend itself to vulnerabilities. The scientists say the work highlights the importance of biological diversity, because if rare members are lost, "the consequences for the community could be disastrous." This would be analogous to attempting to play Hearts without the Queen of Spades. Currently, the hypothesis is limited to microorganisms, but Zinser thinks the hypothesis could be extended to larger free-living organisms. All that is needed is a card which no player wants yet is crucial for the game to be played. http://www.eurekalert.org/pub_releases/2012-04/aaon-smd032712.php Studies: Memory declines faster in years closest to death; mental activity best protection New research finds that a person's memory declines at a faster rate in the two- and-a-half years before death than at any other time after memory problems first begin. ST. PAUL, Minn. - A second study shows that keeping mentally fit through board games or reading may be the best way to preserve memory during late life. Both studies are published in the April 4, 2012, online issue of Neurology®, the medical journal of the American Academy of Neurology. For the study, 174 Catholic priests, nuns and monks without memory problems had their memory tested yearly for six to 15 years before death. After death, scientists examined their brains for hallmarks of Alzheimer's disease called plaques and tangles. "In our first study, we used the end of life as a reference point for research on memory decline rather than birth or the start of the study," said study author Robert S. Wilson, PhD, of Rush University Medical Center in Chicago. The study found that at an average of about two-and-a-half years before death, different memory and thinking abilities tended to decline together at rates that were 8 to 17 times faster than before this terminal period. Higher levels of plaques and tangles were linked to an earlier onset of this terminal period but not to rate of memory decline during it. In an accompanying editorial, author Hiroko H. Dodge, PhD, with Oregon Health and Science University in Portland and a member of the American Academy of Neurology, noted, "The findings suggest that the changes in mental abilities during the two to three years before death are not driven directly by processes related to Alzheimer's disease, but instead that the memory and other cognitive decline may involve some biological changes in the brain specific to the end of life. The study by Wilson and his co-authors deepens our understanding of terminal cognitive decline." The second study, also conducted by Wilson, focused on mental activities and involved 1,076 people with an average age of 80 who were free of dementia. Participants underwent yearly memory exams for about five years. They reported how often they read the newspaper, wrote letters, visited a library and played board games such as chess or checkers. Frequency of these mental activities was rated on a scale of one to five, one meaning once a year or less and five representing every day or almost every day. The results showed that people's participation in mentally stimulating activities and their mental functioning declined at similar rates over the years. The researchers also found that they could predict participants' level of cognitive functioning by looking at their level of mental activity the year before but that level of cognitive functioning did not predict later mental activity. "The results suggest a cause and effect relationship: that being mentally active leads to better cognitive health in old age," said Wilson.
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