Category Archives: Genetics

S.D.N.Y. Holds That Patent Claims on Breast Cancer Genes Are Invalid

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Jake Meyer by Jake Meyer

On March 29th, 2010, Judge Sweet of the United States District Court in the Southern District of New York declared that the challenged patent claims, owned by Myriad genetics, that cover the BRCA1 and BRCA2 breast cancer genes are invalid.  The full opinion is available here.  I had previously blogged about the plaintiffs in the case here, and I previously blogged about Judge Sweet’s denial of the defendant’s motion to dismiss here.  This was the first case to raise the argument that gene sequences and correlations between gene mutations and disease are unpatentable subject matter under 35 U.S.C. section 101.

There were two types of claims at issue in the case:  1) claims to “isolated” DNA containing the BRCA1 or BRCA2 sequence or certain segments of those sequences, and 2) claims to methods of comparing two BRCA1 or BRCA2 sequences to determine whether a mutation that predisposes a subject to cancer is present.  Judge Sweet found that both of these types of claims were invalid subject matter.

U.S. patent law does not allow for the patenting of products of nature.  As Judge Sweet recognizes this in his opinion there is a “judicially created ‘products of nature’ exception to patentable subject matter, i.e. ‘laws of nature, natural phenomenon, and abstract ideas.'”  Judge Sweet applied analysis from the 1980 Supreme Court case Diamond v. Chakrabarty to determine whether the product claims directed to “isolated” DNA were patentable.  The Supreme Court in Chakrabarty held that a genetically engineered bacterium was patentable because the “patentee had produced a new bacterium with markedly different characteristics from any found in nature.”  Sweet found that the requirement that an invention have “markedly different characteristics” from a product of nature to be patentable had been stated (although using different language) in earlier cases as well, such as in the Supreme Court case American Fruit Growers and in the Court of Customs and Patent Appeals case In re Merz.

Judge Sweet held that the “isolated” DNA was not “markedly different” than DNA inside the human body.  The analysis focused on the DNA’s unique role as both a physical molecule and as information.  While the “isolated” DNA was removed from the body, the information embodied by the DNA was not changed:

In light of DNA’s unique qualities as a physical embodiment of information, none of the structural and functional differences cited by Myriad between native BRCA1/2 DNA and isolated BRCA1/2 DNA claimed in the patents-in-suit render the claimed DNA “markedly different.”  This conclusion is driven by the overriding importance of DNA’s nucleotide sequence to both its natural biological function as well as the utility associated with DNA in its isolated form.  The preservation of this defining characteristic of DNA in its native and isolated forms mandates the conclusion that the challenged composition claims are directed to unpatentable products of nature.

The second types of claims to methods of comparing two BRCA1 or BRCA2 sequences to determine whether a mutation that predisposes a subject to cancer is present were found invalid because they involved a law of nature and did not satisfy the Federal Circuit’s machine-or-transformation.  When a method claim makes use of a law of nature, the claimed method must either use a specific machine or apply a transformation to be patentable.  Judge Sweet found that the method did not include a transformation and since the claims did not include the use of a specific machine the method claims were directed to an unpatentable law of nature.

When DNA Takes Center Stage

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Lori Andrews by Lori Andrews

In the wake of the September 11 attacks, Chicagoans Jamil Khoury and Malik Gillani took a unique approach to counter anti-Arab and anti-Muslim sentiment. They formed the Silk Road Theater Company, offering plays which show the complex, multifaceted experiences of people of Asian, Middle Eastern, and Mediterranean descent.  Their productions fight stereotypes with nuanced stories of human similarity and differences.

Now, eight years and multiple awards later, Khoury and Gillani have tackled another complicated and misunderstood phenomenon–genetic testing.  For their latest production, seven playwrights of Silk Road ancestry took genealogical DNA tests and wrote short plays, which are joined together in The DNA Trail.  Performances continue until April 4 at the Silk Road Theater Project, 77 W. Washington, Chicago.

Lori DNA TrailAs the former chair of a federal advisory commission to the Human Genome Project, I was prepared to cringe at any genetic determinism in the plays. I’d been in countless meetings with scientists who tried to reduce complex people to genetic explanations.  One researcher made the controversial claim that, because Maoris were once warriors, he’d searched for and discovered a “warrior” gene in the Maori of New Zealand which makes them more aggressive and violent.  Tariana Turia, a co-leader of the Maori party, questioned why researchers were even looking for the warrior gene in their blood. “Once were warriors?” Turia said to the Daily Telegraph.  “Once were gardeners, once were astronomers, once were philosophers, once were lovers.”

Before the play began, I opened my printed program, which featured bios of the seven playwrights and a brief description of each play.  The first playwright, Elizabeth Wong, started her bio by saying, “I’m in the N9a haplogroup.”  She then went on to say that she thought she was pureblood Chinese, but that the test showed she was linked to a woman out of Africa.

Oh, oh, I thought.  I’d seen data showing that the genealogical tests are not very accurate.  When a journalist sent her DNA to two different companies, she got conflicting results and news that conflicted with her families’ oral history about her ancestry.  The snafu is that 99 percent of our DNA is like anyone else’s, including the people who lived thousands of years ago.  Depending what stretch of the three billion genetic bases the test scrutinizes, I could receive a test result that declares me related to anyone who currently lives or who ever lived.

When the performances began, though, my concerns about determinism vanished.  The playwrights had caught the nuances, complexities, heart-wrenching conflicts, and occasional zaniness of DNA testing.  Wong’s own play, “Finding Your Inner Zulu,” took two sisters on a journey through their DNA that showed how all of us have genetic strengths and weaknesses.  The plays added new twists to questions of identity (Jamil Khoury’s “WASP: White Arab Slovak Pole”) and family (Velina Hasu Houston’s “Mother Road”).  David Henry Hwang’s contribution, “A Very DNA Reunion,” is roaringly funny.  After a son who lives with his parents upsets them by charging a DNA test on their credit card, his purported ancestors–Ghengis Khan, a Ninja, and Cleopatra–show up in his bedroom to help him deal with his folks.  On the other end of the emotional continuum, Shishir Kurup’s captivating and well-acted “Bolt from the Blue” provides a gripping portrait of a family separated by distance dealing with suicide and the propensity to mental illness.

DNA Reunion

Featuring, left to right: Anthony Peeples, Fawzia Mirza, Clayton Stamper, and Khurram Mozaffar.
Photo by Michael Brosilow.

The complexities and significance of genetic testing are laid out in videos on the theater’s website and in essays that cover eight pages in the program.  With the same patience that the Silk Road Theater Project has sought to explain the dreams and goals of discriminated-against people, the Project gives audience members the tools to understand genetic testing.

The extraordinary Nancy Wexler, whose research was responsible for the discovery of the Huntington gene, once said that DNA tests are like card games.  It doesn’t matter what hand you are dealt, it is how you play it.  Once again, the Silk Road Theater Project has played its hand flawlessly.

Should We Clone Neanderthals?

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Lori Andrews by Lori Andrews

In 1856, workers in a limestone mine in the Neander Valley in Germany made a startling discovery.  They came across an assortment of bones — a skull cap, a rib cage and certain leg and arm bones — that they initially believed came from a bear.  But when the bones were examined by anatomist Hermann Schaaffhauesen, the field of paleoanthropology was born.  The bones belonged to a distant relative of humans — a Neanderthal.

Now, a century and a half later, the Neanderthals are again in the news.  A group of scientists have completed the rough draft of the genetic sequence of the Neanderthal and compared it to the genetic sequence of modern humans.  The scientists are asking now asking the question:  What legal and ethical issues would be raised by cloning a Neanderthal?

Neanderthals are the closest relatives of humans and lived from at least 350,000 years ago until about 30,000 years ago.   They survived for about 15,000 years after modern humans appeared.  They lived in Europe, where fossils have been discovered from Spain to Southern Siberia.

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DIY Genetics-Biotechnology by Parents, Artists, and…Potential Terrorists

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Lori Andrews by Lori Andrews

When geneticist Hugh Rienhoff's daughter Beatrice was born six years ago, he noticed a few traits that differed from his other children.  She seemed a little floppy, her feet were slightly bigger than usual, and her fingers didn't seem to stretch completely open.  In the months to come, she ate well, but didn't gain a commensurate amount of weight.  Although Rienhoff had left clinical genetics to join the venture capital and commercial biotech worlds, concern about his daughter pulled him back in.  After consultations with experts didn't bring a satisfactory answer about the cause of her disease, he took matters in his own hands.  He built a lab in his attic and started sequencing her DNA. 

Although his work hasn't yet established a definitive diagnosis or cure, his increased understanding of his daughter's biological pathways did lead her doctor to put her on a drug which strengthened her skeletal muscles.  He's also created a digital community at mydaughtersdna.org where other parents of children with unusual syndromes can share information.   According to an article in Wired, when a Bulgarian man posted information about his 12-year-old daughter's symptoms–inability to shed tears, speech problems, and weak limbs–a geneticist responded by correctly suggesting that the girl should be tested for Triple A syndrome.

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What Do Genetic Testing, Sweaty T-Shirts, and Prairie Voles Have to Do With Love?

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Jake Meyer by Jake Meyer

The internet revolutionized every facet of our lives – work, play, and even our relationships.  With the invention of the internet came numerous matchmaking sites that helped two people find each other for a relationship or marriage.  Match.com allows users to browse through personally created profiles and contact each other, while Eharmony.com matches users based on a test that covers "29 dimensions."  But how is the biotechnology revolution changing relationships?  And how will these technologies alter how we view love and marriage?

One way the biotechnology revolution is changing marriage is through the screening of potential mates to see whether they both carry the genes of a particular disease.  This way the potential mates know whether their children would be more likely to be born with a particular disease and can then make informed decisions about procreation.  For example, in the Ultra-Orthodox Jewish community of New York, where arranged marriages among Ashkenazim (Jews of Eastern European descent) are still common, match makers screen potential matches for a genetic disease known as Tay-Sachs.

People who are of Ashkenazi descent have a one-in-25 chance of having a Tay–Sachs genetic mutation; if two such carriers marry, each child has a one-in-four chance of having the devastating disease.  A child with Tay–Sachs appears normal at birth, but soon loses motor functions, suffers massive neurological deterioration has seizures, and generally dies by age three.  To prevent couples having children with this devastating genetic disease an organization known as Chevra Dor Yeshorim (Association of an Upright Generation) offers Tay–Sachs carrier screening to Ultra-Orthodox Jewish adolescents.  Before a marriage is arranged, the matchmaker calls the program with the identification numbers of the two individuals.  If both individuals are carriers for Tay-Sachs, they are found to be "genetically incompatible."  The program has added screening for other disorders, such as cystic fibrosis, which has generated controversy because these diseases are not necessarily fatal in childhood.

But what about using genetic screening on a mate not to determine whether they carry the genes for a disease, but instead to discover whether mates are genetically compatible?  GenePartner.com does just that –- setting up couples based on genes that would make the couple more naturally attractive to each other.  According to the GenePartner website, the GenePartner project was inspired by a study by Dr. Claus Wedekind at the University of Bern in Switzerland.  Wedekind had female volunteers smell T-shirts that had been worn by men for three consecutive days and then rate the smell of the T-shirts for attractiveness.  Wedekind then analyzed the part of the DNA of the men and women that codes for HLA (human leukocyte antigen) molecules.  HLA molecules control the activation of immunological effectors during an immune response, making them essential for immune resistance.  Wedekind found that the women were most attracted to men with HLA DNA different from their own.  According to GenePartner.com compatible couples have different HLA DNA, leading to varied HLA molecules that allow immunity to a wider variety of diseases.  GenePartner.com also claims that this "gene compatibility" also results in an increased likelihood of forming an enduring and successful relationship, more satisfying sex life, and higher fertility rates.

And so now with the help of genetics you’ve found your genetic compatible mate –- someone with a differing HLA gene and sweaty T-shirts you find irresistible –- but what can genetics do to make the relationship last?  Well perhaps with a little help from genetics you could give your mate a drug — a love potion of sorts — or alter their genes to make them more monogamous.  Dr. Larry Young has studied prairie voles, one of the five percent of mammals that, like humans, are monogamous.  A hormone in the voles, vasopressin, creates urges for bonding and nesting when it is injected in male voles.  Male voles with a genetic mutation that caused a weaker vasopressin response were less likely to find mates.  The same thing has been found in humans as well –- Swedish researchers have reported that human males with a genetically caused weak vasopressin response were also less likely to find a mate.

Armed with this knowledge, it’s possible that we could engineer our mates and ourselves to have a stronger vasopressin response and in turn be more monogamous.  Or if an individual or society decided that monogamy was not desirable, we could engineer ourselves to have less of a vasopressin response.

So as you look in to the eyes of your significant other this Valentine's day, you may find yourself wondering whether you should both get genetic testing, or whether you find his sweaty T-shirt attractive, or if he's more like a vole or more like the 95% of other mammals in the world.  At this point you may realize that genetics (and the internet) have made you think about love and relationships just a bit differently.

Thicket of Uncertainty in the Gene Patent Debate

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Keith Syverson by Keith Syverson

In 1998, Michael Heller and Rebecca Eisenberg wrote that the proliferation of biotechnology patents created a tragedy of the anticommons where "people underuse scarce resources because too many owners can block each other."  This phenomenon is also referred to as a "patent thicket" where there are multiple different patents from different owners.  Over the past 12 years, many studies have been published evaluating the effect of intellectual property rights in medical research and diagnostic testing.  In October 2009, a group of European scientists led by Isabelle Huys investigated whether the proliferation of gene patents or patents on diagnostic methods created a patent thicket.  The article, Legal Uncertainty in the Area of Genetic Diagnostic Testing, concluded that there was no patent thicket with regard to claims that actually claim DNA sequences, but that there were enough different claims on diagnostic methods to create a chilling effect on medical diagnoses and restrict access to care.

The authors provide an empirical analysis of the nature, extent, and scope of patents relating to 22 of the most commonly tested for genetic diseases in Europe which include cystic fibrosis, breast cancer, and colon cancer.  They then compared the claims to the best practice guidelines in Europe and the United States for testing of susceptibility to these genetic disorders to determine if the patents had any effect on access to genetic testing in either country.  The authors concluded that there was not a "thicket" of patents covering only genes because most of these patents could be easily invented around.

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Sorry Darwin, It’s Not All In the Genes.

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Lori Andrews by Lori Andrews
time magazine cover - dna not destinyThis week’s Time features a cover story, “Why Your DNA Isn’t Your Destiny.”  This is a far cry from the sentiment twenty years ago at the start of the Human Genome Project.  At that time, a prominent psychiatrist announced, “The war is over in the nature/nuture debate” — implying that everything was due to genes (nature).  Or when, during the Monica Lewinsky scandal, Time itself ran a cover story proclaiming “Infidelity–It May Be In Our Genes.”

In the intervening two decades, scientists have learned that human traits and behaviors are caused by a complex array of factors.  When researchers begin searching for a gene related to height, they found variations at 20 different points in the genome that were related to a person’s stature.  And even if all 20 were analyzed, that only accounted for 3% of the variation between people in height.

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Zinc Fingers Could Point to Future Cures, But Gene Patents Could Get In The Way

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Jake Meyer by Jake Meyer

A December 29th, 2009 article in The New York Times describes a new technique that allows for the editing of human genes.  The technique uses natural agents called "zinc fingers," two loops of protein that can recognize specific sequences of DNA have multiple potential uses.  Zinc fingers could be used in the future to engineer new crop plants, treat human diseases, and to make alterations to sperm or egg cells –- alterations that would be inheritable. 

Zinc fingers can be used to turn on or off a gene at a specific DNA site.  An agent that turns the gene on or off can be linked to the zinc finger, which recognized and attaches to the specific DNA site.  But zinc fingers have another use which makes them a promising technology for gene therapy –- they can cut out and insert DNA from the gene sequence.

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FDR’s Cancer and Abe Lincoln’s DNA: What Rules Should Govern “Biohistory?”

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Lori Andrews by Lori Andrews

Historians traditionally probed the lives of past presidents by analyzing their speeches, reading their diaries, and tracing the trajectories of their lives.  But now medical and genetic tools have been added to the arsenal of historic inquiry.  And questions have arisen about the ethical and legal ramifications of the emerging field, “biohistory.”

A new book, FDR’s Deadly Secret by neurologist Steven Lomazow and The New York Post reporter Eric Fettmann, hypothesizes that Franklin Delano Roosevelt had cancer.  The authors and came to that conclusion by analyzing photos of small lesion above his eye, thought to be a melanoma.

The assertion is nothing new. For at least half a century, physicians and journalists, including a 1979 Time magazine article, reported on just such a speculation.  But newspaper and blog responses in the past few days are filled with anger about how FDR could have kept this from the public.  There’s even a sense of outrage that his decision-making during World War II might have been impaired due to the spread of the cancer to his brain.  In yesterday’s Post, Fettman accused FDR of endangering the nation by running for president with this supposed malady.

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The Fender Bender Gene: A New Study Suggests Bad Driving May Be Genetically Based

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Jake Meyer by Jake Meyer

While driving in holiday traffic you may be cut-off by a motorist who erratically enters your lane without using a turn signal or you may need to suddenly slam on your brakes to avoid another motorist who brakes with no warning.  And you may find yourself honking your horn and shouting "where did you learn to drive?"  But what if bad drivers didn’t learn to drive like bad drivers, but instead were born bad drivers? 

A recent study by neurologist Dr. Steven Cramer at University of California Irvine suggests that bad driving may be in part genetically based, finding that drivers with a certain gene variant performed 20 percent worse on a driving test than drivers without the gene variant. The study looked at the gene associated with the production of a protein called brain-derived neurotrophic factor (BDNF).  BDNF supports communication among brain cells and keeps them functioning optimally.  Previous studies have shown that people with the BDNF gene variant, when engaged in a task, have a smaller portion of their brain active than those with a normal BDNF gene variant. The study put 29 people in a driving simulator – 22 without the gene variant and 7 with the gene variant – and had them drive 15 laps on track with difficult turns and curves.  Four days later, the participant returned to drive the same 15 laps.  The participants with the gene variant did worse on both tests and also remembered less of the track the second time. 

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