Patent Docs

Myriad Sticks to Its Business Model

    By Kevin E. Noonan --

Myriad Genetics, one of the preeminent gene-based diagnostics companies, has been targeted by the American Civil Liberties Union, Dan Ravicher’s PUBPAT Organization, a raft of medical researchers and their associations, and individual patients in a lawsuit filed in the Southern District of New York; the avowed aim of the plaintiffs is to get the issue of "gene patenting" before the U.S. Supreme Court (see "Association for Molecular Pathology v. U.S. Patent and Trademark Office").  While the case wends its way through the Federal judicial system, Myriad is continuing its pursuit of diagnostically-relevant cancer markers, the most recent of which is a gene related to susceptibility to pancreatic cancer licensed from the Johns Hopkins University.

The gene encodes PALB2, a tumor suppressor gene reported to be involved in susceptibility to pancreatic cancer in the April 10, 2009 issue of Science (Jones et al., 2009, "Exomic Sequencing Identifies PALB2 as a Pancreatic Cancer Susceptibility Gene," Science 324: 217).  The product of the PALB2 gene is a binding partner of BRCA2, originally identified by its association with breast cancer susceptibility.  The two gene products bind to DNA to repair damage, wherein PALB2 localizes and anchors BRCA2 to damaged DNA in the cell nucleus.  More than 3% of familial pancreatic cancer patients had mutations in PALB2 resulting in the production of a truncated version of the encoded protein.  In contrast, no mutations in the PALB2 gene were found in more than 1,000 normal DNA samples.

Myriad contends that the predictive value of detecting such mutations are due to a 10- to 20-fold increase in the likelihood of developing pancreatic cancer by age 70 for individuals bearing the PALB2 mutation (or mutations in BRCA2 or another tumor suppressor gene, p16).  Early detection is particularly important for pancreatic cancer, which is typically detected only after it has progressed past the stage where intervention has any chance of significantly prolonging life.  Pancreatic cancer is diagnosed in about 200,000 patients worldwide each year, and is fatal almost without exception.

The scope of the difficulty in identifying reliable diagnostic genes is reflected in the following synopsis of the extent of mutations found by the Johns Hopkins researchers in tumor DNA from one pancreatic cancer patient.

Among the 20,661 coding genes analyzed, we identified 15,461 germline variants in Pa10 not found in the reference human genome.  Of these, 7318 were synonymous, 7721 were missense, 64 were nonsense, 108 were at splice sites, and 250 were small deletions or insertions (54% in-frame).

The PALB2 mutation found in tumor DNA from this patient exhibited a germline deletion of four basepairs (TTGT) that produced a frameshift mutation at codon 58, resulting in production of a truncated gene product from this gene.  Additional mutations found associated with pancreatic cancer in the PALB2 gene are a G > T transversion at the 5' splice site of exon 6, a deletion of an A residue in exon 11 (at nucleotide 3116) and a C > T transition mutation in exon 12 (at nucleotide 3256).  Fine structure mapping of mutations found in the PALB2 gene in pancreatic cancer, breast cancer, and Fanconi anemia patients was also reported.

The company estimates that a diagnostic genetic test might be on the market by 2010.

Biogen Idec Receives Method-of-Use Patent on Human ß-Interferon

Implications for Patent Protection for Avonex® Anti-Multiple Sclerosis Drug

    By Kevin E. Noonan --

There is a tendency to blame the process when an undesired outcome occurs.  That is happening in the wake of regulatory filings with the Securities and Exchange Commission regarding U.S. Patent 7,588,755 (the '755 patent), issued on September 15, 2009, and owned by Biogen Idec.  The undesired outcome (by some) is the possibility that this patent will protect Biogen Idec's blockbuster multiple sclerosis drug, Avonex® (human interferon beta 1a), from generic competition for an additional 13 years (until September 15, 2026) after expiration of current patents in May 2013.  That may happen, but a review of the history of the application shows that the patenting process worked as it is supposed to, with no evidence that Biogen Idec was not diligent in prosecuting this application within Patent Office rules.  If anything, it is the diligence with which the Office examined the application that resulted in the delay that may extend Biogen Idec's exclusivity period.

The '755 patent claims priority to a first application filed in 1981 and a divisional application filed in 1989, both abandoned.  The application that resulted in the '755 patent was filed on May 25, 1995, and thus has a patent term of 17 years from issue, determined by U.S. law prior to the adoption of the GATT provision limiting U.S. patent term to 20 years from the earliest priority date.  A history of patent prosecution reveals "why it took so long" for this patent to issue:

The longest period of delay extended from March 12, 1998 to January 15, 2003 -- almost five years -- while prosecution was suspended because of a potential interference.  (For those uninitiated in the arcane world of interferences, the most likely reason for this delay was to give a potential interfering application time to be prosecuted until interfering claims were deemed allowable.)  As it turns out, no interference was declared, and the Examiner renewed prosecution by asserting anticipation rejections based on two patents to Sugano (U.S. Patent Nos. 5,514,567 or 5,326,859).  (Ironically, '755 patent applicant Fiers was involved in an earlier interference against Sugano, and a second party, Revel, almost 20 years ago, in which Sugano prevailed in claims for human ß-interferon.)  The second extensive period of delay involved the appeal of the asserted anticipation rejection, which was complicated by the new formalities rules for appeal briefs promulgated (and strictly enforced) by the Office.  This delayed prosecution of the application to allowance by another 3 years, from June 24, 2005 to May 29, 2008.  Ultimately, the Board of Patent Appeals and Interferences reversed the rejections based on the Sugano patents, paving the way for allowance and issue of the '755 patent (a process that took another 16 months).

In addition to these Patent Office delays, the extended term of this patent is, of course, an artifact of the change in patent term in the U.S. -- the reason the term seems so long today is that we have become accustomed to a 20-year maximum from the earliest priority date, and the prior norm of 17 years from grant date seems anomalous, especially when the term is as extended as it is in this case (31 years from the application filing date, and 45 years from the earliest priority date).  Something like this could not occur today.

Besides these procedural aspects, whether the '755 patent will be useful for preventing generic competition for Avonex® will depend on the scope of the granted claims.  The '755 patent has but three claims, set forth below:

1.  A method for immunomodulation or treating a viral conditions, a viral disease, cancers or tumors comprising the step of administering to a patient in need of such treatment a therapeutically effective amount of a composition comprising:
    a recombinant polypeptide produced by a non-human host transformed by a recombinant DNA molecule comprising a DNA sequence selected from the group consisting of:
    (a) DNA sequences which are capable of hybridizing to any of the DNA inserts of G-pBR322(Pst)/HFIF1, G-pBR322(Pst)/HFIF3 (DSM 1791), G-pBR322(Pst)/HFIF6 (DSM 1792), and G-pBR322(Pst)/HFIF7 (DSM 1793) under hybridizing conditions of 0.75 M NaCl at 68.degree. C. and washing conditions of 0.3 M NaCl at 68.degree. C., and which code for a polypeptide displaying antiviral activity, and (b) DNA sequences which are degenerate as a result of the genetic code to the DNA sequences defined in (a);
    said DNA sequence being operatively linked to an expression control sequence in the recombinant DNA molecule.

2.  The method according to claim 1, wherein said DNA sequence is selected from DNA sequences of the formulae:

ATGACCAACAAGTGTCTCCTCCAAATTGCTCTCCTGTTGTGCTTCTCCACTA
CAGCTCTTTCCATGAGCTACAACTTGCTTGGATTCCTACAAAGAAGCAGCAA
TTTTCAGTGTCAGAAGCTCCTGTGGCAATTGAATGGGAGGCTTGAATACTGC
CTCAAGGACAGGATGAACTTTGACATCCCTGAGGAGATTAAGCAGCTGCAGC
AGTTCCAGAAGGAGGACGCCGCATTGACCATCTATGAGATGCTCCAGAACAT
CTTTGCTATTTTCAGACAAGATTCATCTAGCACTGGCTGGAATGAGACTATT
GTTGAGAACCTCCTGGCTAATGTCTATCATCAGATAAACCATCTGAAGACAG
TCCTGGAAGAAAAACTGGAGAAAGAAGATTTCACCAGGGGAAAACTCATGAG
CAGTCTGCACCTGAAAAGATATTATGGGAGGATTCTGCATTACCTGAAGGCC
AAGGAGTACAGTCACTGTGCCTGGACCATAGTCAGAGTGGAAATCCTAAGGA
ACTTTTACTTCATTAACAGACTTACAGGTTACCTCCGAAAC,

and

ATGAGCTACAACTTGCTTGGATTCCTACAAAGAAGCAGCAATTTTCAGTGTC
AGAAGCTCCTGTGGCAATTGAATGGGAGGCTTGAATACTGCCTCAAGGACAG
GATGAACTTTGACATCCCTGAGGAGATTAAGCAGCTGCAGCAGTTCCAGAAG
GAGGACGCCGCATTGACCATCTATGAGATGCTCCAGAACATCTTTGCTATTT
TCAGACAAGATTCATCTAGCACTGGCTGGAATGAGACTATTGTTGAGAACCT
CCTGGCTAATGTCTATCATCAGATAAACCATCTGAAGACAGTCCTGGAAGAA
AAACTGGAGAAAGAAGATTTCACCAGGGGAAAACTCATGAGCAGTCTGCACC
TGAAAAGATATTATGGGAGGATTCTGCATTACCTGAAGGCCAAGGAGTACAG
TCACTGTGCCTGGACCATAGTCAGAGTGGAAATCCTAAGGAACTTTTACTTC
ATTAACAGACTTACAGGTTACCTCCGAAAC.

3.  The method according to claim 1 wherein the polypeptide is selected from polypeptides of the formulae:

Met-Thr-Asn-Lys-Cys-Leu-Leu-Gln-Ile-Ala-Leu-Leu-
Leu-Cys-Phe-Ser-Thr-Thr-Ala-Leu-Ser-Met-Ser-Tyr-
Asn-Leu-Leu-Gly-Phe-Leu-Gln-Arg-Ser-Ser-Asn-Phe-
Gln-Cys-Gln-Lys-Leu-Leu-Trp-Gln-Leu-Asn-Gly-Arg-
Leu-Glu-Tyr-Cys-Leu-Lys-Asp-Arg-Met-Asn-Phe-Asp-
Ile-Pro-Glu-Glu-Ile-Lys-Gln-Leu-Gln-Gln-Phe-Gln-
Lys-Glu-Asp-Ala-Ala-Leu-Thr-Ile-Tyr-Glu-Met-Leu-
Gln-Asn-Ile-Phe-Ala-Ile-Phe-Arg-Gln-Asp-Ser-Ser-
Ser-Thr-Gly-Trp-Asn-Glu-Thr-Ile-Val-Glu-Asn-Leu-
Leu-Ala-Asn-Val-Tyr-His-Gln-Ile-Asn-His-Leu-Lys-
Thr-Val-Leu-Glu-Glu-Lys-Leu-Glu-Lys-Glu-Asp-Phe-
Thr-Arg-Gly-Lys-Leu-Met-Ser-Ser-Leu-His-Leu-Lys-
Arg-Tyr-Tyr-Gly-Arg-Ile-Leu-His-Tyr-Leu-Lys-Ala-
Lys-Glu-Tyr-Ser-His-Cys-Ala-Trp-Thr-Ile-Val-Arg-
Val-Glu-Ile-Leu-Arg-Asn-Phe-Tyr-Phe-Ile-Asn-Arg-
Leu-Thr-Gly-Tyr-Leu-Arg-Asn,

and

Met-Ser-Tyr-Asn-Leu-Leu-Gly-Phe-Leu-Gln-Arg-Ser-
Ser-Asn-Phe-Gln-Cys-Gln-Lys-Leu-Leu-Trp-Gln-Leu-
Asn-Gly-Arg-Leu-Glu-Tyr-Cys-Leu-Lys-Asp-Arg-Met-
Asn-Phe-Asp-Ile-Pro-Glu-Glu-Ile-Lys-Gln-Leu-Gln-
Gln-Phe-Gln-Lys-Glu-Asp-Ala-Ala-Leu-Thr-Ile-Tyr-
Glu-Met-Leu-Gln-Asn-Ile-Phe-Ala-Ile-Phe-Arg-Gln-
Asp-Ser-Ser-Ser-Thr-Gly-Trp-Asn-Glu-Thr-Ile-Val-
Glu-Asn-Leu-Leu-Ala-Asn-Val-Tyr-His-Gln-Ile-Asn-
His-Leu-Lys-Thr-Val-Leu-Glu-Glu-Lys-Leu-Glu-Lys-
Glu-Asp-Phe-Thr-Arg-Gly-Lys-Leu-Met-Ser-Ser-Leu-
His-Leu-Lys-Arg-Tyr-Tyr-Gly-Arg-Ile-Leu-His-Tyr-
Leu-Lys-Ala-Lys-Glu-Tyr-Ser-His-Cys-Ala-Trp-Thr-
Ile-Val-Arg-Val-Glu-Ile-Leu-Arg-Asn-Phe-Tyr-Phe-
Ile-Asn-Arg-Leu-Thr-Gly-Tyr-Leu-Arg-Asn.

The relevance of these claims to Avonex® will depend on whether Avonex® administration falls within the ambit of the method claim, which requires:

a)  immunomodulation or
b)  treating a viral condition, a viral disease, cancers or tumors
c)  administering to a patient in need of such treatment
d)  a therapeutically effective amount of a composition comprising:
e)  a recombinant polypeptide
f)  produced by a non-human host transformed by a recombinant DNA molecule comprising a DNA sequence
g)  encoding human ß-interferon or sequence homolog thereof
h)  which code for a polypeptide displaying antiviral activity

While elements e) through h) are apparently encompassed by Avonex®, whether these claims will be useful for precluding generic entry will depend on whether treatment of MS involves immunomodulation or viral disease (since it is self-evidently neither cancer or a tumor).  In this regard the scientific literature is littered with reports linking MS with a variety of viral infections (including Epstein-Barr virus and measles virus), but no definitive linkage has been established.  While MS treatment is likely to involve some type of immunomodulation, Biogen Idec would have the burden of establishing such a mechanism should they sue an ANDA filer for infringement.

The importance of the question about the scope of this patent, and its effects on generic competition over Avonex® can be appreciated from the sales figures for the drug in the second quarter of 2009, which amount to almost $600 million (or $2.4 billion per year), according to an Associated Press article cited in Forbes magazine.

As the Forbes article suggests, the outcome of the Avonex® patent regime has relevance to the current follow-on biologics legislation, at least because of the emotional appeal regarding the length of patent protection.  Understanding the history of this patent defuses any apprehension about the likelihood of similar outcomes going forward, and the Avonex® patent estate can be seen to be nothing more than a historical accident that cannot be replicated.  However, the tendency for dissatisfaction with outcomes like this one to guide political activity, and legislation, should not be underestimated.

ChemBridge Makes Chemical Libraries Available Via Public Access Database

    By Donald Zuhn --

Last month, ChemBridge Corp. announced that it would make ten of its most popular chemical screening libraries available to researchers via the Collaborative Drug Discovery (CDD) Public Access database.  The CDD Public Access database, a collection of public data from leading vendors, researchers, scientific literature, and patent resources, is hosted by Collaborative Drug Discovery, Inc. as a service to the research community.  Collaborative Drug Discovery provides web-based software for organizing preclinical research data to help scientists more effectively advance new drug candidates.  Researchers can register for free read-only access to the CDD public data sets here; read-and-write access, including the ability to archive, mine, and collaborate around private data and to import and export both private and public data is also available.  Compounds from the ten ChemBridge libraries being added to the Public Access database can be obtained from the San Diego-based discovery chemistry company.

The libraries being offered by ChemBridge include its DIVERSet, a 50,000 diverse small molecule dataset covering a broad range of pharmacophore space; and CNS-Set, which contains 56,000 molecules with an increased probability of blood brain barrier penetration.  ChemBridge noted that more than 600,000 molecules would be available through the CDD database.  CDD CEO Barry Bunin stated that both the CDD community for private access and the entire researcher community for public access would benefit from the addition of the ten ChemBridge libraries.  Prior to the addition of the ChemBridge molecules, the CDD database contained over a million compounds.

Cancer Drug Development in The New York Times

    By Kevin E. Noonan --

The fastest-growing part of the biotech/pharma industry is anticancer drugs, according to an article in The New York Times today ("For Profit, Industry Seeks Cancer Drugs").  Written by Andrew Pollack, one of the paper's senior business and technology writers, the article highlights the interplay between scientific interest and business opportunity driving this phenomenon.

The article supports its thesis on the recent rise in anticancer drugs with some telling statistics:  there are "more than twice the number of experimental drugs for heart disease and stroke combined, nearly twice as many as for AIDS and all other infectious diseases combined, and nearly twice as many as for Alzheimer's and all other neurological diseases combined."  This corresponds to 860 anticancer drugs currently in clinical trials.

The scientific reasons for these efforts stem from the nature of cancer as a disease.  Robert Weinberg (at left) from the Whitehead Institute at MIT is quoted in the article as saying "Cancer is not a single disease.  It's really dozens, arguable hundreds of diseases."  Bert Vogelstein (below right) from Johns Hopkins is quoted as saying that a typical tumor may have 50-100 genetic mutations, with any two patients having the same type of cancer having as few as five mutations in common.  Accordingly, there are many approaches and molecular targets for small molecule, immunological, and other avenues for attacking cancer cells in an effort to find a cure.  In addition, the situation is ripe for "personalized medicine," or efforts to tailor the treatment to the tumor based on the unique signature of genetic mutations and the corresponding phenotype of an individual's cancer and the targets for therapeutic intervention expressed by each individual's tumor.

But this very complexity is the main reason why cancer remains so daunting after 40 years of concerted efforts to find a cure.  On the one hand, individual cancers even of the same type or in the same tissue vary dramatically in changes in gene expression, chromosomal abnormalities, and cancer-associated phenotypes, so that treatments that are effective for some cancer patients are completely ineffective for others.  This has caused the "war on cancer" to resemble a "grinding war of the trenches," according to an uncredited quote by a cancer researcher.  And intractable clinical situations provide a correspondingly broader scope of opportunities for new drugs effective against cancer in some portion of the patient population.

However, on the other hand, the efficacy of many anticancer drugs is limited at best.  The article cites the instance of drugs like Erbitux® used as a "last ditch treatment for colorectal cancer" providing on average about 90 days of additional life to patients.  And Taceva®, used for treating pancreatic cancer (a cancer having a 3% 5-year survival rate that hasn't changed in the past 100 years), extends life for pancreatic cancer patients on average only 12 days (the basis for its approval by the FDA for this indication).

Since 1998, when there were twelve anticancer drugs in the world's 200 medicines having the greatest sales, the number of anticancer drugs has almost doubled (to 23), and 20 of the 126 drugs having revenues of $1 billion are anticancer drugs.  Despite these efforts, however, only a handful of new anticancer drugs are approved each year (two in 2008, one so far in 2009).  Nevertheless, the article cites studies by IMS Health, a pharmaceutical market research company, for evidence that "[c]ancer drugs have been the biggest category of drugs in terms of sales worldwide since 2006 and in the U.S. since 2008."

One factor driving anticancer drug development is the revenues that can be generated from their sales, which carry a hefty price tag.  Taceva® treatments cost about $3,500 a month, according to the article, and Erbitux® costs $10,000 per month (with an "extra" cost per patient averaging $50,000, based on the average length of treatment course).  These costs have resulted in ImClone having revenues of $1.6 billion in 2008 for Erbitux®, revenues that the article asserts motivated "Eli Lilly & Co. to outbid Bristol-Myers Squibb to acquire ImClone for $6.5 billion."

While these costs are exorbitantly high, the article notes that "[p]atients are often desperate, and insurers risk outrage by denying payments for a[n anti]cancer drug," even when there is little chance of benefit from the treatment.  "Cancer is such an emotional issue that the free market doesn't work like it does for bicycle wheels and umbrellas," according to Robert Erwin, head of the Marti Nelson Cancer Foundation.  Money will flow to anticancer drugs "[a]s long as the health care system will pay the price."  This situation raises special concerns for the healthcare system as a whole, particularly under the current economic climate, the pressures to reduce drug costs, and the amount of investment required to determine whether an anticancer drug lead compound will come to market.  These circumstances are characterized as "the biggest bubble you've ever seen," according to Dr. Mark Ratain (at right), a University of Chicago oncologist.

The confluence of the exponential increase in genetic information over the past decade and the technical ability to identify genetic polymorphism and outright mutation with different cancer phenotypes presents an unprecedented opportunity for developing new anticancer therapeutics.  Mr. Pollack's article is a reminder that the science is only part of the equation, and that the economic realities of drug development and the healthcare marketplace will also have a role in determining how many, and which, of these drugs will be available for the next generation of cancer patients.

Leg Length Variation in Dogs and its Relevance to Human Mutations

    By Kevin E. Noonan --

One of the benefits of the exponential increase in genetic information consequent to the determination of the genomic DNA sequence of numerous species (the various "genome projects" that include the Human Genome Project) is that it permits sequence comparisons between related species.  One result of this new knowledge has been to verify the similarity of developmental control genes throughout the animal kingdom (where genes like the Hox genes in nematode worms and fruit flies have been identified in humans, for example).  Within species, decoded genetic information, and the ability to associate genetic variation between individuals in a species with specific phenotypes has elucidated the genes that control such phenotypes.  Several examples have been reported for domesticated dogs, where size is related to inheritance of different alleles of the insulin-like growth factor-1 gene (IGF-1), and coat length, curliness, and other features are related to inheritance of the FGR-5, KRT-71, and RPSO-2 genes.  Artificial human selection for breed characteristics has contributed to the ability to productively perform these types of association studies.

Leg length in dogs is another phenotypic feature subject to the whims of human breed selection and characteristic of different breeds.  In this week's edition of the journal Science, a group from the National Institutes of Health reports on the genetic basis of this variation (termed chondrodysplasia), and associates its results with a form of human dwarfish with similarities to canine chondrodysplasia (wherein the growth plates in the long bones of the leg calcify prematurely, producing shortened bones with a curved appearance) (Parker et al., 2009, "An Expressed Fgf4 Retrogene Is Associated with Breed-Defining Chondrodysplasia in Domestic Dogs," Science 325: 995-98).

The report is from Elaine Ostrander's lab at the NIH, joined by researchers at the Department of Ecology and Evolutionary Biology at UCLA, the WALTHAM Centre for Pet Nutrition in the UK, the Division of Cardiovascular Medicine at the Oregon Health and Human Science University, the Baxter Institute for Animal Health and the College of Veterinary Medicine and the Department of Biological Statistics and Computational Biology, Cornell University, and the Comparative Orthopedic Laboratory at the University of Missouri.  The study is particularly noteworthy as it identifies an expressed retrogene for fibroblast growth factor 4 (FGF4); retrogenes, more commonly termed pseudogenes, represent reverse-transcribed messenger RNA (thus lacking introns) that have been re-introduced into the genome.  Until recently, these genes were believed to be transcriptionally-silent relics of ancient retroviral infection and were not expected to be transcribed.  It is now recognized that such retrotransposition can, and has occurred at sites containing transcriptional regulatory sequences, as it appears to have in these dogs, leading to a novel form of gene duplication.

Genome-wide association studies (GWAS) using Affymetrix single nucleotide polymorphism (SNP) microarrays were performed on DNA from 835 dogs comprising 76 distinct breeds.  Using American Kennel Club (AKC) breed standards, 95 dogs from the chondrodysplastic breeds (including Pekinese, Welsh corgi, and dachshund) were compared to a control group of 64 non-chondrodysplastic dog breeds comprising 702 animals.  The strongest association in these studies specific for the chondrodysplastic breeds was found on canine chromosome 18 (CFA18).  This association was confirmed by studies on heterozygosity in this region of canine chromosome 18, which was expected and was found to be suppressed, consistent with human selection for chondrodysplasia as a part of the breed standard for these breeds of dogs.  Upon further sequencing analysis, the region was found to contain a processed retrogene of canine FGF4, comprising all the coding exon sequences as well as the 3' untranslated region (UTR) and a polyadenine tract (as expected from an mRNA retrotransposon), but lacking the 5' regulatory sequences of the native canine FGF4 gene (which also resides on canine chromosome 18, about 30 Mb from the FGF4 retrotransposon insertion site).  This gene was found in 175 dogs from 19 breeds exhibiting the chondrodysplasia phenotype, and the gene was found to be homozygous in all but seven of these dogs.  Fortuitously, the group found a single transition mutation difference (a G --> A change in the retrogene) that permitted expression to be differentiated between the retrogene and the native FGF4 gene.  Gene expression studies showed that the retrogene was expressed in the articulate cartilage of the long bones from chondrodysplastic dogs, "whereas only the G allele was detected in cDNA and genomic DNA samples from non-chondrodysplastic dogs."

Finally, these authors found that the FGF4 retrogene was expressed using gene regulatory sequences in a copy of a long interspersed nuclear element (LINE) repeat residing at the retrogene insertion site.  However, analysis of the expression pattern of neighboring genes in adult dog tissues showed that neither the native FGF4 nor the FGF4 retrogene were expressed in adult tissues.  Developmental regulation of FGF4 is believed to be mediated by sequences in the 3' UTR element of the native gene, and the presence of these sequences in the FGF4 retrogene suggests that it is also properly regulated during development.

All modern domestic dog breeds are believed to have descended from the gray wolf, and the fact that chondrodysplastic breeds have been developed several times independently (i.e., without direct ancestral relationships) suggests that the retrotransposition event, and the presence of the FGF4 retrogene, should be present in populations of the ancestral gray wolf.  Using hapolotype analysis over the 24 kb region of canine chromosome 18 comprising the FGF4 retrogene and its insertion site, "this combination was not found in any of the non-chondrodysplastic dogs we tested but was identified in wolves from Europe and the Middle East, supporting fossil evidence that these populations contributed to the early development of the dog."

The authors put forth their hypothesis of how the FGF4 retrogene is involved in chondrodysplasia in dogs, and its relevance to humans:

We hypothesize that atypical expression of the FGF4 transcript in the chondrocytes causes inappropriate activation of one or more of the fibroblast growth factor receptors such as FGFR3.  An activating mutation in FGFR3 is responsible for >95% of achondrodysplasia cases, the most common form of dwarfism in humans, and 60 to 65% of hypochondrodysplasia cases, a human syndrome that is more similar in appearance to breed-defining chondrodysplasia.  . . .  FGF4 induces the expression of sprouty genes, which interfere with the ubiquitin-mediated degradation of the FGF receptors including FGFR3, and overexpression of the sprouty genes can cause chondrodysplastic phenotypes in both mice and humans.

The greater significance of the study can be summarized in no better words than the authors' own:

We have found a single retrotransposition event producing a conserved, expressed retrogene that has strongly focused the evolutionary direction of morphological change in the dog because at least 12% of American breeds share a common phenotype and the retrogene.  This retrogene is actively segregating within the species, has a coding sequence that is identical to that of the source gene, and to the best of our knowledge is the only example of a functional retrogene found in morphologically distinct populations of a single species that is actively maintained by selection.  If such rare mutational events or "sports," as Charles Darwin referred to them in "The Origin of Species," happen only in the evolution of domestic animals, then these systems may be less informative for understanding the origin of evolutionary novelty in wild species.  However, if the molecular phenomenon we have observed represents a class of genomic change associated with dramatic phenotypic evolution, then such genetic changes might be keystone molecular innovations.

The Genetic Basis of Coat Variation in Dogs

    By Kevin E. Noonan --

The genetic age, characterized by numerous genome projects (not the least of which is the Human Genome Project) has focused the public's attention on the influence of our genes on our characteristics.  This has led to questions about whether there is a "gene" for risk-taking, or homosexuality, or aggressiveness.  Indeed, the pervasiveness of the "gene" question for complex traits has produced something of a backlash, illustrated by Richard Lewontin's books, Not in Our Genes and It Ain't Necessarily So, making the reasonable point that genetic reductionism has its limitations.

But genes are certainly implicated in a number of characteristics and traits, and one of the consequences of studying genomes has been the elucidation of these relationships.  In 2007, a report in Science disclosed that body size in domesticated dogs is associated with a particular single nucleotide polymorphism (SNP) in the insulin-like growth factor I gene (IGF-1) (see "From Toy Poodle to Rottweiler:  Why Is Fido So Small (or Large)?").  Last week, in Science, a group from the National Institutes of Health report on another canine phenotype, coat variation, and the genes that are associated with variations in several coat related traits (Cadieu et al., 2009, "Coat Variation in the Domestic Dog Is Governed by Variants in Three Genes," Science DOI: 10.1126/science.1177808).

The report, from Elaine Ostrander's lab at the NIH and researchers at the Veterinary Genetics Laboratory at the University of California, Davis, the Biology Department at the University of Utah, the Department of Ecology and Evolutionary Biology at UCLA, Cornell University's Department of Biological Statistics and Computational Biology, the Faculte de Medicine in Rennes, France, and Affymetrix, involves genome-wide association studies (GWAS) for three coat variations:  the presence or absence of "furnishings" (eyebrows and mustaches as arise in wire-haired dogs), coat length, and coat curliness.  The study involved more than 1,000 dogs from 80 breeds of domestic dogs, and resulted in the identification of three genes associated with variations in coat.  These genes are RSPO2, encoding R-spondin-2; FGF5, encoding fibroblast growth factor 5; and KRT71, encoding keratin-71.  These genes, and specifically SNPs associated with each of these genes, were found to be associated with the presence or absence of furnishings (RSPO2), length (FGF5), and curliness (KRT71).

Unlike the situation with body size, these three genes form a combinatorial group of genes that can be independently segregated (i.e., they all reside on different chromosomes) and can thus create a number of different coat variations depending on the different variant alleles inherited by particular breeds of dog (since coat characteristics are frequently important components of the breed standard for different dog breeds).  Three datasets were used in these experiments:  the first comprised DNA from 96 dachshunds varying as wire-haired (with furnishings), smooth and long-haired coats; 76 Portuguese waterdogs, varying in curl type; and 903 dogs form 80 breeds representing "a wide variety of [coat] phenotypes."  The initial results of polymorphisms segregating with the different coat traits were validated using a larger panel of at least 661 dogs from 106 breeds that included the appropriate controls.

From the dachshund (at right) studies was identified the association of RSPO2 with furnishings as a locus residing on canine chromosome 13 (CFA13).  As reported in the paper, "[a] 718 Kb homozygous haplotype in all dogs fixed with furnishings was located within both the original 3.4Mb haplotype observed in the dachshund-only GWAS, and a 2.8 Mb haplotype identified in crossover analysis within the dachshund pedigree."  From this chromosomal location the RSPO2 gene was identified:

Fine-mapping allowed us to reduce the homozygous region to 238 Kb spanning only the R-spondin-2 (RSPO2) gene, excluding the 5'UTR and the first exon (Fig. 1D; fig. S1 and table S3).  RSPO2 is an excellent candidate for a hair growth phenotype as it is known to synergize with Wnt to activate β-catenin . . . , and Wnt signaling is required for the establishment of the hair follicles . . . .  Moreover, the Wnt/β-catenin pathway is involved in the development of hair follicle tumors or pilomatricomas . . . , which occur most frequently in breeds that have furnishings . . . .  Recent studies have shown that a mutation in the EDAR gene, also involved in the Wnt pathway, is responsible for a course East-Asian hair type found in humans . . ., with some similarity to canine wirehair.

The polymorphism associated with the furnishings trait in dachshunds and confirmed in 704 dogs of varying phenotype is a 167 bp insertion within the 3' untranslated region (UTR) of the RSPO2 gene; "297/298 dogs with furnishings were either homozygous (268) or heterozygous (29) for the insertion, while all 406 dogs lacking the trait were homozygous [for 3' UTR lacking the insertion]."  The authors also report a functional consequence of the insertion, wherein there is a 3-fold increase in RSPO2 expression in muzzle skin from dogs with furnishings, suggesting that the insertion in the 3' UTR influences mRNA stability.

For the association of FGF5 with hair length, the same type of GWAS were performed, locating a polymorphism on canine chromosome 32 (CFA32) at the FGF5 locus.  Here, the polymorphism affected the coding sequence of the protein, resulting in a Cys --> Phe change at a conserved residue (95) in exon 1 of the FGF5 gene (corresponding to a G --> T transversion mutation).  This association was not unexpected, as prior work had shown that the FGF5 gene was associated with a long-haired or "fluffy" phenotype in Welsh corgis.  Long hair was associated with the TT genotype, consistent with a genetically recessive mode of inheritance.  The T allele was found in 91% of all long-haired dogs tested and in only 3.9% of short-haired dogs (with medium-haired dogs having an intermediate 30% frequency level for this allele).  Curiously, Afghan hounds that have particularly long hair do not have the Cys95Phe mutation.

Finally, for the curly coat variation GWAS were performed with Portuguese water dogs (PWD) (at left, First Dog Bo).  These studies revealed a SNP on canine chromosome 27 (CFA27) located in the keratin 71 (KRT71) genetic locus.  As reported in the paper, "Non-curly haired dogs carried the CC genotype [and] curly coated dogs had the TT phenotype," and all three genotypes (CC, CT and TT) were found in PWDs, a breed that expressed curl hair to varying extents.  This SNP is also located in the coding sequence (in the second exon) of the gene, causing an Arg --> Trp change at residue 151.  These findings were also rationalized by the authors:

Keratins are obvious candidates for hair growth . . . and mutations in KRT71 have been described in curly coated mice . . . .  The mutation described in our study is within the second exon of the gene and may affect either or both of two protein domains; a coiled-coil and a prefoldin domain.  Conceivably, sequence alterations in these domains could affect cellular targeting, receptor binding or proper folding of the protein after translation.

These three mutations were sufficient to account for the coat phenotype in 95% of the dogs tested, a total of 622 dogs representing 108 of the 160 dog breeds recognized by the American Kennel Club.  The Supplemental Materials contain a combinatorial diagram of the different variations at the three loci that give rise to at least 7 different coat types (representing the majority of coat types in modern breeds):

* The TT genotype was never found in this combination, even though it would likely also display a short phenotype.

The authors set forth the following conclusions.  First, the "ancestral state" of all three genes (Cys95 in FGF5, Arg151 in KRT71, and absence of an insertion in the 3' UTR in RSPO2) is found in short-haired dog breeds (as well as grey wolves, the ancestors of all modern dog breeds).  Wire-haired breeds (which all have furnishings) have the insertion in the RSPO2 gene.  Curly wire hair is found in dogs having both the RSPO2 insertion and the KRT71 mutation, while longer-haired dog breeds have the FGF5 mutation.  Dogs carrying both the FGF5 mutation and the RSPO2 insertion have long, soft coats and furnishings, whereas dogs with the FGF5 and KRT71 mutations have long, curly coats.  Finally, dogs bearing all three of the variants have long, curly coats, and furnishings.

Elucidation of this genetic architecture of observable phenotypic traits is possible because of the large number of different dog breeds and the great variability, on one hand, and the consistent stability, on the other hand, of genetic transmission in these breeds.  This study suggests that these analytical methods can (and will) be applied to assess the genetic bases of other traits in dogs, and the extension of these results to homologous phenotypes in other mammals including humans.

Photograph of mixed breed terrier (above) by Chris Barber, from the Wikipedia Commons under the Creative Commons license.

Efficient Delivery of siRNA

    By Kevin E. Noonan --

A research paper in the June 2009 edition of Nature Biotechnology (Eguchi et al., 2009, "Efficient siRNA delivery into primary cells by a peptide transduction domain–dsRNA binding domain fusion protein," Nature Biotechnology 27: 567-71) describes a new system for introducing short interfering RNAs (siRNAs) into mammalian cells that may help this technology become practicable for therapeutic uses.  The promise of RNA interference, mediated by siRNAs, has revolutionized the prospects for modulating gene expression as a way to achieve therapeutic aims in disease treatment.  First identified in worms (Fire et al., 1998, "Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans," Nature 391: 806–11), plants (Hamilton et al., 1999, "A species of small antisense RNA in posttranscriptional gene silencing in plants," Science 286: 950–52) and then in mammalian cells (Elbashir et al., 2001, "Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells," Nature 411: 494–98), siRNAs form the basis for 81 U.S. patents and 2,125 published patent applications.  Their benefits reside principally in their ability to specifically reduce or even enhance (Li, 2008, "Small RNA-Mediated Gene Activation," In: RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity, Caister Academic Press) gene expression in mammalian cells.

However, a serious impediment to further development of siRNA, particularly for therapeutic uses, is that it is difficult to effectively introduce these molecules into mammalian cells.  siRNAs are double-stranded RNA molecules, typically 21 nucleotides in length and having a 2 nucleotide overhang at the 3' end of each strand.  These molecules are thus large (> 14,000 kDa) and highly negatively charged, and cannot cross the cellular plasma membrane.  Methods for introducing siRNAs have included encapsulation in liposome, complexing with cationic lipids, cholesterol, and condensing polymers, or conjugation with antibodies.  While these methods have proven effective with adherent tumor cells in vitro, they have been less effective in the types of cells that are attractive cellular targets in vivo (such as lymphocytes).  One approach, conjugation with cell-penetrating peptides (PTD) like TAT protein from human immunodeficiency virus or poly(Arg), resulted in cytotoxicity associated with limited siRNA delivery into target cells (Meade et al., 2008, "Enhancing the cellular uptake of siRNA duplexes following noncovalent packaging with protein transduction domain peptides," Adv. Drug Deliv. Rev. 60: 530-36), despite the effectiveness of such PTD carriers in other contexts (Gump et al., 2007, TAT transduction: The molecular mechanism and therapeutic prospects," Trends Molec. Med. 13: 443-48).

The Nature Biotechnology paper is from a group at the Howard Hughes Institute at the University of California, San Diego School of Medicine headed by Steven F. Dowdy.  The paper describes complexes of siRNAs with a fusion protein comprising a TAT-derived PTD conjugated to a double-stranded (ds) RNA-binding domain (DRBD) that binds to siRNA with an avidity of KD ~ 10-9.  A canonical example of such a sequence is the following (provided on-line in supplementary materials):

MGRKKRRQRRRGHSGRKKRRQRRRGHIYPYDVPVPDYAGDPGRKKRRQRRRGDP
AGDLSAGFFMEELNTYRQKQGVVLKYQELPNSGPPHDRRFTFQVIIDGREFPEG
EGRSKKEAKNAAAKLAVEILNEKKAAALEHHHHHH

(where single-underlined sequences are PTD sequences from TAT, the underlined and italicized sequence is an HA-tag, and the boldface sequence is the DRBD from RNA-dependent eIF-2 alpha protein kinase (PKR) protein).  The DRBD sequence non-covalently complexes with siRNA in a way that is distinct from the PTD sequences, which remain competent to mediate transit of the complex through the plasma membrane.

Image obtained from Traversa Therapeutics website.

These complexes were tested in several systems, including human H1299 lung adenocarcinoma cells expressing green fluorescent protein (GFP) and red fluorescent protein, which were used to show specific RNA interference of GFP that was obtained at greater levels than with conventional lipofection techniques.  These results were confirmed by single cell flow cytometry that showed that the entirety of the cell population contained siRNA with no alteration of cellular viability (in contrast with significant cytotoxicity associated with siRNA lipofection).  These results were also confirmed with other cell types, including "primary human fibroblasts, keratinocytes, macrophages and melanoma and glioma cells containing integrated GFP reporter genes."  Substantially similar results were obtained with these cells using siRNAs for glyceraldehyde phosphate dehydrogenase (GAPDH), a housekeeping enzyme.  In these experiments, the effects of the GAPDH siRNAs on the cellular transcriptome were assessed, and were shown to be significantly smaller than the effects of these same siRNAs introduced using lipofection.  In particular, the complexed siRNAs did not activate cellular genes associated with immunogenicity, including interferon-regulated genes, in contrast to lipofected siRNAs.  (siRNA introduction using these complexes did not induce interferon or tumor necrosis factor expression in peripheral blood mononuclear cells, an effect observed with siRNA lipofection.)

In another set of experiments, GFP expression was suppressed in Jurkett T cells, primary murine T cells, and human umbilical vein endothelial cells (HUVEC).  The primary T-cell experiments used siRNAs for CD4 and CD8, and showed specific suppression of each gene by its cognate siRNA and not by the non-cognate siRNA.  (The experiments also showed that expression of an unrelated cell surface marker, CD90, was not affected by siRNA introduction.)  HUVEC cells were treated with GAPDH siRNA and showed significantly lower (essentially undetectable) cytotoxicity and greater delivery than when siRNA were introduced into these cells by lipofection.  Finally, human embryonic stem cells were treated with a number of siRNAs that affected proliferation and differentiation.  Specifically, introduction of complexes of siRNAs for OCT4 caused cell cycle exit and differentiation.

In the most dramatic series of experiments, transgenic mice expressing luciferase in nasal and tracheal passages were treated with luciferase siRNAs complexed with PTD-DRBD.  These experiments showed that luciferase expression could be drastically reduced by these siRNA/PTD-DRBD complexes in vivo.

These results also provide the basis for patent applications in the U.S. and abroad.  The U.S. application is Serial No. 12/278,739, filed August 7, 2008.  Entitled "Transducible Delivery of siRNA by dsRNA Binding Domain Fusions to PTD/CPPS," the application published on April 9, 2009 as U.S. Patent Application Publication No. 2009/0093026, naming Steven F. Dowdy, Jehangir S. Wadia, Bryan Meade, and Akiko Eguchi as inventors.  This application is a U.S. national phase application of International Application No. PCT/US07/03641, filed February 9, 2007 and in turn claiming priority to two U.S. provisional applications (USSN 60/772,787, filed February 10, 2006, and USSN 60/775,638, filed February 21, 2006).  In addition to the experiments disclosed in the research paper, the application also shows EGFR-specific siRNA introduction using PTD-DRBD complexes into EGFR-expressing glioblastoma in mice.  The application also discloses alternative embodiments of PTD and DRBD sequences that can be used in the complexes.

The significance of these results is expressed by the authors as follows:

siRNA delivery has become the rate-limiting barrier to efficient cell culture and preclinical and clinical usage of siRNA therapeutics . . . .  Although current siRNA delivery approaches have merit, they generally do not target the entire population or even a high percentage of cells, especially primary cells, and often result in some degree of cytotoxicity and alternations in cell biology.  In contrast, the PTD-DRBD siRNA delivery approach described here fulfills many of the criteria for and efficient siRNA delivery system for primary cells.  . . .  Because DRBDs bind to dsRNAs (siRNAs) independent of sequence composition, PTD-DRBD could in theory deliver any siRNA into cells.  Lastly, the intranasal knockdown of luciferase demonstrates the in vivo potential of PTD-DRBD-mediated siRNA delivery.

The application is assigned to the Regents of the University of California, but Professor Dowdy is reported to have a start-up biotechnology company, Traversa Therapeutics of La Jolla, CA, and a researcher from Ambion is named on the research paper (but not the patent application).  A serious commitment to commercial development is also evidenced by applicants' recently changing the application status to large entity.

NIH Releases New Stem Cell Rules

    By Kevin E. Noonan --

Yesterday, the National Institutes of Health released guidelines governing requirements (and limitations) for federal funding of research on human embryonic stem cells.  These rules supersede rules promulgated during the Bush administration that so severely constrained the number of funding-eligible human stem cell lines as to effectively prohibit use of federal funds for this research.  These Guidelines were promulgated by Acting Director Raynard S. Kington, and become effective today, July 7, 2009.  The new Guidelines are expected to make up to 700 existing human embryonic stem cell lines eligible for federal funding, a ten-fold increase over the 69 hESC lines approved under the Bush administration (many of which have been acknowledged to be inappropriate for embryonic stem cell research).

The Guidelines were developed by the Institutes in response to Executive Order 13505, entitled "Removing Barriers to Responsible Scientific Research Involving Human Stem Cells" issued March 9, 2009.  Fulfilling a promise President Obama made during his campaign, the Order was intended to permit the Institutes to "support and conduct responsible, scientifically worthy human stem cell research, including human embryonic stem cell (hESC) research, to the extent permitted by law."  The new Guidelines, relating to both intramural and extramural research, "establish policy and procedures under which the NIH will fund such research, and helps ensure that NIH-funded research in this area is ethically responsible, scientifically worthy, and conducted in accordance with applicable law."

The Guidelines are expressly based on the principles that:

1.  Responsible research with hESCs has the potential to improve our understanding of human health and illness and discover new ways to prevent and/or treat illness.

2.  Individuals donating embryos for research purposes should do so freely, with voluntary and informed consent.

Human embryonic stem cells are defined as "cells that are derived from the inner cell mass of blastocyst stage human embryos, are capable of dividing without differentiating for a prolonged period in culture, and are known to develop into cells and tissues of the three primary germ layers," making the distinction that "[a]lthough hESCs are derived from embryos, such stem cells are not themselves human embryos."  The Guidelines establish a new NIH stem cell registry, and stem cells will be eligible for funding if they are listed on the registry or if they comply with Section IIA of the Guidelines.  Cells will be eligible if they are derived from human embryos:

1.  that were created using in vitro fertilization for reproductive purposes and were no longer needed for this purpose;

2.  that were donated by individuals who sought reproductive treatment (hereafter referred to as "donor(s)") and who gave voluntary written consent for the human embryos to be used for research purposes; and

3.  for which all of the following can be assured and documentation provided, such as consent forms, written policies, or other documentation, provided:

a.  All options available in the health care facility where treatment was sought pertaining to the embryos no longer needed for reproductive purposes were explained to the individual(s) who sought reproductive treatment.

b.  No payments, cash or in kind, were offered for the donated embryos.

c.  Policies and/or procedures were in place at the health care facility where the embryos were donated that neither consenting nor refusing to donate embryos for research would affect the quality of care provided to potential donor(s).

d.  There was a clear separation between the prospective donor(s)'s decision to create human embryos for reproductive purposes and the prospective donor(s)'s decision to donate human embryos for research purposes.  Specifically:

i.  Decisions related to the creation of human embryos for reproductive purposes should have been made free from the influence of researchers proposing to derive or utilize hESCs in research.  The attending physician responsible for reproductive clinical care and the researcher deriving and/or proposing to utilize hESCs should not have been the same person unless separation was not practicable.

ii.  At the time of donation, consent for that donation should have been obtained from the individual(s) who had sought reproductive treatment.  That is, even if potential donor(s) had given prior indication of their intent to donate to research any embryos that remained after reproductive treatment, consent for the donation for research purposes should have been given at the time of the donation.

iii.  Donor(s) should have been informed that they retained the right to withdraw consent for the donation of the embryo until the embryos were actually used to derive embryonic stem cells or until information which could link the identity of the donor(s) with the embryo was no longer retained, if applicable.

e.  During the consent process, the donor(s) were informed of the following:

i.  that the embryos would be used to derive hESCs for research;

ii.  what would happen to the embryos in the derivation of hESCs for research;

iii.  that hESCs derived from the embryos might be kept for many years;

iv.  that the donation was made without any restriction or direction regarding the individual(s) who may receive medical benefit from the use of the hESCs, such as who may be the recipients of cell transplants;

v.  that the research was not intended to provide direct medical benefit to the donor(s);

vi.  that the results of research using the hESCs may have commercial potential, and that the donor(s) would not receive financial or any other benefits from any such commercial development;

vii.  whether information that could identify the donor(s) would be available to researchers.

Alternatively (Section IIB), for stem cell lines established prior to promulgation of these Guidelines, eligibility can be established by submitting evidence to a newly-constituted Working Group of the Advisory Committee to the Director showing that "the hESCs were derived from human embryos:  1) that were created using in vitro fertilization for reproductive purposes and were no longer needed for this purpose; and 2) that were donated by donor(s) who gave voluntary written consent for the human embryos to be used for research purposes."

The Guidelines expressly prohibit funding of research on human embryonic stem cells or pluripotent cells introduced into a non-human primate blastocyst or animal breeding experiments involving introduction of human stem cells into non-human primate blastocysts.

The Notice reports that the Institutes received around 49,000 comments in response to the request for public comment published on April 23, 2009 in the Federal Register (74 Fed. Reg. 18578).  These comments came from "patient advocacy groups, scientists and scientific societies, academic institutions, medical organizations, religious organizations, and private citizens," as well as members of Congress.  The Notice contains a synopsis of these comments, which are included in groups identified as title, terminology and background, financial gain, IRB review, donation and informed consent, and monitoring and enforcement actions, among others.  The Notice describes how the draft guidelines were adapted or modified in response to these comments, or the Institutes distinguished or disputed the assertions in the comments.  Of note is the Institutes' assertions that it expects "that stem cell research materials developed with NIH funds, as well as associated intellectual property and data, will be distributed in accordance with the NIH's existing policies and guidance, including ''Sharing Biomedical Research Resources, Principles and Guidelines for Recipients of NIH Grants and Contracts' and 'Best Practices for the Licensing of Genomic Inventions'" (see NIH Policies & Reports page).  In addition, the Institutes will review de novo the circumstances surrounding development of existing stem cell lines rather than grandfathering these cells, applying ethical principles embodied inter alia in the Guidelines and 45 C.F.R. Part 46 Subpart A (Protection of Human Subjects).

The comments section also addresses the potential limitations on federal funding imposed by the Dickey amendment, wherein "an embryo is defined by Section 509, Omnibus Appropriations Act, 2009, Pub. L. 111-8, 3/11/09 . . . as any organism not protected as a human subject under 45 C.F.R. Part 46 that is derived by fertilization, parthenogenesis, cloning or any other means from one or more human gametes or human diploid cells."  The Guidelines state that:

[s]ince 1999, the Department of Health and Human Services (HHS) has consistently interpreted this provision as not applicable to research using hESCs, because hESCs are not embryos as defined by Section 509.  This long-standing interpretation has been left unchanged by Congress, which has annually reenacted the Dickey Amendment with full knowledge that HHS has been funding hESC research since 2001.  These guidelines therefore recognize the distinction, accepted by Congress, between the derivation of stem cells from an embryo that results in the embryo's destruction, for which federal funding is prohibited, and research involving hESCs that does not involve an embryo nor result in an embryo's destruction, for which federal funding is permitted.

While nicely expressing the distinction, it remains to be seen whether Congress acts to refine the Institutes' understanding of these restrictions, in light of the expansion in the scope of human embryonic stem cells intended by these Guidelines to become eligible for federal funding.

The Genetics of Complex Behaviors: It Really Isn't That Simple

    By Kevin E. Noonan --

Early last week, the Journal of the American Medical Association published a study ("Interaction Between the Serotonin Transporter Gene (5-HTTLPR), Stressful Life Events, and Risk of Depression") by Neil Risch at the University of California, San Francisco and colleagues at the National Institutes of Mental Health, Johns Hopkins University, Yale University School of Medicine, the Rockefeller University, the University of Pittsburgh School of Medicine, and Virginia Commonwealth University that showed no statistically-significant link between depression and the short HTT allele.  The study provided a statistical meta-analysis of data accumulated for 14,250 participants from 14 separate studies from the medical literature and a second meta-analysis of 10,943 participants from 10 of these studies.  These results were contrary to the results published by Avshalom Caspi and collaborators (including Terrie E. Moffitt (at right), Knut Schmidt Nielsen Professor, Departments of Psychology and Neuroscience, Psychiatry and Behavioral Sciences, and Institute for Genome Sciences and Policy, Duke University) that individuals bearing at least one copy of a specific genetic polymorphism in a serotonin transporter gene were more susceptible to depression as a consequence of environmental (life) stressors (see Caspi et al., 2003, "Influence of Life Stress on Depression:  Moderation by a Polymorphism in the 5-HTT Gene," Science 301: 386-89).

Dr. Moffitt has graciously provided us with three points in rebuttal to the conclusions of the Risch study, set forth in her own words:

1.    The JAMA article ignores the wider body of scientific evidence.  In the past 6 years, extensive research in experimental neuroscience using both animals and humans has validated the original report by showing that 5-HTTLPR short allele-carriers are excessively vulnerable to stress.  Experimental studies that expose human participants to stressors in the laboratory show that individuals having the 5-HTTLPR short genotype have greater stress responses on measures of cognitive reactivity (e.g., Beevers et al., 2007, J. Abnorm. Psychol. 116: 208-12; Fox et al., 2009, Proc. Biol. Sci. 276: 1747-51), hormonal  reactivity (e.g., Chen et al., 2009, Psychoneuroendocrinology 34: 681-86; Gotlib et al., 2008, Biol. Psychiatry. 63: 847-51), physiological reactivity (e.g., Lonsdorf et al., 2009, Psychol. Sci. 20: 198-206) and reactivity in the brain's emotion-circuitry (e.g., Hariri et al., 2006, Arch. Gen. Psych. 62: 146-52; Canli et al. 2006, Proc. Natl. Acad. Sci. U.S.A. 103: 16033-38).  This vulnerability of 5-HTTLPR S carriers has also been confirmed in animal research (e.g., Carola et al., 2008, Biol. Psychiatry. 63: 840-46; Barr et al., 2004, Biol. Psych. 55: 733-38; Kalin et al., 2008, Mol. Psychiatry. 13: 1021-27, online at DOI: 10.1038/mp.2008.37; Watson et al., 2009, PLoS One, published online January 14, 2009).  Further validation comes from studies which have shown that 5-HTTLPR Short allele carriers are vulnerable not only to depression, but also to other mental-health problems caused by stress, including PTSD and anxiety (e.g., Gunthert et al., 2007, Psychosom. Med. 69: 762-68; Kilpatrick et al., 2007, Am. J. Psychiatry. 164: 1693-99).

2.    The selection of studies for meta-analysis clearly fails to represent the pool of papers in the literature.  4 out of 17 positive replications were included (24%) but 6 out of 9 published negative
studies (67%), a bias that violates a basic requirement of the meta-analysis method to examine a representative sample of the existing literature.  Further, the article opted not to analyze several well-designed studies of individuals exposed to stress.  For example, studies of children who are victims of abuse (e.g., Cicchetti et al., 2007, Dev. Psychopathol. 19: 1161-80; Kaufman et al., 2004, Proc. Natl. Acad. Sci. U.S.A. 101: 17316-21) and patients suffering hip fractures, strokes and coronary heart disease (Kohen et al., 2008, Arch. Gen. Psychiatry. 65: 1296-302; Lenze et al., 2008, Amer. J. Geriatric Psych. 13: 428-32; Otte et al., 2007, Am. J. Psychiatry. 164: 1379-84) have reported positive findings for this "GxE" hypothesis.  Several other positive replications from studies with very strong research designs were omitted from the meta-analysis as well (Kendler et al., 2005, Arch. Gen. Psych. 62: 529-35; Drachmann-Bukh et al., 2009, J. Affect. Disord. 2009 Mar. 30 (e-publ. ahead of print at doi:10.1016/j.jad.2009.02.023); Lazary et al., 2008, Biol. Psychiatry. 64: 498-504).

3.    Within the smaller subset of studies in the meta-analysis, there is important heterogeneity.  The article says this heterogeneity was not statistically significant.  However, we have learned that the test fell just short of statistical significance.  One obvious characteristic that varies widely across studies in the meta-analysis is measurement quality.  As one example, meta-analysis gives more mathematical weight to studies with the largest samples.  But in this case the big studies had to collect their data through telephone calls or self-complete postal questionnaires, which are known to be weak methods of measuring life events and depression.  Not surprisingly, these big studies with weak measures tended not to find positive results, tilting the meta-analysis toward a null finding.  In the existing literature of tests of this GxE hypothesis, 13 studies have replicated the finding, using measures collected in face-to-face clinical assessments, and 10 studies failed to replicate the finding, using measures collected via phone or postal questionnaires.  This clear methodological pattern was ignored in the meta-analysis.  This is one example of heterogeneity could have been followed up in a meta-analysis, there may be others.

Dr. Moffitt concluded her response to Dr. Risch's work by noting that "[w]hat is needed is not less research into gene-environment interaction, as Risch et al. recommend, but more research of better quality, and a more thorough and thoughtful evaluation of it."

Dr. Moffitt has extensive experience in studying the biological basis of complex behaviors, and in addition to her Duke University appointment is also Professor of Social Behaviour and Development, Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, London and Associate Director, Dunedin Multidisciplinary Health and Development Research Unit, Dunedin School of Medicine, Dunedin, New Zealand.

This controversy illustrates one of the many pitfalls frequently faced by academic inventors motivated by the dual (and occasionally conflicting) needs of disseminating the results of their studies as rapidly as possible and protecting the intellectual property aspects of their work to maximize the likelihood that it can be commercialized (and not merely expropriated by others based on its disclosure in the academic literature).  As a result, often the research is not as developed as it might be if it were developed by a commercial concern initially.  This situation presents particular challenges to university technology transfer offices and their clients, university faculty and university administrations.  It is an imperfect system, which motivates some to say there is a flaw in the basic premise of promoting university patenting under the Bayh-Dole regime.  However, the alternative (not protecting university-generated inventions) is indeed worse, since then the public stands no chance of seeing the fruits of these labors helping to finance the next generation of technologies.

The Uncertain Future of Genetic Diagnosis of Human Behavior

    By Kevin E. Noonan --

Sickle cell anemia was the first known human disease associated with a genetic polymorphism (an A→T single nucleotide polymorphism, or SNP), resulting in the substitution of a valine residue (encoded by a GTG codon) for a glutamic acid residue (encoded by a GAG codon) in the beta chain of human hemoglobin.  The work, by Linus Pauling and colleagues at Cal Tech was published in the November 25, 1949 issue of the journal Science, about three and a half years before Watson and Crick deciphered the structure of DNA.  Today, sixty years of molecular biology, including the Human Genome Project, has produced the promise of identifying genetic markers for many human diseases, to be used for molecular diagnosis and particularized treatment going under the generic term of "personalized medicine."

Although monogenic traits have proven amenable to currently-available diagnostic methods (for diseases including cystic fibrosis, Tay-Sachs disease, Huntington's disease, and Duchenne muscular dystrophy), complex traits, particularly psychiatric and other behavioral disorders have proven more resistant to these methodologies.  Thus, it was a particularly exciting development six years ago when Dr. Avshalom Caspi and his colleagues reported in a landmark study in the journal Science that individuals bearing at least one copy of a specific genetic polymorphism were more susceptible to depression as a consequence of environmental (life) stressors (see Caspi et al., 2003, "Influence of Life Stress on Depression:  Moderation by a Polymorphism in the 5-HTT Gene," Science 301: 386-89).  The polymorphism occurs in the promoter region of the serotonin transporter gene (5-HTT), and the alleles are distinguished by the presence of 14 (the "short" allele) or 16 (the "long" allele) copies of a 20-23 basepair repeat motif.  Individuals with the homozygous long/long ("l/l") genotype were shown to express 1.4-1.7 fold greater amounts of the transporter gene mRNA, to have 2-fold higher levels of labeled serotonin uptake and to bind 30-40% more serotonin than the cells of individuals with the heterozygous short/long ("s/l") or homozygous short/short ("s/s") genotypes.

This study was performed on a cohort of 847 non-Maori children in Dunedin, New Zealand, who were followed from ages 3 to 26 (specifically, at ages 3, 5, 7, 9, 11, 13, 15, 18, 21 and 26).  Stressors examined in the study included problems in employment, finances, housing, health, and relationships, as well as childhood maltreatment.  In the study, males experienced more stressors than females; overall, 30% of study participants experienced no stressful life events, 25% experienced one, 20% experienced two, 11% experienced three, and 15% experienced four or more life stressful events.  These results themselves did not have any statistically-significant relationship to the 5-HTT allele genotypes.  17% of study participants were classified as having experienced depression, a level comparable to the results seen in the general population in the U.S.  When these results were compared with the genotypes of the study participants, a statistically-significant correlation (P = 0.02) was found between depression and the presence of the "s" allele, i.e., individuals bearing at least one "s" allele ("s/l" and "s/s" individuals) were more likely to be depressed as a consequence of equivalent numbers of life stressful events.  The authors were careful to emphasize that this correlation did not show a conclusive association between the "s" allele and a predisposition to depression, however.

This study was widely hailed as providing new insight into predicting depression, at least in young adulthood.  The study garnered accolades such as "absolutely spectacular" work, and Steven Pinker opined that the study provided "successful documentation of the elusive phenomena known as 'gene-environment interactions,' [which] are like the weather, according to Mark Twain:  Everyone talks about them, nobody does anything about them -- until now."  The study results also seemed consistent with what was known about neurobiology, in that the serotonin transporter is the target for antidepressants like Prozac®, and was also consistent with other research results that showed more intense brain reactions to fearful stimuli in individuals bearing the "s" allele.

However, the correlation between stress-induced depression and the short promoter of the human HTT gene has not held up.  As widely reported on Tuesday, Neil Risch at the University of California, San Francisco and colleagues at the National Institutes of Mental Health, Johns Hopkins University, Yale University School of Medicine, the Rockefeller University, the University of Pittsburgh School of Medicine, and Virginia Commonwealth University showed no statistically-significant link between depression and the short HTT allele.  The study, published yesterday in the Journal of the American Medical Association (see "Interaction Between the Serotonin Transporter Gene (5-HTTLPR), Stressful Life Events, and Risk of Depression") was a meta-analysis of data accumulated for 14,250 participants of 14 separate studies from the medical literature and a second meta-analysis of 10,943 participants from 10 of these studies.  These statistical analyses by Risch and his colleagues failed to show any increased susceptibility to depression as a result of environmental stressors as reported by the Caspi study for individuals bearing the short promoter variant of the HTT gene in either homozygous (s/s) or heterozygous (s/l) genotypes.  Although these studies are not without their own acknowledged shortcomings, they cast doubt on the validity of the correlations reported six years ago from a much smaller sample size (albeit the earlier study presented more in-depth assessments on the existence, frequency, and significance of the environmental stressors).

These results could not have come at a worse time for Dr. Caspi and his collaborators.  These scientists filed a patent application on their predictive method, published as U.S. Publication No. 2005/0037405.  On May 19th, the U.S. Patent and Trademark Office mailed a Notice of Allowance to the inventors, for claims including the following:

1.    A method for assessing predisposition to depression in a human subject who has experiences a stressful life event, the method comprising the steps of
    determining whether the subject carries one or more copies of a short promoter allele of a 5-HTT gene; and
    concluding that the subject is predisposed to depression if the subject carries the short promoter allele.

At a minimum, the Risch study may have raised a Rule 56 obligation on the inventors, their counsel, and anyone else involved in prosecuting the application that could forestall allowance of this claim.  The results also may raise validity issues of operability and enablement.

There has been justifiable skepticism by some about the capacity for genetic analyses to predict complex behaviors (see, for example, Hamer, 2002, "Rethinking Behavior Genetics," Science 298: 71-72).  These most recent results illustrate once again how difficult it will be to translate the promise of personalized medicine into clinically-validated diagnostic tests, particularly for complex or multigenic traits and diseases.  Of course, these problems make patent protection even more important to support investment in the uncertain promise of personalized medicine.

GSK's Sherry Knowles Responds to Post on BIO Session

    By Donald Zuhn --

On Wednesday, we posted a report on a BIO Super Session entitled "A Model Patent Office for the Future -- Promoting and Protecting Investments in Innovation" (see "Docs at BIO: Panel Offers Suggestions for Fixing the USPTO").  At that session, a panel consisting of Sherry Knowles (at right), Vice President of Corporate Intellectual Property at GlaxoSmithKline Biopharmaceuticals, Inc.; Q. Todd Dickinson, Executive Director for the American Intellectual Property Law Association (AIPLA); John Duffy, Professor of Law at George Washington University Law School; and Jeff Kushan, a Partner at Sidley Austin LLP, provided a long range view of what the model patent office of the future can and should look like to drive innovation and economic growth, and promote investment in IP-intensive industries.  Today, Ms. Knowles sent us a message to let us know that she believed the report did not accurately represent the gist of her comments at the BIO session.  The text of Ms. Knowles' message is provided below:

Don:

Your article inaccurately represented the gist of my comments at BIO.  To be accurate, my position is that the success of the pharmaceutical and biotech industries are directly linked to the success of the US Patent Office.  I said it is not just up to Congress, the courts or the new Commissioner to fix the Patent Office issues, it is up to all of us as stakeholders to play an active role to make sure the PTO's problems are solved.  I concluded the session by saying we should all put the past frustrations and rhetoric behind us and fully support the new PTO Commissioner with a new spirit of cooperation.

Gene Quinn's articles in IPwatchdog.com on the new attitude of Dep. Commissioner Focarino are refreshing and show the PTO is trying to go in the right direction.  We want to work closely with the new administration to accomplish these goals.

The comment about the potential "train wreck" referred to the statistics showing a decreasing allowance rate and decreasing filing rate (which leads to a smaller PTO budget) in combination with an increasing backlog of applications.  This is a matter all of us must proactively propose solutions for.

I am of the opinion that the PTO fee sheet can be used to incentivize behavior and is a better means to regulate filings, submissions and claim presentation than absolute restrictions.  A structure can be implemented that provides relief for small entities and patent applicants for whom this presents a hardship.

I would appreciate it if you post this response.

Sherry Knowles

Our goal in reporting on the BIO session was to provide a fair summary of all of the panelists' comments for Patent Docs readers unable to attend the session.  To the extent that the report did not accomplish this goal, the publication of Ms. Knowles' e-mail should help clarify her intended message.  In addition, as regular readers are well aware, we have previously expressed the opinion that the patent community owes a debt of gratitude to GSK for leading the challenge (along with Dr. Tafas) against the continuation and claims rules (and, as a result, for perhaps playing a role in the USPTO's decision to put the IDS, Markush, and appeals rules packages on hold).  Thus, in publishing our prior report, there was no intent to diminish these important efforts (see links below).

• "Federal Circuit Hears Oral Argument on Tafas Appeal," December 8, 2008
• "GSK Files Brief in Tafas v. Dudas Appeal," September 25, 2008
• "USPTO Posts Comments on New Rules for Alternative Claiming," April 23, 2008
• "No April Fool's Joke -- Tafas and GSK Win on Summary Judgment," April 1, 2008
• "Managing Intellectual Property Releases MIP 50," July 28, 2008
• "U.S. Senate Mailbox Filling with Letters against Passage of Patent 'Reform' Bill," January 18, 2008
• "Enjoined New Rules and Patent Reform Finally Appearing on Biotech Industry's Radar," December 20, 2007
• "Tafas v. Dudas; SmithKline Beecham Corp. v. Dudas (E.D. Va. 2007)," October 31, 2007
• "AIPLA Supports GSK's Lawsuit Against the Patent Office's New Rules," October 25, 2007
• "GSK Brings Out the Big Guns Opposing the New Continuation and Claims Rules," October 24, 2007
• "Hooray! - (Finally) the Big Dogs Have Joined the Hunt," October 11, 2007

Docs at BIO: Lilly Counsel Discusses Patent Issues Regarding Personalized Medicine

    By Donald Zuhn --

In a Breakout Session entitled "The Emerging Promise of Personalized Medicine," a panel consisting of Cindy Collins, Group Vice President at Beckman Coulter, Inc.; Brian Barrett, Associate General Patent Counsel at Eli Lilly & Company; Dr. Courtney Harper, Associate Director for Toxicology at the Office of In Vitro Diagnostic Device Evaluation and Safety of the Food and Drug Administration; and Sheldon Bradshaw, a partner and regulatory attorney at Hunton & Williams, LLP, addressed the business, scientific, and legal challenges for the commercialization of personalized medicine on Tuesday at BIO 2009.  Mr. Barrett's presentation would likely have been of most interest to Patent Docs readers, as his focus at Lilly is on patent procurement.  In Mr. Barrett's portion of the presentation, entitled "Unpredictable Patent Protection and Inadequate Data Protection:  Key Obstacles to Developing Personalized Medicine," he listed a number of patent obstacles for personalized medicine and then briefly touched on data exclusivity with regard to proposed follow-on biologics legislation.

With regard to patent-related obstacles for personalized medicine, Mr. Barrett discussed the recent Association for Molecular Pathology v. U.S. Patent and Trademark Office gene patenting case, and noted that the Supreme Court has not had an opportunity to address the patentability of "isolated DNA."  He also noted that the landmark Diamond v. Chakrabarty decision involved human intervention rather than isolation.  Mr. Barrett also discussed the impact of Laboratory Corp. v. Metabolite Laboratories, Inc. (LabCorp), In re Bilski, and the pending appeal in Prometheus v. Mayo on medical diagnostics.  He next addressed the possible impact of the Supreme Court's decision in KSR International Co. v. Teleflex Inc. on optimization (i.e., tailoring) of therapeutics to individual patients, and then touched on a number of decisions impacting nucleic acid patentability, including In re Fisher, In re Kubin, and Ariad v. Eli Lilly & Co.  Patent Docs readers are no doubt quite familar with the above cases.  Mr. Barrett concluded the patent obstacles portion of his talk by briefly discussing anticipation by experimental use, inherent anticipation, inequitable conduct, compliance with the best mode requirement, inducing infringement, and injunctions in view of eBay Inc. v. MercExchange, L.L.C.

On the topic of data exclusivity, Mr. Barrett highlighted the exclusivity periods in the two pending House follow-on biologics bills (the Waxman and Eshoo bills), and noted that because data protection and patent protection were not additive, the Waxman bill would provide insufficient protection for innovator drug companies.  He stated that innovators, who learn a lot about a therapeutic "deep into" Phase II clinical trials, would be well past the 5.5 years of data protection afforded under the Waxman bill by the time such knowledge had been gathered.  When asked during the question and answer portion of the session whether there was a compromise level of data exclusivity that innovators could live with (i.e., something lower than the maximum 14.5 years provided under the Eshoo bill), Mr. Barrett responded that the Eshoo period "was the compromise" since the data protection period is "currently unlimited" (in the absence of a follow-on biologics regulatory pathway).  Perhaps not surprisingly, Mr. Barrett's response was identical to the one BIO President and CEO Jim Greenwood gave Patent Docs at the BIO IPCC conference in March.

For additional information regarding many of the obstacles discussed in Mr. Barrett's presentation, please see:
• "Association for Molecular Pathology v. U.S. Patent and Trademark Office," May 17, 2009
• "Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co. (Fed. Cir. 2009)," April 6, 2009
• "In re Kubin (Fed. Cir. 2009)," April 5, 2009
• "Second Follow-on Biologics Bill Is Introduced in House," March 18, 2009
• "Waxman Introduces Follow-on Biologics Bill," March 11, 2009
• "Applying In re Bilski to Diagnostic Method Claims," February 5, 2009
• "Personalized Medicine: A Patent Office Perspective," December 11, 2008
• "KSR Int'l Co. v. Teleflex Inc. (2007)," April 30, 2007
• "In re Fisher (Fed. Cir. 2005)," November 9, 2006

Meet the Docs at BIO 2009

The Biotechnology Industry Organization (BIO) is holding its annual BIO International Convention this week at the Georgia World Congress Center in Atlanta.  Founded in 1993, BIO is a nonprofit association seeking supportive biotechnology policies on behalf of more than 1,200 biotechnology companies, state and international affiliates, and related organizations, as well as providing business development services for many emerging biotech companies.

As part of the Convention, more than 2,200 biotech companies, organizations, and institutions are expected to participate in the BIO Exhibition.  Patent Docs Donald Zuhn, Kevin Noonan, Sherri Oslick, Mark Chael, and Andrew Williams will also be attending BIO as part of the MBHB contingent.  Patent Docs readers who may be attending BIO this week are encouraged to stop by booth #4343 to meet the Docs and talk a little biotech patent law.

IPO Releases List of Top 300 Patent Holders for 2008 - Updated

"Biotech/Pharma" Top 43

    By Donald Zuhn --

The Intellectual Property Owners Association (IPO) released its 26th annual list of the top 300 organizations receiving U.S. patents.  Patent Docs Readers may recall that the U.S. Patent & Trademark Office stopped releasing its annual list of top patent recipients in 2006 in order to "discourag[e] any perception that we believe more is better."

The IPO stated that while it does not intend for the report to "encourage or discourage patenting," it would continue to publish its annual list of top recipients because "the number of patents granted is one of the few objective measures of the patent system as a whole and the patenting activities of individual industries and companies."  The IPO compiled its list by counting the number of utility patents granted during 2008 on which an organization or its subsidiary was listed as the owner on the face of the patent.  However, the IPO attributed patents that were granted to two or more organizations jointly to the organization listed first on the patent.  The IPO noted that 157,772 patents were issued in 2008, which was an increase from the 153,283 patents that issued in 2007 (but still lower than the 173,771 patents that issued in 2006).  The top fifteen companies on the IPO Top 300 are listed below.

 

UPDATE:  The IPO has revised its list to indicate that Hitachi finished 3rd with 2,197 patents in 2008.

As with the 2007 and 2008 rankings, we used the IPO's list of top patent holders to compile a list of the top "biotech and pharma" companies and organizations receiving U.S. patents in 2008.  While our list of companies and organizations numbered 51 for 2006 and 47 for 2007, we were only able to compile a list of 43 biotech and pharma companies and organizations for 2008.  Each organization's IPO top 300 ranking for 2008 is indicated in the "'08 IPO Rank" column; the IPO top 300 ranking for 2007 (if available) is indicated in the "'07 IPO Rank" column.  Please note that some of the companies and organizations listed below may be involved in non-biotech or non-pharma work, and therefore, that a portion of the patents granted to these companies may be directed to other than biotech and pharma-related inventions.  In addition, our list is a little inclusive in that we included medical device companies.

UPDATE:  The IPO has revised its list to indicate that Dow Chemical Co. finished 206th with 82 patents in 2008.  In our Biotech/Pharma Top 47 for 2007, Dow Chemical Co. finished 33rd (and 229th overall) with 76 patents.

Interestingly, the so-called Coalition for Patent Fairness, which has lobbied for substantial patent "reforms" that would arguably weaken patent rights in the U.S., placed a significant number of its corporate partners on the IPO's top 300 list.  Of the fourteen corporate partners listed on the group's website, twelve made the top 300 (only Autodesk and Palm did not), and five of these companies placed in the top 25.

For additional information regarding this topic, please see:
• "IPO Releases List of Top 300 Patent Holders," May 22, 2008
• "IPO Posts List of Top 300 Patent Holders," April 20, 2007

Author of Nature Article Provides Rebuttal; Patent Docs Provides Surrebuttal

On Wednesday, we reported on an article, entitled "The dangers of diagnostic monopolies," that appeared in the March 26th edition of Nature (see "Genetic Diagnostic Testing: The 'Anti-Commons' Revisited?").  Today, we received an e-mail from one of the authors of the article, Robert Cook-Deegan (at right), providing some additional comments regarding the article:

This is a very thoughtful take on our article.  I disagree with much of it, but not for the reasons you might predict.  I think if you read through the case studies that underlie this summary commentary in today's Nature, you'll find the reason for specifying the "problems" as we did.

My main point here:  the problems we specify are identified as such by the companies, health professionals who order the tests, and those who get tested -- everyone says they want to avoid them, and the companies say their informal policies are to, for example, permit unfettered basic and clinical research, and to ensure that everyone gets a second opinion and has their test paid for by their insurance or health plan.  If you're prepared to defend patent rights when they cause these problems -- and sometimes they do -- then that's where we can have productive disagreement.

Two other key points where patents in this area differ -- and here I really do urge you to read the case studies and see if you agree.  The word "monopoly" is not a scare word when it describes the reality.  The companies in these case studies -- Athena, Myriad, and Clinical Data/PGxHealth -- do have effective monopolies for testing for some of the conditions (and not others, the point of comparisons); that is their business plan.  It is completely legal, and as the case studies make plain, it's not a slam dunk for either the pro-patent camp or the anti-patent camp (and believe me, we'll get shot at from the other side too).  The tests have been on the market for over ten years in many cases, and in no case has someone "worked around" the key patents when those center on DNA sequences for the consensus sequence or the most common mutations associated with disease.  Myriad has been in effect the sole provider in the US.  (One little aside -- the reason BRCA testing options in Europe are different are because Myriad's patent position has been much weaker there -- so I didn't quite follow your train of argument on that point.)  So it is simply misleading to say such patents do not lead to monopoly effects.  Sometimes they do; and sometimes they don't (other cases also covered in the case studies -- see comparison to colon).  When they do, the problems we note can arise.

The peculiar dynamics of genetic testing  explain why patents on one or a few common mutations can dominate testing for an entire condition caused by many different genes or different mutations in the same gene.  An example:  if you have long-QT syndrome, you don't know which mutation or even which gene might be causing it.  You send your sample for testing to find that out.  Until recently, PGxHealth had a monopoly for such testing by having exclusive rights to Utah patents for some of the most common mutations associated with long-QT.  It was the only place you could send samples to get tested for those and other mutations.  BioReference Labs Inc. has now secured countervailing exclusive rights on other mutations, so that monopoly probably won't continue.  It seems to be an instance of mutually blocking patents -- because neither lab can know in advance whether they are infringing the others' patents until they find out which mutations that particular patient has.  Until BRLI acquired contervailing exclusive rights, no one else was offering testing because PGxHealth had the exclusive rights to common mutations.  Through exclusive rights on the common mutations, PGxHealth has gotten all the business for those mutations as well as patients with long-QT caused by unpatented variants and mutations in undiscovered genes.  This is not necessarily bad (arguments on both sides), and it is unlikely to be catastrophic -- the companies can cross-license or find some other accommodation.  But the situation until recently is fairly and accurately described as a monopoly, and a monopoly not only on the patented inventions but extending to other causes of the same clinical condition.  So I don't agree there is an inherent contradiction in our logic; monopolies can indeed form (but they can also prove unstable in the face of countervailing exclusive rights).

The point about the necessity of the patent incentive is particular to this use of patents, not patents in general.  We do not make these arguments in therapeutics, vaccines, or instruments.  The evidence that a patent incentive is not needed comes from reference labs and academic labs that already offer a test when the exclusively licensed test hits the market.  In that case, it is tautological that the patent incentive was not needed.  The role of patents in that case is to shut down competitors.  That is, of course, a common use of patents and a reason they exist and how they often work; but it is nonetheless evidence that the patent was not needed to create the product or service.  This is not Pfizer keeping Lilly and Merck from making Viagra or Lipitor.  These are commercial labs eliminating testing by reference labs and academic health centers.  We are careful not to judge whether that is a good or bad thing -- there are plenty of arguments on both sides -- but the social benefit of patents in those cases is not that they create tests that would otherwise never come to be.

I do think you're on thin ice and won't be very persuasive if you rest your case on "just live with it" arguments about access to health goods and services.  Here I stick to my guns.  If we can specify problems that could be solved by weakening monopoly rights a little at the margin when they conflict with patient access, then we should do so.  At root, this rests on a premise that patents are instrumental rights balancing net social benefit, not an inherent right, and so constraining them is fair game when doing so promotes social benefit.

But thanks for being first out of the gate in rekindling a debate on this.  Really.  This is great.  And thanks for keeping it civil.

Kevin Noonan (at right), of course, provides a response:

I don't doubt that there are circumstances and situations where the problems you outline in your commentary could occur.  My critique stems from my understanding that the evidence strongly suggests that the problems do not (at present) exist.

As you mention, I have not reviewed the underlying case studies, and we will blog on the HHS White Paper in a future post.  But turning to what I do understand, there are good reasons to believe that the "problems" you outline are not problems at present.  For example, if companies permit basic and clinical research, or ensure that "everyone" gets a second opinion, then the informality of the policies does not trump the consequences -- exactly what you propose be done under threat of patent unenforceability.  If there is an example of a company that has sued a university researcher engaged in basic research, or has refused a patient from getting a second opinion, by all means identify it and let's talk about how to solve the problem.  Revising patent law isn't the only option -- good corporate citizenship seems to be working effectively to prevent the types of predation your commentary warns against.

My reaction to using the term "monopoly" is several-fold.  First, even if not intended, it has a negative connotation.  If that is your opinion, fine, but I will react to it based on its use in anti-patent polemic.  It is also inaccurate because patents by definition have only a limited right -- to exclude others from making, using, selling, offering to sell or importing the patented article or method in the U.S. during the term of the patent.  It does not prevent someone from designing around the patent, and the patent by definition discloses the identity of the gene involved in disease pathology.  All this information is fair game for a competitor to look for other, unpatented ways to achieve the same diagnosis.  You are right that the exclusivity is important for diagnostic companies' business plans -- as I mentioned in my piece, the cost of validating these tests so that they can be reliably used with actual human patients is typically much higher than the cost of the original genetic observation, and without patent exclusivity no one would take the risk on that type of investment.  The fact that no one has "worked around" the patents you cite is, as you much recognize, a very small sample for interrogating a very big question:  it is possible that the earliest genetic diagnostic tests are just robust enough to be hard to design around.  But these tests are ten years old -- how long until they are "off patent" and then fair game for competitors to use for free in perpetuity?

The situation you described between PGxHealth and Bioreference Labs is precisely that which the patent system envisions -- the development of blocking patents between competitors that require cross-licensing.  But as you admit, any "monopoly" is both unstable and short-lived -- the quid pro quo of having the companies disclose their inventions so they can be practiced freely after the patents expire.  The alternatives -- and they are potentially myriad -- are instances where the underlying basis for the diagnostic assay is undisclosed as a trade secret.  In that case (which weakening the patent system would encourage) there would be no disclosure and thus no end to the (non-patent based) monopoly.

I don't intend to rely on "just live with it" arguments.  I merely contend that you identify a host of theoretical or potential problems that, even if they existed would, at their worst, be inherently time-limited and associated with positive benefits for the public.  These benefits include disclosure of the underlying disease-associated polymorphisms, development of the genetic information into robust diagnostic tests, and incentives for others to design-around the patented tests.  I disagree that your proposals would weaken patents at the margins -- the proposals in your commentary would impose your concepts of morality and public benefit -- patient rights -- for mine, or others.  There are certainly instances where that may be appropriate; the Federal government has "march-in" rights for any test developed with Federal grant money, as well as an inherent right to license any patent to any third party for its own use (with compensation through the Court of Claims).  These rights have not been lightly exercised, for good reason, but they exist for instances when they are necessary.  But I think there is little need to impinge on patent rights that underlie investment in genetic diagnostics to solve problems -- such as patient access and insurance coverage -- better addressed by other routes.

Thanks for your response.

Genetic Diagnostic Testing: The "Anti-Commons" Revisited?

    By Kevin E. Noonan --

"Monopoly" is a loaded buzzword when it comes to patents.  It is imprecise, indeed incorrect, but it can be effective in appealing to prejudices that emphasize a negative view of patent rights.  It also effectively telegraphs the writer's own prejudices, so that when it is used in the title of a putatively academic article it can be particularly jarring.

Such an article appears on-line today in the March 26th edition of Nature, in a commentary by Robert Cook-Deegan (lower left), Subhashimi Chandrasekharan, and Mishra Angrist (lower right) of the Institute for Genome Science and Policy at Duke University.  Entitled "The dangers of diagnostic monopolies," it is reminiscent of nothing so much as Eisenberg and Heller's "The Tragedy of the Anti-Commons" in 1998, positing potential problems in the (then) uncertain future of gene patenting, in the context of little support for the espoused position.

The authors of today's Nature commentary admit, in the first paragraph, that the recent report from the Health and Human Services Secretary's Advisory Committee on Genetics, Health and Society disclosed little to no "irreparable" harm to genetic diagnostics from patenting, but assert that "neither have [patents] proven greatly advantageous."  At best, the authors' own research "detect[ed] no pervasive effects of patenting that consistently help or hinder clinical access to genetic testing."  This is consistent with the overwhelming majority of studies showing that the anti-commons aren't tragic after all.  Nonetheless, the authors contend that there are "some" problems that "could be addressed" to benefit everyone -- "patients, researchers, health professionals and companies alike."

The authors' primary concerns are (here we go again) "monopoly situations" -- i.e., when patents are exclusively licensed to one provider.  Why this is a concern is unclear, since they report that "prices of patented and exclusively licensed tests are not dramatically or consistently higher than those of tests without a [wait for it] monopoly."  Moreover, the patent incentive is "usually not necessary."  But the authors go on to state that the effects of patents ("monopolies," of course) on test quality are "equivocal."  And the relationship between quality issues relating to Myriad's BRCA test could not "be ascribed only to the monopoly" (although they assert without support that "[t]est quality is a general problem but monopolies can exacerbate it").  It would be reasonable to conclude from the information discussed in the article to this point that patents are, if anything, neutral with regard to genetic diagnostic tests.

Even benefits associated with sole providers (exclusive patent licensees), such as establishing standards of care, are described as being suspect.  The authors answer the question: "Is a standard of care set by a single provider desirable?" by noting that European companies "take various [alternative] approaches" before performing BRCA tests.  If BRCA tests are reliable, however, what is the benefit of alternative testing?  The authors do not say, merely that "[i]f [if] alternatives are valuable, exclusive licenses limit their availability."  If available alternatives are not patented by the exclusively-licensed single provider, it is unclear how exclusive licenses for BRCA tests could limit availability for those (other, distinct, unpatented) tests.

The authors also bemoan the "fact" that exclusive licenses (actually, the patents underlying them) are difficult to design around.  There is a flaw in the logic behind this assertion, however.  Noting that "[m]ost genetic disorders are heterogeneous -- different genes and mutations lead to clinically similar syndromes," the authors state that "[a]n exclusive license to one or a few common genes or mutations can drive testing to one provider."  On the contrary, the existence of such heterogeneity suggests that it should be difficult for one patentee to cover the entire field, and that continued research on such diseases and the heterogeneous genetic bases thereof should provide a variety of tests controlled by a variety of patentees (much like the co-existence of varieties of pharmaceuticals that address the same underlying pathology).

The authors do raise a legitimate issue -- whether full-genome sequencing efforts will encounter a "patent thicket" comprising patent holders owning rights to specific genetic polymorphisms.  These concerns are real but not realistic, in view of the technical obstacles for the technology (not performing the sequencing but accurately interpreting the data to provide a useful genetic diagnostic test) and the developing legal obstacles to diagnostic testing in general, in view of the Federal Circuit's decisions in Classen Immunodiagnostics, Inc. v. Biogen Idec, In re Bilski, and Justice Breyer's patent musings in the Laboratory Corp. v. Metabolite Labs., Inc. case.  They also ignore the reality that most of the patents existing today will have expired before any of these issues are likely to have been sufficiently resolved to make genomic sequence-based diagnosis a commonly-available diagnostic tool.

The authors eventually arrive at their message -- that "patient rights" should "trump" patent rights for genetic diagnostic tests.  Indeed, the authors identify six "obstructive practices" that should "negate gene patent enforcement," consistent with their goal of whose rights should be trumped.  These include exclusive rights-holders whose policies do not permit:

• Basic and clinical research, including genetic testing in clinical trials or health-services research;
• Performing a test in a form that it does not offer (such as prenatal or preimplantation diagnosis);
• Testing in a territory where the company does not offer a test but has exclusive rights;
• Getting second opinions or verification testing;
• Testing those not covered by its payment agreements with insurers and health plans; and
• Research and development to make testing more comprehensive, more accurate or less expensive.

Opponents of patents frequently raise the issue of "patient rights," typically conflating issues such as reproductive rights or genetic privacy with patent issues, and simplistically framing the issue as one of individual "rights."  These authors do not make these mistakes, but they do seem to forget the realities of the U.S. healthcare system.  The "patient rights" they believe should trump patent rights are solely economic ones (since even the accessibility issues devolve to economics).  But in America, the one right patients don't have when it comes to medical treatment or diagnosis is an economic one.  Healthcare in this country depends intimately on what each individual patient can afford, or if they have benefits through their employer, what their employer provides.  The patent system didn't create this situation and weakening patenting won't solve it.

What weakening the patent system will do is make it less likely that the fundamental research done at universities (where researchers are indeed not motivated by patent concerns) will be translated into useful genetic diagnostic tests.  There is enormous expense required to convert the genetic observations made in a laboratory into a validated diagnostic test that physicians can rely upon in making diagnostic and therapeutic decisions.  This is as it should be -- such tests should be thoroughly vetted before patients are asked to make critical decisions about their health in reliance upon them.  Without the exclusivity provided by patents, there would be little incentive for investors to take the risk that the result of such expenditures will be a robust, reliable genetic diagnostic test.  Restricting patent rights in ways that reduce patent exclusivity can be expected only to reduce these incentives.  This outcome would impinge on a more fundamental patient right than the ones discussed by the authors -- the right to quality and reliable clinical care based on innovation in the genetic bases of human disease.  While the sentiment underlying the authors' commentary may be admirable, they have identified the wrong villain.  In that, of course, (at least lately) they have no monopoly.

President Obama Reaffirms Faith in Science

    By Kevin E. Noonan --

In all the understandable excitement surrounding President Obama's lifting of the Bush Administration's ban on federal funding for embryonic stem cell research, his broader message may have gotten lost.  Overturning the stem cell ban is just a part of a return to the tradition, the guiding principle in Western societies since the end of the Dark Ages, to use the scientific method and its results to understand the world and make rational decisions on policy based on science instead of ideology. 

This tradition was suppressed during the Bush years.  The evidence for this conclusion is rampant:  there have been several books published describing the undue influence of ideology (Seth Shulman's Undermining Science: Suppression and Distortion in the Bush Administration, University of California Press, 2006; Chris Mooney, The Republican War on Science, Basic Books, 2006), as well as dozens of editorials (collected by the Union of Concerned Scientists here).  The Union has also collected its Periodic Table of these abuses).  While the Bush administration's antipathy to the evidence of global warming is well known, there are several other important issues where ideology trumped science, such as abortion and its psychological and medical effects; various specific environmental policies involving endangered species; and political litmus and loyalty tests for scientists appointed to advisory and other federal panels.

President Obama has been on record for some time as being opposed to this philosophy.  In a radio address in December, announcing members of his scientific and technology advisory team, he said:

[T]oday, more than ever before, science holds the key to our survival as a planet and our security and prosperity as a nation.  It is time we once again put science at the top of our agenda and worked to restore America's place as the world leader in science and technology.  Because the truth is that promoting science isn't just about providing resources -- it's about protecting free and open inquiry.  It's about ensuring that facts and evidence are never twisted or obscured by politics or ideology.  It's about listening to what our scientists have to say, even when it's inconvenient -- especially when it's inconvenient.  Because the highest purpose of science is the search for knowledge, truth and a greater understanding of the world around us.  That will be my goal as President of the United States.

A distinct change from the immediate past.

In his remarks on Monday, President Obama reiterated some of these sentiments:

This Order is an important step in advancing the cause of science in America.  But let's be clear:  promoting science isn't just about providing resources -- it is also about protecting free and open inquiry.  It is about letting scientists like those here today do their jobs, free from manipulation or coercion, and listening to what they tell us, even when it's inconvenient -- especially when it's inconvenient.  It is about ensuring that scientific data is never distorted or concealed to serve a political agenda -- and that we make scientific decisions based on facts, not ideology. 

By doing this, we will ensure America's continued global leadership in scientific discoveries and technological breakthroughs.  That is essential not only for our economic prosperity, but for the progress of all humanity.

That is why today, I am also signing a Presidential Memorandum directing the head of the White House Office of Science and Technology Policy to develop a strategy for restoring scientific integrity to government decision making.  To ensure that in this new Administration, we base our public policies on the soundest science; that we appoint scientific advisors based on their credentials and experience, not their politics or ideology; and that we are open and honest with the American people about the science behind our decisions.  That is how we will harness the power of science to achieve our goals -- to preserve our environment and protect our national security; to create the jobs of the future, and live longer, healthier lives.

Amen.

For additional information regarding this or other related topics, please see:
• "President Obama to Life Stem Cell Limits on Monday," March 8, 2009

President Obama to Lift Stem Cell Limits on Monday

    By Donald Zuhn --

The New York Times reported late last week that President Obama will satisfy one of his campaign pledges on Monday when he reverses limits imposed by the Bush administration on embryonic stem cell research.  In August of 2001, the Bush administration ordered that federal research be limited to lines of cells that were already in existence at the time.  President Obama is expected to allow federal research on not only stem cell lines already in existence, but stem cell lines that have yet to be created.  In addition, the President will be asking the National Institutes of Health to come up with new stem cell research guidelines within 120 days of the announcement.

Accompanying the President for the announcement, which is scheduled to take place at 11:45 am (Eastern) in the White House, will be a number of Democratic and Republican legislators who support the reversal.  Among the lawmakers who have been invited to attend the announcement are Senators Dianne Feinstein (D-CA), Tom Harkin (D-IA), Orrin Hatch (R-UT), Edward Kennedy (D-MA), and Arlen Specter (R-PA), and Representatives Michael Castle (R-DE) and Diana DeGette (D-CO).  According to the Times, President Obama will also take the opportunity to speak about a return to "sound science" during his administration, fulfilling a campaign promise to separate politics and science.

In an additional report in today's edition of the Times, officials in the Obama administration noted that the President would be looking -- but perhaps not expressly asking -- for some cooperation from Congress with respect to its own stem cell ban.  In particular, the President would like Congress to overturn the Dickey-Wicker amendment, first passed in 1996, which prohibits the use of tax dollars to create human embryos or to conduct research in which embryos are destroyed, discarded, or knowingly subjected to risk of injury.

Congress has already begun work on the stem cell issue with the introduction last month of three bills in the House (H.R. 872 and H.R. 873) and Senate (S. 487).  The bills would amend the Public Health Service Act to require the Secretary of Health and Human Services to conduct and support research that utilizes human embryonic stem cells, regardless of the date on which the stem cells were derived from a human embryo.  The two House bills, which were sponsored by Rep. DeGette and co-sponsored by Rep. Castle, Tammy Baldwin (D-WI), Mary Bono Mack (R-CA), Lois Capps (D-CA), Russ Carnahan (D-MO), Charles Dent (R-PA), Gene Green (D-TX), Mark Kirk (R-IL), James Langevin (D-RI), Ed Perlmutter (D-CO), and Fred Upton (R-MI), differ in that H.R. 872 also directs the National Institutes of Health to issue guidelines for such stem cell research.  The Senate bill, which was sponsored by Sen. Harkin and co-sponsored by Sen. Feinstein, Hatch, Kennedy, Specter, Harry Reid (D-NV), and Jeanne Shaheen (D-NH), is similar to H.R. 873.  Similar bills were passed by both the House and Senate in 2007, only to be vetoed by then-President Bush.  At a press conference to announce the introduction of the Senate bill, Sen. Specter said the legislation was needed so that "this important policy change . . . does not ping-pong back and forth with each successive President."

New Administration Will Act Quickly to Jump-Start Stem Cell Research

    By Donald Zuhn --

Last week, we reviewed prior Patent Docs reports discussing some aspects of President-elect Barack Obama's technology platform, including his positions on patent issues and follow-on biologics (see "A Second Look at President-elect Obama's Technology Platform").  We also reported on the response by some in the patent community to last week's election (see "Reaction to Historic Presidential Election").  While the results of presidential election -- and shake-up in Congress -- will almost certainly have a significant impact on U.S. patent policy and the creation of a follow-on biologics regulatory pathway, the election results will also impact biotech and pharma research.  No area of the biotech industry is likely to see swifter and more pronounced change than that portion of the industry which is focused on stem cell research.

On Monday, the Washington Post confirmed what many of the President-elect's supporters already knew:  an Obama Administration will be good for stem cell research (see "Stem cell supporters await their Obama moment").  According to the Post, John Podesta, the co-chair of the President-elect's transition team and President Clinton’s Chief of Staff from 1998 to 2001, stated that the President-elect plans to quickly reverse President Bush's 2001 directive limiting federal funding of human embryonic stem cell research.  Geron Corp. CEO David Greenwood and Parkinson's Action Network CEO Amy Comstock Rick expect that as a result of the policy reversal, the industry will see a surge in funding.  The Post notes, however, that for the next few months the industry will have to deal with the Bush Administration's status quo, since President Bush is expected to make no changes in his current stem cell policy.  Addressing the current stem cell climate, White House Press Secretary Dana Perino asserted that "scientists from all over the world, and especially here in our country, have shown their innovation and their abilities to do embryonic stem cell research and make huge leaps in achievement without destroying embryos."

While things look far better for stem cell researchers from a policy standpoint, the Associated Press reported today that stem cell researchers will be facing a new obstacle in 2009:  a lack of funding resulting from the current financial crisis (see "Obama election no panacea for stem cell industry").  The true impact of the financial crisis on stem cell research is hard to gauge, however, since the AP report notes that federal funding restrictions have led to much duplicative spending (as one example, the article cites Harvard's Stem Cell Institute, which purchases one set of equipment for use in federally funded research and another set of equipment for use in non-federally funded research).  In addition, a reversal of the Bush Administration's stem cell policy might lure back stem cell research that moved to China or Singapore.  Any reemergence of the U.S. stem cell industry, however, will depend on an influx of investment dollars, as funding in this country has declined by 65% since 1999.  According to the AP report, one possible group of investors may be drugmakers, who are looking for ways to deal with the loss of patent protection on approximately $24 billion worth of drugs in 2009.

Human embryonic stem cells image: Ryddragyn, Wikipedia Commons

Patents Online Announces New Patent Search Engine

    By Donald Zuhn --

Patents Online, LLC, the company behind FreePatentsOnline, today announced the release of a companion online service, SumoBrain.  The service, which was launched this summer, offers an alternative to patent search pay services by providing free cross-collection searching, portfolios, saved search capabilities, alerts, bulk PDF download capabilities, and collaboration tools.  According to the company's release, SumoBrain was initially conceived as a subscription service, but Patents Online decided to make the service completely free.  Patents Online CEO Erik Reeves noted that the FreePatentsOnline database, from which SumoBrain will draw its search results, currently includes 8,812,656 patents.  SumoBrain permits full-text searching of U.S. patents (1976-present), published U.S. applications (2001-present), European patents and published European applications (1991-present), PCT publications (1978-present), and English abstracts of Japanese patent applications (1996-present).  PDFs can be obtained for U.S. patents (1790-present), published U.S. applications (2001-present), European patents and published European applications (1978-present), and PCT publications (1978-present).