Genetics

The Genomics Law Report has provided ample coverage throughout the litigation over Myriad Genetics’ BRCA1/2 patents. The saga had a rather lengthy procedural history, so a timeline of key landmarks with hyperlinks to GLR coverage as appropriate (in the “where” column) may be useful. When Where Action Citation 1997 USPTO US Patent 5693473 issued to Myriad Genetics Inc.   March 2010 SDNY US Patent 5693473 invalidated AMP v. USPTO, 702 F.Supp.2d 181 July 2011 Fed Cir NY SDNY decision affirmed in part, reversed in part AMP v. USPTO, 653 F.3d 1329. March 2010 SCOTUS Certiorari granted, Fed Cir NY judgment vacated, case remanded to Fed Cir NY AMP v. Myriad, 132 S.Ct. 1794 August 2012 FedCir NY Subsequent determination made (in light of Mayo v. Prometheus) AMP v. USPTO, 689 F.3d 1303 November 2012 SCOTUS Certiorari granted AMP v. Myriad, 133 S.Ct. 694 April 2013 SCOTUS Heard oral arguments   June 2013 SCOTUS Fed Cir decision affirmed in part, reversed in part AMP v. Myriad, 569 US – To understand the Supreme Court’s decision in AMP v. Myriad, announced on June 13, 2013, it’s important to keep in mind what question was before the Court. For a valid patent to issue, the following requirements must be met: • 35 USCA §101 – patentable subject matter • 35 USCA §102 – novelty • 35 USCA §103 – non-obviousness • 35 USCA §112 – adequate, explicit description The only question before the Supreme Court was whether human genes are patentable. (The Court left the methods patent decisions of the Federal Circuit unaffected. In other words, Myriad’s diagnostic method patents are invalid but its therapeutic screening method patent is valid.) Basically, in answering this question, the Supreme Court would decide whether the patents held by Myriad met the first requirement of patentable subject matter (35 USCA §101). The SCOTUS decision The Court unanimously (9-0) answered that isolated DNA is not patentable subject matter but cDNA is patentable subject matter. Justice Thomas wrote the opinion. Justice Scalia wrote a succinct concurring opinion indicating he joined the judgment and all Parts except Part I-A (the scientific discussion). Justice Thomas wrote: …In this case, by contrast [to the facts of Diamond v. Chakrabarty, 447 US 303], Myriad did not create anything. To be sure, it found an important and useful gene, but separating that gene from its surrounding genetic material is not an act of invention. ¶Groundbreaking, innovative, or even brilliant discovery does not by itself satisfy the §101 inquiry. The Court rejected the idea that a products patent (like the isolated DNA patent issued to Myriad) meets §101 by virtue of the extensive research efforts required to isolate the DNA of BRCA1 and BRCA2, that bonds are severed in the process of isolating the DNA from the surrounding genetic material, and of necessary deference to the USPTO practice of granting gene patents of this sort in the past. This last argument was rejected primarily because Congress had not endorsed the USPTO’s practice (in contrast to the example provided by Myriad, i.e., new plant breeds were held patentable as Congress endorsed the practice via its Patent Act amendment). Justice Thomas continued: …the lab technician unquestionably creates something new when cDNA is made. cDNA retains the naturally occurring exons of DNA, but it is distinct from the DNA from which it was derived. As a result, cDNA is not a ‘product of nature’ and is patent eligible under §101, except insofar as very short series of DNA may have no intervening introns to remove when creating cDNA. In that situation, a short strand of cDNA may be indistinguishable from natural DNA. What does the SCOTUS decision mean? John Conley provided analysis of the decision for the GLR here. Robert Cook-Deegan called the recent ruling a “sensible decision” and explained the case highlights Myriad’s mismanagement of its patent portfolio, because cDNAs are useless for diagnostics but invaluable fo

UK legal experts are querying the 2011 Court of Justice of the European Union (CJEU)ruling that the products of research using stem cells derived from human embryos are not patentable (see previous news). ? The UK High Court has itself requested clarification from the CJEU in Luxembourg; depu ...

There is a really interesting article at Slate.Com from Mary Ann Mason, the author of "Do Babies Matter" which I have written about here before. The post is titled "In the Ivory Tower, Men Only". The post tells some of the background behind the book and discusses issues about graduate school, post doctoral positions, applying for faculty jobs and more. The article also has some very good guidance for universities that would like to level the playing field: We all know what structural changes would help to level the playing field in all of these careers and they are quite similar: paid family leave for both mothers and fathers, especially for childbirth, a flexible workplace, a flexible career track, a re-entry policy, pay equity reviews, child care assistance, dual career assistance. Those universities and corporations who have actively created these policies have found an advantage in recruitment and retention. For instance, at Berkeley, after enacting several new policies to benefit parents, including paid teaching leaves for fathers, job satisfaction scored much higher among parents, and more babies are being born to assistant professors. Some good guidance for some of the activities at UC Davis as part of the ADVANCE program in which I am involved. And she ends by recommending It is time for women to “lean in” and demand family policies that will at least give them a fighting chance to have both a successful career and babies. I agree. But it is also time for men to do the same. The more that men also support and demand such policies the quicker things will change. -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------

After what seemed like an eternity, the epic saga known as AMP v. Myriad Genetics has finally come to a close. On June 13, 2013, the Supreme Court ruled (1) that isolated genomic DNA (gDNA) is not patent-eligible under section 101 of the Patent Act, but (2) cDNA is. For once, what the Justices said at oral argument gave accurate clues to what they really thought, and the result was what almost every observer (including this one) had predicted. The opinion—by Justice Thomas—was unanimous and brief: 18 pages. Justice Scalia wrote a one-paragraph concurrence in which he said only that he didn’t know enough to sign on to the Court’s recitation of “the details of molecular biology,” though he agreed with the decision. The 9-0 decision reflects a recent trend in patent decisions (see Mayo v. Prometheus and last month’s Monsanto opinion), and may represent a reaction to the derision that greeted the fractured, multi-opinion mess that was Bilski v. Kappos, the Court’s 2010 business methods case. Beyond the surface unanimity, the Myriad opinion has a no-brainer quality—that is, the opinion does not give any sense of wrestling with a difficult issue, giving the impression that the outcome was so clear that reasonable minds couldn’t possibly differ. Consistent with this approach, the Court cited only the lower court opinions and briefs in the case, a few of its own patent decisions, and a single scientific text (Watson’s Molecular Biology of the Gene). No amicus briefs (except the government’s, to confirm that the Department of Justice had thrown the USPTO under the bus), no scientific or law review articles. The strict legal significance of the decision is pretty straightforward. The Court struck down patent claims on genomic DNA that has been merely “isolated” from the body, where “isolated” means, well, “isolated”—removed and separated from its natural environment in the cell. More specifically, the Court held that genomic DNA does not meet the threshold test of patentable subject matter under section 101. It upheld the subject matter status of cDNA, which it defined as “synthetically created DNA . . . which contains the same protein-coding information found in a segment of natural DNA but omits portions within the DNA segment that do not code for proteins [introns].” Every patent drafted like Myriad’s first and broadest claim—“an isolated DNA coding for [a specified protein]”—is now invalid. Conversely, claims limited to cDNA versions of genes continue to pass the threshold test, though they are still subject to scrutiny under all the other patentability requirements (more on that below). The cDNA/gDNA distinction has its roots in the Federal Circuit’s 1991 decision in Amgen v. Chugai. That case turned on a priority-of-invention contest: who got the rights to the human EPO gene. But the case did, at least implicitly, establish the subject matter status of cDNA. The broadest claim upheld in that case was: “A purified and isolated DNA sequence consisting essentially of a DNA sequence encoding human erythropoietin.” The court treated this as a claim to the cDNA version of the gene, interpreting “purified” as meaning something like “only the coding regions.” It commented that “[i]t is important to recognize that [neither competing inventor] invented EPO or the EPO gene. The subject matter [of this claim] was the novel purified and isolated sequence which codes for EPO.” Thereafter, two things happened. First, the subject matter eligibility of cDNA was never again challenged, until now. And understandably so, if DNA is viewed as a chemical for patent law purposes. cDNA is, in a literal sense, a substance not found in the body; it contains the same coding information as the mature RNA transcript, but it is a different chemical: and, with the noncoding regions excised, it is not exactly replicated in natural DNA. The second thing was less predictable. Amgen set up one of those slippery slopes that lawyers are always talking about. The USPTO

Researchers have analysed the genome sequences of Mycobacterium leprae samples from the teeth and bones of mediaeval skeletons. ? M. leprae is the bacillus that causes leprosy, which was endemic in Europe until mediaeval times; whilst cases have dropped world-wide, it persists in regions outs ...

The Times newspaper has published a front-page story revealing that the Duke of Cambridge, Prince William, and his brother Prince Harry share some Indian ancestry via their mother, based on DNA analysis of distant cousins. ? This in itself is not a particularly controversial revelation &ndash ...

Quick post here ... Some news stories and posts I am checking out today in relation to the UC Davis ADVANCE project in which I am involved. National Geographic: In Her Words: Sylvia Earle on Women in Science – News Watch NY Times Japan's 'Science Women' Seek an Identity NBC News:The Whole World Celebrates 50 Years of Women in Spaceflight Gulf Today: Arab women in science get fellowship boost NY Times: The Unspoken Stigma of Workplace Flexibility -------- This is from the "Tree of Life Blog" of Jonathan Eisen, an evolutionary biologist and Open Access advocate at the University of California, Davis. For short updates, follow me on Twitter. --------

For many many years I have been raising a key questions in relation to open access publishing - how can we measure how open someone's publications are. Ideally we would have a way of measuring this in some sort of index. A few years ago I looked around and asked around and did not find anything out there of obvious direct relevance to what I wanted so I started mapping out ways to do this. When Aaron Swartz died I started drafting some ideas on this topic. Here is what I wrote (in January 2013) but never posted: With the death of Aaron Swartz on Friday there has been much talk of people posting their articles online (a short term solution) and moving more towards openaccess publishing (a long term solution). One key component of the move to more openaccess publishing will be assessing people on just how good a job they are doing of sharing their academic work. I have looked around the interwebs to see if there is some existing metric for this and I could not find one. So I have decided to develop one - which I call the Swartz Openness Index (SOI). Let A = # of objects being assessed (could be publications, data sets, software, or all of these together). Let B = # of objects that are released to the commons with a broad, open license. A simple (and simplistic) metric could be simply OI = B / A This is a decent start but misses out on the degree of openness of different objects. So a more useful metric might be the one below. A and B as above. Let C = # of objects available free of charge but not openly OI = ( B + (C/D) ) / A where D is the "penalty" for making material in C not openly available This still seems not detailed enough. A more detailed approach might be to weight diverse aspects of the openness of the objects. Consider for example the "Open Access Spectrum." This has divided objects (publications in this case) into six categories in terms of potential openness: reader rights, reuse rights, copyrights, author posting rights, automatic posting, and machine readability. And each of these is given different categories that assess the level of openness. Seems like a useful parsing in ways. Alas, since bizarrely the OAS is released under a somewhat restrictive CC BY-NC-ND license I cannot technically make derivatives of it. So I will not. Mostly because I am pissed at PLoS and SPARC for releasing something in this way. Inane. But I can make my own openness spectrum. And then I stopped writing because I was so pissed off at PLOS and SPARC for making something like this and then restricting it's use. I had a heated discussion with people from PLOS and SPARC about this but not sure if they updated their policy. Regardless, the concept of an Openness Index of some kind fell out of my head after this buzzkill. And it only just now came back to me. (Though I note - I did not find the Draft post I made until AFTER I wrote the rest of this post below ... ). To get some measure of openness in publications maybe a simple metric would be useful. Something like the following P = # of publications A = # of fully open access papers OI = Openness index A simple OI would be OI = 100 * A/P However, one might want to account for relative levels of openness in this metric. For example AR = # of papers with a open but somewhat restricted license F = # of papers that are freely available but not with an open license C = some measure of how cheap the non freely available papers are And so on. Given that I am not into library science myself and not really familiar with playing around with this type of data I thought a much simpler metric would be to just go to Pubmed (which of course works only for publications in the arenas covered by Pubmed). From Pubmed one can pull out some simple data. # of publications (for a person or Institution) # of those publications in PubMed Central (a measure of free ava

For the next week or so, 23andMe is pausing updates to the DNA Relatives feature.  This feature provides a list of genetic matches and estimates the range of relationship. According to this week’s 23andMe update entitled “Release Notes: 7 June 2013,” (you must log in to view), “The computation time for DNA Relatives and Ancestry Composition has been growing.” Going into greater detail at “DNA Relatives computations temporarily on hold,” 23andMe explains that due to the increased computational time, and in an effort to reduce the time it takes to generate DNA Relatives matches, updates are paused.  Accordingly, “[t]his means that you won’t be receiving new matches to your existing DNA Relatives list, and if you haven’t received your matches yet there may be some additional waiting time.” It sounds as though this temporary pause will ultimately lead to faster results for 23andMe customers. The full message is below: “DNA Relatives computations temporarily on hold” Posted by Christine M. in Relative Finder Hi everyone, As Mike mentioned in the June 7th Release Notes, the computation time for DNA Relatives has been growing. Part of the effort to reduce the time it takes to generate DNA Relatives matches has required us to pause updates for this feature for the time being. This means that you won’t be receiving new matches to your existing DNA Relatives list, and if you haven’t received your matches yet there may be some additional waiting time. While putting these computations on pause was the best option available while the update is in progress, we understand that it’s not ideal and we appreciate your patience. We expect to re-enable updates to DNA Relatives by the end of next week, June 21st. I will share updates on this thread as necessary. Thanks, Christine Jun 13, 2013 This was brought to my attention by Larry Vick via the ISOGG mailing list.

The US Supreme Court has ruled unanimously that the patents held by Myriad Genetics Inc. for the BRCA1 and BRCA2 gene sequences are invalid, on the basis that they are a product of nature. ? Justice Thomas wrote: “A naturally occurring DNA segment is a product of nature and not patent e ...