Bioinformatics/IT
The Conversation Begins: Recap from Day One of FDA’s LDT Regulatory Meeting
Welcome to Hyattsville, MD, where we have just completed day one of FDA’s two day “Public Meeting on Oversight of Laboratory Developed Tests” (LDTs). The session was civil, well-organized and largely devoid of surprises. It did, however, mark the official kick-off of the FDA’s highly publicized decision to develop a “risk-based application of oversight” for all LDTs.
If you’re interested in the details of what was said and by whom you’ll find links at the bottom to all of the relevant transcripts, video feeds and Twitter coverage. For my part, here are the three key take-away points from day one:
Timing. Last week I wrote that it was unlikely that this meeting, or any of the other myriad regulatory and legislative proposals for LDT regulation, would produce a significant shift in the legal and regulatory landscape any time soon. One day of FDA meetings has done nothing to change that opinion.
Grim Sleeper Awakens Attention to Familial Searching of DNA Databases
Last week, the Los Angeles Police Department announced that it had captured a man suspected of being the “Grim Sleeper”: a serial killer linked with at least 10 murders over 25 years.1 The case marks the first time in the United States that a DNA search technique known as familial searching has led to an arrest in a homicide case.
As we’ve previously discussed, a partial match between two DNA profiles may indicate that the donors of the corresponding samples may be related. In familial searching, a database is searched for the purpose of identifying partial, rather than exact, matches against the sample of unknown origin. Those partial matches are then used as investigatory leads.
Though familial searching has been used with some success in other countries, few states openly endorse its practice. Those states that permit the use of partial matches at all generally prohibit the intentional search for those matches, requiring instead that they be discovered inadvertently. California began using familial searching in 2008 in a first attempt to identify the Grim Sleeper. At the time, the failure to produce a suspect was seen as a strike against the technique: if familial searching could implicate privacy concerns and subject innocent individuals to excessive genetic surveillance, it certainly could not be justified without being able to point to positive results.2 Since then, one DNA profile of particular interest was added to California’s database: that belonging to the son of the man now identified as the Grim Sleeper.
The Unintended Consequences of Katie’s Law: More DNA Samples Collected, More DNA Samples Untested?
Last month, we discussed a bill nicknamed “Katie’s Law” that would give states financial incentives to collect DNA samples from individuals arrested for certain crimes. At the moment, less than half of the states currently collect DNA samples from these arrestees. If Katie’s Law were enacted, the remainder of the states would likely expand the scope of their DNA collection practices, greatly increasing the number of samples collected.
But once DNA samples are collected, when are they actually analyzed? As discussed by Christopher Heaney and Sara Huston Katsanis in The Contra Costra Times, many states currently have considerable backlogs in testing DNA samples, including those collected from convicts, arrestees and victims. Katie’s Law, by increasing the number of samples that require analysis, is likely to exacerbate these backlogs. Worse yet, Heaney and Katsanis point out that other federal funding awards are determined by the size of a state’s backlog—the larger the backlog, the more funds the state can receive. While the intent of Katie’s Law is to expedite the delivery of justice, there is concern that its practical effect may indeed be just the opposite.
Keeping Up With CODIS and Katie’s Law
A few weeks back, we posted a discussion of the issues surrounding the current system of forensic DNA profiling, with an emphasis on the Combined DNA Index System (CODIS). In that post, we noted that the federal government had enacted a policy of taking DNA samples from individuals arrested for certain crimes and retaining the samples in CODIS. To date, 23 states have enacted similar laws, and the federal government may soon give the other 27 states incentives to follow suit.
On May 18, the House of Representatives passed the Katie Sepich Enhanced DNA Collection Act of 2010, informally known as Katie’s Law.1 Under the bill, those states that collect DNA from individuals arrested for certain serious crimes (murder, voluntary manslaughter, serious sexual offenses or serious kidnapping offenses) and compare the samples to those in the CODIS database at least once receive a 5% bonus on certain federal crime prevention grants.2 States that also collect samples from individuals arrested for less serious crimes and submit all profiles collected from arrestees for inclusion in CODIS would instead receive a 10% bonus. The bill is now with the Senate Committee on the Judiciary.
Pigs Fly: Federal Court Invalidates Myriad’s Patent Claims
Late on the afternoon of Monday, March 29, 2010, Judge Robert W. Sweet of the United States District Court for the Southern District of New York issued a jaw-dropping summary judgment ruling (pdf) in Association for Molecular Pathology v. USPTO that invalidates certain of Myriad Genetics’ patents related to the BRCA 1 and 2 breast and ovarian cancer susceptibility genes. In a post written immediately after the release of the opinion, Dan gave a thorough summary of the ruling. Our objective here is to offer a bit more depth on what the ruling means—and what it doesn’t mean. On the one hand, Judge Sweet’s order is radical and astonishing in its sweep. On the other, it will be some time before we have any idea what impact it will ultimately have.
We should first disclose that one of us (John) has a dog in this fight, albeit a small one. In 2003, (along with biologist and patent lawyer Roberte Makowski), John published an article in the Journal of the Patent and Trademark Office Society entitled Back to the Future: Rethinking the Product of Nature Doctrine as a Barrier to Biotechnology Patents (pdf). In that article, Roberte and John laid out an argument for challenging Myriad-style patents on “isolated” genes as claiming products that are only trivially different from the naturally-occurring versions. Judge Sweet cited this article and, in several parts of his opinion, followed the roadmap it created. So, if you oppose the Myriad patents, you’re welcome; if you like them, we’re sorry.
What Summary Judgment Means. As Dan noted, and John first wrote last fall, it is rare for plaintiffs to win on summary judgment. For either side to receive summary judgment, it must show that there are no disputed issues of fact that require a trial to resolve, and that, on the undisputed facts, the law mandates judgment in its favor. This standard is especially hard for a plaintiff to meet, since it bears the burden of proof at trial. At the summary judgment stage, a defendant can usually create an issue of fact and thereby avoid summary judgment just by saying “they have the burden of proof at trial, and a jury might not believe them.” Although this is an unusual case in that the basic facts—most notably Myriad’s patent claims and the fundamental biology and genetics that makes possible those claims—really are not in dispute, a summary judgment ruling for the plaintiffs nonetheless sends a clear message about how strong this particular judge thought their case was—and how weak he thought Myriad’s was.
The Road to Invalidation. The court broke Myriad’s patent claims into two major groups: (i) those claiming isolated DNA sequences and (ii) those claiming methods for comparing or analyzing gene sequences to identify the presence of mutations corresponding to a predisposition to breast or ovarian cancer (p. 2). Both sets of patents were rejected under Section 101 of the Patent Act, which enumerates the permissible categories of patentable subject matter: processes, machines, manufactures, and compositions of matter. As the judge noted, a long history of cases forbids claims on laws of nature, abstract ideas, and natural phenomena, which include products of nature.
Breaking: District Court Rules Myriad Breast Cancer Patents Invalid
The highly anticipated decision in Association for Molecular Pathology v. U.S. Patent and Trademark Office, the frontal attack on Myriad Genetics’ breast cancer gene patents, was handed down today. A copy of the opinion, from Judge Robert Sweet of the Southern District of New York is available here.
The opinion was released late this afternoon and it weighs in at 156 pages, so a more complete analysis will be forthcoming. [Edit 3/30: John Conley and I have published a more detailed review and analysis of the decision here: Pigs Fly: Federal Court Invalidates Myriad's Patent Claims. For just the highlights, continue reading below.] However, there are a few crucial points that deserve an initial reaction.
1. The Plaintiffs Win. The ruling appears to be a nearly complete victory for the plaintiffs and their supporters, including the ACLU. With respect to Myriad’s issued patents on the BRCA1 and BRCA2 genes, Judge Sweet’s ruling invalidates both Myriad’s composition of matter claims (its patents on isolated DNA sequences to all or a portion of the breast cancer genes) and its method claims (those patent claims that relate to analyzing or comparing isolated DNA sequences in order to detect mutations in a patient’s BRCA1/2 genes that might cause breast cancer).
The overall tone of the Court’s ruling is best captured by this passage (from page 135):
The identification of the BRCA1 and BRCA2 gene sequences is unquestionably a valuable scientific achievement for which Myriad deserves recognition, but that is not the same as concluding that it is something for which they are entitled to a patent.
New Tools for Forensic DNA: Keyboards and Cats
Earlier this week James Cass wrote a piece discussing forensic DNA profiling (“The Cost of Making Crime Not Pay: Obama, CODIS and Forensic DNA“). That article prompted GLR readers to write in and point out that, thanks to several recent developments, the next generation of forensic DNA investigations may increasingly involve the use of non-human DNA profiling techniques.
Last week, a paper in the Proceedings of the National Academy of Sciences presented research that every person – even twins whose DNA is practically identical – possesses a unique bacterial signature. It appears that traces of that bacterial signature can be recovered from household surfaces, including a computer keyboard, and potentially used to link a crime scene to a suspected criminal. The researchers’ findings are summarized in ScienceNOW (“CSI’s Latest Clue – Bacteria“).
The Cost of Making Crime Not Pay: Obama, CODIS and Forensic DNA
Earlier this month President Barack Obama appeared on the television show “America’s Most Wanted” to discuss the creation of a national forensic DNA database. In his interview with AMW host John Walsh, President Obama expressed his strong support for a number of law enforcement initiatives, including a proposal to expand the compulsory DNA sampling of individuals arrested and charged with certain crimes.
In this post we’ll take a look at the current system of forensic DNA profiling, starting with the Combined DNA Index System (CODIS), which is the FBI program that oversees DNA profile databanking in the United States. It comprises databases at the local, state and national levels, with the National DNA Index System (NDIS) the crown jewel. The CODIS program operates as a powerful law enforcement tool but, in the eyes of some – including President Obama – it is not yet powerful enough. But even the existing CODIS collection, with its nearly eight million DNA profiles, poses a number of interesting ethical, legal and social issues.
Life Technologies Fires Latest Sequencing Salvo
Another week, another drop in the cost of whole-genome sequencing. The latest announcement comes from Life Technologies, which yesterday announced the launch of its SOLiD 4 sequencing system. The details of the announcement are well-covered by GenomeWeb and Matthew Herper of Forbes.com.
In brief, the SOLiD 4 generates 100 gigabases of data per run at a cost of $6,000 per genome, a cost that appears to account solely for the consumables and does not include the cost of the machine or of interpreting all of that sequence data. According to GenomeWeb, Life is also promising an upgrade to its system – SOLiD 4hq – in the second half of 2010 which it expects to triple the data output at half of the cost: 300 megabases per run, $3,000 per sequence.
As for the impact of Life’s SOLiD 4 announcement, Matthew Herper hits the nail on the head:
But although the news is good for Life and will keep it in the game as the price of decoding the genetic code continues to drop, the specs of this new machine don’t seem good enough to upset Illumina’s place as the first choice of geneticists. “It’s a solid improvement, but I don’t think this changes the game,” says Isaac Ro, an analyst at Leerink Swan who follows both companies.
Meet the New deCODE, Same as the Old deCODE?
When deCODE genetics declared bankruptcy last fall it made a big splash. Geneticists pondered the future of the Icelandic biotechnology company’s one-of-a-kind genetic database and research platform, while investors and creditors wondered if they were going to be left out in the cold.
The initial bankruptcy buzz gave way over the past several months to a steady but relatively unremarkable stream of filings in the United States Bankruptcy Court for the District of Delaware (the case is No. 09-14063). Last week, however, brought a noteworthy docket entry, with the bankruptcy court approving the sale of most of deCODE genetics Inc.’s assets to Saga Investments LLC (pdf) – an investment company whose owners include Polaris Venture Partners, ARCH Venture Partners and genomic sequencing giant (and DTC genomics dabbler) Illumina.
A Holiday Fire-Sale? The sale, as approved by the bankruptcy court, sends substantially all of deCODE genetics Inc.’s assets – including its valuable genetic research engine that is driven in part by its access to its large Icelandic population database – to Saga Investments. As we described back in November, the bankruptcy sale process required a Stalking Horse bidder (Saga Investments) and a sale and auction process that, at least in theory, allowed other interested parties a chance to step in and make a bid for deCODE’s assets. No other bidders came forward, and the sale to Saga Investments was approved in just under two months.
