This article has been updated from a previous version to include comments from a Gene Codes official and an attorney not affiliated with the case.
Gene Codes is suing New York City's Office of Chief Medical Examiner for at least $10 million in damages for allegedly "violating intellectual property rights" through "contractual breaches" and "misappropriation of trade secrets" related to DNA-matching software used to identify victims in the Sept. 11, 2001, terrorist attacks.
In a complaint filed in the US District Court for the Southern District of New York in March, the Ann-Arbor, Mich.-based bioinformatics company claimed that the OCME violated its contract with its subsidiary Gene Codes Forensics by providing the Federal Bureau of Investigation with access to trade secrets and confidential information about the company's Mass Fatality Identification System, or M-FISys, software.
The city fired back, claiming the Gene Codes allegations are nothing but a "fundamental misunderstanding and misinterpretation" of the company's obligations under the agreement and countersued the company for $10 million in damages.
In a statement filed last month, the city further argued that the case should be dismissed because of the "absence of any admissible evidence" to support Gene Codes' allegations.
New York said the Gene Codes complaint provides nothing more than "claims based in unfounded speculation and [is] completely lacking evidentiary support." The city further argued that Gene Codes' claims do not address the "pivotal question" of whether OCME gave the FBI trade secrets and "whether the … secrets are in fact worthy of protection."
M-FISys was developed by Gene Codes in the months following the Sept. 11, 2001, tragedy under a $10 million contract with New York City's OCME. According to the city, that amount was later increased to $13 million.
In its complaint, Gene Codes lists the following as trade secrets incorporated in M-FISys: the proprietary Sequencher program, comprising its internal algorithms and program interfaces; "novel DNA profile matching algorithms;" a novel approach to "collapsing" matching profiles to allow easier management and visualization of large amounts of data; and a database schema for organizing the large amount of different types of data involved in the highly complex identification process. The company added that a "distinctive feature" of M-FISys "is its ability to integrate STR and mitochondrial DNA testing."
The company claims in its suit that the OCME misappropriated the database schema and the company's method for integrating nuclear STR profiles and mitochondrial DNA sequences used on degraded remains.
A New Tool for a Somber Task
Following the destruction of the World Trade Center, New York's Office of the Medical Examiner selected Gene Codes to develop new pattern-matching software because the existing method used for DNA identification, based on the FBI's Combined DNA Index System, or CODIS, was deemed ill-equipped to handle the task of identifying the remains collected from the site.
The company already had an existing relationship with OCME's department of forensic biology, which had used Gene Codes' Sequencher software for its mitochondrial DNA analysis needs.
The resulting software, M-FISys, was used to match DNA from individual remains with DNA from family members and victims’ personal effects; reunify separated pieces of individuals; track collected samples; maintain chains of custody for all submitted swabs and personal effects; and confirm the accuracy of the identifications with rigorous quality assurance tests (BI 7/1/2002).
Gene Codes claims that in response to a "verbal request" from OCME, it "suspended its existing commercial software research and development activities and devoted all of its efforts and energies to developing a new and ground-breaking system of DNA profile matching technology in the span of less than a year."
Furthermore, in May 2003, Charles Hirsch, the chief medical examiner, and Howard Baum, acting director of forensic biology for OCME, expressed support for Gene Code's nomination for the National Medal of Technology, stating in a letter to the US Department of Commerce that "out of a sense of patriotic duty, [Gene Codes] took a major financial risk in the development of M-FISys by shutting down most of their other operations and starting work on M-FISys at their own expense."
The OCME officials added that "M-FISys is the only product to integrate multiple technologies (STR, mitochondrial, and SNP DNA testing)," and said that without the software, "the identification of the remains could not have proceeded so quickly and so smoothly."
Gene Codes Vs. The City of New York
Howard Cash, Gene Codes' president, told BioInform this week that the company was informed in 2009 by an unnamed source that the OCME was assisting the FBI to build similar software by "reverse engineering" the M-FISys database schema, which prompted them to pursue legal action earlier this year.
In its complaint, Gene Codes claims that during a meeting held on Sept. 29, 2001, OCME asked the company to develop DNA-matching software, a request that prompted Gene Codes to "reorganize its business." The company said it handled all the expenses for developing the software without a written contract until M-FISys version one was installed at OCME on Dec. 13, 2001.
Cash said that when his company first became involved with the identification process, it spent the first few months organizing the data, which had been collected by multiple groups and was spread out over multiple databases in multiple formats.
The plan, he said, was to "provide the data in any format that the city requested. What we wouldn’t do, although we were asked several times, was tell them how we would organize the data … [because] our engineering solutions are proprietary."
According to Gene Codes, the partners signed a formal three-year contract on March 1, 2002, that went into effect retroactively beginning Sept. 12, 2001, and was set to expire on Sept. 11, 2004.
According to the complaint, the contract specified that the software had to permit many match searches in a wide variety of configurations; include the ability to account for genetic anomalies; and offer importable functions for a population statistical database to be used to determine the likelihood of direct and kinship DNA identifications among other things.
Furthermore, Gene Codes' contract included a clause where both parties agreed to keep each other's information confidential "by using methods at least as stringent as each party uses to protect its own confidential information," which is what Gene Codes alleges OCME failed to do.
According to Gene Codes, the FBI "specifically sought to obtain and has been provided" information about M-FISys's ability to integrate nuclear STR profiles and mitochondrial DNA sequences, which, the company claims elsewhere in its complaint, is a unique feature of its software.
Listed in the suit are three OCME employees whom Gene Codes claims "participated in printing out the confidential database schema" and "worked directly with the FBI's software engineering personnel and/or contractors for the purpose of enabling the FBI to extract … trade secrets … in order to develop and enhance the functionality of CODIS" in the latter half of 2009. In response to that accusation, the city countered that Gene Codes "has yet to articulate what the alleged trade secrets at issue are."
On this point, James Barta, a partner with Missouri-based law firm Armstrong Teasdale, which is not affiliated with the case, explained to BioInform that one of the challenges for Gene Codes lies in explaining to the court exactly what aspects of the database schema constitute a trade secret — and to do it without revealing more confidential information.
"If you are not a computer person, you [may] have never heard of the word 'schema,' let alone a database schema," he said. "In the computer world it means something fairly specific … the structure and organization of the data within the database, [which] will includes tables and fields and values and specific ways [to] organize a database to make it run better or faster."
A fourth official at OCME, Gene Codes claims, hacked into the M-FISys database "with the knowledge of other senior officials of OCME" and "caused the M-FISys server to fail or crash at the time."
The official, Natarajan Venkataram, who was the head of management information services for OCME during the duration of the contract, is linked to several charges of misconduct mentioned in the suit, which Gene Codes cites as evidence of OCME's "wanton, egregious, and malicious [conduct], rather than an isolated instance of carelessness or oversight."
In addition to claims of misappropriation of trade secrets, Gene Codes asserts that by giving the information to the FBI, the OCME not only violated the contract but did so "to enable the FBI's CODIS software to unfairly compete against [Gene Codes] and its proprietary M-FISys software."
Also, according to Gene Codes, OCME received the "competitive benefit" of the company's IP, while the company "has been deprived of its financial expectation" in developing the software. The firm further alleges that while it fully "performed its obligations," OCME failed to hold up its end of the agreement.
Cash believes that the "FBI plans to develop a competitor to M-FISys and offer it for free to every participating crime lab and medical examiner's office in the country, plus any other country with which the US has diplomatic relations," effectively making it a competitor to Gene Codes.
In its response to the suit dated April 4, OCME denied that integrating STRs and mtDNA is unique to M-FISys and that its officials were complicit in Venkataram's activities. The city also denied making a verbal request to Gene Codes and asking the company for help in the first place.
According to the city's version of events, on Sept. 29, 2001, Cash approached OCME with an offer to develop software and provide resources at a reduced cost to aid the 9/11 victim identification efforts.
In its countersuit, OCME alleges that Gene Codes breached the contract by, among other things, failing to train OCME personnel to upload DNA profiles into M-FISys and failing to provide proper documentation for the operation of the program.
Cash denied that allegation, claiming that the company "repeatedly asked to be relieved" of uploading data both verbally and in writing and that it provided documentation for every feature. Furthermore, he said the company trained "a large number" of OCME personnel to use M-FISys, one of whom Cash said was assigned to assist the FBI in developing the next version of CODIS.
Under the terms of the agreement, the city said that Gene Codes was expected to continue to upgrade the system even after the agreement ended in September 2004, which the company failed to do although it has developed and released several versions of the software since then.
According to Cash, under the terms of the contract, the city was granted a royalty-free perpetual license, meaning that it had "perpetual usability on whatever computers" they used during the duration of the contract.
The license did not include support for upgrades and new features for newer models of computers, which would have required a new "maintenance" contract, which Cash said he sent to the city but "we never ended up executing that."
The city also accused Gene Codes of failing to provide a version of M-FISys that generates data in a CODIS-compatible format; "improperly" using the city's WTC database, which contains the victims' data, as a validation tool without making the resulting improvements to M-FISys available to OCME; and "making statements on its website and in marketing materials" about the work done for OCME "without prior authorization."
Furthermore, OCME argues that by pursuing legal action, Gene Codes breached the terms of a written release signed on Nov. 21, 2006, by Cash agreeing not to file claims against the city for "perceived and/or intellectual property violations."
In a statement filed on Aug. 30, OCME denied allegations that it shared printouts of the database schema or information about the operation and functioning of M-FISys with the FBI and noted that its version of M-FISys "does not have a utility or tool to extract the data stored in M-FISys."
In a response dated Sept. 27, Gene Codes claimed that data from the system could be exported easily with no need for extraction tools. Furthermore, the company claimed that an unnamed senior member of the OCME staff told Cash in September 2009 that an OCME employee was "printing out the data tables from M-FISys specifically to help the FBI develop new software with functions similar to M-FlSys, including integrating different types of DNA testing in the way that M-FISys integrated those different data types."
In its response, OCME dismissed the claims, calling them hearsay and inadmissible in court.
Barta agrees that Gene Codes' complaint seems reliant on hearsay and the words of a confidential source and noted that the laws are clear on what's admissible and material, but noted that the company has a "legitimate right to seek discovery."
"I have seen software licenses/software development contracts that are no more than a couple of pages long and those are the ones that you see that have challenges with them," he said. "When I took a look at the [Gene Codes] contract, it's nearly 50 pages long … this wasn’t just thrown together … it's clear that they put a lot of time and language in there to try to cover different scenarios."
If the case is dismissed, Barta believes that it could have an impact on future relationships between commercial entities and government groups.
"I think Gene Codes would be left scratching their heads and saying, 'What more could we have done at the time?'" he said. "And that would, I think, make everybody step back and [try to] figure out why the court would not consider this case."
Cash said that Gene Codes isn’t pursuing the lawsuit against the city in the hopes of obtaining additional sources of revenue or to slow down the identification process.
"It never occurred to me that we might ever be in this kind of dispute where someone would be saying, 'If we provide your information to a third party, they will give it back to us for free,'" he said. "I want to stop them from doing that because it's unethical and because it's wrong."