Archive for the ‘USPTO’ Category

In re BRCA1- & BRCA2- Based Hereditary Cancer Test Patent Litigation, University of Utah Research Foundation v. Ambry Genetics Corp   Leave a comment


In a follow-up to the Myriad Supreme Court Decision of June 13, 2013, the Federal Circuit issued what has become known as the “Myriad II” decision on December 17, 2014. The decision is available here. Myriad sought to enjoin Ambry from allegedly infringing six claims of three patents. The claims at issue in Myriad II were not previously considered by the Supreme Court in Myriad.


Primer Claims

The composition of matter claims at issue in Myriad II were directed to primers. For example, claim 16 of the ‘282 patent recites:


A pair of single-stranded DNA primers for determination of a nucleotide sequence of a BRCA1 gene by a polymerase chain reaction, the sequence of said primers being derived from human chromosome 17q, wherein the use of said primers in a polymerase chain reaction results in the synthesis of DNA having all or part of the sequence of the BRCA1 gene.

The Federal Circuit panel held that the claims at issue reciting primers were directed to patent-ineligible subject matter. In an opinion drafted by Judge Dyk, the court held that primers necessarily contain the identical sequence of the BRCA strand opposite to the strand to which they are designed to bind. Therefore, the primers were structurally identical to a product of nature. Slip Op at 7.

The court compared the situation to that in In re Roslin Institute (Edinburgh), 750 F.3d 1333, 1337 (Fed. Cir. 2014), where the court held that the cloned sheep Dolly was not patent-eligible subject matter because it was identical to a sheep found in nature and did not possess “markedly different characteristics.” The court held that “[a] DNA structure with a function similar to that found in nature can only be patent eligible as a composition of matter if it has a unique structure, different from anything found in nature.” Myriad, 133 S. Ct. at 2116–17 (citing Chakrabarty, 447 U.S. at 309–10). The court held that primers do not have such a different structure and are patent ineligible. Slip Op. at 9.


Diagnostic Method Claims

The court also considered whether claims directed to diagnostic methods were patent-eligible. One of the claims at issue was directed to a method for screening the germline of a human subject for an alteration of a BRCA1 gene. The diagnostic method claims comprised steps comparing a germline BRCA1 sequence from a tissue sample with a wild-type BRCA1 sequence.


The court held that these claims, like the primer claims, were directed to patent-ineligible subject matter. The court’s rationale for invalidating the method claims was that they were directed to an abstract idea. Slip Op. at 13. The court relied on the two-part Alice test for abstract ideas:

(1) determine if the claim is directed to a patent-ineligible concept

(2) determine what other elements are there in the claim and whether they are enough to transform the claim into a patent-eligible application

Slip Op. at 14.


The court held that the Myriad II claims failed both steps of the Alice test. The court also expressed a concern that allowing such diagnostic method claims would preempt the field of research of breast cancer genes.



In conclusion, claims directed to primers that have a sequence identical to a sequence found in nature are not patent-eligible. However, claims directed to primers made from modified nucleotides, or that have a sequence that is not found in nature, are presumably patent-eligible since they have “markedly different characteristics” to the corresponding product of nature.


Furthermore, claims directed to diagnostic methods that recite “comparing” a germline sequence to a wild-type sequence are not patent-eligible. However, claims that also recite additional steps that narrow the claim enough so that it does not preempt an entire field are more likely to be held patent-eligible. It will also help to recite additional steps that are not seen as conventional and routine.


It remains to be seen how this decision will be interpreted by the USPTO in conjunction with the new Myriad Guidelines that were published on December 16, 2014, available here.

Posted February 5, 2015 by deboraplehn in AIPLA, Myriad, USPTO

USPTO Proposes New Standard for the Disclosure of Sequence Listings Using XML   Leave a comment

In an announcement in the Federal Register on May 15, the USPTO posted a request for comments on the recommendation for the disclosure of sequence listings using XML (Proposed ST.26).   The standard is being revised to require the use of extensible mark-up language (XML) format, to update the standard, and to more closely align requirements of the standard with those of public sequence database providers.  The USPTO is requesting comments to be received on or before July 16, 2012.  No public hearing will be held.

As an explanation for the proposed change, the USPTO explains that in October 2010, the Committee on WIPO Standards (CWS) established a Task Force, designating the European Patent Organization (EPO) as the lead, to propose a revised standard for the filing of nucleotide and/or amino acid sequence listings in XML format, known as the “XML standard.”  It is expected that the XML standard will be adopted at a meeting of the CWS in early 2013.

The text of the current draft of the proposed main body of the sequence listing standard, with its associated Annexes, is available via the Office’s Web site: click here.  The documents are also available below:

1. Recommendation for the disclosure of sequence listings using XML (ST. 26): click here.

2. Annex B1 Controlled Vocabularies: click here.

3. Document Type Definition (DTD for ST. 26): click here.

Some of the highlights of the proposed changes include:

1. The XML standard (paragraph 4) prohibits the inclusion of any branched nucleotide or amino acid sequences or any sequences with fewer than ten specifically defined nucleotides or fewer than four specifically definted amino acids.

2. The XML standard (paragraph 5) specifies inclusion of sequences containing any nucleotides that can be represented using any of the symbols set forth in Annex B.1, paragraph 1, Table 1.  This includes modified nucleotides.

3. The XML standard (paragraph 6) specifies the inclusion of sequences containing D-amino acids.

It remains to be seen how this new XML standard will impact biotech practice, and how burdensome it will turn out to be, or how useful.

Posted June 13, 2012 by deboraplehn in USPTO

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