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Bulk Sequence Applications

Bulk sequence applications are patent applications that disclose an inordinately large number of nucleotide or amino acid sequences–many more sequences than can be properly examined. In some cases, large numbers of sequences are included in the application to provide enablement for the invention, but are not actually claimed. However, there has been a recent trend towards filing applications that disclose large groups of nucleic acid sequences from genome sequencing initiatives and sequencing of EST libraries. These applications often disclose and claim (at least initially) large numbers of sequences; in some cases more than 100,000!


How does the USPTO define bulk sequence applications?

The USPTO defines bulk sequence applications only in terms of the sequence listing length, not on the basis of the number of sequences that are claimed. Applications with sequence listings longer than 300 printed pages are termed “lengthy sequence listings”. Such sequences are only published in electronic form and are not included with the paper patent publication. Lengthy sequences may be searched at the Publication Site for Issued and Published Sequences (PSIPS). Currently the USPTO publishes about half a dozen such filings every two weeks.

Section 2434 of the MPEP outlines the policy in the U.S. for examination of patent applications claiming large numbers of nucleotide sequences.

Do bulk sequence applications result in bulk sequence patents?

Generally, no. In many jurisdictions, restriction or unity of invention practice limit the number of sequences that are examined in a single application, so the majority of granted patents claim fewer than 20 sequences. In addition, many examiners limit their analysis to sequences that are correlated with an established biological function.

What are some of the reasons that bulk sequence applications are filed?

Patent applicants generally seek to have the broadest possible coverage for their invention. As such, it is often advantageous for an applicant to initially claim a large number of sequences, even though the resulting patent is likely to claim only a handful of sequences. Bulk sequence applications may be used to scare off potential infringers, or used as leverage in licensing negotiations (See Provisional rights associated with pending patent applications), even though the final claim scope may be unknown when the application publishes. These activities can have downstream effects that last longer than the patent term itself. On the positive side, sequences that are disclosed but not claimed in patents as issued are considered to be “dedicated to the public”. Therefore, the thousands of sequences that are not claimed in the granted version of the patent are in the public domain, and are precluded from being patented as compositions of matter by anyone else (as long as they are not the subject of another pending application).

Bulk sequence applications can lead to uncertainty as to which sequences are available for public use.

Patents are intended to be a trade of sorts. In exchange for disclosing the details of an invention, the inventor gets a 20 year legal monopoly for his or her invention. An 18 month publication rule has been implemented in most jurisdictions that facilitates this trade by alerting the public about the contents of pending patent applications. Bulk sequence make it difficult for researchers take advantage of the “trade”, since they are unable to determine if their work is free of patent claims until after the patent issues.

In addition to creating uncertainty for other researchers in the area of the bulk sequence patent application, such applications put a large amount of information into the public domain, creating a body of prior art that precludes others from patenting the disclosed sequences.

Updated on October 16, 2020
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