The following has been posted on bionet.molbio.evolution. I felt that it would be of interest to everybody with an interest in systematics, which is why I am posting it here. Please reply to the various authors of the post, not to me. Apologies to those who have already received a copy of this from elsewhere.

-- ******************************************************************************** Dr. Wolfgang Wuster - Research Fellow Snailmail: E-mail: bss166 at bangor.ac.uk School of Biological Sciences Voicemail: +44 1248 383735 University of Wales Fax: +44 1248 371644 Bangor LL57 2UW "If you see a light at the end of the tunnel, Wales, UK it is probably a train coming your way."

---------- Forwarded message ---------- Date: 3 Aug 1995 13:47:59 +0100 From: Frank Wright <fra...@sass.sari.ac.uk> To: "bionet.molbio.evolution mail newsgroup" <bionet-news at dl.ac.uk> Subject: Patent on cladistic analysis involving unknown species

To: bionet.molbio.evolution

I'd like to draw your attention to a European patent (granted in March 1995) that appears to patent phylogenetic/ cladistic analysis when used to identify unknown species. My understanding is that the patent will also apply to the U.S. but not Australia and Japan.

A colleague is challenging the patent (see details appended, from Susan Pryde).

Here is an extract:

"The method of this invention is for the determination of the genus, and then the species, and/or strain, and/or sub species and/or sub-set of a sample of an organism, whether it is eukaryotic or prokaryotic, e.g. a mammal, a bird, a reptile, an amphibian, a fish or an invertebrate.

The method is characterized by the steps of: isolating DNA from a sample; amplifying a defined segment of that DNA; determining the nucleotide sequence of that amplified segment; comparing that DNA sequence with a data base of DNA sequences from known species; and carrying out a cladistic analysis of these sequence data; thereby to determine the identity of the sample."

(under patent number PCT/CA91/00345, of priority date September 25th, 1991 and the corresponding European Patent number 0550491. Inventors are W.S.Davidson and S.E.Bartlett).

Susan (e-mail address: mbsem at seqnet.dl.ac.uk) would be grateful for help in challenging the patent:

(1) Do you know of papers published before the priority date (Sept 25th, 1991) that use phylogenetic/cladistic analysis to identify unknown species?

(2) Would someone be prepared to give advice on terminology? The lawyers are making a big thing that the use of cladistic analysis for identifying unknown species is novel, and that the literature quotes phylogenetic methods. The use of PAUP software is quoted on the Patent.

(3) Any advice on challenging patents would be appreciated.

More details can be obtained from Susan.

... . . . .

If you'd like to object personally then contact (quoting the European Patent Number 0550491):

European Patent Office EPA/EPO/OEB D-80298 Munchen Germany

... . . .

Thanks (in advance) for your help.

Frank Wright Biomathematics & Statistics Scotland University of Edinburgh, Scotland frank at bioss.sari.ac.uk

=========================8< cut here 8=========================== From: mbs...@seqnet.dl.ac.uk Subject: patent

As of March 1995, A European patent has been granted to Bartlett and Davidson on a:

"test to determine an organism's species and/or population identity by direct nucleotide sequence analysis of defined seqments of its genome."

References:

Bartlett,S.E and Davidson., W.S (1991) Identification of Thunnus tuna species by the polymerase chain reaction and direct sequence analysis of their mitochondrial cytochrome b genes. Can. J. Fish.Aquat.Sci. 48:309-317.

Bartlett,S.E and Davidson., W.S (1992) FINS (Forensically Informative Nucleotide Sequencing): A procedure for identifying the animal origin of biological specimens". Biotechniques 12(3):408-411.

The claims of this patent are as follows:

"The method of this invention is for the determination of the genus, and then the species, and/or strain, and/or sub species and/or sub-set of asample of an organism, whether it is eukaryotic or prokaryotic, eg. a mammal, a bird, a reptile, an amphibian, a fish or an invertebrate.

The method is characterised by the steps of: isolating DNA from the sample; amplifying a defined segment of that DNA; determining the nucleotide sequence of that amplified seqment;comparing that DNA sequence with a data base of DNA sequences from known species and carrying out a cladistic analysis of these sequence data; thereby to determine the identity of the sample."

They claim that the novel/inventive part of the patent is in using a cladistic analysis to identify an unknown DNA sequence. ========================================================

At the CSL Food Science Laboratory (Aberdeen, Scotland), our work on tuna species identification has been challenged as a French company (ATLANGENE) have bought a licence from Bartlett and Davidson. ATLANGENE claim to be legally the only European group allowed to use this method for species identification. A letter we recieved from them quoted "We must remind you that the FINS proceedure is patented by BIO-ID Corparation Limited (under patent number PCT/CA91/00345, of September 25th, 1991 and the corresponding European Patent number 0550491). As you know, our laboratory ATLANGENE has, by virtue of an exclusive licence arrangement with BIO-ID Corparation Limited, the exclusive right to use an exploit the FINS technology throughout Europe."

We are currently challenging the patent on the grounds of novelty and obviousness. The "prior art" paper that is the closest related to the patent is:

Rogall et al .(1990) Differentiation of Mycobacterium species by direct sequencing of amplified DNA. J.of Gen. Micro.,136, 1915-1920.

However the European Patent commission have ignored it and granted the patent. Anyone that wishes to challenge this patent should do so before December 1995.

Dr. Susan Pryde CSL Food Science Laboratory P.O. Box 31 135 Abbey Road Aberdeen AB9 8DG Scotland, U.K.

Tel: +44 1224 877071 Fax: +44 1224 874246

e-mail: mbsem at seqnet.dl.ac.uk