Patent on cladistic analysis involving unknown species (fwd)

[Wolfgang Wuster]

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.

--
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Dr. Wolfgang Wuster  -  Research Fellow
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---------- Forwarded message ----------
Date: 3 Aug 1995 13:47:59 +0100
From: Frank Wright <frank at 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: mbsem at 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