Patent on cladistic analysis involving unknown species

Frank Wright frank at sass.sari.ac.uk
Thu Aug 3 07:47:59 EST 1995


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




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