presentation at Leiden STI 2014 conference

1. Gene patents in plant biotechnology: model organisms v. major commercial crops
Koen Jonkers*
European Commission, JRC IPTS
Catalina Martinez
CSIC-IPP, Madrid, Spain
STI 2014 Conference, Leiden, The Netherlands
3-5 September 2014
Disclaimer: The information and views set out in this publication do not necessarily reflect the opinion of the European Commission. The EC does not guarantee the accuracy of the data included in this study. Neither the EC nor any person acting on its behalf may be held responsible for the use which may be made of the information contained herein.

2. Background
•Genetic patenting: scientific, legal and economic importance (e.g. Louwaars et al 2009).
•Global seed market has grown from 18 billion USD in 1985 to 34 billion USD in 2006. Seeds form the basis for a product market which is many times this size and they are of central importance to global food security (Louwaars, 2007).
•The market for genetically modified seeds is growing at a high rate too, from 2.7 billion USD in 2000 to 6.2 billion in 2006 (Le Buanec 2007).
•The past decade has seen a process of concentration of the plant seed sector (Howard 2009).
•Two types of IPR: plant breeders’rights and patents (Louwaars et al 2009).
The focus of the present study is gene patents in plant biotechnology, defined as ‘patent applications including gene sequences of plants’
2

3. Previous research on gene patents
3
Large literature, growing fast, especially on human DNA, but not only, by economic, legal and science scholars (e.g. medicine, biotech):
•Human DNA: e.g. Thomas et al (2002); Hopkins et al (2007); Rosenfeld and Mason (2013)
•Marine genetic resources: e.g. Arrieta et al (2010); Arnaud-Haond et al (2011)
•GM crops: e.g. Regibeau and Rockett (2003); Conti, Regibeau and Rockett (2003); Regibeau and Rockett (2005); Schneider (2011), CAMBIA reports (www.cambia.org)
Main issues: Owmership of patents claiming gene sequences; subject matter of patents with gene sequences; competition issues; effect on follow-on research, access to resources; diffusion, etc.

4. Our data
EPO filings with plant gene sequences from GBPAT files in GENBANK
•We downloaded all the patent sequences files (GBPAT) from NCBI GENBANK flat file release 183.0 (April 2011) which were used to create a relational database and linked those files to patent information from PATSTAT (Sep. 2010). Patent information has been updated for sample using PATSTAT April 2014 and OECD patent quality data July 2014.
•EPO and WIPO sequence information in GBPAT contains information on the source organism.
•Source not provided in the USPTO: BLAST searches for sequence homology is an option.
•We have coded by EPO patent filings by source organism and top plant categories, and EPO granted patents by subject matter (using Derwent family summaries)
•Analysis presented here is at the patent level, but we are doing similar analysis at the family level.
4
EPO filings from GENBANK April 2011
Gene sequences
% Total
Patent applications
% Total
Unclassified
47664
1%
1823
12%
Synthetic
570022
17%
6969
44%
Mammalia
2231844
68%
3316
21%
Bacteria
227932
7%
1352
9%
Plantae
133995
4%
581
4%
Virus
9849
0%
562
4%
Fungi
18344
1%
385
2%
Arthropoda
10201
0%
126
1%
Archae
4590
0%
94
1%
Other
8530
0%
532
3%
Total
3262971
100%
15740
100%

5. Most filings from firms, Public Research Organisations growing fast. Top 5 firms control more than 60% of filings from the private sector (high share of Basf)
0
20
40
60
80
100
120
140
160
1980-2000
2001-2005
2006-2009
Private
Public
Public/Private
0
10
20
30
40
50
60
70
1980-2000
2001-2005
2006-2009
Basf
Bayer
Dupont
Monsanto
Syngenta
Other firms
5
Basf and ‘other firms’ (not top 5) peak in 2001-2006

6. arabidopsis
rice
maize
wheat soybean
tobacco
tomato barley
pea
0
.1 .2 .3 .4
35% of all plant genetic sequence patents filed at EPO between 1981 and
2009 are associated with Arabidopsis thaliana genetic sequences. Rice with
23% and maize with 21% follow. Some patents contain DNA sequences of
more than one type of organism
Distribution of EPO filings by top plants
Genbank (plus some coding) allows to classify by the organism of the gene sequence
included in the patent filing, advantage over using patent classes or keyword search
6

7. Arabidopsis
•No commercial use, except as a research tool
•Arabidopsis DNA sequences in patent claims as an indicator of science relatedness?
•Potentiallly: patent filings with arabidopsis sequences may be used to claim protection for homologous sequences in related plant species (including the dicots tomato and soybean)
•Arabidopsis DNA sequences appear often together with DNA sequences from other organisms in patent filings
7

8. Research questions
•Does the presence of genetic sequences of model organisms such as Arabidopsis indicate more basic/exploratory inventions (science-related) or is it instead a sign of the strategic use of broad claims and homology?
•How could both patterns be disentangled?
•Are patents with Arabidopsis alone more ‘basic’ than patent filings with Arabidopsis listed together with major crops?
8

9. To study the effect of Arabidopsis, with and without major crops, we build four mutually exclusive categories of patents in our sample:
0
20
40
60
80
100
120
140
160
arabidopsis
without major
crops
arabidopsis
and major
crops
major crops
without
arabidopsis
Other
0
10
20
30
40
50
60
70
Major crops
without
Arabidopsis
Arabidopsis
with major
crops
Arabidopsis
without
major crops
Other
9

10. Patent filings with Arabidopsis are less likely withdrawn than patent filings without Arabidopsis
0%
10%
20%
30%
40%
50%
60%
70%
80%
90%
100%
major crops
without
arabidopsis
arabidopsis
without
major crops
arabidopsis
and major
crops
other
withdrawn
refused
pending
granted
unknown
0
10
20
30
40
50
60
70
1981
1984
1987
1990
1993
1996
1999
2002
2005
2008
withdrawn
refused
pending
granted
unknown
But need to control for filing year (more recent filings have had less time to be withdrawn), as we will do later in regressions
10
With Arabidopsis

11. Different business models of the Top 5 firms
11
0
5
10
15
20
25
30
35
Basf
Bayer
Dupont
Monsanto
Syngenta
arabidopsis without major crops
arabidopsis and major crops
major crops without arabidopsis
other

12. Howard, Philip H. 2009.Visualizing Consolidation in the Global Seed Industry: 1996–2008. Sustainability, 1(4), 1266-1287.
12

13. Subject matter of granted EPO patents
improved method
pathogen production
stress yield
"There are two major types of products from plant biotechnology: methods and traits. traits such as disease and
stress resistance, improved yield, product quality [or the production of new compounds] can improve the [direct]
value in the [product] chain. Methods such as molecular marker techniques, transformation techniques [and in
our definition also vectors and regulatory elements] create value in the process of breeding." (Louwaars, 2009)
13
0
5
10
15
20
25
arabidopsis
without major
crops
arabidopsis and
major crops
major crops
without
arabidopsis
other
We manually coded the 130 patent applications which had been granted by July 2014, to
analyse what use was patented - explain. We also considered coding for patents that
were more or less science based, but this proved challenging.

14. PROBIT ANALYS
Statistically significant differences in the characteristics of patents with and without arabidopsis?
14

15. 15
Mean Std. Dev. Min Max Mean Std. Dev. Min Max Without-With e(t)
bulk100 0.14 0.35 0 1 0.08 0.28 0 1 -0.0619* (-2.05)
invnbr 1.33 0.57 0 3 1.26 0.55 0 4 -0.0719 (-1.31)
patent_scope 2.58 1.24 1 7 2.76 1.57 1 8 0.174 (1.20)
claims 16.86 8.22 1 42 18.70 12.83 1 85 1.842 (1.64)
pct 0.23 0.42 0 1 0.19 0.39 0 1 -0.0465 (-1.17)
family_size 8.55 4.17 1 18 8.54 5.29 1 38 -0.0121 (-0.02)
npl_cits 31.50 39.93 0 109 20.30 31.04 0 116 -11.20** (-3.29)
bwd_cits 17.48 26.12 0 120 10.57 21.12 0 122 -6.912** (-3.04)
onefwdcits5 0.04 0.21 0 1 0.12 0.33 0 1 0.0801** (2.78)
largefirmonly 0.41 0.49 0 1 0.51 0.50 0 1 0.102* (2.07)
proonly 0.19 0.40 0 1 0.23 0.42 0 1 0.0395 (0.96)
firmpro 0.03 0.16 0 1 0.05 0.22 0 1 0.0266 (1.34)
smallfirmonly 0.31 0.46 0 1 0.18 0.39 0 1 -0.125** (-3.06)
otheronly 0.06 0.24 0 1 0.02 0.14 0 1 -0.0422* (-2.32)
monsanto 0.06 0.24 0 1 0.11 0.31 0 1 0.0475 (1.65)
bayer 0.05 0.22 0 1 0.08 0.27 0 1 0.0255 (1.04)
basf 0.35 0.48 0 1 0.14 0.35 0 1 -0.214*** (-5.46)
syngenta 0.02 0.14 0 1 0.07 0.26 0 1 0.0535* (2.42)
dupont 0.01 0.08 0 1 0.08 0.27 0 1 0.0696** (3.23)
otherfirms 0.25 0.44 0 1 0.27 0.45 0 1 0.0208 (0.48)
granted 0.27 0.45 0 1 0.30 0.46 0 1 0.0330 (0.73)
withdrawn 0.41 0.49 0 1 0.48 0.50 0 1 0.0671 (1.37)
refused 0.03 0.18 0 1 0.03 0.16 0 1 -0.00386 (-0.23)
pending 0.28 0.45 0 1 0.18 0.39 0 1 -0.100* (-2.47)
With Arabidopsis (N=159) Without Arabidopsis (N=290) Student's T test
Descriptive statistics for first probit analysis

16. (1) (2) (3) (4) (5)
VARIABLES arabidopsis arabidopsis arabidopsis arabidopsis arabidopsis
bulk100 0.0913 0.0562 0.0654 0.0460 0.0621
(0.0889) (0.0914) (0.0938) (0.0901) (0.0922)
linvnbr 0.0309 0.0390 0.0163 -0.115 -0.120
(0.115) (0.118) (0.121) (0.125) (0.127)
lscope 0.0160 0.0170 0.0185 0.0498 0.0582
(0.0516) (0.0524) (0.0529) (0.0541) (0.0550)
pct -0.0105 -0.0372 -0.0553 0.0697 0.0639
(0.0714) (0.0725) (0.0736) (0.0784) (0.0805)
lfamsize 0.0501 0.0580 0.0445 0.0397 0.0388
(0.0457) (0.0476) (0.0492) (0.0482) (0.0497)
lnplcits 0.00369 0.00217 0.00409 -0.0165 -0.0163
(0.0262) (0.0271) (0.0272) (0.0277) (0.0279)
lpatcits 0.0361 0.0518 0.0479 0.0667** 0.0666**
(0.0301) (0.0321) (0.0324) (0.0333) (0.0335)
onefwdcits5 -0.194** -0.189** -0.188** -0.185** -0.182**
(0.0781) (0.0801) (0.0805) (0.0799) (0.0804)
proonly 0.0869 0.0882
(0.0778) (0.0781)
firmpro -0.121 -0.115
(0.122) (0.123)
smallfirmonly 0.187*** 0.199***
(0.0692) (0.0699)
otheronly 0.340*** 0.352***
(0.124) (0.123)
granted -0.0266 0.0187
(0.0736) (0.0763)
withdrawn -0.0634 0.0256
(0.0710) (0.0746)
refused -0.160 -0.132
(0.138) (0.140)
monsanto -0.230*** -0.227***
(0.0734) (0.0739)
bayer 0.00134 -0.00160
(0.134) (0.134)
basf 0.156 0.173*
(0.0950) (0.0976)
syngenta -0.194* -0.197*
(0.114) (0.113)
dupont -0.385*** -0.384***
(0.0360) (0.0361)
otherfirms -0.0587 -0.0585
(0.0701) (0.0704)
filing years yes yes yes yes yes
Log likelihood -254.7344 -247.52309 -246.75343 -237.53659 -237.0001
Pseudo R2 0.0628 0.0893 0.0922 0.1261 0.1281
Observations 406 406 406 406 406
Standard errors in parentheses
*** p<0.01, ** p<0.05, * p<0.1
FIRST PROBIT
arabidopsis or
not
Dependent variable is
‘including gene
sequences of
Arabidopsis in the
claims’
Full sample
Marginal effects
Patent filings with arabidopsis in the
claims are less likely to be cited,
more likely to be filed by small firms
or other (neither firm nor PRO), than
by large firms. When we distinguish
among firms controlled by the top
five firms and other (instead of small
and large) we find that patent filings
with arabidopsis in the claims are
positively associated with Basf, and
negatively with Monsanto, Syngenta
and Dupont reflecting their different
business models. A significant
positive association between having
arabidopsis in the claims and the
number of citations to patent prior
art emerges when this distinction
among the top 5 is made (probably
because these firms build on
previous patents of themselves and
each other, indicating R&D
competition on research using
arabidopsis, something we should
look at in further research).
Neither legal status, scope, nbr of
inventors, nbr of claims, filing route
(PCT or not) or family size are
significantly associated with having
arabidopsis or not in the claims
16

17. 17
Mean Std. Dev. Min Max Mean Std. Dev. Min Max Alone - With Top e(t)
bulk100 0.35 0.48 0 1 0.02 0.14 0 1 -0.330*** (-6.39)
invnbr 1.45 0.62 1 3 1.25 0.52 0 3 -0.197* (-2.15)
patent_scope 2.42 1.14 1 7 2.69 1.30 1 7 0.270 (1.33)
claims 18.90 7.85 1 41 15.63 8.22 2 42 -3.274* (-2.47)
pct 0.37 0.49 0 1 0.15 0.36 0 1 -0.215** (-3.19)
family_size 8.30 3.86 2 16 8.71 4.36 1 18 0.407 (0.60)
npl_cits 27.38 39.50 0 105 33.99 40.19 0 109 6.607 (1.01)
bwd_cits 17.07 26.54 0 106 17.74 25.99 0 120 0.671 (0.16)
onefwdcits5 0.05 0.22 0 1 0.04 0.20 0 1 -0.00960 (-0.28)
largefirmonly 0.32 0.47 0 1 0.46 0.50 0 1 0.148 (1.85)
proonly 0.18 0.39 0 1 0.20 0.40 0 1 0.0187 (0.29)
firmpro 0.02 0.13 0 1 0.03 0.17 0 1 0.0136 (0.53)
smallfirmonly 0.45 0.50 0 1 0.22 0.42 0 1 -0.228** (-3.09)
otheronly 0.03 0.18 0 1 0.08 0.27 0 1 0.0475 (1.19)
monsanto 0.10 0.30 0 1 0.04 0.20 0 1 -0.0596 (-1.50)
bayer 0.05 0.22 0 1 0.05 0.22 0 1 0.000505 (0.01)
basf 0.40 0.49 0 1 0.32 0.47 0 1 -0.0768 (-0.98)
syngenta 0.03 0.18 0 1 0.01 0.10 0 1 -0.0232 (-1.04)
dupont 0.02 0.13 0 1 0.00 0.00 0 0 -0.0167 (-1.29)
otherfirms 0.18 0.39 0 1 0.29 0.46 0 1 0.110 (1.55)
granted 0.13 0.34 0 1 0.35 0.48 0 1 0.220** (3.10)
withdrawn 0.38 0.49 0 1 0.42 0.50 0 1 0.0409 (0.51)
refused 0.07 0.25 0 1 0.01 0.10 0 1 -0.0566* (-1.99)
pending 0.42 0.50 0 1 0.20 0.40 0 1 -0.215** (-2.97)
Arabidopsis with Top crops (N=60) Arabidopsis alone (N=99) Student's T test
Descriptive statistics for second probit analysis

18. 18
(1) (2) (3) (4) (5)
VARIABLES top top top top top
bulk100 0.587*** 0.558*** 0.551*** 0.603*** 0.589***
(0.101) (0.119) (0.131) (0.111) (0.125)
linvnbr 0.309 0.307 0.301 0.440 0.450
(0.253) (0.254) (0.266) (0.292) (0.297)
lscope 0.104 0.137 0.147 0.147 0.141
(0.109) (0.112) (0.115) (0.123) (0.124)
pct 0.102 0.0957 0.0949 0.0692 0.0515
(0.135) (0.139) (0.142) (0.155) (0.155)
lfamsize -0.0201 -0.0626 -0.0484 -0.0387 0.0285
(0.0962) (0.1000) (0.103) (0.117) (0.123)
lnplcits -0.0986* -0.0841 -0.0805 -0.0684 -0.0733
(0.0551) (0.0569) (0.0575) (0.0570) (0.0574)
lpatcits 0.0277 -0.0126 -0.0138 -0.0272 -0.0157
(0.0604) (0.0669) (0.0693) (0.0657) (0.0678)
onefwdcits5 -0.105 -0.0988 -0.0617 -0.0346 -0.00101
(0.216) (0.216) (0.238) (0.242) (0.273)
proonly -0.180 -0.226*
(0.134) (0.128)
firmpro -0.157 -0.223
(0.252) (0.217)
smallfirmonly 0.0794 0.0365
(0.125) (0.127)
otheronly -0.168 -0.217
(0.201) (0.179)
granted -0.183 -0.174
(0.132) (0.138)
withdrawn 0.0987 0.189
(0.151) (0.164)
refused 0.0662 0.0862
(0.399) (0.446)
monsanto 0.574*** 0.644***
(0.128) (0.0984)
bayer 0.474** 0.458**
(0.189) (0.206)
basf 0.152 0.198
(0.173) (0.178)
syngenta 0.600*** 0.633***
(0.111) (0.0833)
otherfirms 0.0481 0.0602
(0.161) (0.166)
filing years yes yes yes yes yes
Log likelihood -75.595764 -73.997626 -71.488517 -67.428357 -63.945154
Pseudo R2 0.2586 0.2743 0.2989 0.3326 0.3671
Observations 152 152 152 151 151
Standard errors in parentheses
*** p<0.01, ** p<0.05, * p<0.1
SECOND PROBIT
Arabidopsis with
top crops or alone
Dependent variable
is ‘including genetic
sequences of top
crops in the claims’
Subsample, only
patents with gene
sequences of
Arabidopsis in the
claims
Marginal effects
Patent filings with arabidopsis and
top crops in the claims are more
likely to contain bulk genetic
sequences (more than 100) and
include less NPL references than
patent filings with arabidopsis alone.
When the types of applicants is
included, the significance of NPL
references disappears and is
replaced by having public research
organisations as applicants than
large firms, which also reflects
science-relatedness of patents
including only Arabidopsis, without
top crops.
When we distinguish among firms
controlled by the top five firms and
other (instead of small and large) we
find that patent filings with
arabidopsis and top crops are
positively associated with
Monsanto, Bayer and Syngenta.
No other variable is significantly
associated to having gene sequences
of arabidopsis with top crops or of
arabidopsis alone in the claims.

19. FURTHER DESCRIPTIVE ANALYSIS (ONLY GRANTED)
19

20. 20
Arabidopsis with crops is more likely to be associated to traits 'pathogen'
and 'yield' (immediately useful for breeders), bulk sequence patents (broad coverage) and PCT (seeking worldwide protection and time to prospect market potential) . They are also more likely to be filed by Syngenta
Arabidopsis alone is therefore less likely to be associated to these variables
Both arabidopsis alone and arabidopsis with crops are equally likely to be
associated with methods and other traits, and the rest of variables that have
non significant differences of means according to the t-test
There are only very few observations. We may try to extend this sample in
further research
Comparison of granted patents of Arabidopsis alone and Arabidopsis with top crops
MeanStd. Dev.MinMaxMeanStd. Dev.MinMaxAlone - With Tope(t) method0,250,46010,430,50010.179(0.92) trait_improved0,250,46010,170,3801-0.0786(-0.50) trait_pathogen0,250,46010,000,0000-0.250**(-3.34) trait_production0,380,52010,310,4701-0.0607(-0.32) trait_stress0,250,46010,170,3801-0.0786(-0.50) trait_yield0,380,52010,090,2801-0.289*(-2.20) bulk1000,130,35010,000,0000-0.125*(-2.18) Granted with Arabidopsis alone (N=35)Granted with Arabidopsis and Top crops (N=8)Student's T test