Transcript Patent constraints

Good
Science
Benefit to
Society
Human genes claimed in granted U.S. patents
Jensen and Murray, Science 310:239-240 (14 Oct. 2005)
“Specifically, this map is based on a
BLAST homology search linking
nucleotide sequences disclosed and
claimed in granted US utility patents to
the set of protein-encoding mRNA
transcripts contained in the NCBI
databases…
…we do not consider claims on genes
defined through amino acid sequences…
Our results reveal that nearly 20% of
human genes [in the NCBI’s gene
database at the time of writing] are
explicitly claimed as U.S. IP.”
Chromosome 20 of the human genome
each horizontal line represents a patent family
Human genes claimed in granted U.S. patents
Jensen and Murray, Science 310:239-240 (14 Oct. 2005)
Ownership of US granted patents on human
genes
Governments,
universities,
research institutions
and hospitals
9%
28%
Private firms
63%
Unclassified
assignees
Human genes claimed in granted U.S. patents
63% of human gene patents privately owned does not tell the full
story…a single patent may cover thousands of genes (Incyte
Pharmaceuticals has IP rights over >2000 genes)
Jensen and Murray, Science 310:239-240 (14 Oct. 2005)
Patents by number
of unique genes
claimed per patent
Don’t think plant-associated bacteria
have a problem?
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703 USPTO applications and patents contain claims to DNA or amino acid
sequences from or used in Pseudomonas
304 of these are granted patents
Here’s claim 1 of a patent on DNA molecules and polypeptides of
Pseudomonas syringae:
1. An isolated nucleic acid molecule comprising a nucleotide sequence which (i) encodes a
protein or polypeptide comprising an amino acid sequence of SEQ. ID. No. 3, SEQ. ID. No. 5,
SEQ. ID. No. 7, SEQ. ID. No. 9, SEQ. ID. No. 11, SEQ. ID. No. 13, SEQ. ID. No. 15, SEQ. ID. No.
17, SEQ. ID. No. 20, SEQ. ID. No. 22, SEQ. ID. No. 24, SEQ. ID. No. 26, SEQ. ID. No. 28, SEQ.
ID. No. 30, SEQ. ID. No. 32, SEQ. ID. No. 34, SEQ. ID. No. 36, SEQ. ID. No.38, SEQ. ID. No. 40,
SEQ. ID. No. 42, SEQ. ID. No. 44, SEQ. ID. No. 46, SEQ. ID. No. 48, SEQ. ID. No. 50, SEQ. ID.
No. 52, SEQ. ID. No. 54, SEQ. ID. No. 56, SEQ. ID. No. 58, SEQ. ID. No. 60, SEQ. ID. No. 62,
SEQ. ID. No. 64, or SEQ. ID. No. 66; or (ii) hybridizes, under stringency conditions comprising a
hybridization medium which includes 0.9M SSC at a temperature of 37° C., to a DNA molecule
comprising a nucleic acid sequence complementary to SEQ. ID. No. 2, SEQ. ID. No.4, SEQ. ID.
No.6, SEQ. ID. No.8, SEQ. ID. No. O, SEQ. ID. No. 12, SEQ. ID. No.14, SEQ. ID. No.16, SEQ. ID.
No.19, SEQ. ID. No.21, SEQ. ID. No. 23, SEQ. ID. No. 25, SEQ. ID. No. 27, SEQ. ID. No. 29,
SEQ. ID. No. 31, SEQ. ID. No. 33, SEQ. ID. No. 35, SEQ. ID. No. 37, SEQ. ID. No. 39, SEQ. ID.
No. 41, SEQ. ID. No. 43, SEQ. ID. No. 45, SEQ. ID. No. 47, SEQ. ID. No. 49, SEQ. ID. No. 51,
SEQ. ID. No. 53, SEQ. ID. No. 55, SEQ. ID. No. 57, SEQ. ID. No. 59, SEQ. ID. No. 61, SEQ. ID.
No. 63, or SEQ. ID. No. 65; or (iii) comprises a nucleotide sequence which is complementary to
the nucleic acid molecules of (i) and (ii).
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12,511 USPTO documents contain sequence claims and description
related to uses in or by Pseudomonas
Here’s a claim from a 2002 patent app that could soon be granted to
Elitra Pharmaceuticals, for use of multifunctional bacterial replicons
in inhibiting growth of Escherichia coli, Staphylococcus aureus,,
Enterobacter cloacae, Helicobacter pylori, Neisseria gonorrhoeae,
Enterococcus faecalis, Streptococcus pneumoniae, Haemophilus
influenzae, Salmonella typhimurium, …Pseudomonas aeruginosa,… or
any species falling within the genera of any of the above
species.
Claim: A method for inhibiting cellular proliferation comprising introducing a
compound which inhibits the activity or reduces the amount of a polypeptide
comprising a sequence selected from the group consisting of SEQ ID NOs.
243-357 and SEQ ID NOs. 359-398 or which inhibits the activity or reduces
the amount of a nucleic acid comprising a nucleotide sequence encoding
said polypeptide into a cell.
Amuse gueule
from a forthcoming patent landscape analysis by CAMBIA BiOS
• ...Three apps are continuations in a single application family
assigned to Mendel Biotechnology, called "Polynucleotides and
polypeptides in plants" which also includes continuations called
"Yield related genes in plants", "environmental stress tolerance
genes", etc all claiming priority to a series of 1998 "bulk
sequence applications". While these 1998 applications
themselves are not published, it can be inferred from the
daughter applications (which by convention maintain the SEQ
ID numbering) that each claimed approximately 2000
sequences, many of which did not have well-characterised
functions in 1998 (that can be inferred from the reference list).
CIPs have been filed as functions have become clear, and
continuations are being kept alive for those for which the
functions are still unclear, these three apps being examples of
the latter. Check out claims 1 & 2 of the particular
daughter app (US 2004/19927) that relates to
transcription factors:
This is not a joke. And it is typical.
Patent App US 2004/19927: Mendel Biotech
What is claimed is:
1. A transgenic plant comprising a recombinant polynucleotide having a polynucleotide
sequence, or a complementary polynucleotide sequence thereof, selected from the group
consisting of: (a) a polynucleotide sequence encoding a polypeptide, wherein said
polypeptide is selected from the group consisting of SEQ ID NO: 2N, wherein N=1-229, SEQ
ID NO: 467; 488-490; 501-503; 505; 512-515; 521-522; 525-526; 528; 530; 534-537;
540; 558-559; 569; 587-594; 597; 607-609; 621-626; 635-639; 665-669; 708-713; 720721; 736-739; 742; 780-807; 824; 835-837; 851-854; 865-867; 890-891; 903-907; 910913; 922-923; 926; 933-934; 943; 953-960; 966-967; 987-988;994; 1011; 1035-1042;
1064-1073; 1081-1090; 1105-1110; 1122; 1129-1133; 1139-1141; 1157-1158; 11761186; 1191; 1200-1201; 1221-1248; 1254-1257; 1263; 1270; 1288-1291; 1302; 13101314; 1324-1327; 1338-1339; 1342-1343; 1362-1364; 1378; 1391-1392; 1395; 13991418; 1433; 1453-1454; 1457-1459; 1466-1467; 1492-1498; 1500-1501; 1503-1504;
1522; 1528; 1533-1535; 1540-1541; 1563-1566; 1572; 1583-1586; 1593-1594; 16211624; 1645-1646; 1655-1658; 1670; 1674; 1681; 1687; 1701-1705; 1710-1713; 1727;
1735-1737; 1743; 1754-1756; 1761-1762; 1765; 1769; 1781; 1785; 1790; 1805; 1813;
1838-1846; 1857; 1863; 1874-1875; 1883-1884; 1897-1901; 1911-1912; 1917-1920;
1929-1930; 1937-1939; 1942-1943; and SEQ ID NO: 2N, wherein N=974-1101; (b) a
polynucleotide sequence encoding a polypeptide, wherein said polynucleotide sequence is
selected from the group consisting of SEQ ID NO: 2N-1, wherein N=1-229, SEQ ID NO:
459-466;468-487; 491-500; 504; 506-511; 516-520; 523-524; 527; 529; 531-533; 538539; 541-557; 560-568; 570-586; 595-596;
Claim 1 cont & claim 2.
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598-606; 610-620; 627-634; 640-664; 670-707; 714-719; 722-735; 740-741; 743-779; 808-823; 825-834;
838-850; 855-864; 868-889; 892-902; 908-909; 914-921; 924-925; 927-932; 935-942; 944-952; 961-965;
968-986; 989-993; 995-1010; 1012-1034; 1043-1063; 1074-1080; 1091-1104; 1111-1121; 1123-1128; 11341138; 1142-1156; 1159-1175; 1187-1190; 1192-1199; 1202-1220; 1249-1253; 1258-1262; 1264-1269; 12711287; 1292-1301; 1303-1309; 1315-1323; 1328-1337; 1340-1341; 1344-1361; 1365-1377; 1379-1390; 13931394; 1396-1398; 1419-1432; 1434-1452; 1455-1456; 1460-1465; 1468-1491; 1499; 1502; 1505-1521; 15231527; 1529-1532; 1536-1539; 1542-1562; 1567-1571; 1573-1582; 1587-1592; 1595-1620; 1625-1644; 16471654; 1659-1669; 1671-1673; 1675-1680; 1682-1686; 1688-1700; 1706-1709; 1714-1726; 1728-1734; 17381742; 1744-1753; 1757-1760; 1763-1764; 1766-1768; 1770-1780; 1782-1784; 1786-1789; 1791-1804; 18061812; 1814-1837; 1847-1856; 1858-1862; 1864-1873; 1876-1882; 1885-1896; 1902-1910; 1913-1916; 19211928; 1931-1936; 1940-1941; 1944-1946, and SEQ ID NO: 2N-1, wherein N=974-1101; (c) a polynucleotide
sequence encoding the polypeptide sequence of (a) with conservative substitutions as defined in Table 2,
wherein said polypeptide sequence of (a) with conservative substitutions is a transcription factor; (d) a variant of
the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and
wherein said sequence variant encodes a polypeptide that is a transcription factor; (e) an orthologous sequence
of the polynucleotide sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and
wherein said orthologous sequence encodes a polypeptide; (f) a paralogous sequence of the polynucleotide
sequences of (a) or (b), which is at least 80% identical to a sequence of (a) or (b), and wherein said paralogous
sequence encodes a polypeptide; (g) a polynucleotide sequence encoding a polypeptide comprising a conserved
domain that exhibits at least 80% sequence homology with the conserved domain of the polypeptide of (a),
wherein said polypeptide comprising a conserved domain of a transcription factor; and wherein said conserved
domain of (a) is bounded by amino acid residue coordinates according to Table 5; and (h) a polynucleotide that
hybridizes to the polynucleotide of (a) or (b) under stringent conditions.
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2. The transgenic plant according to claim 1, wherein: the transgenic plant possesses an altered trait as
compared to a non-transformed plant; or the transgenic plant exhibits an altered phenotype as compared to said
non-transformed plant; or the transgenic plant expresses an altered level of one or more genes associated with a
plant trait as compared to said non-transformed plant; wherein said non-transformed plant does not overexpress
the recombinant polynucleotide.
Entrée (same application)
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AP2 domain found in SEQ IDs 151-217, 243-296
MADS domain found in SEQ IDs 2-57
MYB-related 129-180
Z-CO-like 32-76
Any of you working on any of these? I’m sure the owner
thanks you for adding ‘value’ to their patents.
“First Complete Plant Genetic Sequence Is Determined”
Andrew Pollack in New York Times 14 Dec, 2000
• "There's thousands of applications1 coming down the
pipeline," said Chris Somerville2, director of the department
of plant biology at the Carnegie Institution, professor at
Stanford University and an early organizer of the sequencing
project. 2 "Our goal — and I say we're going to reach it in the
next decade — is to understand plants like little machines.
And we're going to use it to do real engineering.”
I guess he meant patent applications…
2 Also co-founder, Director and now CEO of Mendel
1
Digestif
Here's a method claim from a patent granted to Mendel in 2004
(US 6,835,540):
1. A method of determining whether a member of a pool of cloned
test transcription factor polynucleotides encodes a plant pathway
transcription factor, the method comprising: collecting a pool of
cloned test transcription factor polynucleotides; introducing into a
plant cell a nucleic acid comprising a plant promoter of a pathway
gene operably linked to a reporter gene; introducing into the plant
cell a member of the pool of cloned test transcription factor
polynucleotides, wherein said member is selected on the basis of
structural similarity to a known transcription factor for a pathway
gene; and detecting expression of said reporter gene in the plant
cell, thereby determining whether the member of the cloned test
transcription factor polynucleotide pool encodes a plant pathway
transcription factor.
To date, Ceres has filed patent applications on
QuickTime™ andfunctionally
a
over 50,000 full-length
annotated
TIFF (LZW) decompressor
are needed to see this picture.
genes and over 10,000 promoter sequences.
Forthcoming patent technology landscapes
(2006…we hope)
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The Rice Genome
The Arabidopsis Genome
RNAi
Homologous Recombination
Transcriptional Activators
…..others?