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Resolution INPI/PR No. 144 of March 12, 2015, Introducing the Guidelines for Examination of Patent Applications in the Field of Biotechnology

 Resolution INPI/PR No. 144 of March 12, 2015 (Introducing the Guidelines for Examination of Patent Applications in the Field of Biotechnology)

FEDERAL PUBLIC SERVICE MINISTRY OF DEVELOPMENT, INDUSTRY AND FOREIGN TRADE

NATIONAL INSTITUTE OF INDUSTRIAL PROPERTY

PRESIDENCY March 12, 2015

RESOLUTION N°. 144/2015

SUBJECT MATTER: Introduce the Guidelines for Examining Patent Applications in the Field of Biotechnology.

The PRESIDENT OF THE NATIONAL INSTITUTE OF INDUSTRIAL

PROPERTY (INPI) and the DIRECTOR OF PATENTS, in the exercise of their

authority established in Articles 106, 159 and 161 of Appendix of Ordinance nº

149 of May 15, 2013, and

WHEREAS the need exists to streamline the procedures for processing

applications with a view to enhancing efficiency and ensuring quality,

WHEREAS the INPI’s Directorate of Patents seeks greater transparency

in its administrative procedures, and

WHEREAS the need exists to standardize and update criteria for

analyzing patent applications in the Field of Biotechnology,

HEREBY RESOLVE:

Art. 1 – To introduce the Guidelines for Examining Patent Applications in

the Field of Biotechnology under the terms of document “Guidelines for Examining

Page 1 of 63

Patent Applications in the Field of Biotechnology”, Appended to this Resolution.

Art. 2 – The regulatory effect conferred to items 2.3, 2.4, 2.6, 2.12 to 2.16,

and 2.25 to 2.35 of the “Guidelines for examining patent applications in the fields

of biotechnology and pharmaceuticals filed after December 31, 1994”, as stated in

the written opinion published in issue n°. 1648 of the Industrial Property Gazette

(RPI) dated August 6, 2002, is hereby revoked.

Art. 3 – This Resolution shall enter into effect on the date it is published in

the Online Industrial Property Gazette (Revista Eletrônica da Propriedade

Industrial).

Otávio Brandelli President

Júlio César Castelo Branco Reis Moreira Director of Patents

Page 2 of 63

MINISTRY OF DEVELOPMENT, INDUSTRY AND FOREIGN TRADE

NATIONAL INSTITUTE OF INDUSTRIAL PROPERTY

DIRECTORATE OF PATENTS

Guidelines for Examining Patent

Applications in the Field of

Biotechnology

March 2015

This text shall be an integral part of the Guidelines for Examining

Patent Applications and is designed to define the INPI’s current

understanding in the Field of Biotechnology. Other topics inherent to

examination shall be listed and discussed in said general guidelines.

March 12, 2015

Page 3 of 63

TABLE OF CONTENTS

1 REQUIREMENTS FOR PROTECTION IN BIOTECHNOLOGY.................5

1.1 INDUSTRIAL APPLICATION .........................................................................5

2 CONDITIONS FOR PROTECTION .................................................................... 7

2.1 UNITY OF INVENTION..................................................................................... 7

2.2 FULL DISCLOSURE (ART. 24)......................................................................... 7

2.2.1 DEPOSITING BIOLOGICAL MATERIAL .................................................. 10

2.2.1.1 Cases in which the biological material must be deposited........................... 10

2.2.1.2 Timelines for depositing biological material................................................ 12

2.2.2 FULL DISCLOSURE OF LISTING OF SEQUENCES ................................ 12

2.3 BASIS, CLARITY AND PRECISION (ART. 25) ..........................................13

2.3.1 BASIS IN THE SPECIFICATION ................................................................. 13

3 CLAIMS.................................................................................................................15

3.1 REACH-THROUGH TYPE CLAIMS IN BIOTECHNOLOGY.................15

3.1.1 TECHNICAL EXAMINATION OF CLAIMS

4 MATTER EXCLUDED FROM PROTECTION ACCORDING TO THE

INDUSTRIAL PROPERTY STATUTE ...............................................................18

4.1 DEFINITIONS ...................................................................................................18

4.2 MATTER NOT CONSIDERED INVENTIONS (ART. 10)..........................19

4.2.1 Natural biological products and processes (ART. 10 (IX)) ............................ 19

4.2.1.1 Natural biological products........................................................................... 19

4.2.1.1.1 Compositions containing natural biological product..................................20

4.2.1.1.2 Extracts .......................................................................................................20

4.2.1.1.3 Enriched extracts.........................................................................................20

4.2.1.2 Natural biological processes ..........................................................................21

4.2.1.3 Use of natural products ..................................................................................23

4.3 NON-PATENTABLE INVENTIONS (ART. 18 OF THE INDUSTRIAL

PROPERTY STATUTE) ........................................................................................23

4.3.1 NON-PATENTABLE INVENTIONS BY OF ART. 18 (I) OF THE

INDUSTRIAL PROPERTY STATUTE ...................................................................23

4.3.2 NON-PATENTABLE INVENTIONS BY VIOLATION OF ART. 18 (III) OF

Page 4 of 63

16

THE INDUSTRIAL PROPERTY STATUTE ..........................................................24

5 MICROORGANISMS..........................................................................................26

6 BIOLOGICAL SEQUENCES.............................................................................. 27

6.1 CHARACTERIZATION ................................................................................... 27

6. 1.1 MARKUSH-TYPE SEQUENCES..................................................................29

6.1.2 WHEN IT IS NECESSARY TO FILE THE LISTING OF SEQUENCES IN

CONJUNCTION WITH THE APPLICATION......................................................... 29

6.1.2 NEED TO RESTRICT THE SET OF CLAIMS TO THE SEQUENCES FILED

IN CONJUNCTION WITH THE APPLICATION ................................................... 30

6.2 HOMOLOGY VERSUS IDENTITY................................................................ 31

6.3 SEQUENCES OF NUCLEOTIDES ................................................................. 33

6.3.1 MODIFICATION OF SEQUENCE(S) OF NUCLEOTIDES.......................... 34

6.3.1.1 Modification of sequence(s) by substitutions, insertions or deletions of non-

modified nucleotides................................................................................................... 34

6.3.1.1.1 SNPs............................................................................................................. 35

6.3.1.2 MODIFICATION OF SEQUENCE(S) OF NUCLEOTIDES with modified

derivatives (inclusive with protector groups)

6.3.2 FRAGMENTS ................................................................................................... 36

6.3.3 OLIGONUCLEOTIDES (OR INITIATORS) .................................................. 36

6.3.3.1 Degenerate and modified oligonucleotides .................................................... 37

6.3.4 PROMOTORS ................................................................................................... 37

6.3.5 VECTORS ......................................................................................................... 39

6.3.6 CDNA ................................................................................................................ 42

6.3.7 ESTS – EXPRESSED SEQUENCE TAGS ........................................................ 43

6.3.8 ORFS – OPENREADING FRAMES .......................................................... ........ 43

6.3.9 RNAS ................................................................................................................. 44

6.4 SEQUENCES OF AMINOACIDS.................................................................... 44

6.4.1 CHARACTERIZATION OF AMINOACID SEQUENCES............................ 44

6.4.2 HOMOLOGOUS PROTEINS (PARALOGOUS VERSUS ORTHOLOGOUS)

..................................................................................................................................... 46

6.4.3 PROTEIN FRAGMENTS ................................................................................. 47

6.4.4 SEQUENCE MODIFICATIONS...................................................................... 49

Page 5 of 63

35

6.4.4.1 With natural aminoacids (substitutions, insertions or deletions) ................... 49

6.4.4.2 With non-natural aminoacids (inclusive with protector groups)................... 50

6.4.4.3 Groupings added to the carboxyl or amino terminus ..................................... 50

6.4.5 FUSION PROTEINS ........................................................................................51

6.4.5.1 Naturally-occurring........................................................................................ 51

6.4.5.2 Characterization ............................................................................................. 51

6.4.5.3 Integral Seq ID............................................................................................... 51

6.4.5.4 Definition of just one of the sequences present in the fusion protein ............ 52

6.4.6 ANTIBODIES.................................................................................................... 54

6.4.6.1 Process of obtaining antibodies ...................................................................... 55

6.4.6.2 Hybridomas..................................................................................................... 55

6.4.6.3 Chimeric/humanized antibodies ..................................................................... 56

6.4.6.4 Fragments of antibodies.................................................................................. 57

7 ANIMALS, PLANTS, PARTS THEREOF AND PROCESSES OF

OBTAINING THEM ................................................................................................ 58

7.1 ANIMALS, PLANTS AND PARTS THEREOF ............................................. 58

7.1.1 Products and processes involving stem cells..................................................... 58

7.2 TRANSGENIC PLANTS, PARTS THEREOF AND PROCESSES OF

OBTAINING THEM ................................................................................................ 59

7.3 PROCESS OF OBTAINING PLANTS BY CROSS-BREEDING ................ 60

8 PATENT APPLICATIONS INVOLVING COMPONENTS FROM THE

BRAZILIAN GENETIC HERITAGE.................................................................... 63

9 REFERENCES....................................................................................................... 65

Page 6 of 63

1 Requirements for protection in biotechnology

The requirements of novelty and inventive step are discussed in the Guidelines

for Examining Patent Applications. Only a few specificities of biotechnology patent

applications will be highlighted in this Appendix.

1.1 Industrial application

The concept of industrial application in the field of biotechnology must

comply with that set forth in the Guidelines for Examining Patent Applications (Block

II), and due regard shall be given to the definition of a utility for the invention

claimed.

When the invention involves biological sequences, the requirement of

industrial application is only met when a utility is disclosed for said sequence.

Accordingly, if a patent application identifies a new sequence by homology,

and the homologous sequence described in the state of the art has a known function, a

new sequence identified in the patent application is susceptible to industrial

application provided that this utility is identified in the specification.

Example 1:

The protein of SEQ ID NO: 1 was identified in different patients with prostate

cancer, and no biological function for this protein is known in the state of the art. It is

noted that this protein described in the application is an important marker for

diagnosing prostate cancer.

The inventions related to this protein (for example, use, composition,

diagnosis kit) are susceptible to industrial application since the application clearly

discloses a practical use for this sequence (marker for diagnosing in vitro prostate

cancer), even if its biological function is still unknown.

Example 2:

The application discloses a protein of SEQ ID NO: 1 which was isolated from

yeasts; however, it discloses no function/application for the same and it presents no

homology with any protein having a known function.

The specification discloses a merely speculative list of applications with no

Page 7 of 63

technical basis capable of supporting any practical application for the protein. This

protein and/or its use and/or compositions comprising same are not susceptible to

industrial application, since said subject matters present no defined practical utility.

2 Conditions for protection

2.1 Unity of invention

The patent application shall refer to a single invention or to a group of inter-

related inventions so as to comprise a single general concept (Art. 22 of the Industrial

Property Statute (Law N°. 9,279/96); see Guidelines for Examining Patent

Applications, Block I).

Example 3: Multiple nucleic acid molecules that share a common structure and encode

proteins with common properties.

Claim 1: Modified nucleic acid characterized by being selected from SEQ ID NO: 1, 2,

or 3.

The specification mentions that the three nucleic acids encode dehydrogenases

that include a sequence of conserved motive defining the catalytic site. The three

nucleic acids are isolated from three different sources (mouse, rat and human) and

modified. The specification clearly shows that these three nucleic acids are

homologous based on their global sequence identity (85-95% identity) for both

sequences of nucleotides and aminoacids.

The same technical characteristics or equivalents that are shared among the

nucleic acid molecules lies in their common properties (encoding dehydrogenases) and

their shared structural elements are essential for the common property (the conserved

motive). So, there is a special technical characteristic and SEQ ID NOs: 1, 2, and 3

have unity of invention.

2.2 Full disclosure (Art. 24)

Article 24 of the Industrial Property Statute determines that the specification

must clearly and sufficiently describe the object, to the extent of enabling a person

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skilled in the art to carry it out (see Guidelines for Examining Patent Applications,

Block I). The ‘object’ is understood to be the subject matter for which protection is

sought, that is, the subject matter contained in the set of claims. Accordingly, the

analysis of full disclosure of the matter claimed must be evaluated based on what was

disclosed in the specification, listing of sequences and drawings (as applicable).

When the application pertains to a product or process involving a biological

material, which cannot be described such that a person skilled in the art can

understand and reproduce the subject matter, then the specification must be

supplemented by depositing said material (see item 2.2.1).

Two examples of lack of full disclosure (insufficient description) in the Field

of Biotechnology warrant special attention. The first is that in which the embodiment

of the invention depends on chance. In this situation, even if the person skilled in the

art were to follow the instructions given in the application, there is no guarantee of

obtaining the contended results. These cases must be contested as a result of the

provision laid down in Art. 24 of the Industrial Property Statute (see item 2.2.1.1 and

example 4). The second is when the embodiment of the invention is inherently

impossible. For example, in a method which includes the amplification of a certain

DNA sequence by using a given pair of primers, wherein said primers are not

complementary to any part of the DNA sequence, thus rendering the execution of the

method unfeasible.

Example 4:

The application describes a mutant microorganism obtained by random

mutagenesis with UV radiation. As obtaining the microorganism depends on chance,

full disclosure of the microorganism will only be satisfied by depositing the

microorganism (see item 2.2.1.1). The document of proof of deposit of the

microorganism in question may be presented via explanations, during the technical

examination, provided that the deposit of the microorganism occurred up to the

application filing date (or priority date, as applicable). The microorganism obtained by

UV-induced mutation thus deposited will be in compliance with Art. 10 (IX) provided

that there is no concrete evidence that the microorganism having that characteristic is

Page 9 of 63

noted in nature.

Example 5:

The application describes a new and inventive method of obtaining mutant

microorganisms by random mutagenesis. Since the stages of said method are described

in detail in the specification, it is possible for a person skilled in the art to reproduce the

invention. Therefore, said method presents full disclosure, in compliance with the

provision in Art. 24 of the Industrial Property Statute. If this method is tied to obtaining

just one mutant with specific characteristics, the information on the deposit thereof must

be included in the claim, since there is no guarantee of obtaining the same result.

Example 6:

The application describes a method which uses a mutant microorganism. The

specification furnishes no details of the process of obtaining the microorganism, but

characterizes it by way of its respective filing number. In this case, it is considered

that a person skilled in the art could reproduce the method in question using the

microorganism deposited. Accordingly, the invention meets the condition of full

disclosure.

Example 7:

The specification discloses a protein by way of its access number at the NCBI

database of sequences or by reference to a scientific article, and said protein is essential

for the embodiment of the invention. To comply with the requirement of full disclosure

established in Art. 24 of the Industrial Property Statute, the filing applicant is required

to incorporate the sequence in question to the application, as disclosed in the databases

at the time of filing/priority, in the form of listing of sequences, and this shall not result

in the inclusion of subject matter, since said protein could be identified unequivocally

from its access number or by way of the aforementioned scientific article (see

additionally items 2.2.1.1 and 2.2.2).

Example 8:

Page 10 of 63

The application describes a new dopamine receptor, duly characterized by its sequence

of aminoacids. The application mentions that antagonists and agonists of the receptor

are also useful. Nevertheless, the application does not furnish a technical description

of any antagonist and agonist compounds of the receptor. A person skilled in the art

would not be able to carry out the invention related to the antagonists and agonists

owing to absence of any technical instruction on how to do so, since the mere

description of a receptor does not provide sufficient information concerning the

molecules that might stimulate or prevent its working. Therefore, it is understood that

the subject matters relating to the antagonists or agonists of the enzyme do not fulfill

the condition of full disclosure (see also item 3.1).

2.2.1 Depositing biological material

In the case of biological material that is essential for the practical realization of

the object of the application, which cannot be described in the form of Art. 24 and

which is not publicly accessible, the specification shall be supplemented by depositing

the material at an institution authorized by the INPI or recommended in an

international agreement (Treaty of Budapest; see Guidelines for Examining Patent

Applications, Block I).

Accordingly, it is considered that “biological material”, in this context of

deposit, may refer to any material containing genetic information capable of

exercising direct or indirect self-replication. Representative examples include

bacteria, archaea, protozoa, viruses, fungi, algae, seeds, lineages of animal and

vegetable cells, hybridomas, artificial chromosomes and other vectors, and the host

cell that houses these biological materials, for some of these cases, and in accordance

with the requirements of the chosen depositary center, can be deposited.

2.2.1.1 Cases in which the deposit of biological material must be carried out

It is important to emphasize, as mentioned above, that the Industrial Property

Statute refers to the deposit of biological material which cannot be described pursuant

to Art. 24, that is, it cannot be described clearly and sufficiently in the specification.

Thus, it is concluded that the deposit of the material does not necessarily apply to all

and every biological material involved in a certain invention, since, for example,

Page 11 of 63

polynucleotides and polypeptides shall be described by way of their nucleotide and

aminoacid sequences (N.B.: nevertheless, there is nothing to prevent such materials

from being deposited in addition).

In relation to the microorganisms having different nucleotide sequences from

that found in nature, the application shall present the modified nucleotide sequence by

way of the listing of sequences (see item 2.2.2), or its name known in the art, or the

deposit data of the microorganism. When essential to confer the inventive

characteristic, the description must also include specific promoters, the insertion site

of the heterologous material in the genome, the methodology of obtaining the sample,

among other essential characteristics, such that a person skilled in the art is capable of

carrying out the invention.

In cases where the microorganisms are selected from random mutagenesis and

the genetic alterations which result in a differential effect are not defined in the

application, then in order to comply with Art. 24 of the Industrial Property Statute, the

microorganism shall be deposited at an international depositary authority and the

biological material deposit data (such as declaration of deposit or name of the

institution, number and date of deposit) shall be included in the application (see item

2.2.1). Accordingly, the biological material will be available at the depositary

authority and, therefore, will be considered clear, sufficiently described and

reproducible. If the microorganism is not deposited, the subject matter will not

comply with Art. 24 of the Industrial Property Statute.

When the inventive characteristic obtained by genetic alteration is achieved

only by a specific strain used in the application under examination, it is considered

that the microorganism in itself is essential to carry out the invention and, therefore,

the biological material shall be deposited so that the subject matter complies with Art.

24 of the Industrial Property Statute. Moreover, depositing the biological material is

not necessary when the inventive characteristic can be achieved by various strains or

species of microorganisms available using the methodology described in the

application. Thus, for situations where broadly known organisms are merely

transformed to express a new and surprising characteristic, simply specify the

organism of interest, relating it expressly to the nucleic acid to be used in this

transformation, and assure that this nucleic acid is described clearly and precisely.

Page 12 of 63

In cases where the invention does not lie in a microorganism or biological

material in itself, but rather in the use, modification or cultivation thereof, and a

person skilled in the art is not capable of carrying out the invention without having

said sample in the application, the deposit of the microorganism or the biological

material is also necessary.

2.2.1.2 Timelines for depositing biological material

In connection with the original deposit of biological material for patenting

purposes, IN PR Nº 17/2013 establishes that the biological material shall be deposited

by the filing date of the patent application, and that said data shall be included in the

specification. In the event of a priority claim, the biological material shall be

deposited prior to or by the date of the priority claimed, if applicable, that is, if the

priority rights apply to the biological material.

When the data on proof of deposit of the biological material are not included in

the patent application, and the examiner finds that such data are necessary, an office

action shall be issued for the applicant to reply. If said office action is not complied

with, then the application shall be rejected, by operation of Art. 24 of the Industrial

Property Statute.

2.2.2 Full disclosure of the listing of sequences

If the object of a patent application comprises one or more sequences of

nucleotides and/or aminoacids that are supported by the description of the invention,

then the application shall contain a section of listing of sequences, with a view to

achieving full disclosure as prescribed in Art. 24 of the Industrial Property Statute (see

Guidelines for Examining Patent Applications, Block I). It is emphasized that if the

application uses and makes reference to sequences known in the art, and these are

necessary for the embodiment of the invention, the examiner may issue an office

action for the sequences to be presented. It must also be noted that the sequences shall

correspond to those included in the state of the art at the time of filing/priority (i.e. as

disclosed in the databases), bearing in mind possible refinement or alterations in the

sequences over time.

Resolution INPI Nº 228/09, incorporated into Resolution INPI PR Nº 81/2013,

Page 13 of 63

provides for procedures for presenting the listing of sequences by electronic means

and substitutes item 16.3 of AN 127/97 (see Resolution PR Nº 81/2013 and its

Appendices published in the Official Federal Gazette (DOU) - Section 1, Nº 68, April

10, 2013).

2.3 Basis, clarity and precision (Art. 25)

2.3.1 Basis in the specification

The subject matter that is the object of protection shall be duly supported in the

specification. Accordingly, the description in the specification shall furnish technical

information capable of supporting all the subject matter claimed.

Example 9:

Claim 1: immunogenic protein characterized by consisting of SEQ ID:1, and

fragments thereof.

The specification presents a mutated immunogenic protein (non-natural)

having 600 residues of aminoacids and also discloses an immunogenic fragment of

this mutated protein (non-natural), determined as consisting of residues 320 to 400 of

said protein. The set of claims, in turn, claims protection for the immunogenic protein

and for immunogenic fragments of said protein (claim 1). However, the specification

only discloses one immunogenic fragment of said protein, namely: which starts in

position 320 and ends in position 400 of the protein. In this case, considering that the

patentability requirements prescribed in Art. 8 of the Industrial Property Statute were

met, an office action shall be issued based on Arts. 24 and 25 of the Industrial

Property Statute so that the subject matter claimed is only restricted to that

sufficiently described and effectively supported in the specification, namely the

immunogenic protein and the fragment thereof that comprises residues 320 to 400 of

said protein.

In this example, even if the filing applicant files new information regarding

other immunogenic fragments of said protein which had not been described in the

subject matter initially disclosed, such information could not be considered because

Page 14 of 63

the specification did not mention immunogenic fragments of the aforementioned

protein other than that comprised between aminoacids 320 and 400 thereof.

Therefore, the fact remains that the claim for broad protection of “immunogenic

fragments of the protein” cannot be accepted owing to the absence of full disclosure

and support for the subject matter in the specification.

Example 10:

Claim 1: process for transforming plants characterized by introducing the gene X in

angiosperms and gymnosperms.

The specification presents general information on the process and a detailed

example of the transformation of the gene into an angiosperm. There is evidence for

a person skilled in the art that said process would not be applicable in the same

manner for both groups of plants, and therefore a claim which includes gymnosperms

would not be supported in the specification. This lack of support might be overcome

by evidence that the transformation of gymnosperms could be carried out under the

same conditions already mentioned for angiosperms.

However, if to achieve support for the claim for gymnosperms the data

furnished new parameters or any adaptations that are not trivial for a person skilled

in the art, such information will not be accepted. This is because it would be

necessary to include the data in the specification which would constitute the addition

of subject matter, this being in disagreement with Art. 32 of the Industrial Property

Statute.

3. Claims

There are two basic types of claims: product, related to a physical entity; and

process, related to an activity (see Guidelines for Examining Patent Applications,

Block I).

In the Field of Biotechnology, some non-exhaustive examples of subject

matters considered to be within the “products” category are: nucleic acids, peptides,

polypeptides, proteins, microorganisms, virus, cells, vectors, plants, seeds,

hybridomas, antibodies, probes, vaccines, compositions, kits, expression cassettes,

extracts, food products, and others. For “process claims”, some non-exhaustive Page 15 of 63

examples are: process for producing a compound/composition; process for selecting a

sequence of nucleic acid/polypeptides/peptides; process for producing a transgenic

microorganism/plant/animal; method of purification; processes of extraction/isolation,

among others.

3.1 ‘Reach-through’ type claims in biotechnology

‘Reach-through’ claims are a special type of claim which seek protection for

future inventions based on an invention from the present. That is, this type of claim

seeks protection for inventions that had not been identified by the inventor up to the

time of filing his patent application, but which may be identified in the future by use

of the real invention.

A frequent type of reach-through claim in biotechnology is the product claim,

said product generally corresponding to a “candidate compound”. Such claims seek to

protect compounds that are candidates for modulators of the activity of the real

invention, such as the agents that modulate the biological function of a protein or a

gene.

Reach-through products (drugs, agonists, antagonists, etc.) are usually

identified merely by reference to a material or method used in the identification of

same, without a definition of their chemical structures. Otherwise, such products are

defined in terms of the function associated to the real invention, since this is the only

information available to the inventor. Consequently, both compounds already known

in the state of the art and those yet to be identified are ultimately encompassed within

the scope of the claim, which thus become altogether broad.

The other type of reach-through claim in biotechnology is the process claim

for identifying modulator compounds. In this type of claim, the compound identified

by the process is not defined by its structure but rather by its capacity to modulate the

expression of a protein or a gene involved in a disease, for example, or else by the

screening method used to identify said compound. A common characteristic for these

types of claims is that the subject matter that is the object to be protected is not

known.

3.1.1 Technical examination of reach-through claims

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The subject matters of the reach-through claims typically do not present full

disclosure, clarity, precision and/or basis, thus being in disagreement with Arts. 24

and 25 of the Industrial Property Statute.

Example 11:

Claim 1: Process for identifying an agonist/antagonist of polypeptide X characterized

by comprising (a) contacting said polypeptide with a compound to be screened; and

(b) determining whether the compound affects the activity of said polypeptide.

Claim 2: An agonist/antagonist characterized by being for the polypeptide X as

identified by the process defined in claim 1.

The application pertains to a new and inventive process of screening for

modulators of the activity of a polypeptide already known in the state of the art

(polypeptide X), whose activity was demonstrated as involved in disease Y, though the

compounds identified by said process were not characterized.

Claim 1 defines the main invention of the application which is a method of

screening compounds of therapeutic interest and that modulates the activity of

polypeptide X, being the actual invention, and claim 2 is of the reach-through type,

which in this situation may include in its scope compounds already known and which

are not modified at all by the process used in identifying same, and compounds not yet

known.

Although the application sufficiently describes the screening process

specified in claim 1, and from this aspect could be accepted, claim 2 is not accepted

owing to lack of full disclosure (Art. 24), clarity, precision and support (Art. 25).

Claim 2 uses functional (not structural) characteristics to define the subject matter that

is the object of protection. It so happens that defining a product by functional

characteristics often causes lack of clarity of the subject matter. A person skilled in the

art could not reduce the practice to the definition of the subject matter object claimed,

because the compounds claimed per se (claim 2) have potentially unlimited structural

possibilities, and thus include compounds that are yet to be identified and/or that are

already available in the state of the art and/or are barred by the prohibitions of Art. 10

(IX).

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Claim 2 seeks protection for candidate compounds identified by the screening

method of the invention defined in claim 1. Said compounds were technically defined

only by their activity (that is, functional definition – common wording in this type of claim)

which in the present situation corresponds to a modulation (agonist/antagonist) of the

activity of polypeptide X. The structural characteristics of the candidate compounds were

not defined; said situation would oblige said technician to test innumerous compounds

already known and all the compounds as may be identified in the future using the

screening method of the invention, in order to determine which of these compounds had

the desired activity and that would thus be encompassed by the scope of the claims under

examination.

4 Matter excluded from protection according to the Industrial Property Statute

4.1 Definitions

According to the understanding adopted by this Institute, technically speaking,

the terms and expressions used in these Guidelines are interpreted as follows:

• the “whole” (of natural living beings) refers to plants, animals, microorganisms

and any living being;

• “part of natural living beings” refers to any portion of living beings, such as

organs, tissues and cells;

• “biological materials found in nature” encompass the whole or part of natural

living beings, in addition to extracts, lipids, carbohydrates, proteins, DNA,

RNA, found in nature or isolated therefrom, and parts or fragments of same, as

well as any substance produced from biological systems, for example hormones

and other secreted molecules, viruses or prions. Synthetic molecules that are

identical or indistinguishable from their natural counterparts are also

encompassed within this definition;

• “isolated from nature” is understood to be all and any subject matter extracted

and subjected to a process of isolation or purification, i.e. withdrawn from

natural context;

• “genome” is the set of genetic information of a cell, organism or virus;

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• “germoplasm” is the set of hereditary material of a sample representative of

individuals of a same species;

• “natural biological process” is any biological process that occurs spontaneously

in nature and in which human intervention does not affect the end result;

• “therapy” is a treatment method designed to cure or prevent an infirmity or

defective working of the body;

• “surgery” is defined by the nature of the treatment instead of its purpose, that is,

it does not depend on manual or instrument intervention in the body of the

patient having aesthetic or therapeutic purposes; and

• “diagnosis” refers to the identification of a particular disease.

4.2Subject matters not considered inventions (Art. 10)

4.2.1 Natural biological products and processes (Art. 10 (IX))

In terms of “product” category claims, Art. 10 (IX) of the Industrial Property

Statute establishes that the whole or part of a natural living beings and biological

materials found in nature, or isolated therefrom, including the genome or germoplasm

of any natural living being, are not considered to be inventions.

For “process” category claims, such as processes, methods, uses, applications,

among others, Art. 10 (IX) of the Industrial Property Statute refers solely to natural

biological processes, establishing that these not considered inventions.

Since Art. 10 (IX) of the Industrial Property Statute addresses the whole or

part of natural living beings and biological materials found in nature which are not

considered inventions, documents published subsequent to the priority/deposit date of

the application under analysis can be used as evidence that the subject matter claimed

does not comply with the provisions of Art. 10 (IX) of the Industrial Property Statute,

provided that the information available clearly and unequivocally proves that the

subject matter claimed exists in nature.

4.2.1.1 Natural biological products

The whole or part of natural living beings and biological materials found in

nature – even if isolated therefrom, or produced synthetically which have naturally- Page 19 of 63

occurring correspondents, there being no way of distinguishing them from the natural

ones –, are considered natural biological products, and are not considered to be

inventions because they do not comply with Art. 10 (IX) of the Industrial Property

Statute.

Accordingly, the inclusion of a disclaimer with the term “non-natural” in itself

alone does not overcome the objection in terms of Art. 10 (IX) of the Industrial

Property Statute.

4.2.1.1.1 Compositions containing a natural biological product

A composition claim whose sole characteristic is the presence of a certain

product also confers protection for this product in itself. Accordingly, a composition

claim characterized solely by containing a non-patentable product (for example, a

natural extract), cannot be granted, since it would protect the very non-patentable

product. That is, even more so here than in cases of patentable components, the claim

requires parameters or characteristics which unequivocally determine that it addresses

a de facto composition.

In these cases, special care must be taken in connection to the text of the claim

with regards the other component(s) of the composition in question, so as to prevent it

from ultimately representing a mere dilution (an aqueous solution, for example) of the

non-patentable product. Bearing in mind that the finality of a composition is to place

the active component(s) in a suitable form for the purpose for which it is destined, a

“mere dilution” would be one in which the solvent does not contribute to this end

purpose, being merely the means used for extraction. Thus, it is possible that the

aqueous or ethereal extract of a certain plant, for example, despite containing a

component (extraction solvent) besides the extract itself, does not represent a ready

composition to be used for its end purpose, and this same extract diluted in another

solvent (used for, for example, to make the active ingredient absorbable) represents a

de facto composition as opposed to a “mere dilution”.

4.2.1.1.2 Extracts

Extracts are biological materials isolated from nature and, therefore, are not

considered invention based on Art. 10 (IX).

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Thus, for compositions containing extracts, the same considerations stated

above apply for natural products.

4.2.1.1.3 Enriched extracts

Extracts differentiated from their natural correspondent by being enriched in

any of their components will only be eligible for protection when their composition

presents characteristics that cannot normally be achieved by the species and that result

from direct human intervention.

Attention must also be paid to the case of extract of transgenic bacterial cells.

Although the microorganism in itself may be patentable, its extract is not always

patentable, since there may be cases in which it is not possible to distinguish the

extract from the transgenic cell from the wild extract (for example, the transgenic

microorganism merely superexpresses the endogenous protein).

Example 12:

Claim 1: A vegetable extract characterized by being enriched with isoflavones.

The extract is enriched with isoflavones by the isolation method. In this case, it

is considered that a modification of said extract results from the simple fractioning of a

natural extract isolated from nature, and said claim, therefore, does not comply with

Art. 10 (IX).

Example 13: An extract enriched by genetic manipulation.

Claim: An enriched vegetable extract characterized by comprising human insulin.

The application describes a process of altering the composition of the plant

extract by way of expression of the human insulin gene, resulting in an enriched extract.

In this case, it is considered that the modification of said extract results from the genetic

manipulation of the organism from which it is extracted. Thus, being a material

obtained from plants which present characteristics normally unachievable by the

species, resulting from direct human intervention, said extract is eligible for protection.

4.2.1.2 Natural biological processes

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A “natural biological process” is understood to be any biological process that

occurs spontaneously in nature and in which human intervention does not affect the

end result.

If technical intervention performs an important role in determining the result,

or if its influence is decisive, the process is considered an invention. That is,

processes containing at least a technical stage that has a decisive impact on the end

result, and that cannot be achieved without human intervention, are considered

inventions.

Under this concept, the classic process of obtaining plants or animals is not an

invention. In the same way, processes only having stages which mimic events

occurring in nature, are not considered inventions. In contrast, methods based on

genetic engineering (for example, producing a transgenic plant), where technical

intervention is significant, are eligible for patenting.

Microbiological processes encompass processes that use, apply to, or result in

microorganisms. Although such processes are biological processes, the INPI

considers that they are granted by being an exception from the legal exclusions

permitted under the TRIPS Agreement (Art. 27(3b)).

In the same way, the INPI considers that biological or enzymatic processes for

obtaining chemical compounds, presenting a technical stage that is decisive for the

end result, are eligible for protection.

As in other processes, biological process claims formulated correctly define

the base material, the product obtained and the means of transforming the former into

the latter; the various stages necessary for achieving the intended purpose; or in the

case of use, the material to be used and the purpose of the use.

Examples of suitable claims (N.B.: the level of detail necessary will depend on

the specific invention under examination):

• Process for obtaining compound X characterized by cultivating

microorganism W (bacteria, fungi, yeast, etc.) on Y.

• Process for obtaining compound X characterized by using enzyme E.

• Process for obtaining compound X characterized by cultivating cells of plant

P transformed by gene T.

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4.2.1.3 Use of natural products

When the process claimed involves the whole or part of natural living beings

and biological materials found in nature, including the genome or germoplasm, but

does not consist of a natural biological process, there is no obstacle for the

patentability thereof in light of that prescribed in Art. 10 (IX) of the Industrial

Property Statute. Accordingly, the use of a natural product can be eligible for

protection, provided that is in accordance with patentability requirements.

Example 14:

Claim: Use of a natural resin obtained from Aloe vera plant leaves characterized by

being for preparing cosmetic compositions for the treatment of keratin fibers.

Claims relating to the use of a natural resin for preparing cosmetic compositions can be

accepted, with due regard for adherence to patentability requirements, since no article

in the Industrial Property Statute is contrary to the use of natural products in activities

that do not constitute natural biological processes.

Example 15:

Claim: Use of RNAse characterized by being for cleaving the RNA.

Use of a natural material for carrying out the natural function itself is not considered an

invention according to Art. 10 (IX), because it consists of a natural biological process.

4.3Non-patentable inventions (Art. 18 of the Industrial Property Statute)

4.3.1 Non-patentable inventions by violation of Art. 18 (I) of the Industrial

Property Statute

According to Art. 18 (I), “anything contrary to morality, decency and public

safety, order and health” is not patentable.

Considering that biotechnology is an invention-generating technological field

which addresses subject matter that may raise moral questions and issues of public

order, current doctrine allows the INPI to reject the patenting of these inventions

based on Art. 18 (I) of the Industrial Property Statute.

Non-exhaustive examples include: Page 23 of 63

(a) processes of cloning human beings;

(b) processes of modifying the human genome that cause modification of

the genetic identity of human germinative cells; and

(c) processes involving animals that cause suffering thereto without

resulting in any substantial medical benefit to human beings or

animals from such processes.

In claims worded “process for cloning mammal cells”, it is understood that the

term “mammal” includes human beings. Thus, said claim might adversely affect

morals, order and public health, and, therefore, would not comply with Art. 18 (I) of

the Industrial Property Statute. In this case, the exclusion of human mammals from

the scope of protection would be an acceptable disclaimer, even if human beings are

not excluded in the original specification.

4.3.2 Non-patentable inventions by violation of Art. 18 (III) of the Industrial

Property Statute

According to Art. 18 (III) of the Industrial Property Statute, the following is

not patentable: “living beings, in whole or in part, except for transgenic

microorganisms meeting the three patentability requirements – novelty, inventive step

and industrial application – listed in Art. 8 and which are not mere discoveries”.

Regarding transgenic microorganisms, the sole paragraph of Art. 18 (III) of the

Industrial Property Statute defines that “For the purposes of this law, transgenic

microorganisms are organisms, except for plants and animals, in whole or in part,

that due to direct human intervention in their genetic composition express a

characteristic that cannot normally be achieved by the species under natural

conditions”.

In accordance with this definition, the term transgenic microorganism covers

microorganisms (see item 5) which are obtained by any technique having the

consequence of altering the genetic composition, that cannot be achieved by the

species under natural conditions, by direct human interference. This definition is not

limited to microorganisms which have exogenous genes and/or other organisms

inserted therein.

In the examination of transgenic microorganism claims, it must initially be

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verified whether the term “microorganism” in the application description covers

animal and vegetable cells, which is not eligible for protection, since the whole or part

of plants and animals, even if transgenic, is not patentable. In these cases, the subject

matter claimed must be limited so as to encompass only those transgenic

microorganisms eligible for protection. Additionally, human intervention must be

clear so that it is possible to evaluable whether it is fact addresses a microorganism

that expresses a characteristic not normally achievable by the species under natural

conditions.

Denominations such as “transgenic”, “mutant” or “variant” are not sufficient to

evaluate the patentability of the microorganism, in view of the possibility that the

microorganism, even so-called “transgenic”, “mutant” or “variant”, may occur

naturally or be indistinguishable from the natural one, and therefore not constitute an

invention according to Art. 10 (IX) of the Industrial Property Statute.

5 Microorganisms

The generic term “microorganism” is employed for bacteria, archaea, fungi,

single cell algae not classified in the Plant Kingdom and protozoa. Accordingly,

among the whole or part of living beings, natural or transgenic, the Industrial Property

Statute only allows transgenic microorganisms to be patented.

Examples of suitable formulations for microorganism claims (non-exhaustive list)

• Transgenic microorganism characterized by containing SEQ ID NO: X.

• Transgenic microorganism characterized by containing SEQ ID NO: X inserted in

position Y of the genome.

• Transgenic microorganism characterized by containing sequence xxxxxxx in

position Y of the genome (see item 2.2.2).

• Transgenic microorganism characterized by containing gene X (provided that the

gene is well known).

• Transgenic microorganism characterized by containing gene X with the promoter

Z inserted in position Y of the genome (provided that the gene and the promoter

are well known).

• Transgenic microorganism characterized by containing expression vector X Page 25 of 63

(provided that this vector is well known).

• Transgenic microorganism characterized by being the ATCC-XXXX (filing

number).

Attention must be paid when SEQ ID NO: X, the gene X or the plasmid X were

isolated from a natural and non-modified microorganism. In such case, the claim

bearing the generic title of “microorganism” or “bacteria”, among others, will also

protect the original microorganism that has said gene naturally, and an objection will

be admissible based on prescribed in Art. 10 (IX) of the Industrial Property Statute.

6 Biological sequences

In general terms, in patent applications describing an invention whose

development depends on sequences of aminoacids and/or nucleotides, the following

aspects shall be noted: (i) need to include the sequence in the application for purposes

of full disclosure (Art. 24); (ii) natural occurrence (Art. 10 (IX)); (iii) clarity, precision

and basis (Art. 25) in the form in which such molecules / sequences are claimed; (iv)

novelty (Art. 11); (v) inventive step (Art. 13); and (vi) industrial application (Art. 15).

Full disclosure of biological sequences is specifically addressed in item 2.2.2.

The novelty requirement, when related to biological sequences, follows the

same general principle (see Guidelines for Examining Patent Applications, Block II),

that is, for a sequence of aminoacids or nucleotides to be new in light of the state of

the art, all the aminoacids or nucleotides shall be exactly the same and be in the same

order and, in some cases, additionally have the same structural formula as the

sequence known in the art.

The same points in which unsuitable matters are usually noted will be

addressed in the topics below.

6.1 Characterization

Having complied with the rules established in item 2.2.2 as a way of

guaranteeing clarity and precision of the subject matter claimed, the set of claims shall

refer to the biological sequences in question by way of the corresponding SEQ ID NO:

(see item 2.2.2).

In some cases, other forms characterizing biological sequences can be

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accepted:

a) when the sequences have fewer than four aminoacids or ten

nucleotides, in accordance with Resolution PR Nº 81/2013, they shall

be characterized by the sequence itself;

b) structural formulae accompanied by their corresponding SEQ ID NO: ;

c) Markush formulae accompanied by their corresponding SEQ ID NO: ;

d) deposit number (see item 2.2.1); or

e) by its name or designation, when a biological sequence is already

known in the state of the art and is not the main object of the invention.

It is emphasized that a DNA must be defined by its sequence of nucleotides,

whereas a protein, by its sequence of aminoacids, so as to define with clarity the

subject matter that is the object of protection.

Additionally, attention must be paid to claims of the following types, since

none of them bears clarity (Art. 25).

a) DNA sequence characterized by encoding a protease.

In this type of claim, the product is characterized solely by its

function, which is not sufficient to define with clarity what the product

refers to. In contrast, if this DNA is characterized by its sequence of

nucleotides, the definition of the function may be accepted, as an additional

characteristic of the product.

b) DNA sequence characterized by encoding a polypeptide presenting a

sequence of aminoacids of the protein represented by SEQ ID NO: 1.

This wording defines a DNA by the sequence of aminoacids, which is

not permitted. However, the claim may be altered so as to define the DNA

by the sequence of nucleotides, and their degenerations which generate the

same protein may be accepted. In this situation, at least one sequence of

nucleotides must be present in the application as filed, unless it is a

sequence that is already available in the state of the art and referenced in

the specification.

c) Protein characterized by presenting activity Y.

The product is characterized solely by its function, which does not

enable the scope to be clearly defined. In contrast, if said protein is

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characterized by its sequence of aminoacids, the definition of the function

may be accepted, as an additional characteristic of the product.

d) Protein with activity Y characterized by presenting the following

composition in aminoacids: (percentages of each aminoacid present).

In this type of claim, the product is characterized by its function and

by the percentage of aminoacids, which does not enable the product

claimed to be clearly defined either. The sequence of aminoacids is

necessary.

e) Plasmid characterized by being the pWn.

In this type of claim, the product is characterized by a designation

given by the inventor himself, which does not permit the product to be

defined.

6.1.1 Markush form sequences

Biological sequences can be presented in the form of a Markush formula

containing a base sequence that is substituted by one or more variable substructures,

which are accompanied by a list of definitions of these variable portions, such as, for

example:

Peptide of Formula I

Xaa1 Xaa2 His Xaa4 Pro Gly Ser Phe Ser Asp Glu Gly Asp Trp Leu;

wherein

Xaa1 is His or Thr;

Xaa2 is Ala, Gly or D-Cpa (4-chloro-Phe); and

Xaa4 is Gln, Asn or Pro.

For further details on Markush formulae, see the Guidelines for Examining

Patent Applications, Block II.

6.1.2 When it is necessary to file the listing of sequences in conjunction with the

application

Resolution PR Nº 81/2013 of the INPI establishes in Art. 2 thereof that when

the patent application contains one (or more) sequence(s) of nucleotides and/or

aminoacids, which is (are) fundamental for the description of the invention, said

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sequence(s) shall be presented in a listing of sequences.

When the invention includes the sequence per se, that is, when the set of

claims bears “protein”, “polypeptide”, “nucleic acid” claims, or any other term

designating a biological sequence, such is considered a fundamental part of the

invention, and must be included in the listing of sequences (except for sequences

having fewer than four aminoacids or ten nucleotides, cf. defined in Resolution PR Nº

81/2013).

In contrast, when a molecule in question is solely an illustrative example, said

specific sequence may not be considered a fundamental part of the invention, and

therefore, its sequence does not necessarily need to be presented as part of the

application.

Additionally, care must be taken regarding the possibility that other sequences

used in the application – and not necessarily the encoding genes / sequences – are

fundamental to carry out the invention. Thus, in these cases, it is also important to

evaluate whether the sequence in question is broadly known in the art, and whether its

use is fundamental to carry out the invention.

6.1.3 Need to restrict the set of claims to the sequences filed in conjunction with

the application

When a sequence in question solely represents a molecule that is part of a

process described, but that any other molecule having the same biological function

would present the same result (or in situations where there is no reason to believe that

such molecules would not be effective), said method does not necessarily have to refer

to a single SEQ ID NO:, since said measure would unnecessarily restrict the scope of

the method in question.

Example 16:

The application describes a method of inducing sporulation in bacteria characterized

wherein said bacteria are transformed with a vector containing a sporulation gene

under the control of any promoter. The examples presented in the application use the

spo5 gene. Nevertheless, any gene of the spo family would theoretically allow the

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same result to be achieved. Thus, in theory, there is no reason to demand that a

specific sequence of the spo5 gene be presented in said method claim.

Attention in these cases should lie on the “generic” name given to the sequence of

interest, the so-called “spo gene”, as mentioned above, because if the applicant uses

said denomination in the claims, it must be broadly known and used in the art,

unequivocally referring to a certain gene family.

Example 17: A method for inducing the expression of a given gene under certain

specific conditions.

The specification clearly states that the desired characteristic is a genic

expression in a certain condition, which is only obtained by use of promoter X, since

this promoter is only activated when the means impacts the characteristics of interest

(depletion of glucose, for example).

The application describes the use of different genes under the control of this

promoter X, demonstrating that they are all expressed solely in the conditions of

interest.

In this case, the single fundamental sequence to obtain the desired

characteristic is that of promoter X. Thus, as in the prior example, it is considered that

the presentation of the sequences of genes used is not compulsory; and even if the

applicant presented such sequences, it is not deemed necessary that the subject matter

claimed be restricted to these genes. Nevertheless, the sequence of the promoter,

which is the invention, must be described clearly and precisely by way of its

corresponding SEQ ID NO:.

6.2 Homology versus identity

When aligning and comparing nucleotide or protein sequences with each other,

the terms homology, identity and similarity may be employed. At this stage, it is

important to make the distinction between such terms.

Two sequences (of nucleotides or aminoacids) are homologous solely when

they share a same common ancestor. Therefore, the concept of being “partially

homologous” is non-existent: two sequences are either homologous or not, and it is

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incorrect to speak of percentage of homology. Homologous proteins generally share

may similarities regarding their three-dimensional structures. When two sequences are

homologous, they generally share a significant identity, though there may also be cases

to the contrary: two molecules may be homologous without sharing a statistically

significant identity between their sequences of aminoacids or nucleotides (for example,

as is the case of the family of globins).

Establishing homology between two sequences is not solely based on the

analysis of the identity between these sequences, but also on biological criteria, such

as analyzing the structure and function of the proteins, for example. Results from

comparing sequences by way of algorithms such as BLAST, FASTA and SSEARCH

do not evaluate homology between sequences: they measure the similarity and the

identity between sequences. Whereas homology refers to a qualitative inference,

identity and similarity are quantitative attributes.

The identity between two sequences refers to the occurrence of precisely the

same nucleotides or the same aminoacids in a same position in two nucleotide or

protein sequences aligned and compared to each other. Therefore, if two proteins

present 90% identity, this means that 90% of all the residues of aminoacids contained

in said proteins in corresponding positions are precisely identical.

In contrast, the percentage of similarity between two sequences of proteins

refers to the sum of the identical and similar matches (for example, the aminoacids

glutamate and aspartate are considered similar, since both are acidic). It must be

noted that the similarity can be measured based on different definitions on how related

(similar) an aminoacid residue is to the other.

Applying these terms to the examination of patent applications, the following

types of claims are not accepted:

a) claim of the type “protein (or DNA sequence) characterized by being a SEQ

ID NO: 1 or any other sequence of aminoacid with at least x% homology with

SEQ ID NO: 1” is not clear (in disagreement with Art. 25 of the Industrial

Property Statute), since, technically, the term “% homology” is not applicable,

as highlighted above; and

b) claim of the type “DNA sequence (or protein) characterized by presenting at

least 80% identity (or similarity) with SEQ ID NO: 1” cannot be accepted

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since said as worded it covers innumerous different sequences, and also does

not specify at which sites in the sequence of nucleotides (or aminoacids)

substitutions may occur; therefore, claims of this type cannot be accepted,

since the characterization of the object of protection is not clear and precise,

this being in disagreement with Art. 25 of the Industrial Property Statute.

Furthermore, the characterization of the sequence of interest based on the

identity percentage is highly broad and generally includes in its scope sequences not

supported by the specification or that do not meet patentability requirements. Lastly,

it is also important to note that in these cases, the specification does not generally

provide sufficient information to enable the reproduction of all the countless

sequences covered by said type of definition (this being in disagreement with Art. 24

of the Industrial Property Statute).

6.3 Sequences of nucleotides

Nucleotide sequences can be referred to in patent applications in different

manners: genes, vectors, plasmids, DNA sequence, RNA sequence, nucleic acid,

oligonucleotides, primers, cDNA, and other. Nevertheless, for purposes of

simplification, in these Guidelines, all these molecules will be designated, in general

terms, as “sequences of nucleotides”. This definition is valid despite the size of said

molecule. The items below will address the particular aspects of some of these

molecules.

Said sequences of nucleotides shall be characterized in accordance with the

item 6.1. Nevertheless, it must be emphasized that the molecules defined by a

sequence with fewer than ten nucleotides shall be characterized by the sequence of

nucleotides itself.

6.3.1 Modification of nucleotide sequence(s)

Modifications in nucleotide sequences with the aim of differentiating them

from natural sequences may be carried out in different ways. In theory, any

characteristic introduced into the sequence that was not described as naturally-

occurring is acceptable as a modification so as to comply with Art. 10 (IX) of the

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Industrial Property Statute, with due regard for that prescribed in item 6.3.1.1.

Nevertheless, the simple introduction of terms such as “recombinant” in natural

molecule claims cannot be accepted, since the resulting molecule would be

indistinguishable from its natural counterpart, even if produced in recombinant

manner.

6.3.1.1 Modification of sequence(s) by substitutions, insertions or deletions of

non-modified nucleotides

In general terms, modifications of natural biological sequences by inserting

non-modified nucleotides into the sequence (in the means or at the ends) are

considered sufficient so as to comply with Art. 10 (IX), provided that the resulting

sequence formed is not naturally-occurring either.

If nucleotides are deleted in the means of the sequence claimed, said

modification is, theoretically, enough to differentiate it from the natural molecule.

Nevertheless, even in cases where deleted nucleotides are contiguous and are at the

end of the sequence, this still does not comply with Art. 10 (IX), since the resulting

sequence is still identical to part of the natural sequence (see item 6.3.2).

Regarding the substitution of nucleotides by other non-modified nucleotides, it

is considered that said modification is sufficient to comply with Art. 10 (IX), provided

that there is no description of natural sequences (for instance, in related species)

containing said substitution.

Nevertheless, it should be considered that various substitutions of nucleotides

in a given sequence may not result in any modification in the protein encoded thereby,

owing to degeneration of the genetic code. Thus, in these cases, a nucleotide sequence

modified by substitutions may comply with Art. 10 (IX), whereas the sequence of

aminoacids encoded thereby remains identical to the natural one, and, therefore, does

not comply with Art. 10 (IX).

When analyzing sequences derived from the state of the art, which comply

with Art. 10 (IX), it is important to analyze the inventive step of the modification

(insertion, deletion or substitution) made, taking into account the fact that some

groups of aminoacids present common properties. Thus, the inventiveness of these

alterations in the polynucleotide sequences generally depends on the demonstration of

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an unexpected effect generated by the modification in relation to the state of the art.

6.3.1.1.1 SNPs

The SNP abbreviation refers to “single nucleotide polymorphism” and is used

to designate natural variations that occur in the genome and which involve, as the

name suggests, a single nucleotide. They may be associated to certain characteristics,

thus acting as molecule markers.

Regardless of the utility described, whenever a certain SNP – or any other

polymorphism – is described as being naturally-occurring, it cannot be considered as

an invention, according to Art. 10 (IX) of the Industrial Property Statute.

Nevertheless, the use of a set of SNPs, for example, in an in vitro diagnosis method

(such as DNA fingerprinting) or in the ambit of personalized medicine, may be

eligible for patent protection.

6.3.1.2 Modification of sequence(s) of nucleotides with modified derivatives

(including protector groups)

Inserting nucleotides that are not naturally-occurring (derivatives of natural

nucleotides) are also considered sufficient modifications for the sequences to comply

with Art. 10 (IX). Nevertheless, the presence of these nucleotides and the list of

nucleotides of interest shall be expressed in the claims, so as to prevent the natural

nucleotides from being indirectly included whereby resulting in the natural biological

sequence.

The inclusion of such nucleotides in the sequences presented in patent

applications is addressed in INPI Resolution PR Nº 81/2013, cited in item 2.2.2 of

these Guidelines; and a list with examples of modified nucleotides and the acceptable

abbreviation in their definition is available in Table 2 of the Appendix to this

Resolution (published in the Official Federal Gazette (DOU) – Section 1, Nº 68, April

10, 2013).

6.3.2 Fragments

Special attention in required in analyzing claims involving “Fragments of

sequences”, even if such sequences are inserted into the application. Said

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consideration is due to the fact that the definition of “fragments” of a said sequence

includes all and any subdivision of the sequence presented, resulting in an undefined

number of possible fragments, which do not present any function/relation with the

subject matter described in the application.

Example 18:

An application presents SEQ ID NO: 1 (hypothetican( � agctggttcgactgtctcga.

The claim refers to a “nucleic acid characterized by having a sequence of

nucleotides of SEQ ID NO: 1 and fragments thereof”. As the claim stands, said

claim includes, for example, molecules such as: agct, actg, ctgg, ggtt, ggttc, cgactgt,

and an infinity of others, including many that do not have any function

described/related with the invention.

Thus, it is clear that the reference to fragments of a given sequence cannot

be accepted in the claims, since the subject matter claimed is not supported, nor is it

clearly and precisely defined in accordance with Art. 25 of the Industrial Property

Statute. In these cases, full disclosure of the subject matter may be questioned in

accordance with Art. 24 of the Industrial Property Statute.

Moreover, if the application describes that fragments obtained from a certain

sequence are useful to the finality described in the invention, such fragments may be

claimed, provided that the desired fragments are clearly identified in the claims

(specifying the position of the initial and final nucleotides of this fragment) and are

not natural.

6.3.3 Oligonucleotides (or initiators)

Since they represent segments of sequences complementary to genes and/or

natural mRNAs, it is considered that primers are part of natural biological material,

and therefore, claims that claim such primers do not comply with Art. 10 (IX) of the

Industrial Property Statute (note the possible exceptions in item 6.3.1).

6.3.3.1 Degenerate and modified oligonucleotides

Degenerate oligonucleotides generally consist of a mixture of oligonucleotides

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which can be used for amplifying genes that have similar but not identical sequences

(such as the amplification of orthologous genes in related species), or same genes

unknown.

Attention must be paid to the possibility that one (or some) of the resulting

oligonucleotides are identical to a natural biological sequence (for example, to the

gene sequence intended for amplification), which in this case does not comply with

Art. 10 (IX). Moreover, if they present modifications, which result in a different

sequence of nucleotides to that which occurs in nature, they will comply with Art. 10

(IX) (see item 6.3.1).

Additionally, considering that a mixture of oligonucleotides (for example,

degenerate oligonucleotides, etc.) may not be clearly and precisely defined, the claims

relating to this subject matter will not comply with Art. 25 of the Industrial Property

Statute. Attention is also needed for the description of this mixture in the specification

(compliance with Art. 24 of the Industrial Property Statute).

Furthermore, so that the subject matter claimed is clearly and precisely

defined, a degenerate oligonucleotide may be characterized based on a consensus

sequence, and vary solely by one or a few pre-defined nucleotides. In such cases, the

claims relating to these degenerate oligonucleotides shall cite the consensus sequence

and the variable nucleotide positions.

6.3.4 Promoters

Promoters are the central processor of the regulation of a gene, since it

contains the binding sites for the RNA polymerases, responsible for the genic

transcription. By definition, it comprises the region 5' of the gene. The processes that

provide the transcriptional modulation are highly complex and occur by way of an

intricate network of interactions involving regulatory sequences (TATA box, CCAAT

box etc.) and other elements located further away from the transcription starting point

(enhancer and silencer sequences).

Contrary to gene sequences, which have specific “markers” for their start and

finish (for example: initiation codon, site for polyadenylation, etc.), the sequence of a

promoter does not present such delimitations. Therefore, experimental data shall be

presented to prove that the isolated DNA sequence is indeed capable of leading to the

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expression of gene sequences, that is, it shall present the promoter activity of interest.

There are intermediary cases in which the DNA sequence with promoter

potential is isolated, sequenced and analyzed by bioinformatics to predict its possible

regulatory motives (CCAAT box, TATA box, CpG islands, etc.). said analysis in

silico, though of great importance for preliminary studies, is not sufficient to

demonstrate that the sequence identified is indeed a promoter region, validation with

suitable functional assays being necessary.

In any case, as they are made up of sequences of nucleotides, promoters shall

be represented by a SEQ ID NO: X, as established in items 2.2.2 and 6.1.2.

Example 19:

Claim 1 : DNA sequence characterized by being SEQ ID NO: 1

Said sequence was isolated and presents promoter activity: said claim cannot

be accepted because it does not comply with Art. 10 (IX) of the Industrial Property

Statute.

Nevertheless, in cases where the SEQ ID NO: 1 presents mutations, deletions

and/or insertions, that is, it becomes different to the sequence as found in nature, the

examination of novelty, inventive step and industrial application of the invention is

applicable. It is important to note that deletions may result in fragments that are

considered as part of the natural material, and therefore, would not comply with Art.

10 (IX) (see items 6.3.2 and 6.3.3.1) either.

Example 20:

Claim: Expression cassette characterized by comprising the promoter sequence of SEQ

ID NO: 1 operationally bound to a gene of interest and a terminator sequence.

If SEQ ID NO: 1 was found in nature, but was subsequently modified (via

punctual mutations, deletions and/or insertions), the above claim may be accepted,

provided that the subject matter is considered new and inventive. If SEQ ID NO: 1 is as

found in nature, the claim must be restructured so as to better specify the cassette, with

the introduction of the term “heterologous”, clearly stating that it does not cover

protection for subject matter that does not comply with Art. 10 (IX) of the Industrial

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Property Statute (see item 6.3.5).

Example 21:

Claim: Expression cassette characterized by comprising a promoter sequence

selected from the group of SEQ ID NO: 1 to 3 or fragments and derivatives thereof

operationally bound to a gene of interest and a heterologous terminator sequence.

This type of claim must be analyzed taking into account the observations in the

examples above. Furthermore, the promoter sequence must be restricted solely to

the sequences for which the promoter activity of interest was demonstrated. If

promoter activity was demonstrated solely for SEQ ID NO: 1, for example, a claim

must be limited to said sequence; further, the term “or fragments and derivatives

thereof” cannot be accepted, since the subject matter claimed is not supported, nor is

it clearly and precisely defined in accordance with Art. 25 of the Industrial Property

Statute. In these cases, full disclosure of the subject matter may be questioned in

accordance with Art. 24 of the Industrial Property Statute.

6.3.5 Vectors

A vector is a DNA molecule used as a vehicle for transferring exogenous

genetic material to other cells. Normally, DNA vectors present three characteristics:

(i) they contain an origin of replication that enables the replication thereof, regardless

of the host chromosome; (ii) they contain a selection marker that enables the cells

containing the vector to be easily identified; and (iii) they present single sites for one

or more restriction enzymes. The cloning vector is designed to replicate an insertion

in a host cell. The expression vector contains an expression cassette that enables the

insertion to be expressed in the target cell in an induced or constitutive manner. The

expression cassette contains regulatory sequences, such as transcription promoter and

terminator sequences.

Regarding full disclosure pursuant to Art. 24 of the Industrial Property Statute,

the examiner shall analyze the invention in question and the level of detail necessary

for it to be reproduced, depending, for example, on whether the vector is the main

invention or an accessory invention. In this sense, certain aspects shall be noted in the

specification: Page 38 of 63

• representative drawing of the map of the vector in question, highlighting the

essential characteristics for it to work, that is, the cleavage sites for the

restriction enzymes, the appropriate restriction enzymes, the promoter used,

the repression regions, the termination regions, the marker sequences or

sequences that confer resistance to antibiotics, etc.;

• the sequence to be cloned and/or expressed in the form of SEQ ID NO: X shall

be present in the listing of sequences, pursuant to the Resolution(s) in effect;

• if the preferred codons for expressing the insertion in a given microorganism

are essential to the invention, they must appear in the listing of sequences; and

• the procedures and the conditions for manipulating the DNA/RNA, including

the enzymes used (for example, endonuclease, polymerase, ligase, etc.), the

cloning systems involved, the conditions of transfection/transformation of the

host cell, among other usual techniques.

It is important to point out that when there is no other way of defining the

vector in reproducible form (full disclosure – Art. 24 of the Industrial Property

Statute), the biological material must be deposited (see item 2.2.1).

Below are examples of claims designed to reflect commonplace situations in

which vectors are recombinants. In other words, these examples do not encompass

natural vectors found in bacteria, fungi and plants, especially in mitochondria and

chloroplasts, since these are not considered inventions in light of Art. 10, item IX, of

the Industrial Property Statute.

Example 22: Vector as main invention.

Claim: A vector characterized by consisting of filing number XXXX.

The main invention pertains to a new and inventive vector which can be

employed for cloning and/or expressing a gene of interest. In this case, the vector can

be characterized in a claim by its filing number recorded at an International

Depositary Authority. Therefore, the vector will be defined clearly and precisely,

pursuant to Art. 25 of the Industrial Property Statute.

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Example 23: Vector as main invention.

Claim: A vector that contains the sequence of origin of replication, selection marker

sequence and multiple cloning sites characterized by comprising SEQID NO:X

In this example, the structure of the vector is new and inventive owing to the

specific combination of SEQ ID NO: X with the other elements common to vectors,

such as the sequence of origin of replication, the selection marker sequence (for

antibiotics, etc.) and the sites for the restriction enzymes. Therefore, the essential

elements that distinguish this vector from others in the state of the art shall be the

only elements characterized by their respective SEQ ID NO: X, since the other

components are known by a person skilled in the art. Importantly, in this case, the

SEQ ID No: X does not correspond to the expression cassette.

Example 24: Vector as an inter-related invention.

Claim: Vector characterized by comprising the sequences defined by SEQ ID NO: X

and SEQ ID NO: Y operatively bound to the heterologous promoter and terminator

sequences.

The invention describes two genic sequences involved in the transport of

lysine which were isolated from Corynebacterium glutamicum. SEQ ID NO: X

encodes the lysine-exporter protein (LysE), whereas SEQ ID NO: Y encodes the LysE

regulator protein (LysG). Although SEQ ID NO: X and SEQ ID NO: Y are

endogenous to the host cell Corynebacterium and, therefore, natural, they are flanked

by heterologous sequences of the gene construction present in the recombinant vector.

Accordingly, the vector complies with that prescribed in Art. 10 (IX) of the Industrial

Property Statute.

Example 25: Vector as inter-related invention.

Claim: A vector characterized by comprising a DNA construction consisting of the

sequence defined by SEQ ID NO: X operationally bound to the transcription promoter

and terminator sequences.

The invention refers to a new gene sequence which bears inventive step and

is eligible for cloning/expressing in suitable host cells.

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In cases where SEQ ID NO: X is identical to that found in nature, care must

be taken such that the construction as a whole presents some heterologous sequence

as a way of differentiating it from the natural sequence. However, if SEQ ID NO: X is

altered, the term “heterologous”, as used in example 24, is not necessary.

6.3.6 cDNA

cDNA molecules represent sequences produced from RNAs. In the case of

cDNAs originating from messenger RNA (mRNA), if the originating gene has introns,

the cDNA will be different to the gene that encoded this mRNA, since the cDNA

sequence will only present the sequence of exons. Accordingly, in these cases, it

cannot be considered that a cDNA molecule is identical to a natural molecule, and its

patentability must be evaluated based on the requirements of novelty, inventive step

and industrial application.

When the cDNA addresses molecules produced from mRNAs from genes that

do not have introns, said cDNA will have an identical constitution to the DNA/gene

strand which acted as mold for synthesizing this mRNA. Thus, in these cases, the

cDNA is not considered an invention, according to Art. 10 (IX) of the Industrial

Property Statute.

In cases of cDNA obtained from other types of RNA (such as, for example,

tRNA, snRNA, rRNA), it must be verified whether they are identical to the natural

DNA, a situation in which they would not be considered an invention, according to

Art. 10 (IX).

Additionally, the simple sequencing of the cDNA without association of a

function for same, is not sufficient to guarantee industrial application (see item 1.1)

and support for the subject matter, this being in disagreement with Arts. 15 and 25 of

the Industrial Property Statute, respectively.

6.3.7 ESTs – Expressed Sequence Tags

The term “EST” refers to a partial sequence – or a fragment of the sequence –

obtained from a cDNA (hence the fact of referring solely to expressed sequences).

The simple sequencing of an EST is not sufficient to guarantee industrial

application and support for the subject matter, this being in disagreement with Arts. 15

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and 25 of the Industrial Property Statute, respectively.

Additionally, so as to comply with Art. 10 (IX), the analysis of this subject

matter follows the same criteria used for cDNA; therefore, it is necessary to know

whether said EST represents a sequence fragment of a single exon (in which case it

would be considered part of a natural biological material), or if it extends beyond the

juncture point between two different exons (in which case there would be no natural

equivalent, and therefore, could be considered as an invention).

In contrast, when addressing sequences originating from genes that do not

have introns, any EST is considered a fragment of a natural biological sequence (see

also item 6.3.2).

6.3.8 ORFs – Open Reading Frames

The term ORF refers to potentially encoding sequences, generally obtained

from DNAs sequencing. Additionally, an ORF has an initiator codon (relating to a

methionine, for the majority of organisms) and ends with a terminator codon.

Since this is a region of the genome, the ORF is deemed to be a natural

product, and is not considered an invention according to Art. 10 (IX).

An ORF represents a candidate to an encoding region of a genome that does

not necessarily result in a functional gene product. Thus, in the case of a claim of the

type “vector characterized by comprising an ORF present in SEQ ID NO: 1”, it is

important to evaluate the demonstration of the functionality of the product obtained

from the expression of this ORF, in order to meet the requirement of industrial

application (Art. 15), as well as clarity and precision of the subject matter claimed

(Art. 25).

6.3.9 RNAs

RNAs encoded by natural genes are also natural biological molecules, and

therefore, are not considered inventions according to Art. 10 (IX) of the Industrial

Property Statute.

In contrast, if they are a product of the expression of chimeric genes (such as

genes constructed to express fusion proteins and/or others in existence not found in

nature), such RNA molecules, cannot be considered a natural biological material.

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6.4 Sequences of aminoacids

For definition purposes, it is considered that in analyzing patent applications,

“proteins”, “peptides” and “polypeptides” shall be defined based on their linear

sequence of aminoacids (primary structure), regardless of their size (total number of

residues of aminoacids in accordance with Resolution PR Nº 81/2013). Therefore,

citing any one of these terms (“proteins”, “peptides” or “polypeptides”) in these

Guidelines generally refers to a “sequence of aminoacids” or “protein sequence”.

6.4.1 Characterization of sequences of aminoacids

As stated above, having followed the rules established in items 2.2.2 and 6.1,

as a form of guaranteeing clarity and precision of the subject matter claimed, the set

of claims shall refer to the proteins in question by way of corresponding SEQ ID NO:

and in some cases, additionally, by their structural formula. Sequences with up to 03

(three) residues of aminoacids shall be represented throughout the application solely

by their sequence.

Example 26: Acceptable claims for sequences of aminoacids (provided that these

sequences are not naturally-occurring).

Claim: Protein X characterized by comprising a sequence of aminoacids as defined in

SEQ ID NO: 1.

Claim: Polypeptide characterized by consisting of a sequence of aminoacids as

defined in SEQ ID NO: 1.

Claim: Protein X characterized by consisting of the sequence SEQ ID NO: 1.

Example 27: Claim not acceptable for sequences of aminoacids.

Claim: Protein characterized by consisting of a sequence of aminoacids encoded by

SEQ ID NO: 2 (sequence of nucleotides).

In this situation, an office action shall be issued for the applicant to state the

sequence of aminoacids corresponding to the sequence of nucleotides presented,

without constituting the addition of subject matter.

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Accordingly, the characterization of protein sequences solely by way of their

properties, such as three-dimensional structure, function or biological activity, name,

chemical properties (PI, molecular weight, composition of aminoacids, etc.) will not

be accepted in the claims, since the only way of clearly and precisely defining a

sequence of aminoacids in an unequivocal manner is by the sequence itself.

Additionally, attention must be paid to item 6.2 of these Guidelines, which

address biological sequence claims by way of percentage of identity and/or similarity

to a sequence of reference.

It is important to bear in mind that the use of the terms consist or comprise

results in differences of scope of the claim (see the Guidelines for Examining Patent

Applications, Block I).

Example 28:

The specification of the application describes a mutated protein (non-natural)

characterized by consisting of SEQ ID NO: W. In this case, it would not be possible

to accept a generic claim that sought protection for the mutated protein (non-natural)

characterized by comprising SEQ ID NO: W, as this would imply the possibility of

having any extension in the carboxyl and/or amino terminal regions of the protein that

might cause alterations to the three-dimensional structure of same and/or alterations

of function. Therefore, it would not be possible to assert that any protein comprising

SEQ ID NO: W would work in a similar way to the consisting of SEQ ID NO: W, and

said claim shall be questioned owing to the lack of full disclosure and support in the

specification (Arts. 24 and 25 of the Industrial Property Statute). Even if the

specification discloses certain possible extensions in the sequence of aminoacids of

the protein, such examples would not be sufficient to support that any extension would

achieve the same result.

6.4.2 Homologous proteins (paralogous versus orthologous)

Homologous proteins are proteins that derive from “common ancestral

evolution”. They may be present in a same species, being derived from gene

duplication, originating what is called paralogous (equivalent proteins – with or

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without sequence alterations produced during the course of evolution – present in a

same species). Moreover, they may be present in different species and that have

common ancestry; in this case, such proteins are called orthologous.

These definitions are important for evaluating the inventive step of

applications that describe and claim proteins similar to proteins whose function is

already known, differing solely in relation to the organisms from which the protein

originates.

Example 29:

The patent application describes protein B, isolated from a certain species. This

protein B presents sequence and activity that is highly similar to another protein,

called A, previously described in the state of the art for a different species (A and B

are, therefore, orthologous proteins). In these cases, it is considered that the simple

fact that protein B is isolated from a different organism does not necessarily make it

inventive in light of protein A. Thus, the evaluation of inventive step may consider

whether protein B presents any unexpected characteristic in light of its orthologous A.

Even so, in this case, protein B in itself would not be considered an invention

according to Art. 10 (IX).

Additionally, when the applications involve “variants” or “modifications” of

proteins natural, attention must be paid for compliance with Art. 10 (IX), since such

modifications” may result in another provably natural biological molecule,

originating solely from a different species to the one described in the application.

Example 30:

An application describes modifications in a bovine protein so as to render it suitable for

a certain use, and claims the modified protein itself. Nevertheless, the protein resulting

from the alterations introduced, for example, substitutions, results in a sequence

identical to that of the canine version of said protein, which is already known. In this

case, even though it is not identical to the natural equivalent of the organism in which it

was obtained, the protein claimed is identical to an orthologous protein – natural from

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another species –, and, consequently, does not comply with Art. 10 (IX) either.

6.4.3 Protein fragments

A protein fragment, in the same way as a protein, must be characterized at

least by its sequence of aminoacids (see item 6.4.1). Accordingly, when a protein

fragment is claimed, and characterized solely by its sequence linear, the examiner

must perform a search by the characterizing sequence of aminoacids. If a sequence is

found in the state of the art as part of a protein or peptide of natural origin, the subject

matter claimed will not comply with Art. 10 (IX) of the Industrial Property Statute,

because it constitutes a part of natural living beings and/or biological materials found

in nature.

When a peptide containing few aminoacids is claimed, it is likely found in a

protein in nature, even without a known function in the protein or in a different

context to the subject matter presented in the application under examination. Even so,

the subject matter claimed does not comply with that prescribed in Art. 10 (IX) of the

Industrial Property Statute, since no delimitation is established in the Industrial

Property Statute regarding a minimum size for a fragment to constitute a part of a

natural biological material. Therefore, not any part of natural living beings and

biological materials (i.e. fragments) found in nature shall not be considered to be an

invention.

It is possible for a fragment claimed to be identical to a part of the whole

molecule found in nature. In these cases, even when the fragment claimed presents

innovative activity, function, or chemical properties in light of the state of the art,

since it constitutes a part of a natural living being or a biological material found in

nature, it is not an invention according to Art. 10 (IX) of the Industrial Property

Statute, so it is inappropriate to perform any type of analysis regarding its novelty and

inventive step.

It is important to note that the presence or inclusion of the term “recombinant”

in a natural molecule claim cannot be accepted, since the resulting molecule would be

indistinguishable from its natural counterpart, even if produced in a recombinant

manner.

Therefore, it is clear that any portion of a protein found in nature, regardless of

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the number of aminoacids, must be considered a part of natural living beings and

biological materials found in nature and, therefore, is not considered an invention

according to Art. 10 (IX) of the Industrial Property Statute.

Example 31:

Claim: Peptide characterized by the sequence Ile-Leu-Arg.

Protection is claimed for a biologically active peptide, obtained synthetically,

with immune-regulatory properties, comprised of three aminoacids. The search

revealed that the sequence is contained in various natural proteins. The application

contends that the peptide may be different to the natural polypeptide from various

aspects such as folding, spatial conformation, aggregation and physical-chemical

properties. Although there are differences in the physical-chemical properties of the

molecule claimed with relation to natural polypeptides that comprise the same

sequence, the peptide claimed presents a sequence of aminoacids found in nature,

and this is why the subject matter is not considered an invention according to Art. 10

(IX) of the Industrial Property Statute.

Example 32:

Claim: Protein characterized by presenting SEQ ID NO: 1 wherein positions 1 to 6 have

been deleted.

A cytokine having 76 aminoacids when truncated in the sixth aminoacid amino-

terminal begins to display antagonist activity of the whole cytokine and thus can be used

to manufacture medicines to treat diseases wherein a cytokine antagonist is needed.

Although human interference resulted in an innovative activity, said fact was solely due

to the deletion of part of the molecule, maintaining the sequence obtained identical to

the sequence of aminoacids 6-76 found in the whole natural molecule 1-76. According to

Art. 10 (IX) of the Industrial Property Statute, said analog is not considered an

invention because it is part of the natural molecule, and accordingly is not patentable.

6.4.4 Sequence modifications

Modifications in protein sequences in order to differentiate them from natural

sequences can be carried out in different way. Theoretically, any characteristic Page 47 of 63

introduced into the sequence that was not described as naturally-occurring is

acceptable as modification, for purposes of compliance with Art. 10 (IX) of the

Industrial Property Statute.

6.4.4.1 With natural aminoacids (substitutions, insertions or deletions)

As highlighted above for modifications, in general terms, modifications of

biological sequences by inserting L-natural aminoacids in the sequence (in the means

or at the ends) are considered sufficient for purposes of compliance with Art. 10 (IX),

provided that the resulting sequence formed is not naturally-occurring either.

For deleting aminoacids, the position of the deleted aminoacid results in

different situations to be considered. If it is located in the central part of the sequence

of the protein, said modification is, theoretically, sufficient to differentiate it from the

natural molecule. Nevertheless, even in the case of deleted aminoacids being

contiguous and being at the end of the sequence, same still fails to comply with Art.

10 (IX), since the resulting sequence continues to be identical to a part of the natural

sequence (see example 32).

Regarding the substitution of aminoacids by other natural aminoacids, it is

considered that said modification is sufficient for the sequence to comply with Art. 10

(IX), provided that there is no description of natural proteins in related species

containing said substitution (see item 6.4.2 of orthologous proteins).

When analyzing proteins already described in the state of the art, care must be

taken to evaluate the inventive step of the modification (insertion, deletion or

substitution) made, taking into account the fact that some groups of aminoacids

present common properties. Thus, the inventiveness of these alterations in the protein

sequence generally depends on the demonstration of an unexpected effect generated

by the modification in relation to the state of the art.

6.4.4.2 With non-natural aminoacids (including protector groups)

Insertions of aminoacids which are not naturally-occurring (deriving from

natural aminoacids) are also considered sufficient modifications for the protein

sequences to comply with Art. 10 (IX). Nevertheless, for purposes of clarity and

precision, said aminoacids shall be appropriately identified in the claims, so as to

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avoid the indirect inclusion of natural aminoacids, and thereby result in the natural

biological sequence.

The inclusion of such aminoacids in the sequences presented in patent

applications is also addressed in INPI Resolution PR Nº 81/2013, cited in item 2.2.2 of

these Guidelines; and a list with examples of non-natural aminoacids and the

acceptable abbreviations in the definition thereof is available in Table 4 of Appendix

of this Resolution (published in the Official Federal Gazette (DOU) - Section 1, Nº 68,

April 10, 2013).

6.4.4.3 Grouping added to carboxyl or amino terminus

A protein sequence can also be altered by binding chemical groupings at their

ends, these having the purpose of allowing anchorage to a certain surface or structure,

increase of protein activity, modulation of bioavailability and/or circulating half-life,

etc.

Once again, attention must be paid to the form in which said molecule is

claimed, in order to guarantee the presence of the chemical grouping in said molecule,

since it is this grouping that will differentiate it from its natural equivalent. Fmoc, t-

boc, other chemical groupings, prosthetic groups, lipids, carbohydrates, iron, calcium,

heme, are examples of groupings which when added to proteins may potentially

differentiate them from natural ones.

6.4.5 Fusion proteins

By definition, these proteins are created by union (fusion) of parts of two or

more different protein sequences. Accordingly, a fusion protein involved in a patent

application is formed by at least a “functional” portion, responsible for the property

related to the invention.

Thus, for purposes of definition in accordance with Art. 25, it is important to

underline that in a fusion protein, all the functional portions constituting the end

protein must be described in the application.

6.4.5.1 Naturally-occurring

Rare cases of naturally expressed fusion proteins are noted in some types of

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cancer, owing to chromosome translocation, which may lead to the fusion of different

genes, for example: fusion proteins gag-onc, Bcr-abl, and Tpr-met.

Once the occurrence of a natural identical structure is proven, with due regard

for that prescribed in item 4.2.1 (for example, Bcr-abl, with a portion 1-50 of Bcr

fusioned to the portion 13-78 of abl), such proteins cannot be considered inventions

according to Art. 10 (IX) of the Industrial Property Statute.

6.4.5.2 Characterization

In general terms, in defining fusion proteins, the rules defined for any other

protein sequences apply (see item 6.4.1). Thus, no references are accepted for

percentages of homology/similarity/identity, and the proteins shall be referred to by

way of at least one of their sequences of aminoacids or SEQ ID NO: corresponding to

the functional portion.

6.4.5.3 Integral Seq ID

When the polypeptide sequence described in the patent application is claimed

in the form of a fusion protein, it must always be at least by way of its sequence of

aminoacids or corresponding SEQ ID NO:, for a clear and precise definition of the

subject matter claimed relating to the invention.

When various peptides are related to the property described in the invention,

and all are present in the fusion protein claimed, all these peptides shall be referred to

at least by way of their sequence of aminoacids or corresponding SEQ ID NO:.

Special attention must be paid to cases where the “fusion” protein is in fact

formed by fragments of a same naturally-occurring protein: in accordance with the

form as claimed, the end protein produced (fusion protein) may be an identical result

to the natural molecule.

Example 33:

Claim: Fusion protein characterized by comprising:

a) a first polypeptide that consists of the sequence of aminoacids 41-56 of SEQ

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ID NO: 2;

b) a first spacer of 6-27 aminoacids;

c) a second polypeptide that consists of the sequence of aminoacids 69-84 of

SEQ ID NO: 2;

d) a second spacer of 5-11 aminoacids; and

e) a third polypeptide that consists of the sequence of aminoacids 92-105 of SEQ

ID NO: 2.

In this claim, since the spacers of interest are not defined, said ranges being compatible

with the interval between the sequences defined, the resulting “fusion” protein

encompasses in its scope the very protein whose sequence is described in SEQ ID NO:

2, which is naturally-occurring, and so the claim does not comply with Art. 10 (IX).

6.4.5.4 Definition of just one of the sequences present in the fusion protein

When the protein of interest is fusioned to another other polypeptide that will

solely act as “label/reporter”, said reporter can be defined by way of its sequence of

aminoacids or corresponding SEQ ID NO:, as established previously, to any

polypeptides. Nevertheless, since said polypeptide “reporter” is broadly known in the

art, optionally the reference thereto can be made solely by way of its abbreviation, for

example, to molecules such as GFP (green fluorescent protein), GST (glutathione S-

transferase), CAT, c-Myc, FLAG, among others.

Potentially, an application may present the type of situation in which the

inventive characteristic of the fusion protein is solely in the presence of the protein

described in the application – which can also be the reporter portion – and it can be

fusioned to various others.

Example 34:

The application describes a polypeptide X which, in isolation, has no

surprising activity, but which is capable of enhancing the immunological response of

antigens fusioned thereto. In the set of claims, there is claimed a “fusion protein

characterized by consisting of protein X (defined by SEQ ID NO:) bound to an

antigen”.

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In this case, attention must be paid to clarity and precision of the way in

which the fusion protein is claimed, since the antigen fusioned thereto is not defined

in the claim, and the decision to be taken shall consider the information available in

the specification.

Situation 1: The specification presents examples of X fusion protein with various

different antigens, not related, and demonstrates the indisputable efficiency of all the

resulting proteins for the proposed purpose, so there is no indication that another

antigen would not work in the same manner. In this case, it is not necessary to

require that the application list all the possible antigens for use in the fusion protein,

and it is considered that the claim as worded above is acceptable.

Situation 2: the application presents examples of X fusion protein with various

different antigens, not related, but the results demonstrated do not present

consistency, demonstrating that the fusion protein is effective for some antigens and

not for others. In this case, the very application does not provide full disclosure and

basis in accordance with Arts. 24 and 25 to support that the fusion protein works

with any antigen (it may include antigens for which there is no evidence that they

work as described). Therefore, the set of claims shall be limited to the subject matter

described and supported in the application in accordance with Arts. 24 and 25 of the

Industrial Property Statute, that is, the claims must specify which antigens of interest

are present in the fusion protein claimed.

6.4.6 Antibodies

Antibodies are plasma proteins which bind specifically to substances known as

antigens, and include polyclonals and monoclonals; therefore, they shall be analyzed

as proteins, and also in terms of that prescribed in Art. 10 (IX) (see item 6.4 and

subitems thereof).

Polyclonal antibodies are derived from different lineages of B cells. They are

a mixture of immunoglobulin molecules secreted against a specific antigen, each

recognizing a different epitope. These antibodies are biological products isolated

from nature and, therefore, are not considered inventions according to that prescribed

in Art. 10 (IX) of the Industrial Property Statute. It must be underscored that the

isolation of a specific antibody from this pool of antibodies does not exclude this Page 52 of 63

molecule from compliance with Art. 10 (IX).

Monoclonal antibodies are antibodies from a single specificity, i.e. specific to

a single epitope of an antigen. Through human intervention, a monoclonal antibody

can be obtained by means of different techniques, such as hybridoma (see item

6.4.6.2) or genetic engineering.

Provided that it is obtained by hybridoma and characterized thereby, the

monoclonal antibody cannot be considered natural and, therefore, complies with that

prescribed in Art. 10 (IX). In this situation, this monoclonal antibody can be

additionally defined by its specific sequence (SEQ ID NO:). Since monoclonal

antibodies obtained by genetic engineering, they are defined by their sequence, and

can be accepted provided that they comply with that prescribed in Art. 10 (IX) (see

item 4.2.1).

Example 35: Wording of antibody claim antibody eligible for protection.

Claim: Monoclonal antibody against protein X characterized by the fact that it is

produced by hybridoma HHH, deposited under number YYYY.

Example 36: Unacceptable claims for antibodies.

Claim 1: Antibodies characterized by the fact that they are specific for protein X.

As the antibodies claimed are not clearly and precisely defined, these claims

cannot be accepted since they do not comply with Art. 25 of the Industrial Property

Statute, and may encompass natural molecules, which is contrary to Art. 10 (IX).

Claim 2: Human monoclonal antibody characterized by the fact that it recognizes

protein X and has an affinity of 2x10-9 M.

Claim 3: Monoclonal antibody and fragments thereof characterized by the fact that it is

capable of binding to protein X.

As the antibodies claimed are not clearly and precisely defined, nor which

fragments are being claimed, these claims cannot be accepted, since they do not

comply with Art. 25 of the Industrial Property Statute.

6.4.6.1 Process of obtaining antibodies

The process of producing a polyclonal antibody which consists solely of Page 53 of 63

exposing an animal to an antigen, followed by purification, is considered a natural

biological process, and is not considered invention, thus not complying with Art. 10

(IX). In some cases, however, when there is a non-trivial technical stage involving the

determination of the epitope or modification of the antigen to elicit the immunological

response, it is considered that there is significant human intervention, since it has a

direct action on the molecule, which has a decisive impact on the end result obtained.

In these cases, such processes are eligible for protection.

In contrast, owing to human intervention, the process of producing monoclonal

antibodies is not considered a natural biological process, be it involving the

obtainment of a hybridoma or by genetic engineering techniques.

Regarding the characterization of the process of obtaining antibodies, care

must be taken for the need to define the stages of the process (see item 4.2.1.2).

6.4.6.2 Hybridomas

Hybridomas are the result of a fusion of two cell types, a myeloma with a

lymphocyte B, and produce antibodies. They bear characteristics not achievable by

such cell types under natural conditions, being the product of direct human

intervention. According to the understanding adopted by this Institute, technically

speaking, a hybridoma is considered a transgenic microorganism, and accordingly,

said subject matter is patentable because it complies with Arts. 10 and 18 of the

Industrial Property Statute.

At the same time, since this concerns biological material essential for the

practical realization of the object of the patent application, and cannot be characterized

clearly and precisely in the specification, in order to comply with the sole paragraph of

Art. 24 of the Industrial Property Statute, it is essential to deposit the hybridoma by

the filing date of the patent application or its priority date, and the submission of the

deposit number in the patent application (see item 2.2.1).

6.4.6.3 Chimeric/humanized antibodies

When the monoclonal antibodies of mice, rabbits, etc., are used as therapeutic

agents in humans, the strange proteins are recognized by the immune system of the

human host. The advent of chimeric/humanized antibodies is a mechanism used to

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solve this therapeutic obstacle.

The technology for producing a humanized antibody differs from the

production of a monoclonal antibody because it does not depend on cultivating the

hybrid cell, but implies obtaining the sequence of the immunoglobulin (human Fc

portion and variable portion of the non-human Fab fragment). These sequences are

merged and placed in an expression vector for subsequent cultivation of the

transfected host cell and subsequent stages of purification. Owing to this difference in

the production route, the characterization of humanized antibody requires the

presentation of a SEQ ID NO: X containing a sequence of aminoacids of the variable

portion of the antibody and the definition of the other elements (Fc portion).

Example 37: Wording of antibody claims eligible for protection.

Claim: Humanized antibody against a-actin characterized by comprising the murine

variable region which consists of SEQ ID NO: X and human y chain regions.

Claim: Humanized antibody against a-actin characterized by comprising the murine

complementarity determining regions (CDR1; CDR2; CDR3) which consist of SEQ

ID NO: X, SEQ ID NO: Y and SEQ ID NO: Z in the light chain and SEQ ID NO: A,

SEQ ID NO: B and SEQ ID NO: C in the heavy chain and human y chain regions.

6.4.6.4 Fragments of antibodies

An antibody molecule can be cleaved generating different fragments with

distinct functions. If originating from antibodies found in nature, or are part of other

natural proteins, the fragments in themselves are not patentable owing to Art. 10 (IX)

of the Industrial Property Statute (see item 6.4.3).

Modifications of antibody fragments may also constitute subject matter

eligible for protection, as in the case of single-chain variable fragments (ScFv). The

Fv fragments are not covalently connected, so the heterodimers of the VH and VL

domains can easily dissociate. However, Fv fragments can be constructed so as not to

dissociate, that is, the VH and VL domains can be joined by a connector, creating a

single-chain FV fragment. Despite being an antibody fragment, this construction

complies with Art. 10 (IX) of the Industrial Property Statute, since these fragments are

not found in nature joined by the connector.

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7 Animals, plants, parts thereof and processes of obtaining them

7.1 Animals, plants and parts thereof

If natural/isolated, these are not considered an invention, according to Art. 10

(IX). When resulting from genetic manipulation by the human being, they are not

patentable, according to Art. 18 (III).

7.1.1 Products and processes involving stem cells

Stem cells are undifferentiated cells (totipotent, pluripotent or progenitor)

which can be stimulated to specialize in the tissues that make up the human body.

According to these Guidelines, products and processes involving stem cells

refer exclusively to pluripotent or progenitor stem cells. These cells can be obtained

directly from various tissues of the adult organism (such as, for example, from bone

marrow, from adipose tissue), or even from the umbilical cord, or can be obtained by

de-specializing a specialized adult cell (as in the case of the induced pluripotent stem

cell – IPS).

Alternatively, they can be obtained from the internal mass of the blastocysts

originating from human embryos produced by in vitro fertilization, according to the

provisions of Art. 5 of the Biosafety Act – N°. 11,105/2005.

In accordance with the Industrial Property Statute, the cells themselves

obtained directly from an animal or with some gene modification, are not patentable in

light of that prescribed in Art. 10 (IX) or 18 (III), respectively. Nevertheless,

compositions containing these cells, the processes of obtaining stem cells and

applications (uses) thereof can be considered patentable provided that they do not

imply or include a therapeutic and/or surgical method (Art. 10 (VIII), and provided

that they comply with the provisions of Art. 18 (I) of the Industrial Property Statute.

For example, the following products and processes involving stem cells can be

considered eligible for patenting:

• Compositions containing cells and other ingredients (various implants

containing cells, cell and matrix formulation, cells and growth factors ... ).

• Composition containing mixtures of different types of stem cells. Page 56 of 63

• Processes of purification, preparation, conditioning, specialization, de-

specialization, or any processing of stem cells provided that it is

performed in vitro.

• Uses of cells for preparing medicines to treat disease X.

• Uses of cells for preparing implants to treat disease X.

• Uses of cells for preparing compositions for diagnosing disease X.

• Processes of diagnosis which include stages that employ cells or synthetic

tissues, provided that they are performed in vitro.

• Drug tests which include stages that employ stem cells or synthetic tissues,

provided that they are performed in vitro.

• Processes of cultivating stem cells.

• Conditioned culture means obtained during the cultivation of stem cells.

7.2 Transgenic plants, parts thereof and processes of obtaining them

These are plants that had their genome modified by the introduction of a DNA

manipulated by recombinant DNA techniques, and whose modification would not

occur under natural conditions of cross-breeding or recombination.

Transgenic plants and parts thereof (for example, transgenic cell, tissue

transgenic and transgenic organs) are not considered to be patentable subject matters

according to Art. 18 (III and sole paragraph) of the Industrial Property Statute.

Even if the process of obtaining transgenic plants is patentable, it is important

to emphasize that the intermediary and/or end products of this process, that is, the

transgenic plant and/or parts of this plant constitute subject matters expressly

prohibited from patentability according to Art. 18 (III and sole paragraph) of the

Industrial Property Statute. Nevertheless, there is no restriction on the patenting of the

processes of obtaining these plants.

Examples of claims eligible for protection

• Method of producing a transgenic plant characterized by the fact that it

comprises the stages of:

(a) obtaining an explant from the plant;

(b) exposing the explant to the Agrobacterium tumefaciens culture

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that contains the vector defined by claim X (duly described with

a selection gene, a heterologous gene and the sequence

promoter(s);

(c) cultivation of the explant in a means with the specific conditions

for cultivating a vegetable tissue; and

(d) selecting and cultivating transformed calluses that express the

heterologous gene, to induce the formation of the embryonic

callus.

• Method for producing a transgenic dicotyledonous plant, characterized by

comprising:

(a) transforming plant cells using an Agrobacterium transformation

vector that comprises a chimeric genic construction Y;

(b) obtaining a transformed plant cell; and

(c) regenerating a genetically-transformed plant from a transformed

plant cell.

7.3 Process of obtaining plants by cross-breeding

Article 10 (IX) of the Industrial Property Statute establishes that natural

biological processes are not considered inventions, and therefore excludes patenting of

natural biological processes, including those for producing plants.

A “natural biological process” is understood to be any process that does not use

technical means to obtain biological products or that, even using a technical means, it

would be eligible for occurring in nature without human intervention, consisting

wholly of natural phenomena. In this sense, biological processes are considered non-

natural when human intervention is direct in the genetic composition and are

permanent in character.

Thus, processes involving the cross-breeding of plants genetically-modified by

direct human intervention are eligible for protection.

Example 38: Non-transgenic parentals.

Claim 1: Method for producing a plant of X characterized by comprising the stages

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of:

a) selecting a plant of X homozygote for the gene A;

b) selecting a plant of X homozygote for the gene B; and

c) cross-breeding the plants selected in stages (a) and (b) for producing a

hybrid plant.

Conventional methods of producing plants based on stages of selection, cross-

breeding and propagation are considered natural biological processes, and

do not comply with Art. 10 (IX). In these cases, human interference by way of

selection and induction of specific cross-breeding is not essential for the

process to occur, solely accelerating or limiting that which would occur in

nature.

Example 39: Non-transgenic parentals.

Claim 1: Method for producing a plant of X with high levels of compounds W

characterized by comprising the stages of:

a) identifying the gene markers connected to high levels of W;

b) selecting the individuals comprising the markers identified in stage (a); and

c) cross-breeding the individuals selected in stage (b).

Conventional methods of producing plants based on stages of selection, cross-

breeding and propagation in which human intervention consists solely of providing

additional technical means to facilitate or direct the process – in this case, the

identification of gene markers – are considered natural biological processes, not

complying with Art. 10 (IX). In these cases, human interference is not decisive in order

to obtain the end result, merely accelerating or limiting that which would occur

naturally.

Example 40: Transgenic parentals.

Claim 1: Method of producing hybrid seeds characterized by comprising the cross-

breeding of a herbicide-resistant plant with a plant endowed with an enhanced

nutritional value comprising in its genome a heterologous gene encoding a modified

albumin.

Claim 2: Method of introducing the characteristic of resistance to a herbicide in a plant

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endowed with enhanced nutritional value characterized by comprising the stages of:

a) cross-breeding a plant resistant to at least one herbicide with a plant

comprising in its genome a heterologous gene encoding a modified albumin;

b) developing base populations;

c) evaluating the plants obtained individually; and

d) selecting plants endowed with enhanced nutritional value comprising the

characteristic of herbicide resistance.

This process involves the technical stage that is essential for obtaining plants that do not

occur in nature and, therefore, complies with Art. 10 (IX).

8 Patent applications involving components from the Brazilian genetic heritage

Patent of invention applications for a process or product obtained from a sample of

components of the Brazilian genetic heritage, deposited as of June 30, 2000, shall adhere

to the rules in effect, as established in MP 2186-16/01 dated August 23, 2001, as well as

CGEN Resolution Nº 34 dated February 12, 2009 and INPI PR Nº 69/2013, dated March

18, 2013.

MP 2186-16/01 provides, among other things, on property, rights and obligations

relating to access to components from the Brazilian genetic heritage existing in national

territory, on the continental shelf and in the exclusive economic zone for purposes of

scientific research, technological development or bioprospecting, as well as access to

traditional knowledge associated to the genetic heritage, relevant to the conservation of

biological diversity, to the integrity of the country’s genetic heritage and to the use of

components thereof (Art. 1, items I and II).

In Art. 31, the provisional presidential decree determines that the grant of the

industrial property right over a process or product obtained from a sample of a component

of the genetic heritage requires compliance with the Provisional Presidential Decree (MP),

and the applicant shall inform the origin of the genetic material and the associated

traditional knowledge, as applicable.

The rules established in Provisional Presidential Decree (MP) 2186-16/01 shall be

adhered to for patent applications involving genetic heritage. Non-exhaustive examples

include organisms (plants, animals, fungi, bacteria, archaea, etc.), parts of organisms

(leaves, nails, skin, mucus, blood, roots, extracts, organs, oils, venoms, fangs, etc.),

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molecules isolated from organisms (DNA, RNA, proteins, sugars, lipids, etc.), and their

synthetic correspondents, as well as compositions and processes containing any of the

items mentioned above. In accordance with Art. 3, the MP does not apply to human

genetic heritage.

The applicant shall always furnish information relating to the origin of the material

through petitions established in INPI Resolution PR Nº 69/2013: a petition for access

information or a petition of declaration that the application filed does not involve access

under the terms of MP 2186-16/01. Pursuant to CGEN Resolution Nº 35/2011, for

purpose of regularization, the request protocol for authorization to access a genetic

resource may be accepted, and the allowance of the patent application shall require

presentation of the definitive authorization to access the genetic resource.

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