Transparency tools in gene patenting for informing policy and practice

Jefferson, Osmat Azzam; Köllhofer, Deniz; Ehrich, Thomas H.; Jefferson, Richard A.

doi:10.1038/nbt.2755

Cited by 25 publications

(16 citation statements)

References 21 publications

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“…12-398. Argued April 15, 2013-Decided June 13, 2013 claiming that naturally occurring sequences from the human genome are not patentable may provide a precedent (see Jefferson et al, 2013 for a discussion of the extension of this decision). However, it is not clear how this decision will apply to TEs that may have nearly identical sequences between genomes and may in some cases even move between genomes by horizontal transfer.…”

Section: Discussionmentioning

confidence: 99%

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

Piégu

Bire

Arensburger

et al. 2015

Molecular Phylogenetics and Evolution

138

132

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The increase of publicly available sequencing data has allowed for rapid progress in our understanding of genome composition. As new information becomes available we should constantly be updating and reanalyzing existing and newly acquired data. In this report we focus on transposable elements (TEs) which make up a significant portion of nearly all sequenced genomes. Our ability to accurately identify and classify these sequences is critical to understanding their impact on host genomes. At the same time, as we demonstrate in this report, problems with existing classification schemes have led to significant misunderstandings of the evolution of both TE sequences and their host genomes. In a pioneering publication Finnegan (1989) proposed classifying all TE sequences into two classes based on transposition mechanisms and structural features: the retrotransposons (class I) and the DNA transposons (class II). We have retraced how ideas regarding TE classification and annotation in both prokaryotic and eukaryotic scientific communities have changed over time. This has led us to observe that: (1) a number of TEs have convergent structural features and/or transposition mechanisms that have led to misleading conclusions regarding their classification, (2) the evolution of TEs is similar to that of viruses by having several unrelated origins, (3) there might be at least 8 classes and 12 orders of TEs including 10 novel orders. In an effort to address these classification issues we propose: (1) the outline of a universal TE classification, (2) a set of methods and classification rules that could be used by all scientific communities involved in the study of TEs, and (3) a 5-year schedule for the establishment of an International Committee for Taxonomy of Transposable Elements (ICTTE).

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Section: Discussionmentioning

confidence: 99%

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

Piégu

Bire

Arensburger

et al. 2015

Molecular Phylogenetics and Evolution

138

132

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“…Although sequence use was broadly similar in plantand human-related inventions-on the basis of the categories identified in our human genome study 8 -in plant-related inventions, such use was more intertwined within a single patent document. For example, in US patent 8,692,076 (available at https://www.lens.org/ lens/patent/US_8692076_B2), the sequence identified as SEQ ID No: 1 was mentioned in claim 1 as part of a larger sequence and so would have been categorized as a "Subpart" in The restructuring of the crop agriculture industry over the past two decades has enabled patent holders to exclude, prevent and deter others from using certain research tools and delay or block further follow-on inventions.…”

mentioning

confidence: 86%

“…Thus, considering how divergent and complex the spectrum of interests in gene patenting is becoming and how limited is our understanding of the practices across various economies, we have designed and developed a dynamic platform, the patent sequence (PatSeq) toolkit, to render biological patents and their disclosed genetic sequences more publicly accessible and their contextual navigation more evidence based 8 .…”

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confidence: 99%

The ownership question of plant gene and genome intellectual properties

et al. 2015

Self Cite

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bined the findings from all three genomes to check sequence or patent overlap and redundancy.Results show that only 24% (2,367 out of 9,838), 15% (1,190 out of 7,836) and 24% (2,595 out of 10,634) of the earlier accounted for as maize, rice and soybean referenced sequences, respectively, were actually used in plant-related inventions. These correspond to 846 maize-related patents, 493 rice-related patents and 638 soybean-related patents-or 1,633 granted patents in total, as we found some overlapping patents across the three data sets. The level of overlap among referenced sequences was 9% and redundancy was more than 30%, and only 10% of sequences comprised more than 50 base pairs.According to the US classification codes, in the hand-edited collection, 65% of inventions were related to the processes of introducing or rearranging a nucleic acid molecule into a plant cell or part, either as such or to develop a transgenic plant or plant part; 48% were related to a plant per se (including a higher plant), seedling or plant seed or part; 45% were related to the use of vectors for the introduction of exogenous nucleic acid molecules in host cells; and 33% were related to the transformed plant cell or cell line or to plant proteins used as compounds.Claim analysis, on the other hand, revealed clearer patterns of sequence use. Although sequence use was broadly similar in plantand human-related inventions-on the basis of the categories identified in our human genome study 8 -in plant-related inventions, such use was more intertwined within a single patent document. For example, in US patent 8,692,076 (available at https://www.lens.org/ lens/patent/US_8692076_B2), the sequence identified as SEQ ID No: 1 was mentioned in claim 1 as part of a larger sequence and so would have been categorized as a "Subpart" in The restructuring of the crop agriculture industry over the past two decades has enabled patent holders to exclude, prevent and deter others from using certain research tools and delay or block further follow-on inventions.

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“…al. 2013 have highlighted, sequences may be mentioned in the claims either because they are being claimed or because they are reference sequences (not claimed) for the invention [48]. As such, while references to sequences are extremely common in patent claims more detailed investigation will be required to assess the significance of these references at the level of patent rights.…”

Section: Technology Areas and Topicsmentioning

confidence: 99%

Synthetic Biology - Mapping the Patent Landscape

Oldham

Hall

2018

Preprint

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This article presents the global patent landscape for synthetic biology as a new and emerging area of science and technology. The aim of the article is to provide an overview of the emergence of synthetic biology in the patent system and to contribute to future research by providing a high quality tagged core dataset with 7,424 first filings and 71,887 family members. This dataset is intended to assist with evidence based exploration of synthetic biology in the patent system and with advancing methods for the analysis of new and emerging areas of science and technology.The starting point for the research is recognition that traditional methods of patent landscape analysis based on key word searches face limitations when addressing new and emerging areas of science and technology. Synthetic biology can be broadly described as involving the design, synthesis and assembly of biological parts, circuits, pathways, cells and genomes. As such synthetic biology can be understood as emerging from a combination of overlaps and convergences between existing fields and disciplines, such as biotechnology, genetic engineering, protein engineering and systems biology. More precisely, synthetic biology can be understood as the synthetic phase of molecular biology and genetic engineering. This presents the problem that key word strategies may radically overestimate activity because they involve terms that are widely used in underlying fields that are contributing to synthetic biology.In response to this problem we combined anthropology, scientometrics and data science to map authors from scientific publications on synthetic biology into the international patent system. We mapped 10,816 authors into the international patent system and identified 2,450 authors of articles on synthetic biology who are also inventors in the period to December 2017. By combining this data with citation information and a baseline keyword strategy we are able to describe the global patent landscape for synthetic biology and the wider patent universe in which synthetic biology is situated.This article describes the main features of the global landscape and provides the tagged dataset as a contribution to evidence based debate on intellectual property and synthetic biology and methodological development. We anticipate that the data will prove useful in informing international policy debates on synthetic biology under the United Nations Convention on Biological Diversity.

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Transparency tools in gene patenting for informing policy and practice

Cited by 25 publications

References 21 publications

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

The ownership question of plant gene and genome intellectual properties

Synthetic Biology - Mapping the Patent Landscape

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