The deciphering of the human genetic code in 2003 has been widely acknowledged as a major achievement in genetic science but it has given rise to a number of legal and ethical concerns, most notably that of the protection of genetic information. Universally, there are ongoing attempts to address this concern. This research proposes a suitable approach for South African law. It proceeds from the premise that the privacy paradigm, rather than the anti-discrimination paradigm, is better suited to the protection of genetic information, hence the discourse on genetic privacy. The unique challenges posed by genetic information are identified, with a focus on forensic DNA databases, genetic research databases, life insurance, employment, and genetic research involving human participants. An in-depth analysis of the South African privacy protection framework is undertaken in order to determine its adequacy for the purpose of meeting the legal and ethical demands of genetic information. Aspects of the law of privacy, insurance, labour, evidence; medical law; philosophy and bioethics are accordingly traversed. A cross-jurisdictional review is undertaken with the aim of identifying lessons to be learnt from the experiences of the United Kingdom, Australia, Canada, the Netherlands, and the United States of America. Legislation, common law, codes of practice, court decisions, international conventions, legal literature, ethical guidelines, and industry developments pertaining to the selected jurisdictions, are studied with the aim of identifying strengths and weaknesses in the various approaches. It is found that the current South African position is fragmented, complex, and in urgent need of reform. Another finding is that existing national and international ethical guidelines are not entirely adequate for the protection of genetic privacy. These findings, together with the lessons gleaned from the cross-jurisdictional review, lead to the conclusion that South Africa needs a specific genetic information protection statute for the protection of genetic privacy. This research culminates with recommendations regarding the content of the proposed statute.

This thesis examines the regulation of the direct-to-consumer genetic testing industry through analysis of the industry's use of wrap contracts (clickwrap and browsewrap), A significant portion of the thesis consists of a comparative document review of the publicly available wrap contracts of DTCGT companies provided tests for health purposes. It also considers other regulatory responses to date. Due to the lack of industry specific regulation it argues that the use of wrap contracts can be viewed as a means of industry self-regulation and a form of private legislation. This means that governance is skewed heavily in favour of companies and it creates an imbalance in the respective rights and obligations of the parties - company and consumer - which is likely to result in consumer detriment. It is argued that certain types of terms commonly include in DTCGT contracts, including: unilateral variation clauses; some exclusion clauses; choice of law clauses; indemnity; and consent clauses are likely to be deemed unfair and unenforceable under UK law. It recommends that in the short-term the Competition and Markets Authority should undertake a compliance review of DTCGT contracts in order to improving contracts for consumers. In the long term, companies should also be complying with data protection law, as well as legislation on medical devices and the provisions of the Human Tissue Act and there may be a need for industry specific legislation.

Canada established its National DNA Data Bank (NDDB) in 2000. Since that time, the NDDB has assisted in the solving of numerous criminal investigations. The NDDB has two indexes: the convicted offender index, which holds the identifiable DNA of persons convicted of designated crimes, and the anonymous crime scene index, which holds anonymous DNA collected from crime scenes. A match to a crime scene profile provides criminal investigators with extremely valuable evidence linking a suspect to a crime scene and the NDDB has been used to identify perpetrators in thousands of crimes in Canada. By limiting the identifiable DNA in the NDDB to convicted offenders, Canada has aimed to balance the crime-solving benefits of the data bank with competing rights issues, particularly the individual right to privacy. Some have encouraged expansions to the NDDB scheme in order to increase the number of crimes that can be resolved through the use of DNA evidence. One possible expansion is to introduce familial searching, a technique in DNA analysis that enables suspect identification based on the existence of a partial match between an identifiable DNA profile and an anonymous profile retrieved from the scene of a crime. Where closely matching profiles indicate that a close genetic relationship likely exists between the identifiable offender and an anonymous perpetrator, police will have a useful lead for follow-up and may be able to locate a suspect by testing the DNA of the identified offender’s close relatives. The use of familial searching is controversial. As a crime-solving tool, it has helped solve crimes in other jurisdictions in which it is currently used. At the same time, it introduces legal and ethical questions that have not been fully explored in Canada. One of the crucial questions is whether and to what extent familial searching may discriminate against Canada’s Aboriginal peoples, who suffer the effects of systemic bias in the criminal justice system generally and who are likely to be overrepresented in the NDDB. Applied in an inherently unequal system, familial searching would disproportionately impact Aboriginal peoples and perpetuate or possibly worsen this existing inequality. To help inform Canada’s decision about the use of familial searching as part of NDDB operations, this dissertation examines the issue from a Critical Race Theory perspective. It outlines the various ways in which familial searching would disproportionately impact Aboriginal peoples. The dissertation further examines international approaches to familial searching and evaluates the extent to which these policies protect against racial inequality concerns relating to the use of familial searching in each jurisdiction considered. It argues that Canada should prohibit familial searching of NDDB data in order to avoid a situation in which the technique would perpetuate or worsen systemic bias against Aboriginal peoples in the Canadian criminal justice system.

The analysis of small circular sequences requires specialized tools. While the differences between linear and circular sequences can be neglected in the case of long molecules such as bacterial genomes since in practice all analysis is performed in sequence windows, this is not true for viroids and related sequences which are usually only a few hundred basepairs long. In this contribution we present basic algorithms and corresponding software for circular RNAs. In particular, we discuss the problem of pairwise and multiple cyclic sequence alignments with affine gap costs, and an extension of a recent approach to circular RNA folding to the computation of consensus structures.

L’information génétique est rarement appréhendée directement par le droit, bien que certaines catégories du droit de la propriété intellectuelle, telles que le brevet d’invention ou le certificat d’obtention végétale, en soient des réceptacles privilégiés. De plus, si les Etats ont réaffirmé leur souveraineté sur les ressources génétiques dans le cadre de la Convention sur la diversité biologique et du Protocole de Nagoya, il en résulte un principe de partage juste et équitable des avantages entre fournisseurs et utilisateurs, qui a favorisé la reconnaissance d’un nouveau bien : l’information génétique. Effectivement, selon une approche néocapitaliste de la conservation, la maîtrise de l’information génétique constitue un levier pour la conservation de la biodiversité et un rééquilibrage des relations Nord/Sud. Toutefois, la propriété de la ressource physique s’est révélée déterminante dans les échanges afin de contrôler l’accès à l’information génétique à travers les utilités de la chose.Ce principe d’accès et de partage des avantages entérine un lien spécial entre l’information et son support biologique en ce sens que l’information génétique étudiée par le chercheur demeure le fruit d’un territoire, voire d’un travail de conservation ancestrale d’agriculteurs ou de communautés locales. Il s’agit donc d’une forme atypique de dépendance entre l’information génétique et l’origine géographique de la ressource, devant être articulée avec les droits de propriété intellectuelle qui ne peuvent poursuivre la seule logique de l’innovation, au risque de contourner les engagements internationaux en matière d’accès et de partage des avantages. Par ailleurs, un partage juste et équitable des avantages se comprend largement et n’est pas circonscrit aux avantages découlant du dépôt d’un titre de propriété intellectuelle. La révolution numérique connue par les activités de biotechnologie au travers notamment de la bio-informatique permet la création de nouvelles valeurs, souvent non-appropriables mais largement réservées par les pays du Nord, et auquel l’accès se révèle indispensable dans une véritable perspective de développement des capacités de recherche au Sud. En effet, au-delà des avantages monétaires et du transfert de technologie, ces avantages non monétaires sont essentiels afin de perpétuer les objectifs initiaux de la Convention sur la diversité biologique, malmenés par l’évolution des techniques. Pourtant, le règlement de l’Union européenne du 16 avril 2014 relatif aux mesures concernant le respect par les utilisateurs dans l'Union du protocole de Nagoya sur l'accès aux ressources génétiques et le partage juste et équitable des avantages découlant de leur utilisation et de la loi française pour la reconquête de la biodiversité, de la nature et des paysages du 8 août 2016 peinent à lancer une véritable dynamique de partage autour des pratiques de recherche actuelles, dans un contexte où l’accès au message porté par une séquence d’ADN peut être obtenu indépendamment de la ressource biologique, notamment grâce aux bases de données de bio-informatique ou à la biologie de synthèse. Au-delà du constat réalisé dans cette étude, il est temps de réfléchir à la construction d’une nouvelle forme de gouvernance, englobant l’information génétique au format numérique et répondant aux questions nouvelles soulevées par le big data, ainsi que les pratiques de data mining. L’idée d’un commun contractuel équitable, sur le modèle du Traité international sur les ressources phytogénétiques pour l’alimentation et l’agriculture, nous paraît constituer un enjeu du futur pour une certaine survie des principes de la Convention sur la diversité biologique. / Genetic information is rarely dealt with directly by law, although certain categories of intellectual property law, such as a patent or a plant variety certificate, are privileged receptacles. Moreover, if the states reaffirmed their sovereignty over genetic resources under the Convention on Biological Diversity and the Nagoya Protocol, the result is a principle of fair and equitable sharing of benefits between providers and users, which promoted the recognition of a new good: genetic information. Indeed, using a neocapitalist approach to conservation, mastery of genetic information is a lever for the conservation of biodiversity and a rebalancing of North / South relations. However, the property of the material resource has proved to be a determining trading factor in order to gain control access towards genetic information through its utilities.This principle of access and benefit-sharing enshrines a special link between information and its biological support in the sense that the genetic information studied by the researcher remains a local product or even a work of ancestral preservation by the Farmers or local communities. It is therefore an atypical form of dependence between genetic information and the geographical origin of the resource, that needs to be hinged with intellectual property rights. The latter is unable to solely pursue the logic of innovation without running the risk to bypass the commitments made by the international community on benefits access and sharing. Moreover, a Fair and Equitable sharing of benefits has to be taken broadly and is in no way limited to the benefits ensuing the filing of an IP. The digital revolution experienced by biotechnology activities, especially through Bioinformatics, allows the creation of new values which are mainly non-appropriable although reserved to a very large extent by Northern countries and to which access is essential in a genuine Development of research capacity in the Southern Countries. Indeed, beyond the financial benefits and the technology transfer opportunities, these non-monetary benefits are essentials in order to perpetuate the original goals which are battered by techonological developments. Yet the European Union Regulation of the 16 April 2014 on measures concerning user compliance in the Union with the Nagoya Protocol on access to genetic resources and the fair and equitable sharing of benefits arising from their use and the French Law for the Recovery of Biodiversity, Nature and Landscapes of August 8, 2016 are struggling to trigger and ensure a real dynamic of sharing around modern research practices, in a context where access to the message carried by a DNA sequence can be obtained independently of the biological resource, in particular through bioinformatics databases or synthetic biology.Beyond the findings of this study, it is time to reflect on the construction of a new form of governance, encompassing genetic information in digital format and responding to new questions raised by big data, as well as data mining. The idea of an equitable contractual common good, modeled on the International Treaty on Plant Genetic Resources for Food and Agriculture, seems to us to be a future issue for a certain survival of the principles of the Convention on Biodiversity.

The overall aims of this thesis were to investigate psychological and behavioral effects of receiving cancer genetic counseling for breast, ovarian and colorectal cancer and/or with a family history of these cancer types and to determine whether counselees’ informational needs were met. Study I was performed 3-7 years post-counseling. Participants (n=214) reported a relatively high level of anxiety but a low level of depression compared to cancer patients in general. However, there was no indication that the distress experienced was due to the counseling. Moderate changes in life and family relations, high level of adherence to recommended controls and satisfaction was reported. Study II was a randomized control trial (RCT) intervention study which involved 147 counselees. An increase in the level of knowledge and correct estimation of personal risk was reported in both the intervention and control groups, although this increase declined at later follow-up. Enhanced information led to significantly greater satisfaction with the given information, and the way of informing relatives. Most counselees had shared information with their at-risk relatives. Study III focused on sharing information with at-risk relatives among participants in study II and their relatives (n=81). Counselees were interviewed and answered a questionnaire, whilst their relatives only answered the questionnaire. Counselees reported positive/neutral feelings about communicating genetic information and mostly interpreted their relatives’ reactions as positive/ neutral. Also, approximately 50% of relatives reported positive/neutral reactions and were generally satisfied with the received information. Study IV was conducted in Sweden and Norway based on 235 counselees. Counselees expected counselors to be skillful and thoughtful, take them seriously and provide risk estimations and medical information. Most important issues to counselees were satisfactorily addressed by the counselors. Analyzing importance rankings resulted in five categories of needs: a need for facts, caring communication and medical information, need for understanding and support in sharing genetic information, practical care and medical/practical information. In conclusion, no adverse psychological or behavioral effect on counselees was observed. Apparently, genetic counseling is managed properly and counselors successfully address counselees’ needs. Providing extended information does not seem necessary, however, tailoring information to individual counselees needs may create a more effective counseling.

When biological information about an individual is produced in healthcare or research settings, ethical questions may arise about whether the individual herself should be able to access it. This thesis argues that the individual’s identity-related interests warrant serious attention in framing and addressing these questions. Identity interests are largely neglected in bioethical, policy and legal debates about information access – except where information about genetic parentage is concerned. Even there, the relationship between information and identity, and the interests involved, remain unclear. This thesis seeks to fill this conceptual gap and challenge this exceptionalism. It does so by developing a normative account of the roles that a wide range of information about our health, bodies and biological relationships – ‘personal bioinformation’ – can play in the construction of our self-conceptions. This account is developed in two steps. First, building on existing philosophical theories of narrative self-constitution, this thesis proposes that personal bioinformation has a critical role to play in the construction of identity narratives that remain coherent and support us in navigating our embodied experiences. Secondly, drawing on empirical literature reporting individuals’ attitudes to receiving three categories of personal bioinformation (about donor conception, genetic disease susceptibility, and neuroimaging-based psychiatric diagnoses), the thesis seeks to illustrate, demonstrate the plausibility of, and to refine this theoretically-based proposition. From these foundations, it is argued that we can have strong identity-related interests in whether and how we are able to access bioinformation about ourselves. The practical implications of this conclusion are then explored. It is argued that identity interests are not reducible to other interests (for example, in health protection) commonly weighed in information disclosure decisions. They, therefore, warrant attention in their own right. An ethical framework is developed to guide delivery of this. This framework sets out the ethical responsibilities of those who hold bioinformation about us to respond to our identity interests in information disclosure practices and policies. The framework is informed by indications from the illustrative examples that our interests engaged as much by how bioinformation is communicated as whether it is disclosed. Moreover, these interests are not uniformly engaged by all bioinformation in all circumstances and there is potential for identity detriment as well as benefit. The ethical framework highlights the opportunities for and challenges of responding to identity interests and the scope and limits of potential disclosers’ responsibilities to do so. It also makes recommendations as to the principles and characteristics of identity-supporting disclosure practices.

Evolución dirigida de proteínas: La evolución dirigida es una técnica que nos permite explorar funciones enzimáticas que no son requeridas en el ambiente natural. Esta técnica, simula procesos genéticos naturales y de selección. Esta estrategia se utiliza cuando un diseño racional es muy complicado. Consiste en una repetición de ciclos de diversificación y selección que llevan a la acumulación de mutaciones benéficas. Aquí se presenta dos ejemplos de evolución dirigida con los cuales se ha trabajado directamente: la ADN polimerasa del organismo  Thermus aquaticus usada comúnmente en PCR, y la proteína LacI que regula la expresión de genes usados para el metabolismo de lactosa en E. Coli. / Directed evolution allows us to explore protein functionalities not required in the natural environment. It mimics natural genetic processes and selective pressures. This approach is used when the molecular basis is not completely understood and rational design is a difficult task. This approach consists of serial cycles of consecutive diversification and selection which eventually lead to the accumulation of beneficial mutations. Here are presented two cases where directed evolution is used to modify two different proteins: Taq polymerase, enzyme used for DNA extension in PCR, and the LacI repressor protein which regulates gene expression on E.coli.

Le génome bactérien est classiquement pensé comme constitué de “chromosomes”, éléments génomiques essentiels pour l’organisme, stables et à évolution lente, et de “plasmides”, éléments génomiques accessoires, mobiles et à évolution rapide. La distinction entre plasmides et chromosomes a récemment été mise en défaut avec la découverte dans certaines lignées bactériennes d’éléments génomiques intermédiaires, possédant à la fois des caractéristiques de chromosomes et de plasmides. Désignés par le terme de “chromosomes secondaires”, “mégaplasmides” ou “chromid”, ces éléments sont dispersés parmi les lignées bactériennes et sont couramment décrits comme des plasmides adaptés et modifiés. Cependant, leur véritable nature et les mécanismes permettant leur intégration dans le génome stable reste à caractériser. En utilisant les protéines liées aux Systèmes de Transmission de l’Information Génétique (STIG) comme variables descriptives des éléments génomiques bactériens (ou réplicons), une étude globale de génomique comparative a été conduite sur l’ensemble des génomes bactériens disponibles. A travers l’analyse de l’information contenue dans ce jeu de données par différentes approches analytiques, il apparait que les STIG constituent des marqueurs pertinents de l’état d’intégration des réplicons dans le génome stable, ainsi que de leur origine évolutive, et que les Réplicons Extra-Chromosomiques Essentiels (RECE) témoignent de la diversité des mécanismes génétiques et des processus évolutifs permettant l’intégration de réplicons dans le génome stable, attestant ainsi de la continuité du matériel génomique. / The genome of bacteria is classically separated into essential, stable and slow evolving replicons (chromosomes) and accessory, mobile and rapidly evolving replicons (plasmids). This paradigm is being questioned since the discovery of extra-chromosomal essential replicons (ECERs), be they called ”megaplasmids”, ”secondary chromosomes” or ”chromids”, which possess both chromosomal and plasmidic features. These ECERs are found in diverse lineages across the bacterial phylogeny and are generally believed to be modified plasmids. However, their true nature and the mechanisms permitting their integration within the sable genome are yet to be formally determined. The relationships between replicons, with reference to their genetic information inheritance systems (GIIS), were explored under the assumption that the inheritance of ECERs is integrated to the cell cycle and highly constrained in contrast to that of standard plasmids. A global comparative genomics analysis including all available of complete bacterial genome sequences, was performed using GIIS functional homologues as parameters and applying several analytical procedures. GIIS proved appropriate in characterizing the level of integration within the stable genome, as well as the origins, of the replicons. The study of ECERs thus provides clues to the genetic mechanisms and evolutionary processes involved in the replicon stabilization into the essential genome and the continuity of the genomic material.