Is there a right time to know? The right not to know and genetic testing in children

The increasing implementation of next-generation sequencing technologies in the clinical context and the expanding commercial offer of genetic tests directly-toconsumers has increased the availability of previously inaccessible genetic information. A particular concern in both situations is how the volume of novel information will affect the processing of genetic and genomic information from minors. For minors, it is argued that in the provision of genetic testing, their "right not to know" should be respected as much as possible. Testing a minor early in life eliminates the possibility for the minor to make use of his or her "right not to know." The article discusses the theoretical underpinnings of the right not know, analyzes reasons why various direct-to-consumer companies process samples from minors, and discusses the right not to know in relation to common complex disorders in a pediatric population

Challenges of web-based personal genomic data sharing

In order to study the relationship between genes and diseases, the increasing availability and sharing of phenotypic and genotypic data have been promoted as an imperative within the scientific community. In parallel with data sharing practices by clinicians and researchers, recent initiatives have been observed in which individuals are sharing personal genomic data. The involvement of individuals in such initiatives is facilitated by the increased accessibility of personal genomic data, offered by private test providers along with availability of online networks. Personal webpages and on-line data sharing platforms such as Consent to Research (Portable Legal Consent), Free the Data, and Genomes Unzipped are being utilized to host and share genotypes, electronic health records and family history uploaded by individuals. Although personal genomic data sharing initiatives vary in nature, the emphasis on the individuals’ control on their data in order to benefit research and ultimately health care has seen as a key theme across these initiatives. In line with the growing practice of personal genomic data sharing, this paper aims to shed light on the potential challenges surrounding these initiatives. As in the course of these initiatives individuals are solicited to individually balance the risks and benefits of sharing their genomic data, their awareness of the implications of personal genomic data sharing for themselves and their family members is a necessity. Furthermore, given the sensitivity of genomic data and the controversies around their complete de-identifiability, potential privacy risks and harms originating from unintended uses of data have to be taken into consideration

From the principles of genomic data sharing to the practices of data access committees

Sharing genomic research data through controlled-access databases has increased in recent years. Policymakers and funding organizations endorse genomic data sharing in order to optimize the use of public funds and to increase the statistical power of databases. Well-established data access arrangements and data access committees (DACs)responsible for reviewing and managing requests for access to genomic databasesare therefore central for implementing the policies and principles of data sharing. This article aims to investigate the functionality of DACs through the perspective of existing practices

Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification

SourcePredict is a Python package distributed through Conda, to classify and predict the origin of metagenomic samples, given a reference dataset of known origins, a problem also known as source tracking. DNA shotgun sequencing of human, animal, and environmental samples has opened up new doors to explore the diversity of life in these different environments, a field known as metagenomics (Hugenholtz & Tyson, 2008). One aspect of metagenomics is investigating the community composition of organisms within a sequencing sample with tools known as taxonomic classifiers, such as Kraken (Wood & Salzberg, 2014). In cases where the origin of a metagenomic sample, its source, is unknown, it is often part of the research question to predict and/or confirm the source. For example, in microbial archaelogy, it is sometimes necessary to rely on metagenomics to validate the source of paleofaeces. Using samples of known sources, a reference dataset can be established with the taxonomic composition of the samples, i.e., the organisms identified in the samples as features, and the sources of the samples as class labels. With this reference dataset, a machine learning algorithm can be trained to predict the source of unknown samples (sinks) from their taxonomic composition. Other tools used to perform the prediction of a sample source already exist, such as Source- Tracker (Knights et al., 2011), which employs Gibbs sampling. However, the Sourcepredict results are more easily interpreted since the samples are embedded in a human observable low-dimensional space. This embedding is performed by a dimension reduction algorithm followed by K-Nearest-Neighbours (KNN) classification.Summary Method - Prediction of the proportion of unknown sources - Prediction of the proportion of known sources - Combining unknown and source proportion

Controlled access under review : improving the governance of genomic data access

In parallel with massive genomic data production, data sharing practices have rapidly expanded over the last decade. To ensure authorized access to data, access review by data access committees (DACs) has been utilized as one potential solution. Here we discuss core elements to be integrated into the fabric of access review by both established and emerging DACs in order to foster fair, efficient, and responsible access to datasets. We particularly highlight the fact that the access review process could be adversely influenced by the potential conflicts of interest of data producers, particularly when they are directly involved in DACs management. Therefore, in structuring DACs and access procedures, possible data withholding by data producers should receive thorough attention

Pre- and post-testing counseling considerations for the provision of expanded carrier screening : exploration of European geneticists’ views

Background: Carrier screening is generally performed with the aim of identifying healthy couples at risk of having a child affected with a monogenic disorder to provide them with reproductive options. Expanded carrier screening (ECS), which provides the opportunity for multiple conditions to be screened in one test, offers a more cost-effective and comprehensive option than screening for single disorders. However, implementation of ECS at a population level would have implications for genetic counseling practice. Methods: We conducted semi-structured interviews with sixteen European clinical and molecular geneticists with expertise in carrier screening to explore their views on the implementation of ECS in the clinical setting. Results: Using inductive content analysis, we identified content categories relevant to the pre- and post-test settings. Participants believed ECS would ideally be targeted at couples before pregnancy. There was some disagreement regarding the acceptability of performing ECS in individuals, with several participants actively opposing individual-based screening. In addition, participants discussed the importance of ensuring informed and voluntary participation in ECS, recommending measures to minimize external pressure on prospective parents to undergo testing. A need for adequate counseling to foster informed, autonomous reproductive decision-making and provide support for couples found to be at risk was emphasized. Conclusions: Practical challenges in optimizing pre-test education and post-test counseling should not be underestimated and they should be carefully addressed before implementing ECS in the clinical setting

The use of samples originating from doping control procedures for research purposes : a qualitative study

Doping control samples may be used for research purposes by the World Anti-Doping Agency (WADA)-accredited laboratories after their compulsory storage period has expired. This study investigates opinions of stakeholders toward the governance of antidoping research on these samples and to evaluate the current framework. Semistructured interviews were conducted with stakeholders in antidoping research. The distinction between research and quality assurance in the International Standard for Laboratories (ISL) is neither well-understood nor interpreted uniformly by WADA-accredited labs. Most laboratories would not seek ethics approval for research on doping control samples. Interviewees considered that athletes should be better informed on what antidoping research can entail. A consistent and uniform approach toward the consent should be employed worldwide. Standards and safeguards should be implemented to reduce the risk of reidentification. Centralization of the Informed Consent Form in the ADAMS (Anti-Doping Administration & Management System) database would facilitate providing more information and allow the implementation of the right to withdraw

Genetic testing of children for adult-onset conditions: opinions of the British adult population and implications for clinical practice

This study set out to explore the attitudes of a representative sample of the British public towards genetic testing in children to predict disease in the future. We sought opinions about genetic testing for adult-onset conditions for which no prevention/treatment is available during childhood, and about genetic 'carrier' status to assess future reproductive risks. The study also examined participants' level of agreement with the reasons professional organisations give in favour of deferring such testing. Participants (n=2998) completed a specially designed questionnaire, distributed by email. Nearly half of the sample (47%) agreed that parents should be able to test their child for adult-onset conditions, even if there is no treatment or prevention at time of testing. This runs contrary to professional guidance about genetic testing in children. Testing for carrier status was supported by a larger proportion (60%). A child's future ability to decide for her/himself if and when to be tested was the least supported argument in favour of deferring testing.European Journal of Human Genetics advance online publication, 5 November 2014; doi:10.1038/ejhg.2014.221

Predictive genetic testing in minors for Myocilin juvenile onset open angle glaucoma

Author manuscript made available following 12 month embargo from date of publication (28 Jan 2015) in accordance with publisher copyright policy.Myocilin glaucoma is an autosomal dominant disorder leading to irreversible blindness, but early intervention can minimize vision loss and delay disease progression. The purpose of this study was to discuss the benefits of predictive genetic testing in minors for Myocilin mutations associated with childhood onset glaucoma. Three families with Myocilin mutations associated with an age of onset before 18 years and six unaffected at-risk children were identified. Predictive genetic testing was discussed with the parents and offered for at-risk minors. Parents opted for genetic testing in half of the cases. None carried the familial mutation. The age of disease onset in the family, the severity of the condition, and the age of the child are all factors that appear to influence the decision of the parent to test their children. Predictive genetic testing for early onset Myocilin glaucoma can facilitate early detection of disease or discharge from routine ophthalmic examinations