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

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

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

ITEP Test and Evaluation of Humanitarian Demining Equipment, 2006

The ITEP Work Plan 2006 compiles all test and evaluation activities that will be carried out during 2006 by the ITEP member countries, either as single-country activities or as ITEP collaborative efforts. The following summary provides an update on collaborative test activities initiated during 2005 and continuing in 2006, including also some of the new test and evaluation efforts envisaged

An Update on the ITEP Program and Activities

Since 2000, the International Test and Evaluation Program for Humanitarian Demining has been a crucial instrument in the research and development field, providing comprehensive test and evaluation information to the demining community worldwide. This article summarizes the main ongoing and planned test and evaluation activities carried out by the ITEP participants, either as coordinated efforts or as national projects

CEN Workshop Agreements for Test and Evaluation of Humanitarian Demining Equipment

The Comité Européen de Normalisation has organised workshops to aid the establishment of standard methodologies for demining. This article discusses the workshops and the agreements reached in those workshops. The author includes a list of contacts for additional information on demining equipment and methods

Coming of age of personalized medicine: challenges ahead

A report on the 5th International DNA Sampling Conference 'The age of personal genomics', Banff, Canada, 16-18 September 2009

Expanding the ancient DNA bioinformatics toolbox, and its applications to archeological microbiomes

The 1980s were very prolific years not only for music, but also for molecular biology and genetics, with the first publications on the microbiome and ancient DNA. Several technical revolutions later, the field of ancient metagenomics is now progressing full steam ahead, at a never seen before pace. While generating sequencing data is becoming cheaper every year, the bioinformatics methods and the compute power needed to analyze them are struggling to catch up. In this thesis, I propose new methods to reduce the sequencing to analysis gap, by introducing scalable and parallelized softwares for ancient DNA metagenomics analysis. In manuscript A, I first introduce a method for estimating the mixtures of different sources in a sequencing sample, a problem known as source tracking. I then apply this method to predict the original sources of paleofeces in manuscript B. In manuscript C, I propose a new method to scale the lowest common ancestor calling from sequence alignment files, which brings a solution for the computational intractability of fitting ever growing metagenomic reference database indices in memory. In manuscript D, I present a method to statistically estimate in parallel the ancient DNA deamination damage, and test it in the context of de novo assembly. Finally, in manuscript E, I apply some of the methods developed in this thesis to the analyis of ancient wine fermentation samples, and present the first ancient genomes of ancient fermentation bacteria. Taken together, the tools developed in this thesis will help the researchers working in the field of ancient DNA metagenomics to scale their analysis to the massive amount of sequencing data routinely produced nowadays

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