This paper proposes an original definition of samples as a kind of data within the relational framework of data. The distinction between scientific objects (e.g., samples, data, models) often needs to be clarified in the philosophy of science to understand their role in the scientific inquiry. The relational framework places data at the forefront of knowledge construction. Their epistemic status depends on their evaluation as potential evidence in a research situation and their ability to circulate among researchers. While samples are (...) significant in data-generating science, their role has been underexplored in the philosophy of data literature. I draw on a case study from data-centric microbiology, viz. amplicon sequencing, to introduce specifications of the relational framework. These specifications capture the distinctive epistemic role of samples, allowing the discussion of their significance in the inquiry process. I argue that samples are necessarily transformed to be considered as evidence, portable in the limits of a situation, and they act as world anchors for claims about a phenomenon. I compare these specifications with other data and evidence frameworks and suggest they are compatible. The paper concludes by considering the extension of these criteria in the context of biobanking. The specifications proposed here help analyze other life sciences cases and deepen our understanding of samples and their epistemological role in scientific research. (shrink)

Fusion genes formed by chromosomal rearrangements are common drivers of cancer. Recent innovations in the field of next‐generation sequencing (NGS) have seen a dynamic shift from traditional fusion detection approaches, such as visual characterization by fluorescence, to more precise multiplexed methods. There are many different NGS‐based approaches to fusion gene detection and deciding on the most appropriate method can be difficult. Beyond the experimental approach, consideration needs to be given to factors such as the ease of implementation, processing time, associated (...) costs, and the level of expertise required for data analysis. Here, the different NGS‐based methods for fusion gene detection, the basic principles underlying the techniques, and the benefits and limitations of each approach are reviewed. This article concludes with a discussion of how NGS will impact fusion gene detection in a clinical context and from where the next innovations are evolving. (shrink)

Studies of Y chromosome evolution often emphasize gene loss, but this loss has been counterbalanced by addition of new genes. The DAZ genes, which are critical to human spermatogenesis, were acquired by the Y chromosome in the ancestor of Old World monkeys and apes. We and our colleagues recently sequenced the rhesus macaque Y chromosome, and comparison of this sequence to human and chimpanzee enables us to reconstruct much of the evolutionary history of DAZ. We report that DAZ arrived on (...) the Y chromosome about 38 million years ago via the transposition of at least 1.1 megabases of autosomal DNA. This transposition also brought five additional genes to the Y chromosome, but all five genes were subsequently lost through mutation or deletion. As the only surviving gene, DAZ experienced extensive restructuring, including intragenic amplification and gene duplication, and has been the target of positive selection in the chimpanzee lineage.Editor's suggested further reading in BioEssays Should Y stay or should Y go: The evolution of non‐recombining sex chromosomes Abstract. (shrink)