Investigation into the annotation of protocol sequencing steps in the sequence read archive

BACKGROUND: The workflow for the production of high-throughput sequencing data from nucleic acid samples is complex. There are a series of protocol steps to be followed in the preparation of samples for next-generation sequencing. The quantification of bias in a number of protocol steps, namely DNA fractionation, blunting, phosphorylation, adapter ligation and library enrichment, remains to be determined. RESULTS: We examined the experimental metadata of the public repository Sequence Read Archive (SRA) in order to ascertain the level of annotation of important sequencing steps in submissions to the database. Using SQL relational database queries (using the SRAdb SQLite database generated by the Bioconductor consortium) to search for keywords commonly occurring in key preparatory protocol steps partitioned over studies, we found that 7.10%, 5.84% and 7.57% of all records (fragmentation, ligation and enrichment, respectively), had at least one keyword corresponding to one of the three protocol steps. Only 4.06% of all records, partitioned over studies, had keywords for all three steps in the protocol (5.58% of all SRA records). CONCLUSIONS: The current level of annotation in the SRA inhibits systematic studies of bias due to these protocol steps. Downstream from this, meta-analyses and comparative studies based on these data will have a source of bias that cannot be quantified at present

Untangling the Debate: The Ethics of Human Enhancement

Human enhancement, in which nanotechnology is expected to play a major role, continues to be a highly contentious ethical debate, with experts on both sides calling it the single most important issue facing science and society in this brave, new century. This paper is a broad introduction to the symposium herein that explores a range of perspectives related to that debate. We will discuss what human enhancement is and its apparent contrast to therapy; and we will begin to tease apart the myriad intertwined issues that arise in the debate: (1) freedom & autonomy, (2) health & safety, (3) fairness & equity, (4) societal disruption, and (5) human dignity