Biomedical subjects

Jonathan Lawson

Publications and source records attributed to Jonathan Lawson.

3 recordsLinked to original sources

PubMed2025

Toward ethical provenance tracking: The GA4GH model data access agreement (DAA).

PURPOSE: Standardizing contractual clauses that govern data access enables research institutions to responsibly steward genomic and related health data while enabling its efficient downstream reuse. METHODS: We describe a document analysis study using both qualitative and comparative law analytical approaches to identify the most common categories of clauses from 29 different data access agreements used by human biomedical research consortia globally. We furthermore characterized the legal positions and standard practices for each common element of the agreement and synthesized across them to develop model clauses. A total of 3 discussion sessions were organized virtually to refine the clauses among members of the Ethical Provenance Subgroup of the Global Alliance for Genomics and Health. RESULTS: We developed 15 unique data access clauses corresponding to the most common legal elements identified in the sampled agreements. CONCLUSION: Model clauses can be used to drive administrative efficiencies and institutional compliance for managing access to human genomic data for research. Additional machine-readable consents and software solutions are needed to support traceable "ethical provenance" of human genomic data and communicate data use conditions throughout the data's life-cycle.

Humans↗

PubMed2004

PathoGene: a pathogen coding sequence discovery and analysis resource.

PathoGene is a web-based resource that streamlines the process of predicting genes in microorganisms and designs PCR primers for amplification to facilitate sequence analysis and experimentation. PathoGene currently supports primer design for every complete microbial, viral, and fungal genome as cataloged in GenBank by the National Center for Biotechnology Information (NCBI; http://www.ncbi.nlm.nih.gov/). The resulting primers can then be subjected to a stand-alone Basic Local Alignment Search Tool (BLAST) system called PathoBLAST in which the predicted PCR product and/or primers can be compared against the genome of interest or a similar genome to find related genes or estimate primer quality.

Bacillus anthracis↗

PubMed2004

Organism identification using a genome sequence-independent universal microarray probe set.

There has been increasing interest and efforts devoted to developing biosensor technologies for identifying pathogens, particularly in the biothreat area. In this study, a universal set of short 12- and 13-mer oligonucleotide probes was derived independently of a priori genomic sequence information and used to generate unique species-dependent genomic hybridization signatures. The probe set sequences were algorithmically generated to be maximally distant in sequence space and not dependent on the sequence of any particular genome. The probe set is universally applicable because it is unbiased and independent of hybridization predictions based upon simplified assumptions regarding probe-target duplex formation from linear sequence analysis. Tests were conducted on microarrays containing 14,283 unique probes synthesized using an in situ light-directed synthesis methodology. The genomic DNA hybridization intensity patterns reproducibly differentiated various organisms (Bacillus subtilis, Yersinia pestis, Streptococcus pneumonia, Bacillus anthracis, and Homo sapiens), including the correct identification of a blinded "unknown" sample. Applications of this method include not only pathological and forensic genome identification in medicine and basic science, but also potentially a novel method for the discovery of unknown targets and associations inherent in dynamic nucleic acid populations such as represented by differential gene expression.

Bacillus anthracis↗