Editorials in 2012

The origins of three species and the adaptive evolution of their genomes under natural and agricultural selection are investigated in this issue.

Aging parents transmit an increasing burden of chromosomal aberrations and mutations. There are also epidemiological correlations between parental age and neurodevelopmental disorders, including autism. The citation and interpretation of these two lines of evidence should be carefully evaluated.

Industry and its regulators are increasingly finding value in inviting independent scrutiny of clinical trial data at the participant level. In addition to increasing accuracy and trust, accessible trial data can be used to generate new research hypotheses and validate existing research. Academic trial investigators need to be incentivized to catch up with this encouraging trend.

The impact of the papers we publish depends increasingly on the data they describe. In insisting on data access for referees and readers, we prioritize scientific integrity above all and place the interests of research participants before impact.

Whereas once it was only possible to generate reference genome sequences one at a time, it is now feasible to design genomic experiments to maximize functional comparisons and contrasts among many genomes. Investigating the diversity of a number of related parasite genomes and their transcriptomes in multiple contexts increasingly shows us ways to intervene in the ecological and evolutionary strategies of pathogens.

Familiarity with developments in all areas of genetics—from the trained intuition of dysmorphology to algorithms for SNP calling in next-generation sequencing—is extraordinarily productive in research and clinical translation. Actively organized conferences modeled on the recent European Society of Human Genetics (ESHG) meeting in Nuremberg go a long way in preparing the field for future success.

Because of the usefulness of genome-wide association study (GWAS) data for mapping regulatory variation in the human genome, the journal now asks authors to report the co-location of trait-associated variants with gene regulatory elements identified by epigenetic, functional and conservation criteria. We also ask that authors publish or database the genotype frequencies or association P values for all SNPs investigated, whether or not they reached genome-wide significance.

Animal experimentation in scientific research is a good thing: important, increasing and often irreplaceable. Careful experimental design and reporting are at least as important as attention to welfare in ensuring that the knowledge we gain justifies using live animals as experimental tools.

Belief in the value of DNA sequence led to investment in the technology that made the Human Genome Project possible. But DNA sequences are not in themselves inventions, and gene variants and the conditions in which they cause disease are discovered and held by many stakeholders. So, if patents are to continue to provide incentives of benefit from genomics, they must be licensed for competition that is not a zero-sum game.

The Portable Legal Consent for Common Genomics Research (PLC-CGR) is an experimental bioethics protocol that provides maximum utility to researchers who agree to its terms and protection for the de-identified personal and genomic data volunteered by informed research subjects. Data and resulting publications from this protocol are equally available to all academic, nonprofit and commercial competitors, so that intellectual property claims should arise only on new discoveries based on the data.

An alphabet soup of organizations and initiatives across the world are concerned with identifying, collecting and evaluating disease-causing human gene variants and using them to diagnose and treat rare diseases. Despite increasing standardization of nomenclature and technology, our efforts still need coordination to produce a pipeline leading from discovery to delivery.

Researchers, funders and journals are in broad agreement that data must be accessible to support the conclusions of scientific publications and for the research to have impact. What is lacking is agreement on timing, formatting and attribution.