A study in PLOS Genetics looks at how an individual's genetic background affects the phenotype elicited by various genetic alterations. Using a genome-wide screen for modifiers of a wing-related allele in two Drosophila melanogaster genetic backgrounds, Michigan State University researchers found that almost three-quarters of the modifiers identified had variable effects depending on the broader genetic background. "Such background dependent effects can substantially alter conclusions about how genes influence biological processes, the potential for genetic screens in alternative wild-type backgrounds identifying new loci that contribute to trait expression, and the inferences of the topology of genetic networks," the study's authors say. For more on the study, check out a related story from GenomeWeb Daily News.
A large meta-analysis conducted as part of the International Collaboration for the Genomics of HIV did not unearth any variants that could be conclusively linked to HIV-1 acquisition risk, according to a study appearing in PLOS Pathogens. Investigators from Switzerland, the US, France, and elsewhere brought together SNP data from more than two dozen previous studies — representing 6,334 individuals with HIV-1 and nearly 7,500 without — in an effort to track down variants associated with HIV-1 acquisition. The initial analysis implicated two human leukocyte antigen alleles in this process, but follow-up validation work dissuaded researchers from listing them as risk loci, concluding instead that "genetic influences on HIV acquisition are either rare or have smaller effects than can be detected by this sample size."
In PLOS One, Wageningen University's Freek Bakker and colleagues describe the strategy they took to tackle the sequencing of DNA from preserved specimens of plants, fungi, and insects found at museums or herbariums. The team used multiplex, paired-end Illumina sequencing to assess the genome or exome sequences in the samples — some stretching back as far as 115 years. In the process, the researchers successfully sequenced nuclear DNA from a 43-year-old Arabidopsis thaliana sample, covering much of an existing reference assembly for the plant. They also generated exome sequence data for three fungal species going back as far as 82 years, as well as organelle sequences across the set of plant, fungus, and insect samples.