In PLoS Genetics this week, members of the LACE Consortium present their panel of 446 ancestry-informative markers, or AIMs, which they "optimized to estimate ancestral proportions in individuals and populations throughout Latin America," and applied to genome-wide data from 953 individuals from diverse African, European, and Native American populations. From this, the team selected AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations, selecting markers "on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity." Overall, the authors say their panel and reference genotype information "will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region."
In PLoS Pathogens, investigators at the Broad Institute and elsewhere present "a high-throughput whole HIV-1 genome deep sequencing platform that combines 454 pyrosequencing with novel assembly and variant detection algorithms." Using this, the team identified a variety of mutations, which they say "support the critical need for vaccine-induced CD8+ T cell responses to target more highly constrained regions of the virus in order to ensure the maintenance of immunodominant CD8 responses and the sustained decline of early viremia."
In PLoS One this week, investigators in Germany report on their development and application of a TaqMan real-time PCR assay to interrogate three SNPs "that differentiate a clade within the radiation of methicillin-resistant Staphylococcus aureus." The authors found that their TaqMan-based assay "achieved 98 percent typeability and [that its] results were fully concordant with DNA sequencing."
Writing in PLoS Biology this week, the University of Maine's Michelle Smith presents a teaching activity to help students "learn how one trait, such as deafness or blindness, can be affected by mutations in more than one gene and how geneticists can determine the minimum number of genes involved." Smith's lesson plan also outlines why "strains with dominant mutations cannot be used for complementation testing."