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This Week in PLOS: Apr 11, 2016

In PLOS Genetics, a Stanford University-led team describes de novo and rare variants it identified in an exome sequence-based study of individuals with congenital heart disease. The researchers began by profiling protein-coding sequences in 59 individuals with rare, non-syndromic heart malformations called atrioventricular septal defects, their unaffected parents, and 59 unaffected control trios. By analyzing this exome data in combination with developmental co-expression networks, protein interaction data, and/or inheritance models of loci already linked to congenital heart disease, they narrowed in on candidate congenital heart disease variants that were subsequently tested in another 100 congenital heart disease cases and 533 controls. All told, the analysis highlighted de novo or inherited changes to 19 genes, including transcription factor- and collagen-coding genes.

McGill University researchers reporting in PLOS Neglected Tropical Diseases describe findings from a study that used available transcriptome data to explore host immune response to infection by helminth worms from several species affecting different tissue types. Through a meta-analysis of nine publicly available gene expression sets—representing mice with lung, liver, diaphragm, or intestinal infections by five parasitic helminth worms — the researchers detected some 700 genes that routinely shift in helminth-infected tissues, from a rise in expression of genes involved in immune signaling, pathogen recognition, and immune signaling to declining metabolic gene expression.

Finally, a team from Italy presents a PLOS One study of genetic variability in 10 of that country's most notable horse and pony breeds. Using targeted mitochondrial sequence data for 407 Italian horses samples, representing Italian riding horse and pony breeds such as the Bardigiano, Esperia, or Sardinian Anglo-Arab, the researchers uncovered diverse mitochondrial haplotypes spanning many of the haplogroups previously described in domestic horses, with limited mitochondrial haplotype-based population structure. Through comparisons with mitochondrial sequences from three-dozen Arabian horses, meanwhile, they saw hints that the Arabian horses may have had relatively little impact on the mitochondrial make up of Italian horses breeds despite their past use for improving local breeds.