In PLoS Computational Biology this week, researchers in British Columbia led by Sohrab Shah report on a computational method they developed to detect novel gene fusions in cancer transcriptomes. The researchers say that their method, called deFuse, "considers all alignments and all possible locations for fusion boundaries" in contrast to others that only look for boundaries at the ends of exons. They evaluated deFuse using 40 ovarian cancer patient samples, one ovarian cancer cell line, and three sarcoma patient samples, and say "deFuse exhibits substantially better accuracy than two competing methods and that deFuse is able to discover gene fusions that are not discoverable by more simplistic methods."
Researchers at the University of Massachusetts Medical School report in PLoS Pathogens on their use of high-throughput sequencing to study the genomic variability of human cytomegaloviruses infecting newborns. "We observed substantial intrahost variability that was found throughout the HCMV genome and found evidence of selection both at the intrahost and interhost levels," the researchers write.
The National University of Singapore's Fook Tim Chew and his colleagues took a two-stage genome-wide association study approach to find genetic variants linked to a predisposition to allergic rhinitis or atopy in an ethnic Chinese population. While the team did not find any associations that had genome-wide significance, it saw "suggestive associations at rs8111930, an intronic SNP on MRPL4 gene on chromosome 19p13.2 and rs505010 a 5' flanking SNP to BCAP gene on chromosome 10q24.1." The paper appears in PLoS One.
Researchers in Korea report in PLoS One this week on their use of a genome-wide RNAi screen to study Trypanosoma cruzi infections. The researchers repeated the screen multiple times and used an algorithm to select genes that, when silenced, impaired T. cruzi infection. After validation, the researchers confirmed 14 hits some of which were cellular membrane proteins or involved in the TGF-beta signaling pathway. "This study represents a significant step toward unveiling the key molecular requirements for host cell invasion and revealing new potential targets for antiparasitic therapy," the authors write.