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This Week in Nucleic Acids Research: Oct 2, 2014

University of Minnesota researchers report on a new online resource cataloging the genes that have been implicated as apparent cancer drivers. The Candidate Cancer Gene Database, or CCGD, is designed to house cancer-related information found through transposon mutagenesis studies, the team explains. Along with manually curated data on apparent cancer driver genes, the sites includes information on the precise location of the common transposon insertion sites created during the forward genetic screen studies of mice that were used to define them. Using a gene set enrichment approach, the study's authors demonstrated that pathways with known ties to human cancer are over-represented in CCGD, supporting the notion that it may help in understanding the broad range of tumors that afflict humans.

A team from the Genome Institute of Singapore and other centers in Singapore, the UK, Switzerland, and Australia introduce an approach for deciphering copy number variant and genotype profiles using control-free data generated through long-range targeted resequencing experiments. The researchers developed the algorithm, known as cnvCapSeq, with the help of simulate data representing 21 targeted loci in the human genome. They then went on to verify the approach using targeted resequencing data to profile CNVs in the complement factor H gene cluster in almost 300 individuals of Chinese descent living in Singapore.

Changes in the transcripts and small RNAs expressed by the gastroenteritis-causing pathogen Vibrio parahaemolyticus are altered when the bug successfully infects a host animal, leading to distinct infection-related gene expression patterns, according to another Nucleic Acids Research study. Researchers based at the Broad Institute and Brigham and Women's Hospital did RNA sequencing on V. parahaemolyticus isolates infecting rabbit intestines and compared messenger RNA and small RNA patterns detected there with those present in lab strains of the enteric pathogen. The analysis revealed differential expression involving a wide range of V. parahaemolyticus genes and pathways, offering clues to the processes at play during infection.