In a paper published online in advance this week, a team led by investigators at the Washington University School of Medicine in St. Louis characterized "expressed mutations in highly immunogenic methylcholanthrene-induced sarcomas derived from immunodeficient Rag2−/− mice that phenotypically resemble nascent primary tumor cells" using massively parallel sequencing. Then, using prediction algorithms, the team identified "mutant spectrin-β2 as a potential rejection antigen of the d42m1 sarcoma and validate this prediction by conventional antigen expression cloning and detection," and now show that "cancer immunoediting of d42m1 occurs via a T-cell-dependent immunoselection process that promotes outgrowth of pre-existing tumor cell clones lacking highly antigenic mutant spectrin-β2 and other potential strong antigens."
In another Nature advance online publication, North Carolina State University's Trudy Mackay and her colleagues present the Drosophila melanogaster Genetic Reference Panel, "a community resource for analysis of population genomics and quantitative traits."
The US National Cancer Institute's Ofir Hakim and colleagues this week discuss "the role of nuclear architecture and frequency of DNA damage in the genesis of chromosomal translocations by measuring these parameters simultaneously in cultured mouse B lymphocytes." Taking this approach, the NCI-led team found that "translocations associated with recurrent site-directed DNA damage are proportional to the rate of DNA break formation, as measured by replication protein A accumulation at the site of damage."
Elsewhere in Nature , researchers at the University of Chicago along with their colleagues show that genetic variants that modify chromatin accessibility and transcription-factor binding are major factors leading to gene expression differences among humans. Using DNaseI sequencing on "70 Yoruba lymphoblastoid cell lines, for which genome-wide genotypes and estimates of gene expression levels are also available," the team generated genome-wide maps of chromatin accessibility for each individual, identifying"8,902 locations at which the DNase-seq read depth correlated significantly with genotype at a nearby single nucleotide polymorphism or insertion/deletion," which the researchers dubbed DNase I sensitivity quantitative trait loci, or dsQTLs. "Our observations indicate that dsQTLs are highly abundant in the human genome and are likely to be important contributors to phenotypic variation," the authors write.