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This Week in PNAS: Jun 9, 2015

In the early, online edition of the Proceedings of the National Academy of Sciences, the University of Wisconsin at Madison's David Schwartz and colleagues present findings from a proof-of-principle study of multiple myeloma that used optical mapping and whole-genome sequencing to characterize tumor samples taken from the same individual over time. Along with structural variants in the tumor genome at each time point, the team detected a rise in tumor mutations as the cancer progressed. "Our findings highlight the need to routinely incorporate structural variation analysis at many length scales to understand cancer genomes more comprehensively," the study's authors say. GenomeWeb has more on the study, here.

A team from Italy, the UK, and Switzerland describe an apparent role for the microRNA miR-204 in an inherited form of the eye development disorder retinal dystrophy that includes a type of structural malformation known as bilateral coloboma. Using the medaka fish as a model, the researchers followed up on past findings from linkage, exome sequencing, and gene expression experiments that implicated alterations in the miR-204 seed region in the disease. In fish with higher- or lower-than-usual miR-204 levels, the study's authors saw abnormal photoreceptor development or function, with gain-of-function mutations most closely mimicking those found in patients.

Researchers from the Dana-Farber Cancer Institute, the Broad Institute, and Harvard University investigate the changes in transcription factor binding and gene expression that occur in some tumors. Using an approach called "regression analysis with background integration," or RABIT, the team brought together data from almost 700 chromatin immunoprecipitation sequencing studies performed by members of the ENCODE consortium with genomic profiles for nearly 7,500 tumors from 18 cancer types that were generated by members of the Cancer Genome Atlas. Together, these results revealed some of the regulatory processes at play in tumors, involving new and known transcription factors. Investigators are also attempting to use RABIT to uncover alternative splicing from RNA binding motif data.