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This Week in Genome Research: Dec 26, 2012

The University of Montreal's Philip Awadalla, with Canadian and American collaborators, describes ties between rare alleles in the meiotic recombination-related gene PRDM9 and childhood leukemia in an early, online Genome Research study. The team picked up rare, maternally inherited PRDM9 variants when they tested two French Canadian siblings with B-cell precursor acute lymphoblastic leukemia and their unaffected parents. These less-frequently-found PRDM9 alleles corresponded with off-kilter crossover events in the mother's germline cells — meiotic recombination occurring primarily outside of known hotspots. Rare PRDM9 alleles proved more common-than-usual among parents from nearly two dozen other B-ALL affected French Canadian families, too. And similar patterns turned up in the families of 50 pediatric B-ALL patients treated at the St. Jude Children's Research Hospital in the US. "PRDM9 variability in humans is thought to influence genomic stability," authors write, "and these data support a potential role for PRDM9 variation in risk of acquiring aneuploidies or genomic rearrangements associated with childhood leukemogenesis."

Researchers from Canada and the US present a resource for finding and quantifying isoforms from high-throughput RNA sequence data. The method, known as iReckon, brings this RNA-seq information together with other biological and technical cues to characterize both new and known isoforms, the team notes. For their Genome Research paper, investigators showcase iReckon's capabilities using simulated data as well as transcriptional data representing both a breast cancer sample and a breast cancer cell line. "Our results on simulated and real data demonstrated data demonstrate a superior ability to discover novel isoforms with a significantly reduced number of false positive predictions," they say, "and our abundance accuracy prediction outmatches that of other state-of-the-art tools."

The Scan

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.

New Insights Into TP53-Driven Cancer

Researchers examine in Nature how TP53 mutations arise and spark tumor development.

Mapping Single-Cell Genomic, Transcriptomic Landscapes of Colorectal Cancer

In Genome Medicine, researchers present a map of single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer.

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.