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This Week in Genome Research: Jan 30, 2019

An international team led by investigators at the University Medical Center Rotterdam assesses the collection of circular RNAs found in hundreds of breast cancers. Using RNA sequencing with random-primed complementary DNA and circRNA mapping, the researchers identified almost 96,000 circRNAs in 348 primary breast cancers, including 20,441 that turned up in two or more samples and a handful of circRNAs found in an independent sample set. Through a series of follow-up analyses, the authors found that the circRNAs "are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biology properties" in the breast cancers.

Researchers from the University of Kentucky and the Carnegie Institution for Science present results from an effort to assemble a chromosome-scale genome assembly for the axolotl, Ambystoma mexicanum, a model for development, limb regeneration, and evolutionary analyses. The team did low-coverage genome sequencing on four dozen offspring produced by crossing a homozygous A. mexicanum individual with an A. mexicanum-A.tigrinum hybrid, producing an assembly that spanned 27.3 billion bases and contained some12.6 million SNPs on 14 chromosomes. The chromosomes were further anchored with bacterial artificial chromosome clone fluorescence in situ hybridization data, the authors report, arguing that the assembly "will greatly facilitate studies of the axolotl in biological research." The Scan has more on this, here

Finally, a team from the US and China compare the genomes of three prominent cereal plants — sorghum, rice, and maize — searching for forms of variation that might serve as fodder for the plants' adaptations. The researchers re-sequenced the genomes of 26 sorghum accessions and sequenced transcripts in 40 accessions, considering variants in the accessions alongside those in domesticated and wild sorghum, rice, and maize accessions sequenced for previous studies. With these data, the authors found that "diverse evolutionary mechanisms provide the raw genetic material for adaptation in taxa with divergent histories of genome evolution."

The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.