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This Week in Nucleic Acids Research: Feb 17, 2016

An Italian team has characterized the microRNA repertoire in human retinas using deep, small RNA sequencing on retina samples from 16 individuals and two human retinal pigment epithelium/choroid tissue samples. The researchers estimated that the resulting retinal miRNome encompasses some 90 percent of the miRNAs expressed in the retina, including more than four dozen retina-specific miRNA candidates and thousands of isomiRs, or miRNA variants. "This study is the first to reveal the complexity of the human retina miRNome at nucleotide resolution," they write, "and constitutes a unique resource to assess the contribution of miRNAs to the pathophysiology of the human retina."

Japanese researchers describe a strategy called "Control Sample-based Detection of Structural Variation," or COSMOS, for finding somatic structural variants in cancer genomes. The approach uses an asymmetrical comparison of mapped tumor and normal sequence read statistics, coupled with strand-specific read-depth data, to find and prioritize potential structural variants, the team says. When they applied COSMOS to a structural variant analysis of genome-engineered and gamma-irradiated mouse cells, the investigators found that the method compared favorably with existing approaches, successfully detecting more than 84 percent of the structural variants that could be picked up by PCR.

A group from China and the US introduces a computational pipeline known as UROBORUS for detecting circular RNAs from RNA sequencing data. In their proof-of-principle experiments, the researchers uncovered thousands of candidate circular RNAs when they applied UROBORUS to seven oligodendroglioma, 20 glioblastoma, and 19 normal brain samples. The set included nearly 500 circular RNAs that appear to be differentially expressed in glioma samples compared to typical brain tissue controls, the study's authors report, noting that future versions of UROBORUS are expected to detect still more circular RNAs stemming from intronic regions rather than those falling at exon junctions. 

The Scan

ChatGPT Does As Well As Humans Answering Genetics Questions, Study Finds

Researchers in the European Journal of Human Genetics had ChatGPT answer genetics-related questions, finding it was about 68 percent accurate, but sometimes gave different answers to the same question.

Sequencing Analysis Examines Gene Regulatory Networks of Honeybee Soldier, Forager Brains

Researchers in Nature Ecology & Evolution find gene regulatory network differences between soldiers and foragers, suggesting bees can take on either role.

Analysis of Ashkenazi Jewish Cohort Uncovers New Genetic Loci Linked to Alzheimer's Disease

The study in Alzheimer's & Dementia highlighted known genes, but also novel ones with biological ties to Alzheimer's disease.

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.