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Infectious Disease Tracking Study Compares Genome Sequencing Approaches

For a paper in BMC Genomics, researchers from the Erasmus Medical Center's viroscience department consider sequencing methods for detecting and tracking viruses in genomic epidemiology applications. Using samples containing Flaviviridae family Zika, West Nile, Yellow Fever, or Usutu viruses at a range of concentrations, the team compared metagenomic sequencing, amplicon-based genome sequencing, and capture-based sequencing on Illumina short read or Oxford Nanopore platforms. While capture-based Illumina sequencing was a sensitive strategy for characterizing viral genomes, for example, the authors saw benefits for rapid Nanopore amplicon sequencing when it came to profiling samples in certain viral load ranges. "Choosing a sequencing platform and approach is important for labs adopting genome sequencing, but depends on the stage of an outbreak and the to-be-answered questions in public health decision making," they write, noting that their data "offers a deep insight in the characteristics of each approach and help making this choice."

The Scan

Open Pediatric Brain Tumor Atlas Team Introduces Genomic Data Collection, Analytical Tools

A study in Cell Genomics outlines open-source methods being used to analyze and translate whole-genome, exome, and RNA sequence data from the Pediatric Brain Tumor Atlas.

Neurological Outcomes Linked to Innate Immune Features After Cardiac Arrest

Researchers reporting in Med dig into immune features found a few hours after cardiac arrest that correspond with neurological outcomes.

Mouse Study Finds Circadian Rhythm-Related Gene Expression Changes Linked to Sleep Apnea

A paper in PLOS Biology reveals tissue-specific circadian rhythm and gene expression patterns in an intermittent hypoxia-based mouse model of obstructive sleep apnea.

Polygenic Risk Score to Predict Preeclampsia, Gestational Hypertension in Pregnant Women

Researchers in Nature Medicine provide new mechanistic insights into the development of hypertensive disorders of pregnancy, which may help develop therapeutics.