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This Week in Nature: Apr 25, 2019

In Nature Methods this week, a team led by University of Oxford scientists describes a genomic single-molecule technique for measuring replication fork movement by detecting nucleotide analog signal currents on extremely long nanopore traces. The researchers use the method — dubbed D-NAscent — to study Saccharomyces cerevisiae chromosome biology, generating a whole-genome map of replication dynamics at a single-molecule level and uncovering a class of replication origins that they say could not have been found with established methods.

And in Nature Biotechnology, University of Washington investigators report a method for increasing the accuracy of nanopore DNA sequencing by varying cross-membrane voltage, which changes how a DNA strand moves through the nanopore. This approach, they write, reduces the impact of the two primary error types that affect sequencing accuracy: enzyme mis-steps and sequences with indistinguishable signals. Incorporating the variable-voltage method into nanopore sequencing platforms "will enable wide-scale improvement of all nanopore-based DNA sequencing applications, including species identification, epigenetic mapping, and higher accuracy de novo genome sequencing at lower coverage," the team concludes.

In Nature Medicine, a multi-institute group of scientists discusses the WINTHER trial, a clinical study examining the impact of tumor biopsy-derived DNA sequencing and RNA expression analysis on guiding cancer treatment decisions. Despite the trial's limitations — which include patient pretreatment and the small number of participating patients — it shows that "genomic and transcriptomic profiling are both useful for improving therapy recommendations and patient outcome, and expands personalized cancer treatment," the authors write. GenomeWeb has more on this, here.

Also in Nature Medicine, UK researchers present data from TARGET, a study evaluating the use of circulating tumor DNA sequencing to select patients for early-stage clinical trial enrollment. The investigators state that their findings support the routine implementation of ctDNA sequencing as an adjunct to tumor testing for patient stratification, and that advances in ctDNA assay technology may eventually make it possible to assign certain patients to blood-based testing alone. GenomeWeb also covers this study, here.

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.