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Nature Papers Present Way to Boost Short-Read RNA-seq Transcriptome Accuracy, Sequencing Analysis of Breakthrough Infections

A method that improves the accuracy with which the set of expressed transcripts can be inferred from short RNA sequencing reads is presented in Nature Biotechnology this week. Assembling transcripts from short-read RNA sequencing data is limited by the lack of long-range information contained in each individual short read. At the same time, third-generation technologies are able to read full-length transcripts, but are limited by low throughput, a high error rate, and a high cost per base. To develop an alternative approach, a team led by scientists from Ludwig-Maximilians-Universität turned to an experimental-computational technique — called Ladder-seq — that separates transcripts according to their lengths before sequencing and uses the additional information to improve the quantification and assembly of transcripts. The method, the scientists write, "will allow research facilities to study the composition and dynamics of the transcriptome at an unprecedented level of accuracy based on a technology that has been established for over a decade."

Through an analysis of SARS-CoV-2 sequences from COVID-19 patients in the San Francisco Bay Area, a team led by scientists from the University of California, San Francisco, has found that vaccine breakthrough infections are mostly caused by immune-evading variants. As reported in Nature Microbiology this week, the investigators performed whole-genome sequencing and viral load measurements of nasal swabs, in conjunction with retrospective medical chart review, of 1,373 Bay Area COVID-19 patients between February and June 2021. They discover that vaccine breakthrough infections are overrepresented by immunity-evading variants as compared with unvaccinated infections, probably due to selection pressure in a highly vaccinated community. Notably, the researchers also found that symptomatic breakthrough infection and unvaccinated infections had comparable viral loads, suggesting that symptomatic breakthrough infections may be as efficient in spreading COVID-19 as unvaccinated infections, regardless of the infecting lineage.

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.