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Field-Wide Bias in Differential Expression by High-Throughput Sequencing Found

There is widespread bias in the differential expression profiling field amid unreliability of statistical methods used to analyze high-throughput sequencing data, according to a report appearing in PLOS Biology this week. In recent years concerns have been raised over the quality of experimental science, particularly in terms of reproducibility, replicability, and statistical power to find true effects. Aiming to explore these issues as they relate to expression profiling by high-throughput sequencing, scientists from the University of Tartu analyzed tens of thousands of relevant datasets submitted to the National Center for Biotechnology Information's Gene Expression Omnibus between 2008 and 2020. "Our goal was to study real-world statistical inferences made by working scientists," the study's authors write. "Thus, we study how experimental design choices and analytic decisions of scientists affect the quality of their statistical inferences." The results of the study collectively suggest that the field is largely built on analyzing low-power experiments that are unlikely to identify actual effects while presenting an unknowable number of false discoveries as statistically significant. Although the researchers do not see an apparent single fix for the problem, they say that the development of cheaper ways of conducting experiment could make well-powered experiments practically feasible, which in turn could lead to the development of analytic workflows that work.

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.