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Computational Approach Profiles Splicing, Reduces VUS in Hereditary Cancer Tests

In the Journal of Molecular Diagnostics, Invitae investigators consider the clinical consequences of hereditary cancer syndrome genetic tests that include messenger RNA splicing changes. Using its RNA sequencing-based "splice effect event resolver" (SPEER) workflow — established to interrogate germline genetic variants that disrupt such slicing, including those classified as variants of uncertain significance — the team identified dozens of cancer-related genes in more than 20,300 individuals. The SPEER analysis uncovered transcript splicing changes in 971 of the 3,563 individuals carrying variants expected to alter splicing and, in another 40 individuals, splicing changes linked to variants that were not already profiled. In the process, the author explain, they were also able to reclassify VUSs as pathogenic/likely pathogenic or as benign/likely benign in more than 6 percent of the 20,417 individuals considered. "By combining comprehensive DNA and RNA sequencing with the validated SPEER algorithm," they write, "we will continue to collect data from individuals referred for hereditary cancer syndrome testing, develop deeper insights into the clinical relevance of splicing alterations, and improve the interpretation of inherited DNA variants — leading to a further reduction of uncertainty for hereditary cancer gene testing."

The Scan

Machine Learning Helps ID Molecular Mechanisms of Pancreatic Islet Beta Cell Subtypes in Type 2 Diabetes

The approach helps overcome limitations of previous studies that had investigated the molecular mechanisms of pancreatic islet beta cells, the authors write in their Nature Genetics paper.

Culture-Based Methods, Shotgun Sequencing Reveal Transmission of Bifidobacterium Strains From Mothers to Infants

In a Nature Communications study, culture-based approaches along with shotgun sequencing give a better picture of the microbial strains transmitted from mothers to infants.

Microbial Communities Can Help Trees Adapt to Changing Climates

Tree seedlings that were inoculated with microbes from dry, warm, or cold sites could better survive drought, heat, and cold stress, according to a study in Science.

A Combination of Genetics and Environment Causes Cleft Lip

In a study published in Nature Communications, researchers investigate what combination of genetic and environmental factors come into play to cause cleft lip/palate.