A Systematic Method for Detecting Abnormal mRNA Splicing and Assessing Its Clinical Impact in Individuals Undergoing Genetic Testing for Hereditary Cancer Syndromes.

Autor:	Kamps-Hughes N; Invitae Corporation, San Francisco, California., Carlton VEH; Invitae Corporation, San Francisco, California., Fresard L; Invitae Corporation, San Francisco, California., Osazuwa S; Invitae Corporation, San Francisco, California., Starks E; Invitae Corporation, San Francisco, California., Vincent JJ; Invitae Corporation, San Francisco, California., Albritton S; Invitae Corporation, San Francisco, California., Nussbaum RL; Invitae Corporation, San Francisco, California., Nykamp K; Invitae Corporation, San Francisco, California. Electronic address: keith.nykamp@invitae.com.
Jazyk:	angličtina
Zdroj:	The Journal of molecular diagnostics : JMD [J Mol Diagn] 2023 Mar; Vol. 25 (3), pp. 156-167. Date of Electronic Publication: 2022 Dec 21.
DOI:	10.1016/j.jmoldx.2022.12.002
Abstrakt:	Nearly 14% of disease-causing germline variants result from the disruption of mRNA splicing. Most (67%) DNA variants predicted in silico to disrupt splicing are classified as variants of uncertain significance. An analytic workflow-splice effect event resolver (SPEER)-was developed and validated to use mRNA sequencing to reveal significant deviations in splicing, pinpoint the DNA variants potentially involved, and measure the deleterious effects of the altered splicing on mRNA transcripts, providing evidence for assessing the pathogenicity of the variant. SPEER was used to analyze leukocyte RNA encoding 63 hereditary cancer syndrome-related genes in 20,317 patients. Among 3563 patients (17.5%) with at least one DNA variant predicted to affect splicing, 971 (4.8%) had altered splicing with a deleterious effect on the transcript, and 40 had altered splicing due to a DNA variant located outside of the reportable range of the test. Integrating SPEER results into the interpretation of variants allowed variants of uncertain significance to be reclassified as pathogenic or likely pathogenic in 0.4%, and as benign or likely benign in 5.9%, of the 20,317 patients. SPEER-based evidence was associated with a significantly greater effect on classifications of pathogenic or likely pathogenic and benign or likely benign in nonwhite versus non-Hispanic white patients, illustrating that evidence derived from mRNA splicing analysis may help to reduce ethnic/ancestral disparities in genetic testing. (Copyright © 2023 Association for Molecular Pathology and American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
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