1. Improving Genetic Testing in Hereditary Cancer by RNA Analysis
- Author
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Conxi Lázaro, Mireia Menéndez, Eva Tornero, Marta Pineda, Jesús del Valle, Lídia Feliubadaló, Paula Rofes, Mónica Salinas, Gardenia Vargas-Parra, Alex Teulé, Joan Brunet, Eva Montes, Carolina Gómez, Sara González, Gabriel Capellá, and Ares Solanes
- Subjects
0301 basic medicine ,Sanger sequencing ,medicine.medical_specialty ,medicine.diagnostic_test ,Genetic counseling ,Genomics ,Computational biology ,Biology ,Pathology and Forensic Medicine ,03 medical and health sciences ,Exon ,symbols.namesake ,030104 developmental biology ,0302 clinical medicine ,030220 oncology & carcinogenesis ,RNA splicing ,medicine ,symbols ,Molecular Medicine ,Medical genetics ,Gene ,Genetic testing - Abstract
RNA analyses are a potent tool to identify spliceogenic effects of DNA variants, although they are time-consuming and cannot always be performed. We present splicing assays of 20 variants that represent a variety of mutation types in 10 hereditary cancer genes and attempt to incorporate these results into American College of Medical Genetics and Genomics (ACMG) classification guidelines. Sixteen single-nucleotide variants, 3 exon duplications, and 1 single-exon deletion were selected and prioritized by in silico algorithms. RNA was extracted from short-term lymphocyte cultures to perform RT-PCR and Sanger sequencing, and allele-specific expression was assessed whenever possible. Aberrant transcripts were detected in 14 variants (70%). Variant interpretation was difficult, especially comparing old classification standards to generic ACMG guidelines and a proposal was devised to weigh functional analyses at RNA level. According to the ACMG guidelines, only 12 variants were reclassified as pathogenic/likely pathogenic because the other two variants did not gather enough evidence. This study highlights the importance of RNA studies to improve variant classification. However, it also indicates the challenge of incorporating these results into generic ACMG guidelines and the need to refine these criteria gene specifically. Nevertheless, 60% of variants were reclassified, thus improving genetic counseling and surveillance for carriers of these variants.
- Published
- 2020
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