Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis

• Published in: Frontiers in genetics 2023-04, Vol.14, p.1122985-1122985
• Main Authors: Tran Mau-Them, Frédéric, Overs, Alexis, Bruel, Ange-Line, Duquet, Romain, Thareau, Mylene, Denommé-Pichon, Anne-Sophie, Vitobello, Antonio, Sorlin, Arthur, Safraou, Hana, Nambot, Sophie, Delanne, Julian, Moutton, Sebastien, Racine, Caroline, Engel, Camille, De Giraud d'Agay, Melchior, Lehalle, Daphne, Goldenberg, Alice, Willems, Marjolaine, Coubes, Christine, Genevieve, David, Verloes, Alain, Capri, Yline, Perrin, Laurence, Jacquemont, Marie-Line, Lambert, Laetitia, Lacaze, Elodie, Thevenon, Julien, Hana, Nadine, Van-Gils, Julien, Dubucs, Charlotte, Bizaoui, Varoona, Gerard-Blanluet, Marion, Lespinasse, James, Mercier, Sandra, Guerrot, Anne-Marie, Maystadt, Isabelle, Tisserant, Emilie, Faivre, Laurence, Philippe, Christophe, Duffourd, Yannis, Thauvin-Robinet, Christel
• Format: Article
• Language: English
• Subjects: developmental anomalies; diagnostic improvement; exome sequencing (ES); Genetics; genomic database; GREP; intellectual disability
• ISSN: 1664-8021; 1664-8021
• DOI: 10.3389/fgene.2023.1122985

Exome sequencing has a diagnostic yield ranging from 25% to 70% in rare diseases and regularly implicates genes in novel disorders. Retrospective data reanalysis has demonstrated strong efficacy in improving diagnosis, but poses organizational difficulties for clinical laboratories. We applied a reanalysis strategy based on intensive prospective bibliographic monitoring along with direct application of the GREP command-line tool (to "globally search for a regular expression and print matching lines") in a large ES database. For 18 months, we submitted the same five keywords of interest [( , ( ) , and ( ) )] to PubMed on a daily basis to identify recently published novel disease-gene associations or new phenotypes in genes already implicated in human pathology. We used the Linux GREP tool and an in-house script to collect all variants of these genes from our 5,459 exome database. After GREP queries and variant filtration, we identified 128 genes of interest and collected 56 candidate variants from 53 individuals. We confirmed causal diagnosis for 19/128 genes (15%) in 21 individuals and identified variants of unknown significance for 19/128 genes (15%) in 23 individuals. Altogether, GREP queries for only 128 genes over a period of 18 months permitted a causal diagnosis to be established in 21/2875 undiagnosed affected probands (0.7%). The GREP query strategy is efficient and less tedious than complete periodic reanalysis. It is an interesting reanalysis strategy to improve diagnosis.