دورية أكاديمية
Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis
| العنوان: | Combining globally search for a regular expression and print matching lines with bibliographic monitoring of genomic database improves diagnosis |
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| المؤلفون: | Frédéric Tran Mau-Them, Alexis Overs, Ange-Line Bruel, Romain Duquet, Mylene Thareau, Anne-Sophie Denommé-Pichon, Antonio Vitobello, Arthur Sorlin, Hana Safraou, Sophie Nambot, Julian Delanne, Sebastien Moutton, Caroline Racine, Camille Engel, Melchior De Giraud d’Agay, Daphne Lehalle, Alice Goldenberg, Marjolaine Willems, Christine Coubes, David Genevieve, Alain Verloes, Yline Capri, Laurence Perrin, Marie-Line Jacquemont, Laetitia Lambert, Elodie Lacaze, Julien Thevenon, Nadine Hana, Julien Van-Gils, Charlotte Dubucs, Varoona Bizaoui, Marion Gerard-Blanluet, James Lespinasse, Sandra Mercier, Anne-Marie Guerrot, Isabelle Maystadt, Emilie Tisserant, Laurence Faivre, Christophe Philippe, Yannis Duffourd, Christel Thauvin-Robinet |
| المصدر: | Frontiers in Genetics, Vol 14 (2023) |
| بيانات النشر: | Frontiers Media S.A. |
| سنة النشر: | 2023 |
| المجموعة: | Directory of Open Access Journals: DOAJ Articles |
| مصطلحات موضوعية: | GREP, intellectual disability, developmental anomalies, genomic database, diagnostic improvement, exome sequencing (ES), Genetics, QH426-470 |
| الوصف: | Introduction: 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.Patients and methods: 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 [(intellectual disability, (neuro)developmental delay, and (neuro)developmental disorder)] 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.Results: 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%).Conclusion: The GREP query strategy is efficient and less tedious than complete periodic reanalysis. It is an interesting reanalysis strategy to improve diagnosis. |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| تدمد: | 1664-8021 |
| العلاقة: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1122985/fullTest; https://doaj.org/toc/1664-8021Test; https://doaj.org/article/c14e4795329344a3bad7a62c2a7011bdTest |
| DOI: | 10.3389/fgene.2023.1122985 |
| الإتاحة: | https://doi.org/10.3389/fgene.2023.1122985Test https://doaj.org/article/c14e4795329344a3bad7a62c2a7011bdTest |
| رقم الانضمام: | edsbas.D781EE30 |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 16648021 |
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| DOI: | 10.3389/fgene.2023.1122985 |