Exome sequencing and targeted gene panels: a simulated comparison of diagnostic yield using data from 158 patients with rare diseases
Next-generation sequencing (NGS) has altered clinical genetic testing by widening the access to molecular diagnosis of genetically determined rare diseases. However, physicians may face difficulties selecting the best diagnostic approach. Our goal is to estimate the rate of possible molecular diagno...
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Published in | Genetics and molecular biology Vol. 44; no. 4; pp. 1 - 20210061 |
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Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English Portuguese |
Published |
Ribeirao Preto
Sociedade Brasileira de Genetica
01.01.2021
Sociedade Brasileira de Genética |
Subjects | |
Online Access | Get full text |
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Summary: | Next-generation sequencing (NGS) has altered clinical genetic testing by widening the access to molecular diagnosis of genetically determined rare diseases. However, physicians may face difficulties selecting the best diagnostic approach. Our goal is to estimate the rate of possible molecular diagnoses missed by different targeted gene panels using data from a cohort of patients with rare genetic diseases diagnosed with exome sequencing (ES). For this purpose, we simulated a comparison between different targeted gene panels and ES: the list of genes harboring clinically relevant variants from 158 patients was used to estimate the theoretical rate of diagnoses missed by NGS panels from 53 different NGS panels from eight different laboratories. Panels presented a mean rate of missed diagnoses of 64% (range 14%-100%) compared to ES, representing an average predicted sensitivity of 36%. Metabolic abnormalities represented the group with highest mean of missed diagnoses (86%), while seizure represented the group with lowest mean (46%). Focused gene panels are restricted in covering select sets of genes implicated in specific diseases and they may miss molecular diagnoses of rare diseases compared to ES. However, their role in genetic diagnosis remains important especially for well-known genetic diseases with established genetic locus heterogeneity. |
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Bibliography: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Associate Editor: Roberto Giugliani Author Contributions: CRDACQ; MJRO; SFP; APD; CHC; CAK: provided the conception and design of the study, acquisition of data, analysis and interpretation of data, drafting the article, revised it critically for important intellectual content. CMM; GMNF; PRSB; MGP; RRFS; VPC; JEPC; MCP; MMN: provided acquisition of data, analysis and interpretation of data, drafting the article, revised it critically for important intellectual content. RAS; MNPS; ARSF; ALB; MB; RFR; ENF; OJEP; DP; CO; GMS; WARB: revised the article critically for important intellectual content. All authors read and approved the final version. Conflict of Interest: The following authors are employees (received salary and other bonuses) of Fleury Medicina e Saúde: Caio Robledo D’Angioli Costa Quaio; Sandro Felix Perazzio; Aurelio Pimenta Dutra; Christine Hsiaoyun Chung; Caroline Monaco Moreira; Gil Monteiro Novo Filho; Patricia Rossi Sacramento-Bobotis; Michele Groenner Penna; Rafaela Rogerio Floriano de Sousa; Vivian Pedigone Cintra; Juliana Emilia Prior Carnavalli; Rafael Alves da Silva; Monize Nakamoto Provisor Santos; Maria Carolina Pintao; Alexandre Ricardo dos Santos Fornari; Matheus Burger; Rodrigo Fernandes Ramalho; Elisa Napolitano e Ferreira; Otavio Jose Eulalio Pereira; Daniele Paixão; Caroline Olivati; Gustavo Marquezani Spolador; Miguel Mitne-Neto; Wagner Antonio da Rosa Baratela. |
ISSN: | 1415-4757 1678-4685 1678-4685 |
DOI: | 10.1590/1678-4685-GMB-2021-0061 |