Cargando…
Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort
PURPOSE: Retinoblastoma (Rb) is the most common primary intraocular cancer of childhood and one of the major causes of blindness in children. India has the highest number of patients with Rb in the world. Mutations in the RB1 gene are the primary cause of Rb, and heterogeneous mutations are distribu...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Molecular Vision
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4985049/ https://www.ncbi.nlm.nih.gov/pubmed/27582626 |
_version_ | 1782448012615745536 |
---|---|
author | Singh, Jaya Mishra, Avshesh Pandian, Arunachalam Jayamuruga Mallipatna, Ashwin C. Khetan, Vikas Sripriya, S. Kapoor, Suman Agarwal, Smita Sankaran, Satish Katragadda, Shanmukh Veeramachaneni, Vamsi Hariharan, Ramesh Subramanian, Kalyanasundaram Mannan, Ashraf U. |
author_facet | Singh, Jaya Mishra, Avshesh Pandian, Arunachalam Jayamuruga Mallipatna, Ashwin C. Khetan, Vikas Sripriya, S. Kapoor, Suman Agarwal, Smita Sankaran, Satish Katragadda, Shanmukh Veeramachaneni, Vamsi Hariharan, Ramesh Subramanian, Kalyanasundaram Mannan, Ashraf U. |
author_sort | Singh, Jaya |
collection | PubMed |
description | PURPOSE: Retinoblastoma (Rb) is the most common primary intraocular cancer of childhood and one of the major causes of blindness in children. India has the highest number of patients with Rb in the world. Mutations in the RB1 gene are the primary cause of Rb, and heterogeneous mutations are distributed throughout the entire length of the gene. Therefore, genetic testing requires screening of the entire gene, which by conventional sequencing is time consuming and expensive. METHODS: In this study, we screened the RB1 gene in the DNA isolated from blood or saliva samples of 50 unrelated patients with Rb using the TruSight Cancer panel. Next-generation sequencing (NGS) was done on the Illumina MiSeq platform. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. RESULTS: We were able to detect germline pathogenic mutations in 66% (33/50) of the cases, 12 of which were novel. We were able to detect all types of mutations, including missense, nonsense, splice site, indel, and structural variants. When we considered bilateral Rb cases only, the mutation detection rate increased to 100% (22/22). In unilateral Rb cases, the mutation detection rate was 30% (6/20). CONCLUSIONS: Our study suggests that NGS-based approaches increase the sensitivity of mutation detection in the RB1 gene, making it fast and cost-effective compared to the conventional tests performed in a reflex-testing mode. |
format | Online Article Text |
id | pubmed-4985049 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Molecular Vision |
record_format | MEDLINE/PubMed |
spelling | pubmed-49850492016-08-31 Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort Singh, Jaya Mishra, Avshesh Pandian, Arunachalam Jayamuruga Mallipatna, Ashwin C. Khetan, Vikas Sripriya, S. Kapoor, Suman Agarwal, Smita Sankaran, Satish Katragadda, Shanmukh Veeramachaneni, Vamsi Hariharan, Ramesh Subramanian, Kalyanasundaram Mannan, Ashraf U. Mol Vis Research Article PURPOSE: Retinoblastoma (Rb) is the most common primary intraocular cancer of childhood and one of the major causes of blindness in children. India has the highest number of patients with Rb in the world. Mutations in the RB1 gene are the primary cause of Rb, and heterogeneous mutations are distributed throughout the entire length of the gene. Therefore, genetic testing requires screening of the entire gene, which by conventional sequencing is time consuming and expensive. METHODS: In this study, we screened the RB1 gene in the DNA isolated from blood or saliva samples of 50 unrelated patients with Rb using the TruSight Cancer panel. Next-generation sequencing (NGS) was done on the Illumina MiSeq platform. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. RESULTS: We were able to detect germline pathogenic mutations in 66% (33/50) of the cases, 12 of which were novel. We were able to detect all types of mutations, including missense, nonsense, splice site, indel, and structural variants. When we considered bilateral Rb cases only, the mutation detection rate increased to 100% (22/22). In unilateral Rb cases, the mutation detection rate was 30% (6/20). CONCLUSIONS: Our study suggests that NGS-based approaches increase the sensitivity of mutation detection in the RB1 gene, making it fast and cost-effective compared to the conventional tests performed in a reflex-testing mode. Molecular Vision 2016-08-16 /pmc/articles/PMC4985049/ /pubmed/27582626 Text en Copyright © 2016 Molecular Vision. http://creativecommons.org/licenses/by-nc-nd/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited, used for non-commercial purposes, and is not altered or transformed. |
spellingShingle | Research Article Singh, Jaya Mishra, Avshesh Pandian, Arunachalam Jayamuruga Mallipatna, Ashwin C. Khetan, Vikas Sripriya, S. Kapoor, Suman Agarwal, Smita Sankaran, Satish Katragadda, Shanmukh Veeramachaneni, Vamsi Hariharan, Ramesh Subramanian, Kalyanasundaram Mannan, Ashraf U. Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort |
title | Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort |
title_full | Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort |
title_fullStr | Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort |
title_full_unstemmed | Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort |
title_short | Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort |
title_sort | next-generation sequencing-based method shows increased mutation detection sensitivity in an indian retinoblastoma cohort |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4985049/ https://www.ncbi.nlm.nih.gov/pubmed/27582626 |
work_keys_str_mv | AT singhjaya nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT mishraavshesh nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT pandianarunachalamjayamuruga nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT mallipatnaashwinc nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT khetanvikas nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT sripriyas nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT kapoorsuman nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT agarwalsmita nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT sankaransatish nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT katragaddashanmukh nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT veeramachanenivamsi nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT hariharanramesh nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT subramaniankalyanasundaram nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort AT mannanashrafu nextgenerationsequencingbasedmethodshowsincreasedmutationdetectionsensitivityinanindianretinoblastomacohort |