Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort

Singh, Jaya and Mishra, Avshesh and Pandian, Arunachalam Jayamuruga and Mallipatna, Ashwin C and Khetan, Vikas and Sripriya, S and Kapoor, Suman and Agarwal, Smita and Sankaran, Satish and Katragadda, Shanmukh and Veeramachaneni, Vamsi and Hariharan, Ramesh and Subramanian, Kalyanasundaram and Mannan, Ashraf U (2016) Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort. In: MOLECULAR VISION, 22 . pp. 1036-1047.

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Abstract

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.

Item Type:	Journal Article
Publication:	MOLECULAR VISION
Additional Information:	Copy right for this article belongs to the MOLECULAR VISION, C/O JEFF BOATRIGHT, LAB B, 5500 EMORY EYE CENTER, 1327 CLIFTON RD, N E, ATLANTA, GA 30322 USA
Department/Centre:	Division of Electrical Sciences > Computer Science & Automation
Date Deposited:	21 Dec 2016 07:12
Last Modified:	21 Dec 2016 07:12
URI:	http://eprints.iisc.ac.in/id/eprint/55255

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