title: Next-generation sequencing-based method shows increased mutation detection sensitivity in an Indian retinoblastoma cohort.
abstract: 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.
  
  
  
  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.
  
  
  
  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).
  
  
  
  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.
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Jaya
authors: J
authors: Singh
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Avshesh
authors: A
authors: Mishra
authors: Sankara Nethralaya ONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India.
authors: Arunachalam Jayamuruga
authors: AJ
authors: Pandian
authors: Department of Pediatric Ophthalmology and Strabismology, Narayana Nethralaya, Bangalore, India.
authors: Ashwin C
authors: AC
authors: Mallipatna
authors: Department of Vitreo Retina, Sankara Nethralaya, Chennai, India.
authors: Vikas
authors: V
authors: Khetan
authors: Sankara Nethralaya ONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, India.
authors: S
authors: S
authors: Sripriya
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Suman
authors: S
authors: Kapoor
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Smita
authors: S
authors: Agarwal
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Satish
authors: S
authors: Sankaran
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Shanmukh
authors: S
authors: Katragadda
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Vamsi
authors: V
authors: Veeramachaneni
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India; Department of Computer Science and Automation, Indian Institute of Science, Bangalore, India.
authors: Ramesh
authors: R
authors: Hariharan
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Kalyanasundaram
authors: K
authors: Subramanian
authors: Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bangalore, India.
authors: Ashraf U
authors: AU
authors: Mannan
mesh_terms: D000328:Adult; D044466:Asian People / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D018389:Codon, Nonsense; D015331:Cohort Studies; D004252:DNA Mutational Analysis; D005091:Exons / Q000235:genetics; D005260:Female; D016161:Genes, Retinoblastoma; D005820:Genetic Testing / Q000379:methods; D018095:Germ-Line Mutation; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007194:India; D007223:Infant; D008297:Male; D008875:Middle Aged; D009154:Mutation; D016133:Polymerase Chain Reaction; D019572:Retinal Neoplasms / Q000235:genetics*; D012175:Retinoblastoma / Q000235:genetics*; D056286:Retinoblastoma Binding Proteins / Q000235:genetics*; D044767:Ubiquitin-Protein Ligases / Q000235:genetics*; D055815:Young Adult
chemical_list: D018389:Codon, Nonsense; C000606393:RB1 protein, human; D056286:Retinoblastoma Binding Proteins; D044767:Ubiquitin-Protein Ligases