Predicting Pathogenic Missense Mutations in the Human c-MET Oncogene Using a Nucleotide Scoring Function

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Year 2018 Vol 7 Issue 4
Document Type : ORIGINAL ARTICLE
¹Padmini Arunkumar , Kumar Sankaran2 , Shivangi Naik2 and Prashantha Karunakar3* ²Kumar Sankaran, ³Shivangi Naik, ⁴Prashantha Karunakar
¹Department of Biotechnology, PES Institute of Technology, Bengaluru- 560085
²Leucine Rich Bio Pvt. Ltd. 283 M. K. Puttalingaih Road, Padmanabhanagar, Bengaluru - 560070
³Leucine Rich Bio Pvt. Ltd. 283 M. K. Puttalingaih Road, Padmanabhanagar, Bengaluru - 560070
⁴Department of Biotechnology, PES University, Bengaluru - 560085
Abstract
Background: Many nucleotide variations in the human genome remain uncharacterized even more than ten years after the first draft was published. Objective: A three-parameter nucleotide-based scoring function was designed to predict the possible pathogenicity of 163 uncharacterized but validated missense mutations of the c-MET oncogene. Methodology: The parameters used by the scoring function were: surrounding consensus regions in a multiple sequence alignment of the human c-MET oncogene and five orthologous variants, inter-species allele frequency of each human missense mutation, and the nature of the mutation. Results: Out of 163 variants of unknown significance, 99 and 52 mutations were characterized as likely pathogenic and pathogenic respectively. An analysis of nine variants of known significance revealed that this scoring function could classify six out of nine (66.67%) variants with a reasonable accuracy.



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