Identification of novel SNPs in differentially expressed genes and its association with horn cancer of Bos indicus bullocks by next-generation sequencing
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- 作者：P. G. Koringa ; S. J. Jakhesara ; D. N. Rank ; C. G. Joshi
- 关键词：SNPs ; Horn cancer (HC) ; Bos indicus ; BPIFA1 ; Ion Torrent PGM
- 刊名：3 Biotech
- 出版年：2016
- 出版时间：December 2016
- 年：2016
- 卷：6
- 期：1
- 全文大小：670 KB
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- 作者单位：P. G. Koringa (1) <br> S. J. Jakhesara (1) <br> D. N. Rank (1) <br> C. G. Joshi (1) <br><br>1. Department of Animal Biotechnology, College of Veterinary Science and Animal Husbandry, Anand Agricultural University, Anand, Gujarat, India <br>
- 刊物主题：Biotechnology; Agriculture; Cancer Research; Bioinformatics; Stem Cells; Biomaterials;
- 出版者：Springer Berlin Heidelberg
- ISSN：2190-5738
文摘
The use of polymorphic markers like SNPs promises to provide comprehensive tool for analysing genome and identifying genomic regions that contribute to cancer phenotype. Horn cancer is the most common cancer among Bos indicus animals. Increased expression of some genes due to polymorphisms increases risk of HC incidence. We successfully amplified 91 SNPs located in 69 genes in 52 samples, each of HC and HN. Equimolar concentration of amplicons from 69 PCR products of each sample was pooled and subjected to sequencing using Ion Torrent PGM. Data obtained were analysed using DNASTAR software package and case control analysis using SAS software. We found SNP present in BPIFA1 gene of B. indicus shows association with event of HC which reflects its potential to be a genetic marker. Bioinformatic analysis to detect structural and functional impact nsSNP of BPIFA1 added another layer of confirmation to our result. We successfully identified SNP associated with HC as well as demonstrated efficient approach for limited number of SNP discovery and validation in targeted genomics regions in large number of samples combining PCR amplification and Ion Torrent PGM sequencing which suits small-scale laboratories with limited budget. Keywords SNPs Horn cancer (HC) Bos indicus BPIFA1 Ion Torrent PGM