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Genome-wide association study of cat mammary tumor using 63,000 SNP chip through PLINK data analysis toolset

By: Rashid Saif, Leslie Lyons, Barbara Gandolfi, Maleeha Ahmad, Ramlah Ejaz, Muhammad Wasim

Key Words: GWAS, LD plot, Pakistani siamese cat, 63K Chip, PLINK

Int. J. Biosci. 11(1), 75-82, July 2017.

DOI: http://dx.doi.org/10.12692/ijb/11.1.75-82

Certification: ijb 2017 0010

Abstract

Genome wide case-control association study using Illumina Infinium Feline 63K I Select DNA array was performed with7 cancer cases and 23 controls from the Siamese cat breed. The purpose of this study to identify the SNPs associated with mammary tumor in cats. PLINK data analysis toolset was used to analysis the SNP data obtained through microarray genotyping experiment. Zerovalue of Mendel error was observed, Similarly, deviations from the HWE was also detected which depicts the excessive in breeding within the sampled population. Allelic association test highlighted ten most associated SNPs through Manhattan plot. Linkage-disequilibrium plots were also drawn through these associated SNPs, which showed that, one of the SNP at locus ChrC1:202,770,816 on chromosome 8 exist in haplotype, which is part of RFTN2 gene and belongs to raftlin protein family. This protein is involved in the activation of B type immune cells. Another SNP ChrE1:53,681,930 on chromosome 14 was found to be in linkage disequilibrium with 4 genes named C7orf64, APPBP2, PPMID and BCAS3, all of these genes are highly expressed in breast cancers. This study revealed, that outbreak of mammary tumor in cats may be associated be with aforementioned SNPs and simultaneously outbreak of this cancer is a micro-evolutionary process and cumulative effect of number of SNPs located on different chromosomes.

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Genome-wide association study of cat mammary tumor using 63,000 SNP chip through PLINK data analysis toolset

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Rashid Saif, Leslie Lyons, Barbara Gandolfi, Maleeha Ahmad, Ramlah Ejaz, Muhammad Wasim.
Genome-wide association study of cat mammary tumor using 63,000 SNP chip through PLINK data analysis toolset.
Int. J. Biosci. 11(1), 75-82, July 2017.
http://www.innspub.net/ijb/genome-wide-association-study-cat-mammary-tumor-using-63000-snp-chip-plink-data-analysis-toolset/
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