NDLI: Identification of putative SNPs in progressive retinal atrophy affected Canis lupus familiaris using exome sequencing

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Identification of putative SNPs in progressive retinal atrophy affected Canis lupus familiaris using exome sequencing

Content Provider	Springer Nature Link
Author	Reddy, Bhaskar Kelawala, Divyesh N. Shah, Tejas Patel, Anand B. Patil, Deepak B. Parikh, Pinesh V. Patel, Namrata Parmar, Nidhi Mohapatra, Amit B. Singh, Krishna M. Men, Ramesh Pandya, Dipal Jakhesara, Subhash J. Koringa, Prakash G. Rao, Mandava V. Joshi, Chaitanya G.
Copyright Year	2015
Abstract	Progressive retinal atrophy (PRA) is one of the major causes of retinal photoreceptor cell degeneration in canines. The inheritance pattern of PRA is autosomal recessive and genetically heterogeneous. Here, using targeted sequencing technology, we have performed exome sequencing of 10 PRA-affected (Spitz = 7, Cocker Spaniel = 1, Lhasa Aphso = 1 and Spitz-Labrador cross breed = 1) and 6 normal (Spitz = 5, Cocker Spaniel = 1) dogs. The high-throughput sequencing using 454-Roche Titanium sequencer generated about 2.16 Giga bases of raw data. Initially, we have successfully identified 25,619 single nucleotide polymorphisms (SNPs) that passed the stringent SNP calling parameters. Further, we performed association study on the cohort, and the highly significant (0.001) associations were short-listed and investigated in-depth. Out of the 171 significant SNPs, 113 were previously unreported. Interestingly, six among them were non-synonymous coding (NSC) SNPs, which includes CPPED1 A>G (p.M307V), PITRM1 T>G (p.S715A), APP G>A (p.T266M), RNF213 A>G (p.V1482A), C>A (p.V1456L), and SLC46A3 G>A (p.R168Q). On the other hand, 35 out of 113 unreported SNPs were falling in regulatory regions such as 3′-UTR, 5′-UTR, etc. In-depth bioinformatics analysis revealed that majority of NSC SNPs have damaging effect and alter protein stability. This study highlighted the genetic markers associated with PRA, which will help to develop genetic assay-based screening in effective breeding.
Starting Page	638
Ending Page	649
Page Count	12
File Format	PDF
ISSN	09388990
Journal	Mammalian Genome
Volume Number	26
Issue Number	11-12
e-ISSN	14321777
Language	English
Publisher	Springer US
Publisher Date	2015-10-29
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Cell Biology Animal Genetics and Genomics Human Genetics
Content Type	Text
Resource Type	Article
Subject	Genetics

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