Title

Light Whole Genome Sequence for SNP Discovery Across Domestic Cat Breeds

Authors

James C. Mullikin, National Institutes of Health at Bethesda
Nancy F. Hansen, National Institutes of Health at Bethesda
Lei Shen, Agencourt Bioscience Corporation
Heather Ebling, Agencourt Bioscience Corporation
William F. Donahue, Agencourt Bioscience Corporation
Wei Tao, Agencourt Bioscience Corporation
David J. Saranga, Agencourt Bioscience Corporation
Adrianne Brand, Agencourt Bioscience Corporation
Marc J. Rubenfield, Agencourt Bioscience Corporation
Alice C. Young, National Institutes of Health at Bethesda
Pedro Cruz, National Institutes of Health at Bethesda
Carlos Driscoll, National Cancer Institute at Frederick
Victor David, National Cancer Institute at Frederick
Samer W. K. Al-Murrani, Hill's Pet Nutrition Inc.
Mary F. Locniskar, Hill's Pet Nutrition Inc.
Mitchell S. Abrahamsen, Hill's Pet Nutrition Inc.
Stephen J. O'Brien, National Cancer Institute at FrederickFollow
Douglas R. Smith, Agencourt Bioscience Corporation
Jeffrey A. Brockman, Hill's Pet Nutrition Inc.

Document Type

Article

Publication Date

2010

Publication Title

BMC Genomics

ISSN

1471-2164

Volume

11

Issue/No.

406

First Page

1

Last Page

8

Abstract

Background

The domestic cat has offered enormous genomic potential in the veterinary description of over 250 hereditary disease models as well as the occurrence of several deadly feline viruses (feline leukemia virus -- FeLV, feline coronavirus -- FECV, feline immunodeficiency virus - FIV) that are homologues to human scourges (cancer, SARS, and AIDS respectively). However, to realize this bio-medical potential, a high density single nucleotide polymorphism (SNP) map is required in order to accomplish disease and phenotype association discovery.

Description

To remedy this, we generated 3,178,297 paired fosmid-end Sanger sequence reads from seven cats, and combined these data with the publicly available 2X cat whole genome sequence. All sequence reads were assembled together to form a 3X whole genome assembly allowing the discovery of over three million SNPs. To reduce potential false positive SNPs due to the low coverage assembly, a low upper-limit was placed on sequence coverage and a high lower-limit on the quality of the discrepant bases at a potential variant site. In all domestic cats of different breeds: female Abyssinian, female American shorthair, male Cornish Rex, female European Burmese, female Persian, female Siamese, a male Ragdoll and a female African wildcat were sequenced lightly. We report a total of 964 k common SNPs suitable for a domestic cat SNP genotyping array and an additional 900 k SNPs detected between African wildcat and domestic cats breeds. An empirical sampling of 94 discovered SNPs were tested in the sequenced cats resulting in a SNP validation rate of 99%.

Conclusions

These data provide a large collection of mapped feline SNPs across the cat genome that will allow for the development of SNP genotyping platforms for mapping feline diseases.

Comments

©Mullikin et al; licensee BioMed Central Ltd. 2010

NSUWorks Citation

Mullikin, James C.; Nancy F. Hansen; Lei Shen; Heather Ebling; William F. Donahue; Wei Tao; David J. Saranga; Adrianne Brand; Marc J. Rubenfield; Alice C. Young; Pedro Cruz; Carlos Driscoll; Victor David; Samer W. K. Al-Murrani; Mary F. Locniskar; Mitchell S. Abrahamsen; Stephen J. O'Brien; Douglas R. Smith; and Jeffrey A. Brockman. 2010. "Light Whole Genome Sequence for SNP Discovery Across Domestic Cat Breeds." BMC Genomics 11, (406): 1-8. https://nsuworks.nova.edu/cnso_bio_facarticles/767

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015