title: Prospecting for pig single nucleotide polymorphisms in the human genome: have we struck gold?
abstract: Gene-to-gene variation in the frequency of single nucleotide polymorphisms (SNPs) has been observed in humans, mice, rats, primates and pigs, but a relationship across species in this variation has not been described. Here, the frequency of porcine coding SNPs (cSNPs) identified by in silico methods, and the frequency of murine cSNPs, were compared with the frequency of human cSNPs across homologous genes. From 150,000 porcine expressed sequence tag (EST) sequences, a total of 452 SNP-containing sequence clusters were found, totalling 1394 putative SNPs. All the clustered porcine EST annotations and SNP data have been made publicly available at http://sputnik.btk.fi/project?name=swine. Human and murine cSNPs were identified from dbSNP and were characterized as either validated or total number of cSNPs (validated plus non-validated) for comparison purposes. The correlation between in silico pig cSNP and validated human cSNP densities was found to be 0.77 (p < 0.00001) for a set of 25 homologous genes, while a correlation of 0.48 (p < 0.0005) was found for a primarily random sample of 50 homologous human and mouse genes. This is the first evidence of conserved gene-to-gene variability in cSNP frequency across species and indicates that site-directed screening of porcine genes that are homologous to cSNP-rich human genes may rapidly advance cSNP discovery in pigs.
authors.affiliation: Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA.
authors.forename: L
authors.initials: L
authors.lastname: Grapes
authors.forename: S
authors.initials: S
authors.lastname: Rudd
authors.forename: R L
authors.initials: RL
authors.lastname: Fernando
authors.forename: K
authors.initials: K
authors.lastname: Megy
authors.forename: D
authors.initials: D
authors.lastname: Rocha
authors.forename: M F
authors.initials: MF
authors.lastname: Rothschild
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D051379:Mice; D016366:Open Reading Frames / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D013223:Statistics as Topic / Q000379:methods; D034421:Sus scrofa / Q000235:genetics*