Prion gene haplotypes of U.S. cattle

BMC Genetics

Volumn 7, Issue , 2006, Pages

  Clawson, Michael L ^a   Heaton, Michael P ^a   Keele, John W ^a   Smith, Timothy P L ^a   Harhay, Gregory P ^a   Laegreid, William W ^a  

^a U S MEAT ANIMAL RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; PRION PROTEIN;

3' UNTRANSLATED REGION; ALLELE; ARTICLE; BEEF CATTLE; BOVINE SPONGIFORM ENCEPHALOPATHY; CATTLE; CONTROLLED STUDY; DAIRY CATTLE; DISEASE PREDISPOSITION; DNA POLYMORPHISM; EXON; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENETIC ASSOCIATION; GENOME; HAPLOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRION; PROMOTER REGION; PROTEIN POLYMORPHISM; PROTEIN VARIANT; SEQUENCE ANALYSIS;

3' UNTRANSLATED REGIONS; ALLELES; ANIMALS; CATTLE; EXONS; GENE FREQUENCY; GENE REGULATORY NETWORKS; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID AMPLIFICATION TECHNIQUES; POLYMORPHISM, SINGLE NUCLEOTIDE; PRIONS; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; UNITED STATES;

BOS TAURUS;

EID: 33751319933     PISSN: 14712156     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-7-51     Document Type: Article

References (32)

1. Aguzzi A, Sigurdson CJ: Antiprion immunotherapy: to suppress or to stimulate? Nat Rev Immunol 2004, 4(9):725-736.
2. Wells GA, Scott AC, Johnson CT, Gunning RF, Hancock RD, Jeffrey M, Dawson M, Bradley R: A novel progressive spongiform encephalopathy in cattle. Vet Rec 1987, 121:419-420.
3. Bruce ME, Will RG, Ironside JW, McConnell I, Drummond D, Suttie A, McCardle L, Chree A, Hope J, Birkett C, Cousens S, Fraser H, Bostock CJ: Transmissions to mice indicate that 'new variant' CJD is caused by the BSE agent. Nature 1997, 389(6650):498-501.
4. Hill AF, Desbruslais M, Joiner S, Sidle KC, Gowland I, Collinge J, Doey LJ, Lantos P: The same prion strain causes vCJD and BSE. Nature 1997, 389(6650):448-450.
5. Wadsworth JD, Asante EA, Desbruslais M, Linehan JM, Joiner S, Gowland I, Welch J, Stone L, Lloyd SE, Hill AF, Brandner S, Collinge J: Human prion protein with valine 129 prevents expression of variant CJD phenotype. Science 2004, 306(5702):1793-1796.
6. Prusiner SB, Scott MR: Genetics of prions. Annu Rev Genet 1997, 31:139-175.
7. Baylis M, Goldmann W: The genetics of scrapie in sheep and goats. Curr Mol Med 2004, 4(4):385-396.
8. Barron RM, Baybutt H, Tuzi NL, McCormack J, King D, Moore RC, Melton DW, Manson JC: Polymorphisms at codons 108 and 189 in murine PrP play distinct roles in the control of scrapie incubation time. J Gen Virol 2005, 86(Pt 3):859-868.
9. Sander P, Hamann H, Pfeiffer I, Wemheuer W, Brenig B, Groschup MH, Ziegler U, Distl O, Leeb T: Analysis of sequence variability of the bovine protein gene (PRNP) in German cattle breeds. Neurogenetics 2004, 5:19-25.
10. Seabury CM, Womack JE, Piedrahita J, Derr JN: Comparative PRNP genotyping of U.S. cattle sires for potential association with BSE. Mamm Genome 2004, 15:828-833.
11. Heaton MP, Leymaster KA, Freking BA, Hawk DA, Smith TP, Keele JW, Snelling WM, Fox JM, Chitko-McKown CG, Laegreid WW: Prion gene sequence variation within diverse groups of U.S. sheep, beef cattle, and deer. Mamm Genome 2003, 14(11):765-777.
12. Seabury CM, Honeycutt RL, Rooney AP, Halbert ND, Derr JN: Prion protein gene (PRNP) variants and evidence for strong purifying selection in functionally important regions of bovine exon 3. Proc Natl Acad Sci USA 2004, 101(42):15142-15147.
13. Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R: Ascertainmant bias in studies of huamn genome-wide polymorphism. Genome Res 2005, 15:1496-1502.
14. Soldevila M, Andres AM, Ramirez-Soriano A, Marques-Bonet T, Calafell F, Navarro A, Bertranpetit J: The prion protein gene in humans revisited: Lessons from a worldwide resequencing study. Genome Res 2006, 16:231-239.
15. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D: The structure of haplotype blocks in the human genome. Science 2002, 296(5576):2225-2229.
16. Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P, Chamberlain AT, Sykes BC, Bradley DG: Genetic evidence for Near-Eastern origins of European cattle. Nature 2001, 410:1088-1091.
17. Consortium HM: A haplotype map of the human genome. Nature 2005, 437:1299-1320.
18. Biacabe AG, Laplanche JL, Ryder S, Baron T: Distinct molecular phenotypes in bovine prion diseases. EMBO Rep 2004, 5(1):110-115.
19. Casalone C, Zanusso G, Acutis P, Ferrari S, Capucci L, Tagliavini F, Monaco S, Caramelli M: Identification of a second bovine amyloidotic spongiform encephalopathy: molecular similarities with sporadic Creutzfeldt-Jakob disease. Proc Natl Acad Sci U S A 2004, 101(9):3065-3070.
20. Yamakawa Y, Hagiwara K, Nohtomi K, Nakamura Y, Nishijima M, Higuchi Y, Sato Y, Sata T: Atypical proteinase K-resistant prion protein (PrPres) observed in an apparently healthy 23-month-old Holstein steer. Jpn J Infect Dis 2003, 56(5-6):221-222.
21. Heaton MP, Chitko-McKown CG, Grosse WM, Keele JW, Keen JE: Interleukin-8 haplotype structure from nucleotide sequence variation in commercial populations of U.S. beef cattle. Momm Genome 2001, 12:219-226.
22. Heaton MP, Keen JE, Clawson ML, Harhay GP, Bauer N, Shultz C, Green BT, Durso L, Chitko-McKown CG, Laegreid WW: Use of bovine single nucleotide polymorphism markers to verify sample tracking in beef processing. J Am Vet Med Assoc 2005, 226(8):1311-1314.
23. Hills D, Schlaepfer J, Comincini S, MacLean I, Dolf G, Ferretti L, Olsaker I, Williams JL: Sequence variation in the bovine and ovine PRNP genes. Animal Genetics 2003, 34:183-190.
24. Hills D, Comincini S, Schlaepfer J, Dolf G, Ferretti L, Williams JL: Complete genomic sequence of the bovine prion gene (PRNP) and polymorphisms in its promoter region. Animal Genetics 2001, 32:231-233.
25. Clawson ML, Heaton MP, Chitko-McKown CG, Fox JM, Smith TPL, Snelling WM, Keele JW, Laegreid WW: Beta-2-microglobulin haplotypes in U.S. beef cattle and association with failure of passive transfer in newborn calves. Mamm Genom 2004, 15:227-236.
26. Smith TP, Godtel RA, Lee RT: PCR-based setup for high-throughput cDNA library sequencing on the ABI 3700 automated DNA sequencer. Biotechniques 2000, 29(4):698-700.
27. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8(3):186-194.
28. Ewing B, Hillier L, Wendl MC, Green P: Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998, 8(3):175-185.
29. Nickerson DA, Tobe VO, Taylor SL: PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res 1997, 25(14):2745-2751.
30. Gordon D, Abajian C, Green P: Consed: a graphical tool for sequence finishing. Genome Res 1998, 8(3):195-202.
31. Barrett JC, Fry B, Mailer J, Daly MJ: Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21(2):263-265.
32. Bandelt HJ, Forster P, Rohl A: Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999, 16(1):37-48.