Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene

REFERENCES

• Brenig B, Schmeitz E, Hardt M, Scheuermann P, Freick M. A 20 bp Duplication in Exon 2 of the Aristaless-Like Homeobox 4 gene (ALX4) is the candidate causative mutation for tibial hemimelia syndrome in galloway cattle. PLoS One 2015; 10(6):e0129208; PMID:26076463; http://dx.doi.org/10.1371/journal.pone.0129208
   PubMedGoogle Scholar
• Behl JD, Mishra P, Verma NK, Niranjan SK, Dangi PS, Sharma R, Behl R. Nucleotide polymorphisms in the bovine lymphotoxin A gene and their distribution among Bos indicus zebu cattle breeds. Gene 2016; 579(1):82-94; PMID:26724420; http://dx.doi.org/10.1016/j.gene.2015.12.049
   PubMed Web of Science ®Google Scholar
• Rosse Ida C, Steinberg Rda S, Coimbra RS, Peixoto MG, Verneque RS, Machado MA, Fonseca CG, Carvalho MR. Novel SNPs and INDEL polymorphisms in the 3′UTR of DGAT1 gene: in silico analyses and a possible association. Mol Biol Rep 2014; 41(7):4555-63; PMID:24676595; http://dx.doi.org/10.1007/s11033-014-3326-z
   PubMed Web of Science ®Google Scholar
• Zhang YE, Liu GY, Ji AB, Sun JP. The application of the mathematical expectation in the disease census. J Math Med 2003; 16(1):83-4 (in Chinese)
   Google Scholar
• Guo LJ, Zhang Y. As application examples of the mathematical expectation. The public science and technology 2006; 7:169. ( in Chinese)
   Google Scholar
• Stephen C. Newman. Biostatistical Methods in Epidemiology; 1rd ed. New York; John Wiley & Sons Publishers; 2001
   Google Scholar
• Prusiner SB. Prions. Proc Natl Acad Sci USA 1998; 95(23):13363-83; PMID:9811807; http://dx.doi.org/10.1073/pnas.95.23.13363
   PubMed Web of Science ®Google Scholar
• Maheshwari A, Fischer M, Gambetti P, Parker A, Ram A, Soto C, Concha-Marambio L, Cohen Y, Belay ED, Maddox RA, et al. Recent US case of variant Creutzfeldt-Jakob disease-global implications. Emerg Infect Dis 2015; 21(5):750-9; PMID:25897712; http://dx.doi.org/10.3201/eid2105.142017
   PubMed Web of Science ®Google Scholar
• Sigurdson CJ, Miller MW. Other animal prion diseases. Br Med Bull 2003; 66:199-212
   PubMed Web of Science ®Google Scholar
• Kashkevich K, HumeNanyang A, Ziegler U, Groschup MH, Nicken P, Leeb T, Fischer C, Becker CM, Schiebel K. Functional relevance of DNA polymorphisms within the promoter region of the prion protein gene and their association to BSE infection. FASEB J 2007; 21(7):1547-155; PMID:17255470; http://dx.doi.org/10.1096/fj.06-7522com
   PubMed Web of Science ®Google Scholar
• Nakamura I, Xue G, Sakudo A, Saeki K, Matsumoto Y, Ikuta K, Onodera T. Novel single nucleotide polymorphisms in the specific protein 1 binding site of the bovine PRNP promoter in Japanese Black cattle: impairment of its promoter activity. Intervirology 2007; 50(3):190-6; PMID:17283444; http://dx.doi.org/10.1159/000099217
   PubMed Web of Science ®Google Scholar
• Xue G, Sakudo A, Kim C, Onodera T. Coordinate regulation of bovine prion protein gene promoter activity by two Sp1 binding site polymorphisms. Biochem Biophys Res Commun 2008; 372(4):530-5; PMID:18505676; http://dx.doi.org/10.1016/j.bbrc.2008.05.085
   PubMed Web of Science ®Google Scholar
• Sander P, Hamann H, Drögemüller C, Kashkevich K, Leeb T. Bovine prion protein (PRNP): promoter polymorphisms modulated PRNP expression and may be responsible for differences in bovine spongiform encephalopathy susceptibility. J Biol Chem 2005; 280(45):37408-14; PMID:16141216; http://dx.doi.org/10.1074/jbc.M506361200
   PubMed Web of Science ®Google Scholar
• Msalya G, Shimogiri T, Nishitani K, Okamoto S, Kawabe K, Minesawa M, Maeda Y. Indels within promoter and intron 1 of bovine prion protein gene modulate the gene expression levels in the medulla oblongata of two Japanese cattle breeds. Anim Genet 2009a; 41(2):218-21http://dx.doi.org/10.1111/j.1365-2052.2009.01983.x
   PubMed Web of Science ®Google Scholar
• Brandsma JH, Janss LL, Visscher AH. Association between PrP genotypes and litter size and 135 days weight in texel sheep. Livest Prod Sci 2004; 85:59-64; http://dx.doi.org/10.1016/S0301-6226(03)00116-7
   Google Scholar
• Lan XY, Zhao HY, Li ZJ, Li AM, Lei CZ, Chen H, Pan CY. A novel 28-bp insertion–deletion polymorphism within goat PRNP gene and its association with production traits in Chinese native breeds. Genome 2012a; 55(7):547-52; http://dx.doi.org/10.1139/g2012-040
   PubMed Web of Science ®Google Scholar
• Lan XY, Zhao HY, Wu CY, Hu SR, Pan CY, Lei CZ, Chen H. Analysis of genetic variability at codon 42 within caprine prion protein gene in relation to production traits in Chinese domestic breeds. Mol Biol Rep 2012b; 39(4):4981-8; http://dx.doi.org/10.1007/s11033-011-1294-0
   PubMed Web of Science ®Google Scholar
• Alexander BM, Stobart RH, Russel WC, O'Rourke KI, Lewis GS, Logan JR, Duncan JV, Moss GE. The incidence of genotypes at codon 171 of the prion protein gene (PRNP) in five breeds of sheep and production traits of ewes associated with those genotypes. J Anim Sci 2005; 83:455-9; PMID:15644519
   PubMed Web of Science ®Google Scholar
• De Vries F, Borchers H, Hamann H, Drogemuller C, Reinecke S, Lupping W, Distl O. Associations between the prion protein genotype and performance traits of meat breeds of sheep. Vet Rec 2004; 155:140-3; PMID:15338706; http://dx.doi.org/10.1136/vr.155.5.140
   PubMed Web of Science ®Google Scholar
• Ioannides IM, Mavrogenis AP, Papachristoforou C. Analysis of PrP genotypes in relation to reproductive and production traits in Chios sheep. Livest Sci 2009; 122(2–3):296-301; http://dx.doi.org/10.1016/j.livsci.2008.09.022
   Web of Science ®Google Scholar
• Walawski K, Czarnik U. Prion octapeptide-repeat polymorphism in Polish Black-and-White cattle. J Appl Genet 2003; 44(2):191-5; PMID:12773797
   PubMed Web of Science ®Google Scholar
• Zhu XY, Feng FY, Xue SY, Hou T, Liu HR. Bovine spongiform encephalopathy associated insertion/deletion polymorphisms of the prion protein gene in the four beef cattle breeds from North China. Genome 2011; 54(10):805-11; PMID:21923635; http://dx.doi.org/10.1139/g11-043
   PubMed Web of Science ®Google Scholar
• Czarnik U, Grzybowski G, Zabolewicz T, Strychalski J, Kaminski S. Deletion/insertion polymorphism of the prion protein gene (PRNP) in Polish red cattle, Polish White-backed cattle and European bison (Bison bonasus L., 1758). Genetika 2009; 45(4):519-25; PMID:19507705
   PubMedGoogle Scholar
• Pan CY, Wu CY, Jia WC, Xu Y, Hu SR, Lei CZ, Lan XY, Chen H. A critical functional missense mutation (H173R) in the bovine PROP1 gene significantly affects growth traits in cattle. Gene 2013; 531(1):398-402; PMID:24029076; http://dx.doi.org/10.1016/j.gene.2013.09.002
   PubMed Web of Science ®Google Scholar
• Zhang S, Dang Y, Zhang Q, Qin Q, Lei C, Chen H, Lan X. Tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) rapidly identified a critical missense mutation (P236T) of bovine ACADVL gene significantly affecting growth traits. Gene 2015; 559(2):184-8; PMID:25620159; http://dx.doi.org/10.1016/j.gene.2015.01.043
   PubMed Web of Science ®Google Scholar
• Lan XY, Pan CY, Chen H, Zhang CL, Li JY, Zhao M, Lei CZ, Zhang AL, Zhang L. An AluI PCR-RFLP detecting a silent allele at the goat POU1F1 locus and its association with production traits. Small Ruminant Res 2007; 73(1):8-12; http://dx.doi.org/10.1016/j.smallrumres.2006.10.009
   Web of Science ®Google Scholar
• Shimogiri T, Msalya G, Myint SL, Okamoto S, Kawabe K, Tanaka K, Mannen H, Minezawa M, Namikawa T, Amano T, et al. Allele distributions and frequencies of the six prion protein gene (PRNP) polymorphisms in Asian native cattle, Japanese breeds, and mythun (Bos frontalis). Biochem Genet 2010; 48(9–10):829-39; PMID:20623331; http://dx.doi.org/10.1007/s10528-010-9364-x
   PubMed Web of Science ®Google Scholar
• Uchida L, Heriyanto A, Thongchai C, Hanh TT, Horiuchi M, Ishihara K, Tamura Y, Muramatsu Y. Genetic diversity in the prion protein gene (prnp) of domestic cattle and water buffaloes in Vietnam, Indonesia and Thailand. J Vet Med Sci 2014; 76(7):1001-8; PMID:24705506; http://dx.doi.org/10.1292/jvms.13-0642
   PubMed Web of Science ®Google Scholar
• Sander P, Hamann H, Pfeiffer I, Wemheuer W, Brenig B, Groschup MH, Ziegler U, Distl O, Leeb T. Analysis of sequence variability of bovine prion protein gene (PRNP) in GermaNanyang cattle breeds. Neurogenetics 2004; 5(1):19-25; PMID:14727152; http://dx.doi.org/10.1007/s10048-003-0171-y
   PubMed Web of Science ®Google Scholar
• Seabury CM, Womack JE, Piedrahita J, Derr JN. Comparative PRNP genotyping of US cattle sires for potential association with BSE. Mamm Genome 2004; 15(10):828-33; PMID:15520885; http://dx.doi.org/10.1007/s00335-004-2400-6
   PubMed Web of Science ®Google Scholar
• Hou J, An X, Song Y, Gao T, Lei Y, Cao B. Two mutations in the caprine MTHFR 3′ UTR regulated by microRNAs are associated with milk production traits. PLoS One 2015; 10(7):e0133015; PMID:26186555; http://dx.doi.org/10.1371/journal.pone.0133015
   PubMedGoogle Scholar