New Prediction Model for Probe Specificity in an Allele-Specific Extension Reaction for Haplotype-Specific Extraction (HSE) of Y Chromosome Mixtures

PLoS ONE

Volumn 7, Issue 9, 2012, Pages

  Rothe, Jessica ^a   Watkins, Norman E ^b   Nagy, Marion ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b DNA Software Inc ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; ALLELE; ALLELE SPECIFIC EXTENSION REACTION; ARTICLE; COMPUTER PROGRAM; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DNA BASE COMPOSITION; DNA EXTRACTION; DNA PROBE; ENERGY; FREE ENERGY; GENETIC PARAMETERS; GENETIC PROCEDURES; HAPLOTYPE SPECIFIC EXTRACTION; HUMAN; HYBRIDIZATION; MALE; MELTING POINT; PREDICTION; PROBE DESIGN; PROBE LENGTH; PROBE MATCH; PROBE MISMATCH; PROBE SPECIFICITY; SHORT TANDEM REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; Y CHROMOSOME;

EID: 84866654229     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0045955     Document Type: Article

References (21)

1. Cai Y, Yuan Y, Lin Q, Chan P, (2010) Allele-specific extension allows base-pair neutral homozygotes to be discriminated by high-resolution melting of small amplicons. Anal Biochem 406: 29-33.
2. Chan K, Yam I, Yuen J, Yuen MF, Lai CL, et al. (2011) A comprehensive HBV array for the detection of HBV mutants and genotype. Clin Biochem 44: 1253-1260.
3. Litos IK, Ioannou PC, Christopoulos TK, Tzetis M, Kanavakis E, et al. (2011) Quadruple-allele dipstick test for simultaneous visual genotyping of A896G (Asp299Gly) and C1196T (Thr399Ile) polymorphisms in the toll-like receptor-4 gene. Clinica Chimica Acta 412: 1968-1972.
4. Dapprich J, Magira E, Samonte MA, Rosenman K, Monos D, (2007) Identification of a novel HLA-DPB1 allele (DPB1*1902) by haplotype-specific extraction and nucleotide sequencing. Tissue Antigens 69: 282-284.
5. Endres RO, Redman H, Scavello GS, (2007) A novel HLA-B*51 allele, HLA-B*5149. Tissue Antigens 70: 259-260.
6. Lim J, Kim Y, Cho B, Chung NG, Bok JN, (2009) A novel HLA-Cw*0436 allele identified by haplotype-specific extraction and sequence-based typing. Tissue Antigens 73: 78-79.
7. Ulrich S, Posch U, Helmberg W, Lanzer G, (2008) A new HLA-B*44 variant, B*4453, identified by haplotype-specific extraction and sequencing-based typing. Tissue Antigens 71: 91-92.
8. Dapprich J, Cleary MA (2001) Method for selectively isolating a nucleic acid, U.S. Patent Application #20010031467: Australian Patent #785211.
9. Dapprich J, Witter K, Gabel HW, Murphy NB, Albert ED, (2007) Identification of a new HLA-B allele (B*1576) by haplotype specific extraction. Hum Immunol 68: 418-421.
10. Gabriel A, Dapprich J, Kunkel M, Gresham D, Pratt SC, et al. (2006) Global mapping of transposon location. PLoS Genet 2: e212.
11. Huang MM, Arnheim N, Goodman MF, (1992) Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR. Nucleic Acids Res 20: 4567-4573.
12. Rothe J, Roewer L, Nagy M, (2011) Individual specific extraction of DNA from male mixtures-First evaluation studies. Forensic Science International: Genetics 5: 117-121.
13. Kwok S, Kellogg DE, McKinney N, Spasic D, Goda L, et al. (1990) Effects of primer-template mismatches on the polymerase chain reaction: human immunodeficiency virus type 1 model studies. Nucleic Acids Res 18: 999-1005.
14. Onodera K, (2007) Selection for 3′-end triplets for polymerase chain reaction primers. Methods Mol Biol 402: 61-74.
15. Ayyadevara S, Thaden JJ Shmookler Reis RJ, (2000) Discrimination of primer 3′-nucleotide mismatch by taq DNA polymerase during polymerase chain reaction. Anal Biochem 284: 11-18.
16. SantaLucia J Jr, Hicks D, (2004) The thermodynamics of DNA structural motifs. Annu Rev Biophys Biomol Struct 33: 415-440.
17. SantaLucia J Jr, (2007) Physical principles and visual-OMP software for optimal PCR design. Methods Mol Biol 402: 3-34.
18. Allawi HT, SantaLucia J Jr, (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36: 10581-10594.
19. Watkins NE Jr, SantaLucia J Jr, (2005) Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes. Nucleic Acids Res 33: 6258-6267.
20. SantaLucia J Jr, (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A 95: 1460-1465.
21. Dapprich J, Ferriola D, Magira EE, Kunkel M, Monos D, (2008) SNP-specific extraction of haplotype-resolved targeted genomic regions. Nucleic Acids Res 36: e94.