Microarray-based STR genotyping using RecA-mediated ligation

Nucleic Acids Research

Volumn 38, Issue 17, 2010, Pages

  Herrmann, David ^a,c   Rose, Emily ^a   Müller, Uwe ^b   Wagner, Robert ^a  

^a Gene Check Inc   (United States)

^b UWILA International Consulting   (United States)

^c CARGILL INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; RECA PROTEIN; AUTOANTIGEN; IODIDE PEROXIDASE; IRON BINDING PROTEIN; MICROSATELLITE DNA; TPO PROTEIN, HUMAN;

ACCURACY; AMPLICON; ARTICLE; AUTOMATION; BASE PAIRING; CATALYSIS; CONTROLLED STUDY; FORENSIC MEDICINE; GENETIC PROCEDURES; GENOME SIZE; GENOTYPE; HUMAN; MICROARRAY ANALYSIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RECA MEDIATED LIGATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SHORT TANDEM REPEAT; ALLELE; CHEMISTRY; DNA MICROARRAY; GENETICS; METABOLISM; PROCEDURES;

ALLELES; AUTOANTIGENS; GENOTYPE; HUMANS; IODIDE PEROXIDASE; IRON-BINDING PROTEINS; MICROSATELLITE REPEATS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; REC A RECOMBINASES;

EID: 77957230669     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq657     Document Type: Article

References (30)

1. Wells,R.D., Goodman,T.C., Hillen,W., Horn,G.T., Klein,R.D., Larson,J.E., Müller,U.R., Neuendorf,S.K., Panayotatos,N. and Stirdivant,S.M. (1980) DNA structure and gene regulation. Prog. Nucleic Acid Res. Mol. Biol., 24, 167-267.
2. Williams,W.L. and Müller,U.R. (1987) Effects of palindrome size and sequence on genetic stability in the bacteriophage phi X174 genome. J. Mol. Biol., 196, 743-755.
3. Müller,U.R., Perkins,B.K. and Williams,W.L. (1988) Effects of palindromes on in vivo DNA replication and mutagenesis in bacteriophage phi X174 RF DNA. Nucleic Acids Res., 16, 10733-10750.
4. Müller,U.R. and Wilson,C.L. (1987) The effect of supercoil and temperature on the recognition of palindromic and non-palindromic regions in phi X174 replicative form DNA by S1 and Bal31. J. Biol. Chem., 262, 3730-3738.
5. Müller,U.R. and Turnage,M.A. (1986) Insertions of palindromic DNA sequences into the J-F intercistronic region of bacteriophage phi X174 interfere with normal phage growth. J. Mol. Biol., 189, 285-292.
6. Zahra,R., Blackwood,J.K., Sales,J. and Leach,D.R. (2007) Proofreading and secondary structure processing determine the orientation dependence of CAG{middle dot}CTG trinucleotide repeat instability in Escherichia coli. Genetics, 176, 27-41.
7. Goldfless,S.J., Morag,A.S., Belisle,K.A., Sutera,V.A. Jr. and Lovett,S.T. (2006) DNA repeat rearrangements mediated by DnaK-dependent replication fork repair. Mol. Cell, 21, 595-604.
8. Wang,G. and Vasquez,K.M. (2006) Non-B DNA structure-induced genetic instability. Mutat. Res., 598, 103-119.
9. Bichara,M., Wagner,J. and Lambert,I.B. (2006) Mechanisms of tandem repeat instability in bacteria. Mutat Res., 598, 144-163.
10. Rubinstein,D.C. and Hayden,M.R.E. (1998) Analysis of Triplet Repeat Disorders. BIOS Scientific Publishers, Oxford, Washington, DC.
11. Edwards,A., Civitello,A., Hammond,H.A. and Caskey,C.T. (1991) DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. Am. J. Hum. Genet., 49, 746-756.
12. Saker,A., Benachi,A., Bonnefont,J.P., Munnich,A., Dumez,Y., Lacour,B. and Paterlini-Brechot,P. (2006) Genetic characterization of circulating fetal cells allows non-invasive prenatal diagnosis of cystic fibrosis. Prenat. Diagn., 26, 906-916.
13. Fundia,A.F., De Brasi,C. and Larripa,I. (2004) Feasibility of a cost-effective approach to evaluate short tandem repeat markers suitable for chimerism follow-up. Mol. Diagn, 8, 87-91.
14. Budowle,B. and Moretti,T.R. (1999) Genotype profiles for six population groups at the 13 CODIS short tandem repeat core loci and other PCR based loci. Forensic Sci. Commun., 1, http://www.fbi.gov/hq/lab/fsc/backissu/july1999/budowle.htm.
15. Butler,J.M. (2005) Constructing STR multiplex assays. Methods Mol. Biol., 297, 53-66.
16. Kimpton,C.P., Gill,P., Walton,A., Urquhart,A., Millican,E.S. and Adams,M. (1993) Automated DNA profiling employing multiplex amplification of short tandem repeat loci. PCR Methods Appl., 3, 13-22.
17. Butler,J.M., McCord,B.R., Jung,J.M., Lee,J.A., Budowle,B. and Allen,R.O. (1995) Application of dual internal standards for precise sizing of polymerase chain reaction products using capillary electrophoresis. Electrophoresis, 16, 974-980.
18. Lazaruk,K., Walsh,P.S., Oaks,F., Gilbert,D., Rosenblum,B.B., Menchen,S., Scheibler,D., Wenz,H.M., Holt,C. and Wallin,J. (1998) Genotyping of forensic short tandem repeat (STR) systems based on sizing precision in a capillary electrophoresis instrument. Electrophoresis, 19, 86-93.
19. Schmalzing,D., Koutny,L., Adourian,A., Belgrader,P., Matsudaira,P. and Ehrich,D. (1997) DNA typing in thirty seconds with a microfabricated device. Proc. Natl Acad. Sci. USA, 94, 10273-10278.
20. Goedecke,N., McKenna,B., El-Difrawy,S., Gismondi,E., Swenson,A., Carey,L., Matsudaira,P. and Ehrlich,D.J. (2006) Microdevice DNA forensics by the simple tandem repeat method. J. Chromatogr. A, 1111, 206-213.
21. Goedecke,N., McKenna,B., El-Difrawy,S., Carey,L., Matsudaira,P. and Ehrlich,D. (2004) A high-performance multilane microdevice system designed for the DNA forensics laboratory. Electrophoresis, 25, 1678-1686.
22. Wang,Y., Wallin,J.M., Ju,J., Sensabaugh,G.F. and Mathies,R.A. (1996) High-resolution capillary array electrophoretic sizing of multiplexed short tandem repeat loci using energy-transfer fluorescent primers. Electrophoresis, 17, 1485-1490.
23. Gao,Q., Pang,H.M. and Yeung,E.S. (1999) Simultaneous genetic typing from multiple short tandem repeat loci using a 96-capillary array electrophoresis system. Electrophoresis, 20, 1518-1526.
24. Butler,J.M., Li,J., Shaler,T.A., Monforte,J.A. and Becker,C.H. (1999) Reliable genotyping of short tandem repeat loci without an allelic ladder using time-of-flight mass spectrometry. Int. J. Legal Med., 112, 45-49.
25. Sosnowski,R., Heller,M.J., Tu,E., Forster,A.H. and Radtkey,R. (2002) Active microelectronic array system for DNA hybridization, genotyping and pharmacogenomic applications. Psychiatr Genet., 12, 181-192.
26. Pourmand,N., Caramuta,S., Villablanca,A., Mori,S., Karhanek,M., Wang,S.X. and Davis,R.W. (2007) Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays. Proc. Natl Acad. Sci. USA, 104, 6146-6151.
27. Landegren,U., Kaiser,R., Sanders,J. and Hood,L. (1988) A ligase-mediated gene detection technique. Science, 241, 1077-1080.
28. Landegren,U., Samiotaki,M., Nilsson,M., Malmgren,H. and Kwiatkowski,M. (1996) Detecting genes with ligases. Methods, 9, 84-90.
29. Bianco,P.R., Tracy,R.B. and Kowalczykowski,S.C. (1998) DNA strand exchange proteins: a biochemical and physical comparison. Frontiers Biosci., 3, 570-603.
30. Shen,P. and Huang,H. (1989) Effect of base pair mismatches on recombination via the RecBCD pathway. Mol. Gen. Genet., 218, 358-360.