Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Patent
1997-05-27
1999-09-21
Campbell, Eggerton A.
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
435 912, C12Q 168, C12P 1934
Patent
active
059552760
DESCRIPTION:
BRIEF SUMMARY
FIELD OF INVENTION
The present invention relates the use of perfect, compound simple sequence repeats (SSR) as self-anchoring primers for the identification and analysis of DNA sequence polymorphisms. More specifically it has been observed that any one type of simple sequence repeat (SSR) in both plant and animal genomes often exists directly adjacent to an SSR of a different type, usually with perfect periodicity of one of the component nucleotides shared by both SSRs. This observation has allowed the design of self-anchoring 15 primers in new variations of polymerase chain reaction-based multiplexed genome assays, including inter-repeat amplification and amplified fragment length polymorphism assays. These method variations collectively have been termed selective amplification of microsatellite polymorphic loci (SAMPL).
BACKGROUND
The ability to map eukaryotic genomes has become an essential tool for the diagnosis of genetic diseases, and for plant breeding and forensic medicine. An absolute requirement for elucidation of any genetic linkage map is the ability to identify DNA sequence variation. The realization that genetic (DNA) polymorphisms between phenotypically identical individuals are present and can be used as markers for genetic mapping has produced major advances in the art of developing eukaryotic linkage maps.
Techniques for identifying genetic polymorphisms are relatively few and to date have been time consuming and labor intensive. One of the most common techniques is referred to as restriction fragment length. polymorphism or RFLP (Botstein et al. Am. J. Hum. Genet. 342, 314, (1980)). Using RFLP technology, genetic markers based on single or multiple point mutations in the genome may be detected by differentiating DNA banding patterns from restriction enzyme analysis. As restriction enzymes cut DNA at specific target site sequences, a point mutation within this site may result in the loss or gain of a recognition site, giving rise in that genomic region to restriction fragments of different length. Mutations caused by the insertion, deletion or inversion of DNA stretches will also lead to a length variation of DNA restriction fragments. Genomic restriction fragments of different lengths between genotypes can be detected with region-specific probes on Southern blots (Southern, E. M., J. Mol. Biol. 98, 503, (1975). The genomic DNA is typically digested with nearly any restriction enzyme of choice. The resulting fragments are electrophoretically size-separated, transferred to a membrane, and then hybridized against a suitably labelled probe for detection of fragments corresponding to a specific region of the genome. RFLP genetic markers are particularly useful in detecting genetic variation in phenotypically silent mutations and serve as highly accurate diagnostic tools. RFLP analysis is a useful tool in the generation of codominant genetic markers but suffers from the need to separate restriction fragments electrophoretically and often requires a great deal of optimization to achieve useful background to signal ratios where significant polymorphic markers can be detected. In addition, the RFLP method relies on DNA polymorphisms existing within actual restriction sites. Any other point mutations in the genome usually go undetected. This is a particularly difficult problem when assaying genomes with inherently low levels of DNA polymorphism. Thus, RFLP differences often are difficult to identify.
Another method of identifying polymorphic genetic markers employs DNA amplification using short primers of arbitrary sequence. These primers have been termed `random amplified polymorphic DNA`, or "RAPD" primers, Williams et al., Nucl. Acids. Res., 18, 6531 (1990) and U.S. Pat. Nos. 5,126,239; (also EP0 543 484 A2, WO 92/07095, WO 92/07948, WO 92/14844, and WO 92/03567). The RAPD method amplifies either double or single stranded nontargeted, arbitrary DNA sequences using standard amplification buffers, dATP, dCTP, dGTP and TTP nucleotides, and a thermostable DNA polymerase such as Taq polymerase.
REFERENCES:
patent: 5126239 (1992-06-01), Livak et al.
patent: 5206137 (1993-04-01), Ip et al.
Senior et al Genomics 36:884-889, 1993.
Grist et al Biotechniques 15:304-309, 1993.
Moore, S.S., et al., Genomics, 10, 654-660 (1991).
Epplen, J.T., The Journal Of Heredity, 79(6), 409-417 (1988).
Weber, J.L., et al., Genomics, 11, 695-700 (1991).
Wu, K. et al., Mol. Gen. Genet., 241, 225-235 (1993).
Weber, J.L., In Tilgman, S., Daves, K. (Eds.), Genome Analysis Vol. 1: Genetic and Physical Mapping, Cold Spring Harbor Labratory Press, 159-181 (1990).
Hing, A.V. et al., Am. J. Hum. Genet., 55, 509-517 (1993).
Beckmann, J.S. et al., Bio/Technology, 8, 930-932 (1990).
Litt, M. et al., Am. J. Hum. Genet., 44, 397-401 (1989).
Ellegren, H. et al., Animal Genetics, 23, 133-142 (1992).
Weber, J.L. et al., Am. J. Hum. Genet., 44, 388-396 (1989).
Slettan, A. et al., Animal Genetics, 24, 195-197 (1993).
Condit, R. et al., Genome, 34, 66-71 (1991).
Browne, D.L. et al., Nucleic Acids Research, 20(1) (1991).
Beckmann, J.S. et al., Genomics, 12, 627-631 (1992).
Botstein, D. et al., Am. J. Hum. Genet., 32, 314-331 (1980).
Buchanan, F.C. et al., Mammalian Genome, 4, 258-264 (1993).
Weber, J.L., Genomics, 7, 524-530 (1990).
Zietkiewicz, E. et al., Genomics, 20, 001-007 (1994).
Wu, K., et al., Nucleic Acids Research, 22(15), 3257-3258 (1994).
Morgante, M. et al., The Plant Journal, 3(1), 175-182 (1993).
Akkaya, M.S. et al., "Length Polymorphisms Of Simple Sequence Repeat DNA In Soybean", Soybean And Alfalfa Res. Lab., US Dept. Of Ag. Res. Service, Beltsville Ag Res. Ctr., Beltsville, MD 20705-2350 (1992).
Southern, E.M., J. Mol. Biol., 98, 503-517 (1975).
Williams, J.G.K. et al., Nucleic Acids Res., 18(22), 6531-6535 (1990).
Zietkiewicz et al., "Genomic Fingerprinting By SSR Anchored Polymerase Chain Reaction" Genomics 20: 176-183, 1994.
Buchanan et al., "Microsatellites And Associated Repetitive Elements In The Sheep Genome" Mammalian Genome 4:258-264, 1993.
Weber, "Human DNA Polymorphisms Based On Length Variations In Simple-Sequence Tandem Repeats" In Genome Analysis vol. 1: Genetic And Physical Mapping, pp. 159-181, 1990, CSHP.
Morgante Michele
Vogel Julie Marie
Campbell Eggerton A.
E.I. Du Pont de Nemours and Company
LandOfFree
Compound microsatellite primers for the detection of genetic pol does not yet have a rating. At this time, there are no reviews or comments for this patent.
If you have personal experience with Compound microsatellite primers for the detection of genetic pol, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Compound microsatellite primers for the detection of genetic pol will most certainly appreciate the feedback.
Profile ID: LFUS-PAI-O-78973