Multiplex Allele-specific Target Amplification Based on PCR Suppression

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2001 Jan 3

PMID 11136256

Citations 21

Authors

N E Broude

L Zhang

K Woodward

D Englert

C R Cantor

Affiliations

Soon will be listed here.

Abstract

We have developed a strategy for multiplex PCR based on PCR suppression. PCR suppression allows DNA target amplification with only one sequence-specific primer per target and a second primer that is common for all targets. Therefore, an n-plex PCR would require only n + 1 primers. We have demonstrated uniform, efficient amplification of targeted sequences in 14-plex PCR. The high specificity of suppression PCR also provides multiplexed amplification with allele specificity. Multiplexed PCR was used to develop assays for genotyping DNA samples from cystic fibrosis-affected individuals. The new approach greatly simplifies primer design, significantly increases the PCR multiplexing level, and decreases the overall primer cost. In addition, this assay is more readily amenable to automation and is therefore suitable for high-throughput genetic diagnostics.

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References

Brownie J, Shawcross S, Theaker J, Whitcombe D, Ferrie R, Newton C . The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res. 1997; 25(16):3235-41. PMC: 146890. DOI: 10.1093/nar/25.16.3235. View

Gerry N, Witowski N, Day J, Hammer R, Barany G, BARANY F . Universal DNA microarray method for multiplex detection of low abundance point mutations. J Mol Biol. 1999; 292(2):251-62. DOI: 10.1006/jmbi.1999.3063. View

Chamberlain J, Gibbs R, Ranier J, Nguyen P, Caskey C . Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. Nucleic Acids Res. 1988; 16(23):11141-56. PMC: 339001. DOI: 10.1093/nar/16.23.11141. View

Cotton R . Detection of single base changes in nucleic acids. Biochem J. 1989; 263(1):1-10. PMC: 1133383. DOI: 10.1042/bj2630001. View

Norby S, Lestienne P, Nelson I, Rosenberg T . Mutation detection in Leber's hereditary optic neuropathy by PCR with allele-specific priming. Biochem Biophys Res Commun. 1991; 175(2):631-6. DOI: 10.1016/0006-291x(91)91612-g. View

Zielenski J, Rozmahel R, Bozon D, Kerem B, Grzelczak Z, Riordan J . Genomic DNA sequence of the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Genomics. 1991; 10(1):214-28. DOI: 10.1016/0888-7543(91)90503-7. View

Cha R, Zarbl H, Keohavong P, Thilly W . Mismatch amplification mutation assay (MAMA): application to the c-H-ras gene. PCR Methods Appl. 1992; 2(1):14-20. DOI: 10.1101/gr.2.1.14. View

Barnes W . PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates. Proc Natl Acad Sci U S A. 1994; 91(6):2216-20. PMC: 43341. DOI: 10.1073/pnas.91.6.2216. View

Edwards M, Gibbs R . Multiplex PCR: advantages, development, and applications. PCR Methods Appl. 1994; 3(4):S65-75. DOI: 10.1101/gr.3.4.s65. View

10.

Siebert P, Chenchik A, Kellogg D, Lukyanov K, Lukyanov S . An improved PCR method for walking in uncloned genomic DNA. Nucleic Acids Res. 1995; 23(6):1087-8. PMC: 306810. DOI: 10.1093/nar/23.6.1087. View

11.

Launer G, Lukyanov K, Tarabykin V, Lukyanov S . Simple method for cDNA amplification starting from small amount of total RNA. Mol Gen Mikrobiol Virusol. 1994; (6):38-41. View

12.

Rychlik W . Selection of primers for polymerase chain reaction. Mol Biotechnol. 1995; 3(2):129-34. DOI: 10.1007/BF02789108. View

13.

Lukyanov K, Launer G, Tarabykin V, Zaraisky A, Lukyanov S . Inverted terminal repeats permit the average length of amplified DNA fragments to be regulated during preparation of cDNA libraries by polymerase chain reaction. Anal Biochem. 1995; 229(2):198-202. DOI: 10.1006/abio.1995.1402. View

14.

Matsunaga J, Tomita Y, Tagami H . Detection of point mutations in human tyrosinase gene by improved allele-specific amplification. Exp Dermatol. 1995; 4(6):377-81. DOI: 10.1111/j.1600-0625.1995.tb00063.x. View

15.

Li D, Vijg J . Multiplex co-amplification of 24 retinoblastoma gene exons after pre-amplification by long-distance PCR. Nucleic Acids Res. 1996; 24(3):538-9. PMC: 145645. DOI: 10.1093/nar/24.3.538. View

16.

Diatchenko L, Lau Y, Campbell A, Chenchik A, Moqadam F, Huang B . Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci U S A. 1996; 93(12):6025-30. PMC: 39182. DOI: 10.1073/pnas.93.12.6025. View

17.

Shuber A, Grondin V, Klinger K . A simplified procedure for developing multiplex PCRs. Genome Res. 1995; 5(5):488-93. DOI: 10.1101/gr.5.5.488. View

18.

Stuven T, Griese E, Kroemer H, Eichelbaum M, Zanger U . Rapid detection of CYP2D6 null alleles by long distance- and multiplex-polymerase chain reaction. Pharmacogenetics. 1996; 6(5):417-21. DOI: 10.1097/00008571-199610000-00005. View

19.

Rines R, van Orsouw N, Sigalas I, Li F, Eng C, Vijg J . Comprehensive mutational scanning of the p53 coding region by two-dimensional gene scanning. Carcinogenesis. 1998; 19(6):979-84. DOI: 10.1093/carcin/19.6.979. View

20.

van Orsouw N, Zhang X, Wei J, JOHNS D, Vijg J . Mutational scanning of mitochondrial DNA by two-dimensional electrophoresis. Genomics. 1998; 52(1):27-36. DOI: 10.1006/geno.1998.5410. View