Methods and compositions for multiplex amplification of nucleic acids

#The polymerase chain reaction (PCR) is a simple and versatile method to amplify in vitro a specific segment of DNA for subsequent study (Saiki et al., Science 230:1350 (1985); Saiki et al; Science 235:487 (1985)). The PCR method has gained widespread use in biomedical research, and has revolutionized the accurate and early diagnosis of many inherited and acquired genetic disorders (Eisenstein, N. Engl J. Med. 322:178 (1990)), particularly those caused by point mutations or small insertions or deletions including sickle cell anemia (Saiki et al; Science 230:1350 (1985)), hemophilia A (Kogan et al; N. Engl. J. Med. 317:985 (1987)), Tay-Sach's disease (Myerowitz, Proc. Natl. Acad. Sci. USA 85:3955 (1988); Myerowitz et al; J. Biol. Chem. 263:18587 (1988)), cystic fibrosis (Riordan et al., Science 245:1066 (1989)), and many others. With PCR, it is also possible to detect heterozygotic carriers in recessive disorders.

#Polymerase chain reaction (PCR) is used for a variety of purposes. PCR can be used to amplify genomic DNA or other sources of nucleic acids for analysis. It is often desirable to be able to achieve equimolar yields of different length amplicons when performing multiplex PCR or multiple PCR reactions. Having an approximately equimolar yield of amplicons is particularly useful, for example, when approximately equal representation of certain regions of genomic DNA amplified after multiplex PCR is desired. Prior to the methods of present invention, finding the appropriate experimental conditions useful to achieve this result has been difficult because PCR amplifies nucleic acids having different lengths with different efficiencies. The yield of longer amplicons is often less than the yield of shorter amplicons because of those differences in PCR amplification efficiency. FIG. 1 shows the difference in yields that one might expect, for example, when starting with equal primer concentrations used to amplify amplicons of varying lengths: A, B, C. There is a continuing need in the art for methods which permit the amplification of different sequences with the same efficiency so that approximately equimolar products result.

#It is an object of the present invention to provide a method of performing multiplex PCR which achieve approximately equimolar products.

#FIG. 1 shows the difference in yields that one might expect, for example, when starting with equal primer concentrations used to amplify amplicons of varying lengths: A, B, C.

#FIG. 2 illustrates the relationship for given values X and LL,using the amplicons from different exons of the human p53 gene as an example.

#It is a discovery of the present invention that approximately equimolar yields of amplicons of varying lengths can be easily produced by multiplex PCR. It has been determined that varying the primer concentrations as a function of the lengths of amplicons yields approximately equimolar amounts of amplicons of varying lengths. The relationship between primer concentration and the length of amplicons is as follows:

#CA=CL(LA/LL)X

#wherein