Patent ID: 8728766

Claim:
A method for processing a genomic DNA sample, comprising: (a) hybridizing a genomic sample comprising a population of initial target DNA molecules with a population of first primers that comprise: (i) a 3′ target-specific sequence that hybridizes to a sequence in said initial target DNA molecules, (ii) different degenerate base region (DBR) sequences, each of which is 5′ to said target-specific sequence, wherein said DBR sequences comprise at least one nucleotide base selected from: R, Y, S, W, K, M, B, D, H, V, N and modified versions thereof; and (iii) a generic primer sequence that is 5′ to each of said DBR sequences, thereby producing duplexes comprising an initial target DNA molecule of said population of initial target DNA molecules and a primer of said first primers; (b) subjecting the duplexes of step (a) to one, two or three rounds of primer extension to extend the population of first primers in said duplexes, thereby producing a mixture comprising tagged copies of said initial target DNA molecules, wherein each of said tagged copies comprises a DBR sequence of said DBR sequences and the generic primer sequence of said first population of primers; (c) removing any of said population of first primers that have not been extended in step (b) from the mixture of step (b) or inactivating any of said population of first primers that have not been extended in step (b) in the mixture of step (b); and (d) amplifying said tagged copies of said initial target DNA molecules after step c), thereby producing a plurality of different amplicons, wherein each of the different amplicons comprises multiple copies of the same polynucleotide, and wherein: i) the amplifying step is done by polymerase chain reaction (PCR) using a primer pair that comprises a generic primer that hybridizes to the complement of the generic primer sequence of the first primers of step (a); and ii) each of at least some of the different amplicons has a different DBR sequence of said DBR sequences.