Patent ID: 7202039

Claim:
A method for analyzing a first nucleic acid sample comprising: obtaining a second nucleic acid sample by: fragmenting the first nucleic acid sample to produce double stranded fragments; ligating one or more adaptors to the double stranded fragments; digesting the adaptor ligated double stranded fragments to produce single stranded half molecules; adding a homopolymeric tail to the 3′ end of the single stranded half molecules, hybridizing a primer to the homopolymeric tail and extending the primer to generate double stranded half fragments from the single stranded half molecules; and amplifying a plurality of the double stranded half fragments by a polymerase chain reaction (PCR) wherein the size of the amplified fragments is modulated by varying one or more reaction conditions or reagents to reduce the complexity of the first nucleic acid sample; providing a nucleic acid array; hybridizing the second nucleic acid sample to the array; and analyzing a hybridization pattern resulting from the hybridization.