A method for whole genome amplification by multiple displacement amplification, comprising: (a) performing a plurality of separate multiple displacement amplification reactions, wherein each reaction is performed in the presence of: a primer set, wherein each primer of the primer set comprises a self-complementary sequence at its 5' terminus and a random sequence or a semi-random sequence at its 3' terminus, and wherein the self-complementary sequences in each primer set are the same, but different from the self-complementary sequences in another primer set and wherein the primers are resistant to 3'→5' exonuclease proofreading activity, and wherein each primer has the sequence 5'-S-L-S'-R-3' wherein (i) S and S' are two sub-sequences that are complementary to each other in the antiparallel orientation, (ii) L is an optional sequence between sub-sequences S and S', and (iii) R is a random sequence or a semi-random sequence; a DNA polymerase having a strand displacement activity, and target genomic DNA from one or more different single cells, wherein the target genomic DNA in the separate multiple displacement reactions comes from different samples, and (b) pooling the nucleic acids amplified from the plurality of multiple displacement amplification reactions together thereby generating a sequencing library, wherein the self-complementary sequences of the primers in each primer set is indicative of the sample source from which target genomic DNAs in each multiple displacement amplification reaction were obtained. (a) performing a plurality of separate multiple displacement amplification reactions, wherein each reaction is performed in the presence of: a primer set, wherein each primer of the primer set comprises a self-complementary sequence at its 5' terminus and a random sequence or a semi-random sequence at its 3' terminus, and wherein the self-complementary sequences in each primer set are the same, but different from the self-complementary sequences in another primer set and wherein the primers are resistant to 3'→5' exonuclease proofreading activity, and wherein each primer has the sequence 5'-S-L-S'-R-3' wherein (i) S and S' are two sub-sequences that are complementary to each other in the antiparallel orientation, (ii) L is an optional sequence between sub-sequences S and S', and (iii) R is a random sequence or a semi-random sequence; a DNA polymerase having a strand displacement activity, and target genomic DNA from one or more different single cells, wherein the target genomic DNA in the separate multiple displacement reactions comes from different samples, and a primer set, wherein each primer of the primer set comprises a self-complementary sequence at its 5' terminus and a random sequence or a semi-random sequence at its 3' terminus, and wherein the self-complementary sequences in each primer set are the same, but different from the self-complementary sequences in another primer set and wherein the primers are resistant to 3'→5' exonuclease proofreading activity, and wherein each primer has the sequence 5'-S-L-S'-R-3' wherein (i) S and S' are two sub-sequences that are complementary to each other in the antiparallel orientation, (ii) L is an optional sequence between sub-sequences S and S', and (iii) R is a random sequence or a semi-random sequence; (i) S and S' are two sub-sequences that are complementary to each other in the antiparallel orientation, (ii) L is an optional sequence between sub-sequences S and S', and (iii) R is a random sequence or a semi-random sequence; a DNA polymerase having a strand displacement activity, and target genomic DNA from one or more different single cells, wherein the target genomic DNA in the separate multiple displacement reactions comes from different samples, and (b) pooling the nucleic acids amplified from the plurality of multiple displacement amplification reactions together thereby generating a sequencing library, wherein the self-complementary sequences of the primers in each primer set is indicative of the sample source from which target genomic DNAs in each multiple displacement amplification reaction were obtained.