A method for whole genome amplification and analysis of multiple target molecules in a biological sample including genomic DNA and target molecules comprising the steps of: a) providing the biological sample; b) contacting the biological sample with at least one binding agent, which is directed to at least one of the target molecules, conjugated with a tagged oligonucleotide, the tagged oligonucleotide comprising: i) a payload sequence of nucleic acid comprising a binding-agent barcode sequence and a unique molecular identifier sequence, and ii) at least one first tagged oligonucleotide amplification sequence of nucleic acid (5-TOS); so that - when at least one target molecule is present in the biological sample - the at least one binding agent binds to the at least one target molecule; c) carrying out a separating step to selectively remove unbound binding agent thus obtaining a labeled biological sample; d) carrying out on the labeled biological sample: - a whole genome amplification of said genomic DNA by: i) deterministic restriction-site whole genome amplification (DRS-WGA), or ii) Multiple Annealing and Looping Based Amplification Cycles whole genome amplification (MALBAC), and - an amplification of the tagged oligonucleotide conjugated with the at least one binding agent, wherein whole genome amplification and amplification of the tagged oligonucleotide are carried out simultaneously; e) preparing a massively parallel sequencing library from the amplified tagged oligonucleotide; f) sequencing the massively parallel sequencing library; g) retrieving the sequences of the binding-agent barcode sequence and unique molecular identifier sequence from each sequencing read; h) counting the number of distinct unique molecular identifier sequences for each binding agent. a) providing the biological sample; b) contacting the biological sample with at least one binding agent, which is directed to at least one of the target molecules, conjugated with a tagged oligonucleotide, the tagged oligonucleotide comprising: i) a payload sequence of nucleic acid comprising a binding-agent barcode sequence and a unique molecular identifier sequence, and ii) at least one first tagged oligonucleotide amplification sequence of nucleic acid (5-TOS); so that - when at least one target molecule is present in the biological sample - the at least one binding agent binds to the at least one target molecule; i) a payload sequence of nucleic acid comprising a binding-agent barcode sequence and a unique molecular identifier sequence, and ii) at least one first tagged oligonucleotide amplification sequence of nucleic acid (5-TOS); so that - when at least one target molecule is present in the biological sample - the at least one binding agent binds to the at least one target molecule; c) carrying out a separating step to selectively remove unbound binding agent thus obtaining a labeled biological sample; d) carrying out on the labeled biological sample: - a whole genome amplification of said genomic DNA by: i) deterministic restriction-site whole genome amplification (DRS-WGA), or ii) Multiple Annealing and Looping Based Amplification Cycles whole genome amplification (MALBAC), and - an amplification of the tagged oligonucleotide conjugated with the at least one binding agent, wherein whole genome amplification and amplification of the tagged oligonucleotide are carried out simultaneously; - a whole genome amplification of said genomic DNA by: i) deterministic restriction-site whole genome amplification (DRS-WGA), or ii) Multiple Annealing and Looping Based Amplification Cycles whole genome amplification (MALBAC), and i) deterministic restriction-site whole genome amplification (DRS-WGA), or ii) Multiple Annealing and Looping Based Amplification Cycles whole genome amplification (MALBAC), and - an amplification of the tagged oligonucleotide conjugated with the at least one binding agent, wherein whole genome amplification and amplification of the tagged oligonucleotide are carried out simultaneously; e) preparing a massively parallel sequencing library from the amplified tagged oligonucleotide; f) sequencing the massively parallel sequencing library; g) retrieving the sequences of the binding-agent barcode sequence and unique molecular identifier sequence from each sequencing read; h) counting the number of distinct unique molecular identifier sequences for each binding agent.