Varietal counting of nucleic acids for obtaining genomic copy number information

A method comprising:

• a) generating unique tagged nucleic acid molecules, comprising:
• i) subjecting mRNA transcripts in a sample to a polymerase reaction in the presence of primers capable of hybridizing to the polyA tails of the mRNA transcripts under conditions that promote the formation of only one complement of the mRNA transcripts, thereby generating first order derivative strands;
• ii) adding a polynucleotide tail to an end of the first order derivative strands, thereby generating first order derivative strands comprising the polynucleotide tail;
• and
• iii) subjecting the first order derivative strands comprising the polynucleotide tail to a polymerase reaction in the presence of primers capable of hybridizing to the polynucleotide tail added in step (ii) under conditions that promote the formation of only one complement of the first order derivative strands comprising the polynucleotide tail, thereby generating second order derivative strands,
• wherein the primers of step (i) or (iii) comprise nucleic acid tags, such that each of the tagged nucleic acid molecules is unique, and the first order derivative strands and the second order derivative strands are the tagged nucleic acid molecules;
• b) subjecting each of the tagged nucleic acid molecules to a polymerase chain reaction (PCR), thereby generating amplified tagged nucleic acid molecules;
• c) generating tag associated sequence reads by sequencing the amplified tagged nucleic acid molecules of step (b);
• d) assigning each of the amplified tagged nucleic acid molecules to a location on a cDNA library produced from the mRNA transcripts by mapping the subsequence of each tag associated sequence read of said tag associated sequence reads of step (c) to a location on the cDNA library;
• and
• e) at a plurality of locations on the cDNA library, counting the number of the amplified tagged nucleic acid molecules having a different tag that have been assigned to the same location on the cDNA library based on the mapping step, thereby obtaining a count for each location of the plurality of locations on the cDNA library.