Methods for making polynucleotide libraries, polynucleotide arrays, and cell libraries for high-throughput genomics analysis

A method for high-throughput genomics analysis, to identify the therapeutic or diagnostic utility of genes, entails the use of a construct to disrupt a gene or alleles of a gene in cells of interest. Arrays of such cells can be used to monitor such disrupted cells phenotypically in the context, for example, of testing drug candidates. Polynucleotides that comprise part of the disrupted genes can be recovered from such "knockout" cells, by virtue of an origin of replication or a host cell selection marker sequence that is part of the construct. The recovered polynucleotides can be used to identify the disrupted genes or to make homologous recombination vectors, which in turn can be employed to make multi-allele knockout cells. Double-stranded RNA molecules designed to target the recovered polynucleotide are used to down regulate the polynucleotide in vitro and in vivo, following determination of a therapeutically effective dosage of the RNAi molecule.