A method to identify and verify one or more pharmacogenomic biomarkers, which method comprises: a) isolating DNA from archived clinical samples, from a previously conducted clinical trial, of five or more patients exhibiting different values in a relevant phenotype; b) amplifying said isolated DNA, wherein the amplification is whole-genome amplification, and the resulting DNA is whole-genome amplified DNA (wgaDNA); c) obtaining high-density genotyping data of said amplified DNA by using a genome-wide genotype calling algorithm, wherein the call rate cut-off value of the genome-wide genotype calling algorithm is adjusted multiple times to include or exclude samples, whereby the call rate cut-off value is optimized based on sequence information from said amplified DNA, the optimized call rate cut-off value is less than 95%, and genotypes are calculated based on the sequence information and the optimized call rate cut-off value; d) performing association analysis based on said genotyping data and said different values in said relevant phenotype to identify one or more pharmacogenomic biomarkers of said relevant phenotype, e) obtaining additional genotyping data from archived clinical samples of additional patients from the previously conducted clinical trial by using a verification genotype calling algorithm, wherein the call rate cut-off value of the verification genotype calling algorithm is adjusted multiple times to include or exclude samples, f) comparing the additional genotyping data obtained by using the verification genotype calling algorithm to the genotyping data obtained by using the genome-wide genotype calling algorithm, and g) performing association analysis based on said additional genotyping data to verify association between the one or more pharmacological biomarkers identified in step d) and said relevant phenotype, wherein a subset of the pharmacogenomic biomarkers identified in step d) is verified in step g), for retrospective study of archived clinical samples from the previously conducted clinical trial, wherein the archived clinical samples are plasma samples, and wherein the isolated DNA is suboptimal genomic DNA which is inferior in quality and/or in quantity to genomic DNA isolated from whole blood. a) isolating DNA from archived clinical samples, from a previously conducted clinical trial, of five or more patients exhibiting different values in a relevant phenotype; b) amplifying said isolated DNA, wherein the amplification is whole-genome amplification, and the resulting DNA is whole-genome amplified DNA (wgaDNA); c) obtaining high-density genotyping data of said amplified DNA by using a genome-wide genotype calling algorithm, wherein the call rate cut-off value of the genome-wide genotype calling algorithm is adjusted multiple times to include or exclude samples, whereby the call rate cut-off value is optimized based on sequence information from said amplified DNA, the optimized call rate cut-off value is less than 95%, and genotypes are calculated based on the sequence information and the optimized call rate cut-off value; d) performing association analysis based on said genotyping data and said different values in said relevant phenotype to identify one or more pharmacogenomic biomarkers of said relevant phenotype, e) obtaining additional genotyping data from archived clinical samples of additional patients from the previously conducted clinical trial by using a verification genotype calling algorithm, wherein the call rate cut-off value of the verification genotype calling algorithm is adjusted multiple times to include or exclude samples, f) comparing the additional genotyping data obtained by using the verification genotype calling algorithm to the genotyping data obtained by using the genome-wide genotype calling algorithm, and g) performing association analysis based on said additional genotyping data to verify association between the one or more pharmacological biomarkers identified in step d) and said relevant phenotype,