Human genes: HPRT1, hypoxanthine phosphoribosyltransferase
1; HPRT1, hypoxanthine phosphori bosyltransferase 1; RPLPO, ribosomal protein, large, PO; ERBB2, v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2; AR, androgen receptor; ERBB4, v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4.
Details on the measurement of mRNAs encoded by CDH16  (cadherin 16, KSP-cadherin), HIF1A [hypoxiainducible factor 1, a subunit (basic helix-loop-helix transcription factor)], HPRT1 (hypoxanthine phosphoribosyltransferase
1), PPIA [peptidylprolyl isomerase A (cyclophilin A)], KLK3 (kallikrein-related peptidase 3; also known as PSA), and TBP (TATA box binding protein) are provided in Supplemental Text 1, Table 2, A and B, and Fig.
2004) reported data on hypoxanthine phosphoribosyltransferase
(HPRT) gene mutant frequency (HPR[T.sub.mf]) in a subset of the subjects participating in the present study.
The production of HPRT1 (hypoxanthine phosphoribosyltransferase
1) mRNA was used for data normalization (14) according to the expression [2.sup.-[DELTA]Cq], where Cq is the quantification cycle.
 Human genes: RPLPO, ribosomal protein, large, P0; PPIA, peptidylprolyl isomerase A (cyclophilin A); TNFRSF1A, tumor necrosis factor receptor superfamily, member 1A; CCL11, CCL17, CCL19, CCL22, CCL3, CCL4, chemokine (C-C motif) ligand 11, 17, 19, 22, 3, and 4; CL5 chemokine (C-C motif) ligand 5; CCR1, CCR7, CCR8, chemokine (C-C motif) receptor 1, 7, and 8; CD86, CD86 molecule; CXCL12, chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1); CXCL2, chemokine (C-X-C motif) ligand 2; CXCR4, chemokine (C-X-C motif) receptor 4; L128, interleukin 12B (natural killer cell-stimulating factor 2, cytotoxic lymphocyte maturation factor 2, p40); IL15, IL4, IL8, interleukin 15, 4, and 8; HPRT1, hypoxanthine phosphoribosyltransferase
1; PGK1, phosphoglycerate kinase 1.
Concentrations of the target genes, expressed relative to our housekeeping set [low-abundance housekeeping gene hydroxymethylbilane synthase (HMBS, formerly porphobilinogen deaminase, PBGD), medium-abundance hypoxanthine phosphoribosyltransferase
(HPRT), and highabundance [[beta].sub.2]-microglobulin (B2M)], were quantified as follows: mRNA target = [2.sup.(mean Ct housekeeping--mean Ct target)] as described (21).
We evaluated 5 housekeeping genes (housekeeping gene selection set; Roche): [delta]-aminolevulinate synthase 1 (ALAS1), [[beta].sub.2]-microglobulin (B2M), glucose-6-phosphate dehydrogenase (G6PD), hypoxanthine phosphoribosyltransferase
1 (HPRT1), and hydroxymethylbilane synthase (HMBS; formerly PBGD, porphobilinogen deaminase), as potential references for relative quantification.
RNA integrity of all CDNA preparations was tested by real-time PCR amplification of the HPRT (hypoxanthine phosphoribosyltransferase
) gene (LightCycler-h-HPRT, Roche).
TPMT catalyzes the conversion of thiopurines to nontoxic or less toxic methylated compounds, as opposed to their metabolic activation by hypoxanthine phosphoribosyltransferase
(EC 126.96.36.199), ultimately leading to active 6-thiopurine nucleotides (7).
The quality of the RNA was checked by examining ribosomal RNA bands after agarose gel electrophoresis and by amplifying hypoxanthine phosphoribosyltransferase
(HPRT) as a control (see below).