Sheet 1: MIQE checklist.

All essential information (E) and Desirable information (D) are submitted in the current manuscript. Sheet 2: Data of DNA stock solutions. h—healthy, nfai—non-functioning adrenal incidentaloma, sv—simple virilizing congenital adrenal hyperplasia, sw—salt wasting congenital adrenal hyperplasia; g—good quality, p—population, b—bad quality; Q—Qiagen QIAcube wtih QIAamp DNA blood mini kit, R—Roche DNA isolation kit for mammalian blood, 5P - 5 Prime ArchivePure DNA cell/tissue kit; i—intact, sd—slightly degraded, pd—partially degraded. Sheet 3: Raw Cq values of the main qPCR experiments. Outliers were not identified using quartile ± 1.5 * interquartile range criterion. NTC—no template control. Sheet 4: Raw peak heights of MLPA probes. Coffalyser software with the default settings was used for the determination. Sheet 5: Raw dosage quotient of CYP21A1P and CYP21A2 MLPA probes. Coffalyser software with the default settings was used for the determination. Sheet 6: Raw Cq values for the repeatability and reproducibility values of the robustness experiments. Outliers were not identified using quartile ± 1.5 * interquartile range criterion. NTC—no template control; FAMM—TaqMan fast advance master mix, UMM2—TaqMan universal master mix II, GS7—GeneStudio 7 qPCR instrument, 7500F - 7500 Fast qPCR instrument. Sheet 7: Raw Cq values for the detailed CYP21 robustness experiments. Outliers were not identified using quartile ± 1.5 * interquartile range criterion. NTC—no template control; FAMM—TaqMan fast advance master mix, UMM2—TaqMan universal master mix II, GS7—GeneStudio 7 qPCR instrument, 7500F - 7500 Fast qPCR instrument. Sheet 8: Detailed gene copy number results. GCN—gene copy number, avr—average, SD—standard deviation, lwr—lower, upr—upper, CI—95% confidence interval, CV%—coefficient of variation %, DQ—dosage quotient, CGH—comparative genome hybridization; wd—with dilution, wod—without dilution; g—good quality, p—population, b—bad quality; orange number or amb—ambiguous result, red number—misclassification, orange background—not all MLPA probes were used for a CYP21 gene due to chimeric gene, red background—MLPA was inconclusive probably due to double chimeric genes. Sheet 9: Expected gene copy numbers. GCN—gene copy number, avr—average, exp—expected, dev—deviation, mod—modified SD—standard deviation, lwr—lower, upr—upper, CI—95% confidence interval, CV%—coefficient of variation %, DQ—dosage quotient, CGH—comparative genome hybridization; g—good quality, p—population, b—bad quality; orange number—ambiguous result, red number—misclassification at GCN or a deviation above 0.4 at avr dev GCNs or a misclassification at rounded GCNs. Sheet 10: Detailed results of linear discriminant analyses. The estimated total integer gene copy number (GCN) differed from the input class in sample NA11839 (the only sample having inconsistency in its input classes) and in sample H005 which has a relatively low probability value of classification. Cross-validation, when the estimated integer GCN of one sample is estimated without its input class and is based on the data of all other samples, supported the estimation in the former case, and led to a different classification in the latter one. A deviated classification of C4 genes was also observed by cross-validation in sample NA11839. The cross-validation of CYP21 genes could not be performed in two samples (H004 and H010) with the rare 3 GCN of CYP21A2, because their classes consisted of only one sample. avr—average, P—probability, red number—inconsistent input class, orange background—low probability or difference between input, resultant or cross-validation class, yellow background—cross-validation cannot be applied, red background—ambiguous estimated integer GCN. (XLSX)