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Table S1. List of all environmental chemicals (= 121) measured in 130 breast milk samples from Denmark and Finland 1997–2011.

Table S2. Environmental Chemicals (= 15) excluded from statistical analysis due to very low or undetectable levels.

Table S3. (a) Logistic regression analysis of individual chemical concentrations in 65 Danish breast milk samples from mothers with healthy (controls) or cryptorchid boys (cases). The results are corrected for multiple testing with Holm’s method. (b) Logistic regression analysis of individual chemical concentrations in 65 Danish breast milk samples from mothers with healthy (controls) or cryptorchid boys (cases). The results are not corrected for multiple testing.

Table S4. Logistic regression analysis of individual chemical concentrations in 65 Finnish breast milk samples from mothers with healthy (controls) or cryptorchid boys (cases). The results are not corrected for multiple testing.

Table S5. (a and b) Performance of PLS (Partial Least Square) analysis in predicting cases (boys with cryptorchidism) and controls (healthy boys) from measurements of 106 persistent environmental chemicals in maternal breast milk samples, accounting for confounders. Chemicals were used as predictor variables, while case/control status and confounding factors were added as response variables. (a) Danish samples. (b) Finnish samples.

Table S6. (a and b) Performance of PLS (Partial Least Square) analysis in predicting cases (boys with cryptorchidism) and controls (healthy boys) from measurements of 106 persistent environmental chemicals in maternal breast milk samples, without accounting for confounders. Chemicals were used as predictor variables, while case/control status and confounding factors were added as response variables. (a) Danish samples. (b) Finnish samples.

Table S7. (a and b) Performance of SVM (Support Vector Machine) analysis in predicting cases (boys with cryptorchidism) and controls (healthy boys) from measurements of 106 persistent environmental chemicals in maternal breast milk samples, without accounting for confounders. Chemicals were used as predictor variables, while case/control status and confounding factors were added as response variables. (a) Danish samples. (b) Finnish samples.

Table S8. (a and b) Performance of nnet (neural network classifier) analysis in predicting cases (boys with cryptorchidism) and controls (healthy boys) from measurements of 106 persistent environmental chemicals in maternal breast milk samples, without accounting for confounders. Chemicals were used as predictor variables, while case/control status and confounding factors were added as response variables. (a) Danish samples. (b) Finnish samples.

Table S9. List of environmental chemicals measured in 65 Danish breast milk samples sorted according to their regression coefficient (Coef.) in the PLS (Partial Least Square) analysis (adjusted for confounders and using different handlings of values close to LOQ).

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