cge1879-sup-0001-FigureS1.docxapplication/acrobat204K Fig. S1. Targeted sequencing diagnostic pipeline. Bar-coded genomic DNA was pooled and captured to sequence 2.5 Mb of genomic DNA corresponding to the genes known to be important in sex development. All data was aligned to the human reference genome hg18 and then put through the subsequent bioinformatics analysis to identify copy number variants and sequence variants and estimate sex chromosome dosage.
cge1879-sup-0002-FigureS2.docxapplication/acrobat153K Fig. S2. Copy number variant analysis for disorders of sex development genes. We performed copy number variant analysis on all known genes of sex development. Genes located on the X- or Y-chromosome were separated based on the number of each sex chromosome in the sample. For each autosomal gene, all samples were analyzed together. No outliers were detected among these samples (DAX1 with duplication is illustrated in Fig. 2).
cge1879-sup-0003-TableS1.docxapplication/acrobat218K Table S1. Captured genomic intervals. All targeted genomic intervals are based on the reference genome hg18. (A) All captured genomic intervals for 35 genes known to be important in mammalian sex development. Both exonic and intronic regions were captured for these regions. (B) For sex chromosome dosage analysis, we captured regions along the X- and Y-chromosomes spaced approximately 10 Mb apart.
cge1879-sup-0004-TableS2.docxapplication/acrobat112K Table S2. Sequencing quality statistics. For each sample, capture specificity, mean coverage, and percent of targeted bases covered by 10 or more reads are shown. After optimization, we were able to pool six samples together (DSDPts 7–12), with higher on-target rate (capture specificity >0.5) and sufficient coverage with majority of the targeted bases covered at 10× or greater. Coverage for the autosomes, X- and Y-chromosomes are given separately.
cge1879-sup-0005-AppendixS1.docapplication/acrobat723K Appendix S1. Supplementary methods.

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