Supplementary Figures S1 - S18

Supplementary Figure S1 shows independent estimation of circulating tumor DNA fraction using whole exome sequencing.

Supplementary Figure S7 shows the concordance of gene coverage logratios between 72-gene targeted sequencing and whole exome sequencing

<p>Supplementary Figure S17 provides whole exome somatic mutation profiles in patients that did not show temporal changes in 72-gene panel mutation profiles</p>

Supplementary Figure S8 shows that exome-wide sequencing supports ctDNA fraction estimates inferred with the 72-gene panel

Supplementary Figure S13 shows temporal changes in copy number profiles detected via 72-gene targeted sequencing

Supplementary Figure S10 provides Kaplan-Meier plots showing duration of treatment response in patients with different baseline circulating tumor DNA fractions

Supplementary Figure S25 shows concordant identification of intragenic copy number changes inside the androgen receptor (AR) gene based on a coverage-based approach and breakpoint-based approach

Supplementary Figure S24 shows that amplification of the enhancer region 640 kb upstream of the androgen receptor (AR) is common.

Supplementary Figure S12 shows the re-detection rate for somatic mutations identified in an earlier cfDNA sample

Supplementary Figure S14 shows temporal changes in whole exome somatic mutation profiles in patients that had evidence for somatic mutation profile change based on 72-gene targeted sequencing.

<p>Supplementary Figure S17 provides whole exome somatic mutation profiles in patients that did not show temporal changes in 72-gene panel mutation profiles</p>

Supplementary Figure S19 shows the complete switch of circulating tumor DNA profile in patient 026 between baseline and first progression timepoints

Supplementary Figure S20 shows genomic changes in selected prostate cancer driver genes after treatment with abiraterone/enzalutamide

Supplementary Figure S16 shows patients without evidence for somatic mutation profile change after treatment progression based on 72-gene targeted sequencing

Supplementary Figure S23 provides AR region copy number profiles for all 20 patients that showed a change in the structure of androgen receptor (AR) amplifications after treatment with abiraterone/enzalutamide

Supplementary Figure S15 shows temporal changes in whole exome copy number profile in patients that had evidence for copy number profile change in 72-gene targeted sequencing

Supplementary Figure S9 shows the correlation between serum prostate-specific antigen (PSA) levels and plasma circulating tumor DNA fraction.

Supplementary Figure S18 provides whole exome copy number profiles in patients that did not show temporal changes in their 72-gene copy number profile

Supplementary Figure S5 provides an overview of per patient ctDNA fraction and sequential treatment response (best prostate-specific antigen (PSA) decline and duration of response).