Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

Correlation between pCN and tumor fraction in plasma where z=((2*(1-x))+(y*x)), and x is set from 0 to 100% as tumor fraction. Centiles of ERBB2 pCN in the Guardant Health database were as follows: copy number 2.4 but 4.0 ({greater than or equal to}90th percentile).</p

Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

Copy number plots from two pre-treatment HERACLES A samples. X axis represents chromosome (chr) number across the Guardant360 genomic footprint. Y axis represents observed copy number in plasma. Colored dots represent probe-specific copy number signals at each chromosomal position and light green horizontal line represents the sample-specific normalized diploid copy number. The 18 reported gene amplifications are labelled, including ERBB2 on chromosome 17. The sample represented in panel 2A is suggestive of chromosome 17 aneuploidy, as all 5' probe specific signals adjacent to and including ERBB2 are increased (ERBB2 observed pCN = 52.8). In contrast, panel 2B shows clear focal amplification of ERBB2 only (ERBB2 observed pCN = 7.7).</p

Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

Copy number plots from two pre-treatment HERACLES A samples. X axis represents chromosome (chr) number across the Guardant360 genomic footprint. Y axis represents observed copy number in plasma. Colored dots represent probe-specific copy number signals at each chromosomal position and light green horizontal line represents the sample-specific normalized diploid copy number. The 18 reported gene amplifications are labelled, including ERBB2 on chromosome 17. The sample represented in panel 2A is suggestive of chromosome 17 aneuploidy, as all 5' probe specific signals adjacent to and including ERBB2 are increased (ERBB2 observed pCN = 52.8). In contrast, panel 2B shows clear focal amplification of ERBB2 only (ERBB2 observed pCN = 7.7).</p

Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

Digital Sequencing-based ctDNA assay workflow. (a) cfDNA is extracted from stabilized peripheral whole blood, (b) labeled with oligonucleotide barcodes at high efficiency, and (c) up to 30ng is used for library preparation. (d) Sequencing libraries are enriched using hybrid capture and sequenced to an average depth of ~15,000x. (e) Individual unique input molecules are then bioinformatically reconstructed using barcode and sequence data to suppress analytical error modes. (f) Somatic variants are deconvoluted from germline and reported by clinical priority with both treatment and clinical trial annotations.</p

Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

The ctDNA panel (Guardant360{trade mark, serif}) utilized here employs digital sequencing to detect mutations in 73 genes. Whole gene sequencing is performed in 19 cancer genes, critical exons coverage in 54 genes and amplifications (18 genes), fusions (6 genes) and indels (23 genes).</p

Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

Supp. Table 1 Summary of tissue and ctDNA results and response data</p

Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

Figure legends for the supp figures</p

Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

ERBB2 pCN (pCN), RAS/RAF status and maximum mutant allele fraction (Max MAF) in 4,294 plasma samples from mCRC patients in the Guardant Health historical database. An observed pCN cutoff of 2.4 (>50th %ile) allowed for exclusion of 84% of all KRAS, NRAS, and BRAF driver mutations in the historical cohort. Dark blue dots - ERBB2 amplified and clonal RAS/RAF mutation positive; Light blue dots ERBB2 amplified and sub-clonal RAS/RAF mutation positive; Red dots - ERBB2 amplified and RAS/RAF mutation not detected.</p

Supplementary Data from Plasma HER2 (<i>ERBB2</i>) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer

Supp. Table 2 ROC analysis to determine adjusted plasma copy number cutoff</p

Figure S10 from Genome-wide Copy-number Alterations in Circulating Tumor DNA as a Novel Biomarker for Patients with High-grade Serous Ovarian Cancer

The levels of ctDNA of 15 HGS-EOC patients are shown in relation to the patient's clinical history. The TF% in cfDNA is reported for each plasma sample (purple line) withdrawn against the CA-125 levels (green line). Red bars refer to the tumor volume calculated from TC analysis as described in Supplementary methods (). * indicates patients for whom TC scan is not available at time of diagnosis and/or at recurrence. Figures S11 and S12 specifically show cases where the TF% in cfDNA does not anticipate tumor progression.</p