Cancer treatment response monitoring of CAIRO5 patients with metastatic CRC using cell-free DNA (cfDNA) sequencing

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Dataset ID	Description	Technology	Samples
EGAD00001009718	This dataset consists of 39 noncancerous donor and 62 cancer patient plasma samples (including 29 patients with CRC across a total of 13 tumor types) that were analyzed with the PGDx elio plasma resolve assay. The PGDx elio plasma resolve assay is a hybrid capture approach targeting 33 genes with sequencing performed using the Illumina NextSeq with 150bp paired-end reads. The bam files provided have been adapter masked and contain duplicate reads.	NextSeq 500	101
EGAD00001009719	The dataset "PGDx elio™ plasma resolve assay: targeted sequencing analyses of plasma cfDNA" includes paired end FASTQ reads of 183 cfDNA samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 33 genes, covering over 237,000 bp, targeting 25,000x depth across the targeted regions.	NextSeq 500	183
EGAD00001009720	The dataset "PGDx elio™ tissue complete assay: targeted sequencing analyses of tissue DNA" includes paired end FASTQ reads of 28 tissue samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 505 genes, targeting 2,500x depth across the targeted regions.	NextSeq 500	28
EGAD00001009721	The dataset "PGDx elio™ plasma resolve assay: targeted sequencing analyses of WBC DNA" includes paired end FASTQ reads of 49 white blood cell (WBC) genomic DNA samples from metastatic colorectal cancer patients. Sequencing was performed using a panel consisting of 33 genes, covering over 237,000 bp, targeting 25,000x depth across the targeted regions.	NextSeq 500	49
EGAD50000000630	The dataset "DELFI low-coverage WGS of plasma cfDNA" includes paired FASTQ files produced by WGS of 689 plasma cfDNA samples from 153 patients with colorectal cancer. WGS (100bp PE) was performed on a NovaSeq 6000 with a target depth of coverage of 8x.	Illumina NovaSeq 6000	689

Publications	Citations
Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells. van 't Erve I, Medina JE, Leal A, Papp E, Phallen J, Adleff V, Chiao EJ, Arun AS, Bolhuis K, Simmons JK, Karandikar A, Valkenburg KC, Sausen M, Angiuoli SV, Scharpf RB, Punt CJA, Meijer GA, Velculescu VE, Fijneman RJA. Clin Cancer Res 29: 2023 899-909	8
Cancer treatment monitoring using cell-free DNA fragmentomes. van 't Erve I, Alipanahi B, Lumbard K, Skidmore ZL, Rinaldi L, Millberg LK, Carey J, Chesnick B, Cristiano S, Portwood C, Wu T, Peters E, Bolhuis K, Punt CJA, Tom J, Bach PB, Dracopoli NC, Meijer GA, Scharpf RB, Velculescu VE, Fijneman RJA, Leal A. Nat Commun 15: 2024 8801	0