Supplementary Table S5 from Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes
Year: 2023
Type: supplementary-materials
Abstract: Unsupervised model predictions and patient/validation cohort sequencing metrics Sheet 1: DFCI Cohort I: Tumor phenotype by histology and estimates of tumor fraction, subtyping score, and inferred subtype calls using ctdPheno. Sheet 2: DFCI cohort I: Tumor phenotype by histology and estimates of tumor fraction, subtyping score, and inferred phenotypic subtype calls using different ATAC-seq site restricted analysis using ctdPheno. Sheet 3: DFCI cohort I: Tumor phenotype by histology and estimates of tumor fraction, subtyping score, and inferred phenotypic subtype calls using different ATAC-seq site restricted analysis using Keraon. Sheet 4: DFCI Cohort II: Tumor phenotype by histology, summary of clinical correlatives and estimates of tumor fraction, subtyping score, and inferred subtype calls using ctdPheno. Sheet 5: Histology, tumor fraction, subtype score, NEPC fraction, and subtype calls for WGS and ULP patient samples (UW cohort). Sheet 6: Complete sequencing metrics for DFCI cohort I. Sheet 7: Complete sequencing metrics for DFCI cohort II (ULP). Sheet 8: Complete sequencing metrics for DFCI cohort II (deep WGS) Sheet 9: Complete sequencing metrics and ichorCNA estimated tumor fractions for the UW cohort (ULP). Sheet 10: Complete sequencing metrics for the UW cohort (deep WGS) Sheet 11: Complete sequencing metrics for the healthy donor cohort. Sheet 12: Clinical data summary for UW cohort.
Authors: Navonil De Sarkar, Robert D. Patton, Anna-Lisa Doebley, Brian Hanratty, Mohamed Adil, Adam J. Kreitzman, Jay F. Sarthy, Minjeong Ko, Sandipan Brahma, Michael P. Meers, Derek H. Janssens, Lisa S. Ang, Ilsa M. Coleman, Arnab Bose, Ruth F. Dumpit, Jared M. Lucas, Talina A. Nunez, Holly M. Nguyen, Heather M. McClure, Colin C. Pritchard, Michael T. Schweizer, Colm Morrissey, Atish D. Choudhury, Sylvan C. Baca, Jacob E. Berchuck, Matthew L. Freedman, Kami Ahmad, Michael C. Haffner, R. Bruce Montgomery, Eva Corey, Steven Henikoff, Peter S. Nelson, Gavin Ha
Language: English
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Open Access status: gold
OpenAlex ID: W4362552017