The QSEA R package37(v.1.16) was used to analyze BAM files, with the use of a custom R package to extend QSEA (https://github.com/cruk-mi/mesa). The entire genome was tiled into 300-bp non-overlapping windows, with the removal of windows lying within the encode exclusion list regio...
Multi-modal cfDNA feature sets We adopted a multi-modal set of genome-wide and targeted features from [9] to combine with our deconvolution scores derived from the TSMA. This set included genome-wide methylation density (GWMD), targeted region methylation density (TMD), genome-wide fragmentation...
. Data are presented as median values with maximums and minimums. ESCC esophageal squamous cell carcinoma, IEN intraepithelial neoplasia, LGIEN low-grade IEN, HGIEN high-grade IEN, HC healthy control, WGS whole-genome sequencing, WGBS whole-genome bisulfite sequencing, MAPQ mapping quality, MDS ...
Whole genome or probe hybridization-based NGS methods can capture cfDNA fragments of native sizes. However, amplicon-based NGS assays are not directly amenable to cfDNA size analysis due to predetermination of amplicon sizes by design. Here we present a method to extract relative distribution of ...
human genome (GRCh37) using bitmapperBS (version 1.0.2.1)44. The aligned BAM files were sorted and indexed using SAMtools (version 1.11)45. PCR and optical duplicates were marked and removed using GATK tools (version 4.2.3.0) MarkDuplicates46, generating a final BAM file for feature ...
Abstract In the current era of precision medicine, the identification of genomic alterations has revolutionised the management of patients with solid tumours. Recent advances in the detection and characterisation of circulating tumour DNA (ctDNA) have enabled the integration of liquid biopsy into clinical...
library preparation. The first workflow is for targeted enrichment of frequently mutated regions from DNA (Fig.1E); the second is for known and unknown fusion detection from RNA input (Supplementary Fig.1), the third is whole sample (a.k.a. whole genome) library preparation (Supplementary ...
2.3. Whole-Genome Bisulfite Sequencing To evaluate the performance ofsingle- anddouble-strandedlibrarypreparation (ssLP and dsLP) for methylation analysis of cfDNA from urine and plasma, we used plasma cfDNA samples of two healthy volunteers and three liver transplant and four kidney transplant recipie...