Supplemental Figure 1, Supplemental Figure 2, Supplemental Figure 3 from Bias-Corrected Targeted Next-Generation Sequencing for Rapid, Multiplexed Detection of Actionable Alterations in Cell-Free DNA from Advanced Lung Cancer Patients
Year: 2023
Type: supplementary-materials
Abstract: Supplemental Figure 1: Comparison of targeted sequencing of cfDNA using standard hybridization selection versus Resolution methods. (A) UCSC genome browser depiction of read coverage in the TP53 vicinity. The coverage track representing hybridization selection of cfDNA was created by mapping the reads from sample SRR1197557 of Newman et al 2014. The other coverage track represents unique reads from Sample 511 in this paper. The off-target noise outside of the TP53 gene is higher in SRR1197557 compared with Sample 511. (B) Genome-wide calculation of off-target versus on-target coverage for the two samples. The percentage of read coverage overlapping the declared target regions (widened by an extra 100 nucleotides on each side) was calculated using bedtools. Supplemental Figure 2: Sensitivity of mutant allele detection as a function of dilution. A total of four gene fusions (orange open squares), thirteen point mutations (black circles) and one indels (orange open squares), were assayed at varying mutant allele concentrations (Supplemental Table 1). All 18 lesions were detected in the 2.5%, 1.0%, and 0.4% pools, while fourteen out of the 18 were detected at 0.1%. We expect gene fusions to be more difficult to detect because adequate sequence coverage demands a larger assay footprint than point mutations and probe orientation is unidirectional rather than bidirectional. Consistent with this expectation, the ROS1 fusion in cell line HCC78 and the ALK fusion in cell line H3122 were underrepresented. Supplemental Figure 3: Schematic of predicted genomic junctions for 5 translocations identified in plasma specimens.
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4361884859