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This prospective study explores the prognostic value of circulating tumor DNA (ctDNA) and positron emission tomography/computed tomograpy (PET/CT) in unresectable locally advanced non-small cell lung cancer (LA-NSCLC) treated with definitive chemoradiotherapy (CRT). The discovery set includes 62 patients, with 62 baseline and 53 post-CRT plasma samples. PET/CT is performed at baseline, and 33 patients undergo mid-treatment scans after 40 Gy. Baseline ctDNA is detected in 71.0% of patients. Pre-treatment ctDNA concentration correlates with total metabolic tumor volume (TMTV) (p < 0.001) and total lesion glycolysis (TLG) (p = 0.001) but not treatment response or survival. However, patients with undetectable ctDNA and low TMTV show significantly longer progression-free survival (PFS) (34.2 vs 10.1 months, p = 0.027). Post-CRT, ctDNA is detected in 47.2% of patients, while ctDNA concentration (p = 0.005) and variant allele frequency (VAF) (p = 0.005) significantly decline. Undetectable post-CRT ctDNA associates with longer PFS (p < 0.001) and overall survival (OS) (p = 0.001). Higher ∆TMTV correlates with improved PFS and OS. Similar findings were obtained in a test of 19 patients. These results highlight post-CRT ctDNA and ∆TMTV as robust prognostic markers, potentially identifying patients who may forgo ICI consolidation.
Pubmed ID: 40089870
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A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)
View all literature mentionsJava toolset for working with next generation sequencing data in the BAM format.
View all literature mentionsCommercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.
View all literature mentionsSoftware Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
View all literature mentionsA software tool for copy number variation (CNV) detection for whole-exome data from paired tumour/matched normal samples.
View all literature mentionsAn efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)
View all literature mentionsConversion software that both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
View all literature mentionsProvides digital infrastructure, data analytics and decision support tools to help in diagnosis, treatment and monitoring of patients.
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