Unknown

Dataset Information

0

Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC.


ABSTRACT: Liquid biopsy has recently emerged as an important tool in clinical practice particularly for lung cancer patients. We retrospectively evaluated cell-free DNA analyses performed at our Institution by next generation sequencing methodology detecting the major classes of genetic alterations. Starting from the graphical representation of chromosomal alterations provided by the analysis software, we developed a support vector machine classifier to automatically classify chromosomal profiles as stable (SCP) or unstable (UCP). High concordance was found between our binary classification and tumor fraction evaluation performed using shallow whole genome sequencing. Among clinical features, UCP patients were more likely to have ≥ 3 metastatic sites and liver metastases. Longitudinal assessment of chromosomal profiles in 33 patients with lung cancer receiving immune checkpoint inhibitors (ICIs) showed that only patients that experienced early death or hyperprogressive disease retained or acquired an UCP within 3 weeks from the beginning of ICIs. UCP was not observed following ICIs among patients that experienced progressive disease or clinical benefit. In conclusion, our binary classification, applied to whole copy number alteration profiles, could be useful for clinical risk stratification during systemic treatment for non-small cell lung cancer patients.

SUBMITTER: Tosello V 

PROVIDER: S-EPMC11316016 | biostudies-literature | 2024 Aug

REPOSITORIES: biostudies-literature

altmetric image

Publications

Binary classification of copy number alteration profiles in liquid biopsy with potential clinical impact in advanced NSCLC.

Tosello Valeria V   Grassi Angela A   Rose Dominic D   Bao Loc Carlo LC   Zulato Elisabetta E   Dalle Fratte Chiara C   Polano Maurizio M   Del Bianco Paola P   Pasello Giulia G   Guarneri Valentina V   Indraccolo Stefano S   Bonanno Laura L  

Scientific reports 20240809 1


Liquid biopsy has recently emerged as an important tool in clinical practice particularly for lung cancer patients. We retrospectively evaluated cell-free DNA analyses performed at our Institution by next generation sequencing methodology detecting the major classes of genetic alterations. Starting from the graphical representation of chromosomal alterations provided by the analysis software, we developed a support vector machine classifier to automatically classify chromosomal profiles as stabl  ...[more]

Similar Datasets

| S-EPMC10833088 | biostudies-literature
| S-EPMC8361064 | biostudies-literature
| S-EPMC8268955 | biostudies-literature
| S-EPMC10925597 | biostudies-literature
2011-09-12 | GSE31798 | GEO
| S-EPMC7710584 | biostudies-literature
2011-09-11 | E-GEOD-31798 | biostudies-arrayexpress
| S-EPMC4121784 | biostudies-literature
| S-EPMC3966983 | biostudies-literature
| S-EPMC9179452 | biostudies-literature