GEO series

A Multivariate Cell-Based Liquid Biopsy for Lung Nodule Risk Stratification: Analytical Validation and Early Clinical Evaluation

GSE275699 Homo sapiens (human) RNA-seq (gene expression) 249 samples Submitted 2025/08/07 Platform GPL20301

At a glance

RNA-seq (gene expression) · human · 249 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Topic: Lung cancerThis series is part of our curated briefing on it.
Samples: 249 samples: 218 distinct titles, 3 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: A multivariate cell-based liquid biopsy for lung nodule risk stratification: Analytical validation and early clinical evaluationThe journal of liquid biopsy · 2025

Summary (written by the submitters)

The iCAP is a tool for blood-based diagnostics that addresses the low signal-to-noise ratio of blood biomarkers by using cells as biosensors. The assay exposes patient serum to standardized cells in culture and classifies disease by AI analysis of gene expression readouts from the cells. This method simplifies the complexity of blood into a concise readout in a scalable cell-based assay.

Read the full summary ↓

We developed the LC-iCAP as a rule-out test for nodule management in CT-based lung cancer screening. The assay achieved an AUC of 0.63 (95% CI 0.50-0.75) in blind temporal validation with retrospective samples. When integrated with CT data after validation, it demonstrated 90% sensitivity, 67% specificity and 95% NPV using an estimated 25% prevalence, significantly outperforming the Mayo Clinic model and potentially reducing unnecessary follow-up procedures. Analytical validation demonstrated LC-iCAP reproducibility, identified unwanted variation from long-term sample storage and indicated enrichment of hypoxia signaling in the differential assay readout.

Published in

A multivariate cell-based liquid biopsy for lung nodule risk stratification: Analytical validation and early clinical evaluation

Berndt JD, Duffy FJ, D'Ascenzo MD et al. · The journal of liquid biopsy 2025 · PMID 40831733 · doi:10.1016/j.jlb.2025.100313

This dataset

Open GSE275699 in finder → Find more human RNA-seq datasets → Lung cancer landscape →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE275699_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1152596 and SRA study SRP528726. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40831733) ↗

Study design

218 distinct titles, 3 of them repeated

16HBE cells, 5% serum reference control, 24h, ×14 16HBE cells, 5% case serum pool 20200917, 24h, ×10 16HBE cells, 5% control serum pool 20200917, … ×10

Supports a case/control comparison: 215 samples read as cases, 24 as controls.

How we read this: Read from 249 sample titles: 218 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8482743 16HBE cells, 5% patient serum 524330, 24h, rep1
GSM8482744 16HBE cells, 5% patient serum 517604, 24h, rep1
GSM8482745 16HBE cells, 5% patient serum 521697, 24h, rep1
GSM8482746 16HBE cells, 5% patient serum 529706, 24h, rep1
GSM8482747 16HBE cells, 5% patient serum R000030, 24h, rep1
GSM8482748 16HBE cells, 5% case serum pool 20200917, 24h, rep1
GSM8482749 16HBE cells, 5% control serum pool 20200917, 24h, rep1
GSM8482750 16HBE cells, 5% patient serum 571209, 24h, rep1
GSM8482751 16HBE cells, 5% patient serum 524314, 24h, rep1
GSM8482752 16HBE cells, 5% patient serum 517267, 24h, rep1
GSM8482753 16HBE cells, 5% patient serum 581507, 24h, rep1
GSM8482754 16HBE cells, 5% patient serum 537495, 24h, rep1
GSM8482755 16HBE cells, 5% patient serum 508617, 24h, rep1
GSM8482756 16HBE cells, 5% patient serum 615973, 24h, rep1
GSM8482757 16HBE cells, 5% patient serum 555845, 24h, rep1
GSM8482758 16HBE cells, 5% patient serum 509905, 24h, rep1
GSM8482759 16HBE cells, 5% patient serum 565175, 24h, rep1
GSM8482760 16HBE cells, 5% case serum pool 20200917, 24h, rep2
GSM8482761 16HBE cells, 5% control serum pool 20200917, 24h, rep2
GSM8482762 16HBE cells, 5% patient serum 516417, 24h, rep1
GSM8482763 16HBE cells, 5% patient serum 511967, 24h, rep1
GSM8482764 16HBE cells, 5% patient serum 507726, 24h, rep1
GSM8482765 16HBE cells, 5% patient serum 525167, 24h, rep1
GSM8482766 16HBE cells, 5% patient serum R000001, 24h, rep1
GSM8482767 16HBE cells, 5% patient serum 579594, 24h, rep1
GSM8482768 16HBE cells, 5% patient serum 530132, 24h, rep1
GSM8482769 16HBE cells, 5% patient serum 565428, 24h, rep1
GSM8482770 16HBE cells, 5% patient serum 531233, 24h, rep1
GSM8482771 16HBE cells, 5% patient serum 521005, 24h, rep1
GSM8482772 16HBE cells, 5% case serum pool 20200917, 24h, rep3
GSM8482773 16HBE cells, 5% control serum pool 20200917, 24h, rep3
GSM8482774 16HBE cells, 5% patient serum 579012, 24h, rep1
GSM8482775 16HBE cells, 5% patient serum 510431, 24h, rep1
GSM8482776 16HBE cells, 5% patient serum 512853, 24h, rep1
GSM8482777 16HBE cells, 5% patient serum 509597, 24h, rep1
GSM8482778 16HBE cells, 5% patient serum 587413, 24h, rep1
GSM8482779 16HBE cells, 5% patient serum 530000, 24h, rep1
GSM8482780 16HBE cells, 5% patient serum 670584, 24h, rep1
GSM8482781 16HBE cells, 5% patient serum 521271, 24h, rep1
GSM8482782 16HBE cells, 5% patient serum 512343, 24h, rep1

+ 209 more — browse all 249 samples with per-sample file links →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.