# Comprehensive Analysis of Best Practices for Clinical Testing of Malignant Pleural Effusion Specimens

> **NIH NIH U01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2023 · $369,431

## Abstract

PROJECT SUMMARY/ABSTRACT
Patients with advanced cancers often develop malignant pleural effusions (MPEs), a collection of fluid that
develops between the surface of the lung and the chest wall that contains malignant tumor cells and benign
inflammatory cells. In many cases, percutaneous or transbronchial tissue biopsies may be pauci-cellular or
difficult to obtain, thus MPEs may be the only specimen available for pathologic evaluation and molecular testing.
Thoracentesis removes this fluid, alleviating symptoms and also providing diagnostic material that can be used
for downstream molecular analysis. In current clinical practice, the thoracentesis fluid is typically centrifuged and
the cell-rich pellet is used to generate a formalin fixed paraffin embedded (FFPE) cell pellet that is subsequently
used to make a hematoxylin & eosin (H&E) stained slide for diagnosis along with additional unstained slides for
ancillary studies. Recent studies have highlighted the fact that pleural fluid samples often contain abundant cell-
free DNA (cfDNA) within the supernatant fraction and this may represent an alternative source of DNA for
molecular testing. Similar to cfDNA isolated from plasma, cfDNA isolated from MPEs could in theory circumvent
the problem of intra-tumoral heterogeneity and tissue accessibility while at the same time obviate the time
needed to create a cell block and reduce/eliminate the labor-intensive steps of scraping and extracting DNA from
unstained slides. Despite its promise, there are no established guidelines for the collection, storage, processing,
and molecular testing of cfDNA isolated from MPEs. Our proposal systematically tests several preanalytical
variables as well as directly compares three different cfDNA isolation techniques to identify the best practices for
processing cfDNA from MPEs. We predict that optimization and harmonization of the these preanalytical steps
will lead to reduced false negative results, increased reproducibility, improved efficiency, and reduced turn-
around-time in the testing of MPEs. We will leverage our collective expertise in cytopathology, molecular
pathology, and test validation to develop standard operating procedures that can be easily adapted into existing
clinical workflows. Finally, we will validate these pre-analytical protocols using a CLIA/CAP certified multi-gene
sequencing assay.

## Key facts

- **NIH application ID:** 10703794
- **Project number:** 1U01CA275514-01A1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Walter Patrick Devine
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $369,431
- **Award type:** 1
- **Project period:** 2023-09-05 → 2028-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10703794

## Citation

> US National Institutes of Health, RePORTER application 10703794, Comprehensive Analysis of Best Practices for Clinical Testing of Malignant Pleural Effusion Specimens (1U01CA275514-01A1). Retrieved via AI Analytics 2026-05-27 from https://api.ai-analytics.org/grant/nih/10703794. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*