Identification of novel mutations in FFPE lung adenocarcinomas using DEPArray sorting technology and next-generation...

Area of Science:

• Oncology
• Genomics
• Molecular Pathology

Background:

• Formalin-fixed paraffin-embedded (FFPE) tissues are standard in pathology but face challenges with tissue admixture and limited normal samples for somatic mutation detection.
• Accurate cancer diagnosis relies on precise identification of somatic mutations, which can be hindered by non-tumor cell contamination in FFPE samples.

Purpose of the Study:

• To evaluate the efficacy of Di-Electro-Phoretic Array (DEPArray) technology for isolating pure tumor cells from FFPE lung adenocarcinoma tissues.
• To improve the accuracy of somatic mutation detection and identify novel mutations using next-generation sequencing (NGS) on DEPArray-sorted cells.

Main Methods:

• Isolation of pure tumor cells from 22 FFPE lung adenocarcinoma samples using DEPArray technology.
• Analysis of somatic mutations via next-generation sequencing (NGS) on both sorted and unsorted cells.
• Comparison of mutation detection rates and allele frequencies between sorted and unsorted samples.

Main Results:

• DEPArray sorting improved allele frequencies of gene mutations by 1.2 times overall (1.3-10.1 times for tumor suppressor genes, 1.3-2.6 times for oncogenes).
• 16 novel somatic mutations were identified in sorted cells, compared to only 4 in unsorted cells.
• Key genes including TP53, EGFR, PTEN, RB1, KRAS, and CTNNB1 were found to be somatically mutated in multiple lung adenocarcinomas.

Conclusions:

• DEPArray technology enables precise isolation of pure tumor cells from FFPE lung adenocarcinomas, significantly enhancing somatic mutation detection.
• This approach establishes a more accurate genomic landscape for lung adenocarcinoma, aiding in diagnosis and potentially guiding treatment decisions.
• The findings offer new insights for the diagnosis and treatment of lung adenocarcinomas, including squamous cell lung cancers.