Robust detection of translocations in lymphoma FFPE samples using targeted locus capture-based sequencing

Area of Science:

• Oncology
• Genomics
• Pathology

Background:

• Formalin-fixed, paraffin-embedding (FFPE) is standard for preserving tissue morphology but causes DNA fragmentation.
• DNA fragmentation in FFPE samples compromises the accurate detection of chromosomal rearrangements crucial for cancer diagnosis and treatment.
• Chromosomal rearrangements are key drivers in many hematolymphoid malignancies and solid tumors.

Purpose of the Study:

• To develop and validate a novel method for detecting chromosomal rearrangements in FFPE tissue specimens.
• To introduce FFPE-targeted locus capture (FFPE-TLC) and the PLIER computational framework for analyzing FFPE DNA.
• To improve the sensitivity and specificity of rearrangement detection compared to existing methods.

Main Methods:

• FFPE-targeted locus capture (FFPE-TLC) was developed for targeted sequencing of proximity-ligation products in FFPE tissues.
• The PLIER computational framework was created for automated identification and characterization of rearrangements at selected loci.
• FFPE-TLC was blindly applied to 149 lymphoma and control FFPE samples.

Main Results:

• FFPE-TLC successfully identified known and novel rearrangement partners in FFPE samples.
• The method demonstrated superior sensitivity and specificity compared to fluorescence in situ hybridization (FISH).
• FFPE-TLC outperformed standard capture-Next-Generation Sequencing (NGS) methods, detecting rearrangements in repetitive sequences.

Conclusions:

• FFPE-TLC is a powerful new tool for accurate, targeted rearrangement detection in FFPE specimens.
• This method overcomes limitations of DNA fragmentation in FFPE samples for genomic analysis.
• FFPE-TLC offers significant advantages for clinical diagnostics in oncology.