Desktop transcriptome sequencing from archival tissue to identify clinically relevant translocations

Area of Science:

• Oncology
• Genomics
• Molecular Diagnostics

Background:

• Somatic mutations are crucial for cancer diagnosis and treatment prediction.
• Current clinical assays are limited, assessing one mutation at a time.
• High-throughput sequencing (HTS) offers a comprehensive approach to mutation detection.

Purpose of the Study:

• To demonstrate the feasibility of diagnosing sarcoma translocations using desktop HTS on FFPE tissues.
• To evaluate the potential of a single transcriptome HTS assay for comprehensive cancer mutation analysis.

Main Methods:

• Full transcriptome sequencing was performed on FFPE tissues from various sarcoma types using the MiSeq platform.
• Reads were mapped to the 'sarcomatome' (83 known sarcoma genes).
• A novel algorithm was used to rank fusion candidates and identify exact breakpoints.

Main Results:

• Pathognomonic fusions and breakpoints were identified in synovial sarcoma, myxoid liposarcoma, and clear cell sarcoma from FFPE samples.
• Ewing sarcoma fusion genes required greater sequencing depth for detection in FFPE material.
• Desktop HTS successfully diagnosed translocations in FFPE sarcoma tissues.

Conclusions:

• A single transcriptome HTS assay using FFPE tissue can effectively diagnose sarcoma translocations.
• This approach has the potential to replace conventional molecular diagnostic methods.
• FFPE samples are viable for comprehensive mutation analysis via desktop HTS.