Pitfalls of improperly procured adjacent non-neoplastic tissue for somatic mutation analysis using next-generation...

Area of Science:

• Oncology
• Genomics
• Pathology

Background:

• Next-generation sequencing (NGS) is crucial for detecting somatic alterations in neoplasms.
• Matched non-neoplastic tissue is required for filtering germline polymorphisms.
• Low-level somatic mutations in adjacent non-neoplastic tissues complicate variant filtering.

Purpose of the Study:

• To investigate if neoplastic cell contamination causes low-level somatic mutations in non-neoplastic tissues.
• To develop and test a systematic protocol for collecting non-neoplastic tissue samples to minimize contamination.

Main Methods:

• Applied a systematic protocol to collect multiple non-neoplastic tissues from two breast cancer lumpectomy specimens.
• Used whole-exome sequencing to identify somatic mutations and assess their presence in adjacent tissues.
• Employed ultra-deep targeted sequencing to quantify contamination levels under different collection conditions.

Main Results:

• Contamination levels in non-neoplastic tissues varied significantly (up to 20.9%), correlating with grossing and procurement methods.
• A carefully controlled collection protocol successfully eliminated detectable contamination in both cases.
• Demonstrated that tissue procurement processes contribute to neoplastic cell contamination.

Conclusions:

• Tissue procurement methods significantly impact neoplastic cell contamination in adjacent non-neoplastic tissues.
• A standardized protocol for acquiring non-neoplastic tissue can minimize contamination to undetectable levels.
• Implementing such protocols is essential for accurate somatic mutation detection in NGS studies.