B-250 Core Needle Biopsy FFPET Samples: Enhanced Application of the AVENIO Tumor Tissue CGP Automated Assay

Background Small tissue biopsies, particularly core needle biopsy samples, are the preferred method for oncology as they offer a less invasive way of obtaining tissue samples than traditional surgical resections. However, sequencing-based comprehensive genomic profiling (CGP) of these small tissues preserved as formalin-fixed, paraffin-embedded tissue (FFPET) samples remains technically challenging due to the limited tissue volume and often suboptimal quality of DNA extracted from these samples. The AVENIO Tumor Tissue CGP Automated Assay (for Research Use Only, not for use in diagnostic procedures) offers an automated, end-to-end solution for CGP of FFPET specimens. The assay’s tissue extraction method is designed to achieve high DNA yield and quality, which is crucial for analyzing samples with limited tissue volumes. This study assessed the performance of the AVENIO Tumor Tissue CGP Automated assay on these challenging core needle biopsy FFPE tumor tissue specimens. Methods A set of 70 unique FFPET samples originating from breast, lung, and prostate core needle biopsy procedures was processed in duplicates through the AVENIO Tumor Tissue CGP Automated Assay. FFPET blocks were collected from 3 collection sites to represent the various qualities of the samples. Four 10-micron-thick tissue curls were used as input for the assay to increase the input volume. Sequencing QC metrics were compared to evaluate the sample pass rates per collection site. The variants reported were compared within the replicates to assess the reproducibility of the assay. Results FFPET samples from core needle biopsy procedures typically have a smaller tissue volume than those from surgical resection. In this study, tissue volumes for the assay ranged from 0.06mm³ to 1.8mm³, with the smallest volume that met the 40ng DNA input requirement being 0.09mm³. A positive correlation was observed between the tissue volume and DNA yield. Samples from different collection sites showed distinct DNA quality resulting in different sample pass rates, likely due to variations in formalin fixation and specimen processing procedures. In core needle biopsies collected from Site A (breast and lung) and Site B (prostate), 97% (33/34) and 95% (38/40) of samples met the 40ng DNA input requirement, respectively; 100% (34/34) from Site A and 95% (38/40) from Site B passed overall sequencing QC. In contrast, collection Site C showed a substantially lower ratio of samples passed the DNA input at 38% (25/66) and a poor sample pass rate of 24.2% (16/66). Variants reported from the core needle biopsy samples that passed the sequencing QC presented high reproducibility with >90% overall positive call rate within replicates. Conclusion This study demonstrates that the AVENIO Tumor Tissue CGP Automated Assay can effectively process core needle biopsy FFPET specimens, achieving a high sample pass rate and consistent variant detections.