RESUMO
INTRODUCTION: Mutational analysis is becoming the standard of diagnostic workup. Sufficient amounts of and quality tumor tissue can be challenging when faced with a small biopsy or biopsy by fine-needle aspiration (FNA). MATERIALS AND METHODS: We reviewed the failures of FNA and surgical biopsy to yield sequencing data and causes thereof over a 3-year period. We executed a search of the laboratory information system for requests to perform our targeted 50-gene assay by massively parallel sequencing on surgical biopsies and FNAs and compared the results. RESULTS: Three failure causes were assigned: insufficient tissue as defined by the pathologist, failure to meet quality control indicating library preparation or sequencing failure, and failure of pre-qualifying step for DNA integrity. A total of 327 of 354 cases were successfully sequenced (92%), including 151 FNA cases and 203 biopsies, with 16 (10.6%) and 11 (5.4%) failures, respectively. The Fisher's exact test two-tailed P-value equals 0.050381, making the difference between FNA and biopsy not statistically significant. Insufficient tissue, quality control failure, and DNA integrity were identified as the cause of the failure in 10 (62%), 3 (19%), and 3 (19%) FNA biopsies, and in 5 (45.5%), 1 (9%), and 5 (45.5%) surgical biopsies. The most common cause of failure of FNA was insufficient tissue. For surgical biopsies, DNA integrity and insufficient tissue were equally as likely to be implicated. Both FNA and surgical biopsy have a low failure rate overall without statistical significance between them. CONCLUSIONS: Although surgical biopsy is considered the gold standard, these findings support FNA as an equal modality.
