Abstract
Context Targeted needle biopsies are increasingly performed for the genetic characterization of cancer. While the nucleic acid content of core needle biopsies after standard pathology processing (i.e., formalin fixation and paraffin embedding (FFPE)) has been previously reported, little is known about the potential yield for molecular analysis at the time of biopsy sample acquisition. Objectives Our objective was to improve the understanding of DNA and RNA yields from commonly used core needle biopsy techniques prior to sample processing. Methods We performed 552 ex vivo 18 and 20G core biopsies in the lungs, liver, and kidneys. DNA and RNA were extracted from fresh-frozen core samples and quantified for statistical comparisons based on needle gauge, biopsy site, and tissue type. Results Median tumor DNA yields from all 18G and 20G samples were 5880 ng and 2710 ng, respectively. Median tumor RNA yields from all 18G and 20G samples were 1100 ng and 230 ng, respectively. A wide range of DNA and RNA quantities (1060–13,390 ng and 370–6280 ng, respectively) were acquired. Median DNA and RNA yields from 18G needles were significantly greater than those from 20G needles across all organs (p < 0.001). Conclusions Core needle biopsy techniques for cancer diagnostics yield a broad range of DNA and RNA for molecular pathology, though quantities are greater than what has been reported for FFPE processed material. Since non-formalin-fixed DNA is advantageous for molecular studies, workflows that optimize core needle biopsy yield for molecular characterization should be explored.
Highlights
Image-guided solid tumor needle biopsies are frequently the starting point for modern cancer care
Increased emphasis on molecular characterization has highlighted the role of targeted tissue biopsies in oncology, routinely obtained for personalized treatment planning and for correlative studies in clinical trials
Gene sequencing for mutation profiling can be challenging for solid tumors as formalin fixatives can disrupt Deoxyribonucleic acid (DNA) integrity [14]
Summary
Image-guided solid tumor needle biopsies are frequently the starting point for modern cancer care. The ability to genomically characterize tumors has amplified the importance of tissue biopsies for cancer treatment selection, determining eligibility for clinical trials and understanding disease progression. A high-quality, high-value biopsy is defined by sufficient cancer cellularity for diagnosis and genomic analysis [4]. Diagnostic rates for contemporary targeted biopsies are high, but procedural practice guidelines have been slow to consider additional sampling requirements associated with molecular characterization [5]. The quantity of genetic material that can be obtained from small tumors is not defined due to many factors influencing biopsy yield, including normal tissue versus solid tumor cellularity and variable density of tumor nuclei per volume of tissue. Single-site biopsies may not sufficiently portray intratumoral genetic heterogeneity [7]
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