Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics

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.

Figure 1

DNA content by tissue type and needle gauge in (a) lung tumors, (b) liver tumors, and (c) kidney tumors (N18 = normal tissue/18 gauge, T18 = tumor tissue/18 gauge, N20 = normal tissue/20 gauge, and T20 = tumor tissues/20 gauge). The dark bar represents median DNA quantity, the surrounding box encompasses the 25–75% interquartile range (IQR), and the brackets reflect 1.5^∗IQR. Diamonds represent statistical outliers.

Figure 2

Logarithmic scale of RNA content by tissue type and needle gauge in (a) lung tumors, (b) liver tumors, and (c) kidney tumors (N18 = normal tissue/18 gauge, T18 = tumor tissue/18 gauge, N20 = normal tissue/20 gauge, T20 = tumor tissues/20 gauge). The dark bar is the median, the box encompasses the 25–75 interquartile range (IQR), the dotted brackets are 1.5^∗IQR, and dots are outliers.