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

Date Published: December 10, 2018

Publisher: Hindawi

Author(s): Mikhail T. Silk, Nina Mikkilineni, Tarik C. Silk, Emily C. Zabor, Irina Ostrovnaya, Ari A. Hakimi, James J. Hsieh, Etay Ziv, Natasha Rekhtman, Stephen B. Solomon, Jeremy C. Durack.


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.

Our objective was to improve the understanding of DNA and RNA yields from commonly used core needle biopsy techniques prior to sample processing.

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.

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). 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.

Partial Text

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. In recent years, the brisk pace of discoveries revealing the genetic basis for malignant transformation has empowered oncologists, enabling therapies targeting specific molecular aberrations [1–3]. Needle biopsies can provide material for targeted genetic mutation analysis or to assess response to treatment, obviating the need for surgical biopsy.

We performed an Institutional Review Board-approved prospective study of surgically resected specimens at a comprehensive cancer center with a waiver of informed consent. Biopsies were performed in a tissue procurement service facility under direct visualization within 2 hours of surgical excision using 18-gauge (18G) and 20-gauge (20G) core biopsy needles (Temno Evolution, CareFusion, Waukegan, IL). Each surgical specimen was first dissected to allow direct visualization of the tumor and surrounding normal tissues. Biopsies were acquired from a variety of locations in normal parenchyma and tumor, avoiding areas of visible necrosis, and each 2 cm long core needle sampling tray was visually inspected. Core specimens that did not fill at least 85% of the sampling tray were discarded. Biopsies were performed in triplicate using 18G and 20G needles for both DNA and RNA processing. Biopsy sample sizes were estimated based on the number of samples required to achieve statistical significance from a preliminary kidney biopsy cohort. Each specimen was immediately placed in a 1.7 ml Eppendorf tube and snap frozen in liquid nitrogen. Samples were then stored in a −80°C freezer until molecular extractions were performed.

In the recent years, cancer genetic technologies such as next-generation sequencing (NGS) have evolved, offering insights beyond traditional histopathologic or radiographic diagnoses [13]. Increased emphasis on molecular characterization has highlighted the role of targeted tissue biopsies in oncology, now routinely obtained for personalized treatment planning and for correlative studies in clinical trials. Gene sequencing for mutation profiling can be particularly challenging for solid tumors as formalin fixatives can disrupt DNA integrity [14]. As nucleic acid yield is not enumerated at the time of biopsy, even when on-site cytopathology review is performed, it can be difficult to determine whether sufficient genetic material has been obtained [15].




0 0 vote
Article Rating
Notify of
Inline Feedbacks
View all comments