Prospective evaluation of unprocessed core needle biopsy DNA and RNA yield from lung, liver, and kidney tumors: Implications for cancer genomics Journal Article


Authors: Silk, M. T.; Mikkilineni, N.; Silk, T. C.; Zabor, E. C.; Ostrovnaya, I.; Hakimi, A. A.; Hsieh, J. J.; Ziv, E.; Rekhtman, N.; Solomon, S. B.; Durack, J. C.
Article Title: 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.
Journal Title: Analytical Cellular Pathology
Volume: 2018
ISSN: 2210-7177
Publisher: Hindawi Publishing Corporation  
Date Published: 2018-01-01
Start Page: 2898962
Language: English
DOI: 10.1155/2018/2898962
PUBMED: 30652067
PROVIDER: scopus
PMCID: PMC6311765
DOI/URL:
Notes: Export Date: 1 February 2019 -- Source: Scopus
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MSK Authors
  1. Natasha Rekhtman
    210 Rekhtman
  2. Emily Craig Zabor
    121 Zabor
  3. Stephen Solomon
    266 Solomon
  4. Jeremy Charles Durack
    84 Durack
  5. Abraham Ari Hakimi
    129 Hakimi
  6. Mikhail Thomas Silk
    11 Silk
  7. Tarik Christopher Silk
    7 Silk
  8. Etay   Ziv
    26 Ziv