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Front-end genomics: using an alternative approach for the recovery of high-quality DNA from core needle biopsies
  1. Wilfrido D Mojica1,
  2. Tieying Hou1,
  3. Don Sykes2,
  4. Rama Dey-Rao3
  1. 1Department of Pathology and Anatomical Sciences, University at Buffalo, Buffalo, New York, USA
  2. 2Department of Medicine, University at Buffalo, Buffalo, New York, USA
  3. 3Department of Dermatology, University at Buffalo, Buffalo, New York, USA
  1. Correspondence to Dr Wilfrido D Mojica, Department of Pathology and Anatomical Sciences, University at Buffalo, 100 High Street, Buffalo, NY 14203, USA; mojica{at}buffalo.edu

Abstract

Aims Determine whether a simple prewash step will provide adequate amounts of high-quality DNA from core needle biopsies for molecular sequencing studies.

Methods The quantitative and qualitative metrics of DNA recovered from core needle biopsies processed either by 1) formalin fixation and paraffin embedding (FFPE), 2) cells recovered after the core needle biopsy was washed, and 3) frozen sections of the core needle biopsy tissue were evaluated and compared to one another.

Results Fairly equivalent amounts of DNA can be obtained from cells recovered from a prewash step relative to the FFPE and frozen section samples. The number of amplifiable DNA in the wash sample was greater than that from the FFPE samples. The average molecular size of DNA in the wash sample was greater than that of both the FFPE and frozen samples.

Conclusions Although more starting material in terms of the number of cells was present in both the FFPE and frozen section samples than the wash samples, equivalent to better results were obtained from the latter with regard to quality. This approach may be a means to better aliquot the diminutive amounts of tissue associated with core needle biopsies, allowing dissociated cells to be dedicated for molecular studies while keeping the tissue intact for morphological studies.

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Footnotes

  • Handling editor Cheok Soon Lee

  • Contributors WDM designed, performed and analysed the data of the experiment as well as wrote the manuscript. TH helped with data analysis and the writing of the manuscript. DS helped with experiments. RDR helped with the experiment and analysis of the data.

  • Competing interests None declared.

  • Provenance and peer review Not commissioned; externally peer reviewed.

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