Optimizing DNA Extraction from Archival Prostate Biopsy Samples.

PURPOSE: In this paper, we compare the performance of three distinct nucleic acid extraction protocols in a large population-based prostate cancer cohort, aiming to optimize DNA yield from limited tumor samples in prostate needle biopsies. MATERIAL AND METHODS: We utilized two commercially available extraction kits and identified the minimum digitally measured tumor area yielding sufficient DNA for sequencing panels (defined as >50 ng of total DNA). Representative FFPE prostate cancer biopsies were processed from 643 patients recruited through population-based U.S. cancer registries as part of the multi-institutional RESPOND study. Scanned whole slide images were used to annotate and measure the tumor region prior to manual macrodissection and DNA isolation using the extraction kits. RESULTS: The QIAamp® FFPE Advanced® kit resulted in the highest median DNA yield compared to combined RNA/DNA or DNA extraction using the AllPrep® kit (4.3 vs 2.1 or 2.1 ng per mm2 total tumor, p=0.0004 and p<0.0001, respectively). DNA yield significantly correlated with total tumor area for both kits. Using a tumor area cutoff of 2 mm2 for the Advanced® kit, or 5 mm2 for the AllPrep® DNA/RNA kit, with macrodissection across ten 4 μm tissue sections, 86% to 94% of samples generated more than 50 ng of total DNA. Both kits resulted in comparable panel-based sequencing quality metrics, including percentage duplicated reads and median insert length. For DNA quantity and median target coverage at sequencing, the Advanced® kit outperformed the AllPrep® kit, but it does not allow simultaneous RNA extraction. CONCLUSIONS: For a DNA yield of at least 50 ng, we suggest a cutoff of 2 mm2 of tumor area with ten 4 μm macrodissected tissue sections for a prostate cancer needle core biopsy to be considered sufficient for DNA extraction.