I am working on breast tissue and comparing mutations in tumour tissue with adjacent normal breast tissue for somatic mutations in the tumour. While our yields from tumour tissue are satisfactory, for the normal tissue with high content of adipose tissue I am facing difficulties in getting both adequate quantity and quality of DNA. Any one with suggestions / experience in improving DNA content from FFPE Adipose rich tissue.

We are using the Qiagen's QiaAMP DNA FFPE Tissue Kit for extraction. We have an additional elution and wash step at the end of the protocol which has greatly improved our yields for tumour tissue. We use nanodrop for DNA quantitation and are getting 30 to 80 ng of DNA with good ratios, curve and band on electrophoresis. But with the normal tissue we rarely get more than 3-5 ng/uL DNA and the curve is flat with very low ratios, the 260/230 hovering around 0.5 - 1.0. Additional elution and wash seem to worsen the issue. I am using ARMS PCR array and need atleast 15- 20 ng of good quality DNA per sample.

WE have ruled out Formalin and fixation issues. Paired toumour normal samples have adequate yields in the tumour and poor yield in the normal tissue of the same sample. We have tried increasing the number of sections taken and varying the digestion times but has not helped. Any help would be welcome.