Detection of Copy Number Changes in DNA from Formalin Fixed Paraffin Embedded Tissues Using Paralogue Ratio Tests

作者：Saldanha Gerald^*; Potter Linda; Dyall Lovesh; Bury Danielle; Hathiari Nisreen; Ehdode Abdlrzag; Hollox Edward; Pringle James Howard

来源：Analytical Chemistry, 2011, 83(9): 3484-3492.

DOI：10.1021/ac200153j

The purpose of this study was to evaluate whether paralogue ratio tests (PRT) using real-time PCR can accurately determine the DNA copy number (CN) using formalin fixed paraffin embedded (FFPE) tissue. Histopathology diagnostic archives are an enormous resource of FFPE tissue, but extracted DNA is of poor quality and may be unsuitable for CN assessment, thus representing a missed opportunity for studies of genetic association and somatic change in cancer in large cohorts of easily accessible samples. Assays with paralogues on chromosomes 18 and 20 (18 vertical bar 20 PRT) and chromosomes 13 and X (13 vertical bar X PAT) were tested using archived FFPE pathology samples with known CN, including tonsil, placentae, and FFPE melanoma cell lines. The assay proved accurate over the dynamic range from 1:1 to 1:3 and gave precise results when repeated four times over several weeks. The precision of the assay was marginally reduced once the CT value for 10 ng of FFPE DNA increased above 30 cycles, reflecting importance of DNA quality. The assays distinguished changes in CN ratio with high sensitivity and specificity. The 13 vertical bar X PRT could detect cells with distinct genotypes microdissected from within the same FFPE sample. Therefore, PRTs are suitable for analyzing CN in FFPE tissues.

• 出版日期2011-5-1