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Genomic Analysis of Formalin-Fixed Paraffin Embedded (FFPE) Tissues through the use of Whole Genome Amplification (WGA)

The past is a source of knowledge, and the future is a source of hope.
S. Ambrose (1936-2002) Ernest Mueller

Preserved samples from medical, forensic, museum and other archival collections represent a rich source of study material, much of it meticulously collected, characterized and preserved through many decades of work by experts in the field. While the majority of this material was originally collected and preserved with morphological studies in mind, the advent of molecular genetic techniques have caused many scientist to eye archival collections as a precious source of biological data.

There are many preservation methods that have been applied to tissues, including alcohol preservation, formalin treatment, freezing and sequestration in waxes and other materials. Molecular diagnostic research groups began working with formalin-fixed paraffin embedded (FFPE) tissues in the late 1980s and early 1990s .1,2 Their results showed some early successes. Unfortunately, many of the preservation methods used in the past, of which formalin treatment has been the most popular, have been found to degrade DNA and RNA. Common techniques of extraction and molecular analysis that worked well with fresh and frozen samples were found to work poorly on samples stored in unbuffered formalin or FFPE preserved samples. This so-called formalin problem appears to be worse for samples that have been stored over longer periods. It has been hypothesized that while the immediate adducts created by formalin are reversible, the slower reactions are irreversible and leave nucleic acids unsuitable for PCR, hybridization and other molecular biology methods.3,4 Strand breaks or formaldehyde lesions in the DNA are equally able to ruin amplification.

Researchers have attempted to characterize the effect of long-term formaldehyde preservation on DNA. While the conditions of f
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