barcoding,1 the ultimate goal is to obtain genome sequences for other studies.
Biologists have used different methods for extracting DNA from formalin-flxed samples, and some have yielded DNA sequence information, but only under narrow conditions. However, those nominal successes suggest that the problem of recovering DNA sequence information from formalin-flxed samples is solvable. This workshop brought a group of experts together to discuss potential solutions and alternative methods. Crothers clarifled that the specimens in question had been flxed and stored in 5 to 10 percent formalin solution or had been flxed in formalin solution for a few days and then preserved in ethanol. Workshop cochair Ann Bucklin (University of Connecticut), explained that in some cases the formalin for preservation or storage was unbuffered and therefore acidic.
Mark Rubin (Brigham and Women’s Hospital) and David Schindel (Consortium for the Barcode of Life; CBOL) suggested that, although the workshop’s focus was on biological samples stored in aqueous solution, much could be learned from protocol development for DNA extraction from formalin-flxed and paraffln-embedded samples. Marvin Caruthers (University of Colorado) said that paraffln embedding creates a more stable environment for the formalin-flxed sample than storage in aqueous formalin or alcohol. For example, whereas the pH of the paraffln does not change, the formaldehyde in formalin can be oxidized to formic acid by exposure to atmospheric oxygen, thereby reducing its pH.
To begin the discussion on the effect of formalin exposure on DNA, Crothers showed a slide that sums up the reactions that occur in formaldehyde flxation of a drug, adriamycin (Figure 1). During flxation,
“DNA barcoding is a technique for characterizing species of organisms using a short DNA sequence from a standard and agreed-upon position in the genome. DNA barcode sequences are very short relative to the entire genome, and they can be obtained reasonably quickly and cheaply. The cytochrome c oxidase subunit 1 mitochondrial region (COI) is emerging as the standard barcode region for higher animals. It is 648 nucleotide base pairs long in most groups, a very short sequence relative to 3 billion base pairs in the human genome, for example” (“DNA barcoding,” Consortium for the Barcode of Life, http://barcoding.si.edu/DNABarCoding.htm).