Advisers to the Nation on Science, Engineering, and Medicine

The National Academy of Sciences is a private, nonprofit, self-perpetuating society of distinguished scholars engaged in scientific and engineering research, dedicated to the furtherance of science and technology and to their use for the general welfare. Upon the authority of the charter granted to it by the Congress in 1863, the Academy has a mandate that requires it to advise the federal government on scientific and technical matters. Dr. Ralph J. Cicerone is president of the National Academy of Sciences.

The National Academy of Engineering was established in 1964, under the charter of the National Academy of Sciences, as a parallel organization of outstanding engineers. It is autonomous in its administration and in the selection of its members, sharing with the National Academy of Sciences the responsibility for advising the federal government. The National Academy of Engineering also sponsors engineering programs aimed at meeting national needs, encourages education and research, and recognizes the superior achievements of engineers. Dr. Wm. A. Wulf is president of the National Academy of Engineering.

The Institute of Medicine was established in 1970 by the National Academy of Sciences to secure the services of eminent members of appropriate professions in the examination of policy matters pertaining to the health of the public. The Institute acts under the responsibility given to the National Academy of Sciences by its congressional charter to be an adviser to the federal government and, upon its own initiative, to identify issues of medical care, research, and education. Dr. Harvey V. Fineberg is president of the Institute of Medicine.

The National Research Council was organized by the National Academy of Sciences in 1916 to associate the broad community of science and technology with the Academy’s purposes of furthering knowledge and advising the federal government. Functioning in accordance with general policies determined by the Academy, the Council has become the principal operating agency of both the National Academy of Sciences and the National Academy of Engineering in providing services to the government, the public, and the scientific and engineering communities. The Council is administered jointly by both Academies and the Institute of Medicine. Dr. Ralph J. Cicerone and Dr. Wm. A. Wulf are chair and vice chair, respectively, of the National Research Council.

www.national-academies.org

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Museums catalogue our knowledge of the Earth’s biodiversity, and their collections represent many decades of work by experts. Access to DNA sequence information in archival specimens would greatly extend knowledge of the genetic relationships within our biosphere. However, molecular genetic analysis of museum specimens has been slowed by the usual practice of fixation of samples in formalin and storage in alcohol or formalin. The fixation and storage induce changes in DNA that are not fully understood. With more frequent use of morphological and molecular characters for taxonomic and systematic analysis, the “formalin problem” has grown in significance. For example, a global effort to determine DNA barcodes (short DNA sequences for species recognition and discovery) for life on earth could be markedly expedited by sequencing DNA from specimens in museum collections. Molecular analysis of formalin-fixed tissue would allow biologists to address retrospective questions about how patterns in the genetic diversity of plant and animal species have changed over time. With application of molecular genetic analysis to formalin-fixed museum specimens, new insights about biodiversity, population dynamics, and ecosystem function can be gained from collections sampled years and perhaps decades ago.

There are many technical challenges to solving the “formalin problem,” beginning with the wide variation in curatorial practices for specimen storage. Some organisms are fixed in formalin only for a short time and then transferred to alcohol for long-term storage; others are fixed and stored in

formalin permanently. The rapid reactions of formalin with double helical DNA generally are reversible, but over the long term, especially with denaturation of the DNA, a variety of reactions can occur, many of which have not been characterized. Those reactions can be irreversible, and they can either mask the nature of the modified nucleotide in enzymatic replication, or they can block chain elongation altogether, resulting in failure of polymerase chain reaction amplification. To further complicate matters, oxidation of formaldehyde in formalin to formic acid produces an acidic solution in which depurination reactions and subsequent chain scission are greatly accelerated. Given the variation in preservation practices, and the variable age of the samples, it is unlikely that the “formalin problem” can be solved for all samples. However, with better understanding of the chemistry of formalin reactions and their effect on DNA integrity, and with better knowledge of curatorial history and practices, it should be possible to select likely candidates for intensive DNA isolation and sequencing experiments, with the goal of reconstructing significant portions of the genome.

On May 8-9, 2006, the Board on Life Sciences of the National Academies convened a workshop, “Recovering DNA from Formalin-Fixed Biological Samples.” Participants were experts—biophysicists, chemists, molecular biologists, and bioinformaticians—who discussed the path to successfully obtaining DNA sequence information from formalin-fixed biological samples. Unlike study committees of the National Research Council, workshops do not reach conclusions or present recommendations. However, participants in this workshop spent much time considering the research and experimentation that could be done to advance retrieval of genomic information from formalin-fixed samples. We thank all of the workshop participants for sharing their expertise and experience and for the stimulating discussions and insightful suggestions.

Ann C. Bucklin

Donald M. Crothers

Cochairs, Steering Committee for the

Workshop on Recovering DNA from

Formalin-Fixed Biological Samples

This document presents the author’s summary of the workshop discussion and does not necessarily reflect the views of the roundtable members or other participants.

This summary has been reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise, in accordance with procedures approved by the National Research Council Report Review Committee. This independent review is intended to provide candid and critical comments that will assist the institution in making its published workshop summary as sound as possible and to ensure that the workshop summary meets institutional standards for objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We wish to thank the following individuals for their review of this workshop summary:

Although the reviewers have provided many constructive comments and suggestions, they were not asked to endorse the content nor did they

see the final draft of the workshop summary before its release. The review of this workshop summary was overseen by Marvalee Wake, University of California, Berkeley. Appointed by the National Research Council, she was responsible for making certain that an independent examination of this workshop summary was carried out in accordance with institutional procedures and that all review comments were carefully considered. Responsibility for the final content of this workshop summary rests entirely with the institution.

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