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ILAR Journal V34(4) [FORMERLY ILAR NEWS]
ILAR Reports

Standardized Nomenclature for Transgenic Animals

Committee on Transgenic Nomenclature
Institute of Laboratory Animal Resources
Commission on Life Sciences
National Research Council

Preface

As part of its mission to promote efficient, cost-effective, ethical research with animals, and to those ends to identify valuable laboratory animal resources, the Institute of Laboratory Animal Resources (ILAR) of the National Research Council's Commission on Life Sciences was charged with addressing a new and rapidly developing application of molecular biology to animal experimentation termed transgenic technology. The development of a large number of new strains of animals with this technology has been accompanied by some specific deficiencies, as follows:


To address those deficiencies, the ILAR Council organized an advisory panel,a which recommended a series of initiatives to assist scientists who work with or care for transgenic animals.

In recognition that the lack of a widely accepted standardized nomenclature for transgenic animals greatly complicates efforts to catalog existing resources, the recommended first initiative was that ILAR develop such a nomenclature. Accordingly, ILAR established the Committee on Transgenic Nomenclature to undertake this task and to delineate a means by which the nomenclature could be used to create a catalog of existing transgenic resources. The committee was constituted to include experts in the production of transgenic animals by various means, scientists with experience in issues related to animal nomenclature, and a member and an invited participant who are involved in the development of a data base on transgenic animals.

The committee felt that it would be sensible to establish a nomenclature that is compatible with the storage and efficient retrieval of information from the data base on transgenic animals. The nomenclature that it developed, therefore, includes the relevant differences in the various approaches to making transgenic animals, encompasses the diversity and complexity of the DNA elements that are introduced into the germline, and provides the conciseness required for the convenient use and efficient storage of information.

The committee acknowledges the assistance of the staff of ILAR, which has made this report possible.

Jon W. Gordon, Chairman
Committee on Transgenic Nomenclature

Footnote

a Melvin W. Balk (Chairman), Charles River Laboratories, Inc., Wilmington, Massachusetts; Jon W. Gordon, Department of Obstetrics and Gynecology, Mt. Sinai School of Medicine, New York, New York; Steven P. Pakes. University of Texas Southwestern Medical Center. Dallas, Texas; Fred W. Quimby, New York State College of Veterinary Medicine, Cornell University, Ithaca, New York; J. Wesley Robb, University of Southern California School of Medicine, Los Angeles. California; and John L. Seidman, Department of Genetics, Harvard University School of Medicine, Boston, Massachusetts.

Committee on Transgenic Nomenclature

Jon W. Gordon (Chairman), Department of Obstetrics and Gynecology, Mt. Sinai School of Medicine, New York, New York
John M. Coffin, Department of Molecular and Microbiology, Tufts University School of Medicine, Boston, Massachusetts
Muriel T. Davisson, The Jackson Laboratory, Bar Harbor, Maine
Thomas J. Gill III, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh. Pennsylvania
Clement L. Markert, Department of Animal Science, North Carolina State University, Raleigh
Richard P. Woychik, Biology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee

Invited Participant
Monica Lee-Tischler, Biology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee

Staff
Dorothy D. Greenhouse, Senior Program Officer
Amanda E. Hull, Program Assistant


Contents

INTRODUCTION

The ability to achieve controlled genetic modifications of multicellular eukaryotic species by the insertion of genetic material, termed transgenic technology, has led to an explosion of research in developmental genetics, attracting the interest of many investigators who previously were not engaged in animal research. However, although many new animal models have been produced, there has been no organized effort to identify and catalog them. The lack of a catalog might keep research with the new technology from being conducted with maximal efficiency and effectiveness for several reasons:
It is obvious that some registry of transgenic strains and their characteristics is essential. To that end, the Oak Ridge National Laboratory, Oak Ridge, Tennessee, under contract Y01 -ES10067 from the National Institute of Environmental Health Sciences of the National Institutes of Health has undertaken the development of a data base for cataloging transgenic animals: the Transgenic Animal Data Base (TADB). For the TADB to be effective and to promote effective communication between scientists in different laboratories, a widely accepted standardized nomenclature for transgenic animals is necessary.

ISSUES IN DEVELOPING A TRANSGENIC NOMENCLATURE

For developing a transgenic nomenclature, the committee defined a transgenic organism as an organism in which new genetic material has been experimentally introduced into the germ cells. The new DNA can be derived from the homologous species and need not be genetically active; however, it should be heritable. Thus, animals with new gene insertions resulting from ecotropic retroviral infection are not transgenic, nor are those receiving DNA only in somatic cells. In contrast, mice with an additional mouse b-globin gene that has been inserted into a site other than that of the endogenous gene and transmitted to progeny as a Mendelian trait are transgenic. Animals with genetic modifications introduced by homologous recombination in embryonic stem cells are considered transgenic if the purpose of the homologous recombination approach is to target functional genetic elements into specific sites in the genome.

A transgenic nomenclature must incorporate information related to both the methods used to produce transgenic animals and the diversity of genetic elements that can be inserted into animals. It must also be concise enough to make it easily recognized and remembered. Thus, there is a potential conflict between the need for conciseness and the need for completeness of information. The same conflict was encountered by the International Committee on Standardized Genetic Nomenclature for Mice, which began work on nomenclature for transgenes in 1984. That committee proposed a general form that followed the format used for chromosomal anomalies: an abbreviation of the word transgenic, followed by parenthetic information on the inserted segment, followed by a unique laboratory code and a numerical designation. Although this nomenclature was widely circulated for review and the comments of experts in transgenic mice were incorporated, neither it nor the revised nomenclature published a few years later (Lyon, 1989a) has been widely used. A major problem has been deciding how much information on the inserted segment to include. Opinions vary from a three-character symbol to all the information known (the latter would sometimes mean a symbol that requires several lines of text).

Given that history and the present committee's own perception of the problems presented in creating a usable transgenic nomenclature, the committee decided that brief, unique identifiers of transgenic insertions would be most effective for transgene symbols. The full history and description of each transgenic insertion should be recorded in the TADB (described in detail in Appendix II).

In determining the elements of the transgene symbol, the committee concentrated its deliberations on the following issues:

IMPLEMENTATION OF THE NEW NOMENCLATURE

For the nomenclature to contribute to better transgenic-resource management and preservation of transgenic animals, it must first be accepted for use by the major investigators in the field and then be made available to all those developing or using transgenic animals. To achieve the first objective, the committee sent the proposed nomenclature to several major laboratories involved in transgenic research, including two that use species other than the mouse. Comments from those laboratories have been considered in developing the nomenclature.

To achieve the second objective, the committee solicited and has received endorsement of the nomenclature rules from the International Committee on Standardized Genetic Nomenclature for Mice and, in the absence of a functional international nomenclature committee for rats, from the ILAR Committee on Rat Nomenclature. In addition, membership on the present committee of one of the developers of the TADB has allowed us to develop a nomenclature that is compatible with the data base. Promulgation of the nomenclature will simultaneously increase awareness of the existence of the data base.

The committee also identified several other strategies for implementation, including sending the nomenclature for publication in journals that commonly contain papers involving research with transgenic animals and recommending that the editors of the journals make the nomenclature a requirement for acceptance of papers in this field. Moreover, this report has been sent to the categorical institutes of NIH that have an interest in transgenic technology with the request that the rules be provided to the appropriate grantees and contractors and to the study sections that evaluate grant and contract proposals involving transgenic animals.

In the next section, the committee formally proposes its transgene nomenclature. Information on obtaining assistance with naming transgenes or recording transgenes in the data base is contained in Appendix I.

RULES FOR NAMING TRANSGENES

Transgenes are named according to the following conventions.

Symbol

A transgene symbol consists of three parts, all in Roman type, as follows:


where TgX = mode,
Mode. The first part of the symbol always consists of the letters Tg (for "transgene") and a letter designating the mode of insertion of the DNA: N for nonhomologous insertion, R for insertion via infection with a retroviral vector, and H for homologous recombination. The purpose of this designation is to identify it as a symbol for a transgene and to distinguish among three fundamentally different organizations of the introduced sequence relative to the host genome, not simply to indicate the method of insertion or nature of the vector. For example, mice derived by infection of embryos with MULV vectors will be designated TgR, and mice derived by microinjection or electroporation of MULV DNA into zygotes will be designated TgN; mice derived from ES cells by introduction of DNA followed by recombination with the homologous genomic sequence will be designated TgH, while mice derived by insertions of the same sequence by nonhomologous crossing-over events will be designated TgN.

When a targeted mutation introduced by homologous recombination does not involve the insertion of a novel functional sequence, the new mutant allele (often called a "knockout" mutation) will be designated in accordance with the guidelines for gene nomenclature for each species. The gene nomenclature will also be used when the process of homologous recombination results in integration of a novel functional sequence, if that sequence is a functional drug-resistance gene. For example, Mbpm l D n, would be used to denote the first targeted mutation of the myelin basic protein (Mbp) in the mouse made by Muriel T. Davisson (Dn). In this example, the transgenic insertion, even if it contains a functional neomycin-resistance scene, is incidental to "knocking out" or mutating the targeted locus (see also Lyon, 1989b). The mode symbol TgH is reserved for a time in the future when homologous recombination might be employed to transfer genes to specific sites in the genome using cloned DNA from the target cite to produce a homologous recombination vector. Such target loci might be anonymous, but might exhibit important regulator features that render them desirable for targeting transgenes. A hypothetical example is given on page 50.

Insert designation. The second part of the symbol indicates the salient features of the transgene as determined by the investigator. It is always in parentheses and consists of no more than eight characters: letters (capitals or capitals and lower-case letters) or a combination of letters and numbers. Italics, superscripts, subscripts, internal spaces, and punctuation should not be used. The choice of the insert designation is up to the investigator, but the following guidelines should be used:
An(anonymous sequence),
Ge(genomic clone),
Im(insertional mutation),
Nc(noncoding sequence),
Rp(reporter sequence),
Sn(synthetic sequence),
Et(enhancer trap construct), and
Pt(promoter trap construct).

This list will be expanded as needed and maintained by appropriate international nomenclature committees.

Laboratory-assigned number and laboratory code. The third part of the symbol consists of two components. The laboratory-assigned number is a unique number that is assigned by the laboratory to each stably transmitted insertion when germline transmission is confirmed. As many as five characters (numbers as high as 99,999) may be used; however, the total number of characters in the insert designation plus the laboratory-assigned number may not exceed 11. No two lines generated within one laboratory should have the same assigned number. Unique numbers should be given even to separate lines with the same insert integrated at different positions. The number can have some intralaboratory meaning or simply be a number in a series of transgenes produced by the laboratory. The laboratory code is uniquely assigned to each laboratory that produces transgenic animals. A laboratory that has already been assigned such a code for other genetically defined mice and rats or for DNA loci should use that code. The registry of these codes is maintained by the Institute of Laboratory Animal Resources (ILAR) (see Appendix I).

The complete designation identifies the inserted site, provides a symbol for ease of communication, and supplies a unique identifier to distinguish it from all other insertions. Each insertion retains the same symbol even if it is placed on a different genetic background. Specific lines of animals carrying the insertion should be additionally distinguished by a stock designator preceding the transgene symbol. In general, this designator will follow the established conventions for the naming of strains or stocks of the particular animal used. If the background is a mixture of several strains, stocks, or both, the transgene symbol should be used without a strain or stock name.

Examples

Abbreviations

Transgene symbols can be abbreviated by omitting the insert. For example, the full symbol TgN(GPDHIm)lBir would be abbreviated TgN1Bir. The full symbol should be used the first time the transgene is mentioned in a publication; thereafter, the abbreviation may be used.

Insertional Mutations and Phenotypes

The symbol should not be used to identify the specific insertional mutation or phenotype caused directly or indirectly by the transgene. If an insertional mutation that produces an observable phenotype is caused by the insertion, the locus so identified must be named according to standard procedures for the species involved (see Appendix I). The allele of the locus identified by the insertion can then be identified by the abbreviated transgene symbol (see above) according to the conventions adopted for the species.

Examples

REFERENCES

APPENDIX I
Resources Available for Assistance with Transgenic Nomenclature

Before naming a transgene, an investigator should obtain a laboratory code from ILAR at the address given in the list below. An investigator who has already been assigned such a code for other genetically defined mice and rats or for DNA loci should use the same code. The transgene should be named as stated in the rules. Assistance in selecting transgene symbols is available from several organizations (see below). Lists of named genes for mice and rats are published periodically in Mouse Genome (Oxford University Press, Journal Subscriptions Department, Pinkhill House, Southfield Road, Eynsham, Oxford OX8 1JJ, UK) and Rat News Letter (Dr. Viktor Stolc, editor, Rat News Letter, 2542 Harlo Drive, Allison Park, Pittsburgh, PA 15101). The list of mouse genes is also maintained in GBASE, a genomic data base for the mouse maintained by Dr. Don P. Doolittle, Dr. Alan L. Hillyard, Ms. Lois J. Maltais, Dr. Muriel T. Davisson, Dr. Thomas H. Roderick, and Mr. John N. Guidi at The Jackson Laboratory (see below). Human gene symbols are recorded in the Genome Data Base (GDB), which is maintained at The Johns Hopkins University (see below).

Institute of Laboratory Animal Resources (ILAR). Assigns laboratory codes; assists in naming transgenes; provides rules for naming transgenes. Contact: Dr. Dorothy D. Greenhouse, ILAR, National Research Council, 2101 Constitution Avenue, NW, Washington, DC 20418. Tel: 1-202-334-2590; Fax: 1-202-334-1687; Bitnet: DGREENHO@NAS).

The Jackson Laboratory. Assists in naming transgenes; provides rules for standardized nomenclature for mice; provides lists of named mouse genes. Contact: Dr. Muriel T. Davisson, The Jackson Laboratory, Bar Harbor, ME 04609. Tel: 1-207-288-3371; Fax: 1-207-288-8982).

Medical Research Council Radiobiology Unit. Assists in naming transgenes; provides lists of named mouse genes. Contact: Dr. Josephine Peters, MRC Radiobiology Unit, Chilton, Didcot, Oxford OX11 ORD, UK. Tel: 44-235-834-393; Fax: 44-235-834-918.

Transgenic Animal Data Base (TADB). Records, stores, and provides information on transgenic animals, including standardized nomenclature and a complete description of each transgenic animal; maintains rules for transgenic nomenclature on electronic bulletin board. Contact: Ms. Karen Schneider, TADB Coordinator, Oak Ridge National Laboratory, PO Box 2008, MS 6050, Oak Ridge, TN 37831-6050. Tel: 1-615-574-7776; Fax: 1-615-574-9888; Bitnet: TUG@ORNLSTC; Internet: OWENSET@IRAVAX.HSR.ORNL.GOV.

Genome Data Base (GDB). Records, stores, and provides information on mapped human genes and clones. Contact: GDB, Welch Medical Library, The Johns Hopkins University, 1830 East Monument Street, Baltimore, MD 21205. Tel: 1-301-955-9705; Fax: 301-955-0054. For assistance in naming human genes, the contact is Dr. Phyllis J. McAlpine, GDB Nomenclature Editor, University of Manitoba, Department of Human Genetics, 250 Old Basic Sciences Building, 770 Bannatyne Avenue, Winnipeg, Manitoba, Canada R3E 0W3. Tel: 1-204-788-6393; Fax: 1-204-786-8712; Bitnet: GENMAP@UOFMCC).

APPENDIX II
The Transgenic Animal Data Base

The Transgenic Animal Data Base (TADB) is intended to be a comprehensive, online, computerized record of all lines of transgenic animals and animals with targeted mutations that have been generated worldwide. Although the data base now includes only mice, it will be expanded to include other animal species. Transgenic animals of little interest to one researcher might be of enormous interest to others. This situation is addressed through the data base by making available to the scientific commu-nity extensive information about transgenic constructs, including methods, expressions, and phenotypes. Standardized nomenclature should be used to enter information into the data base.

Scientists provide data on their own lines of transgenic animals. The TADB office faxes a set of specific questions to each scientist, who answers the questions on a floppy disk with a word-processing program. The floppy disk is returned to the TADB office, where the data are formatted and transferred to the online computer. The result is that pertinent information, published or unpublished, on each line of animals is organized in the data base by the categories listed below. The data base has an easy-to-use, menu-driven interface that enables new users to search for and retrieve relevant records rapidly.

The data base also furnishes an opportunity for users to enter messages to the system administrator. This feature enables the system administrator to assist users who report difficulties and to make necessary adjustments in data base operations to maximize its usefulness. Information on various topics related to use of the data base can be accessed online.

The TADB is stored on an IBM RS6000/320 workstation Server using BRS, a full-text searching software, for retrieval. It is accessible internationally via a toll-free number through the Tymnet telecommunications network. Access through Telnet is also available. Users need a personal computer, a terminal emulation program (such as White Knight, Versaterm, Procom, or Kermit), and a modem to access the data base. Users can get information at no cost from the TADB office. Contact: Ms. Karin Schneider, TADB Coordinator, Oak Ridge National Laboratory, PO Box 2008, MS 6050, Oak Ridge, TN 37831-6050. Tel: 1-615-574-7776; Fax: 1-615-574-9888; Bitnet: TUG@ORNLSTC; Internet: OWENSET@IRAVAX.HSR.ORNL.GOV.

Development of the TADB is sponsored by the National Institute of Environmental Health Sciences, National Institutes of Health, under contract Y01-ES10067.

Categories in the Transgenic Animal Data Base

DOCNBRS-Assigned Accession Number
DESGDesignation (Standardized Nomenclature) of Transgenic Line
METHMethod Used
DNADNA Fragment Introduced
COPYCopy Number
BACKGenetic Background of Host Embryo or ES Cells
EXPRExpression of Transgene or Targeted Gene
PHENPhenotype Due to Expression of Transgene or Targeted Gene
INTGDescription of Integration Site
CROSCrosses with Other Transgenic Lines
IGENGenetics of Host Insertional Mutation
ICOMComments on Genetics of Host Insertional Mutation
ICLNIs Flanking Sequence Cloned?
ICHRIs Mutant Locus Characterized?
IALLIs Mutation Allelic with Existing Mutations?
IPHNPhenotype of Insertional Mutation
FCOMFurther Comments Relating to Transgenic Line
MNTIs Line Being Maintained?
HNDLSpecial Handling Instructions for the Animals
QDTEIs This Line Presently Available to Other Investigators?
CADDName and Address of Contact Person
GADDName and Address of Author(s) Entering This Record
PUBLReferences for Publications Relating to Line
DATEDate Document Was Entered or Updated






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