ILAR Journal Volume 34, Number 4 1992 Pages S1-S26

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NOTICE: The project that is the subject of this report was approved by the Governing Board of the National Research Council, whose members are drawn from the councils of the National Academy of Sciences, National Academy of Engineering, and Institute of Medicine. The members of the committee responsible for the report were chosen for their special competencies and with regard for appropriate balance.

This report has been reviewed by a group other than the authors according to procedures approved by a Report Review Committee consisting of members of the National Academy of Sciences, National Academy of Engineering, and Institute of 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. Frank Press 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. Robert M. White 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. Kenneth I. Shine is president of the Institute of Medicine.

The National Research Council was established 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 National Academy of Engineering in the conduct of their 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. Frank Press and Dr. Robert M. White are chairman and vice-chairman, respectively, of the National Research Council.

The Institute of Laboratory Animal Resources (ILAR) was founded in 1952 under the auspices of the National Research Council. A component of the Commission on Life Sciences, ILAR serves as a coordinating agency and a national and international resource for compiling and disseminating information on laboratory animals, promoting education, planning and conducting conferences and symposia, surveying existing and required facilities and resources, upgrading laboratory animal resources, and promoting high quality, humane care of laboratory animals in the United States.

This study was supported through grant number 1R13RR06884-01-R by the Comparative Medicine Program, National Center for Research Resources; Biology of Aging Program, National Institute on Aging; and Division of Cancer Biology, Diagnosis, and Centers, National Cancer Institute. Support was also provided by the Division of Cancer Treatment, National Cancer Institute through contract number NO1-CM-07316; the National Toxicology Program, National Institute of Environmental Health Sciences, through purchase order PR242640; the Japanese Ministry of Education, Science, and Culture; Chugai Pharmaceutical Co., Ltd.; Mitsubishi Kasei Co., Ltd.; and Otsuka Pharmaceutical Co., Ltd. Additional support was provided by the B & K Universal Group Ltd., Charles River Laboratories, Inc.; CLEA Japan, Inc.; Harlan Sprague Dawley, Inc.; and Taconic Farms, Inc. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the committee and do not necessarily reflect the views of the National Institutes of Health; Japanese Ministry of Education, Science, and Culture; or other sponsors, nor does the mention of trade names, commercial products, or organizations imply endorsement by the U.S. or Japanese governments.

ILAR's core program is supported by grants from the National Center for Research Resources, National Institutes of Health; National Science Foundation; American Cancer Society, Inc.; and U.S. Army Medical Research and Development Command, which is the lead agency for combined Department of Defense funding also received from the Human Systems Division, Air Force Systems Command; Armed Forces Radiobiology Research Institute; Uniformed Services University of the Health Sciences; and U.S. Naval Medical Research and Development Command.

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National Research Council
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Washington, DC 20418

To encourage the use of standardized nomenclature for rats by revising and updating, the rules for standardized nomenclature.

To resolve problems that have arisen because of the inappropriate use of nomenclature in naming, rat strains.

To ensure high genetic quality of rats by developing criteria for determining appropriate techniques for genetic monitoring.

To encourage sharing of unique genetically defined strains by developing criteria for investigators to use in distributing animals to other investigators and to commercial companies.

To ensure continued availability of unique genetically defined rat strains by developing criteria for determining what strains are of most value to the scientific community and by what mechanism they might be preserved.

To develop a strategy for establishing communication between rat geneticists and investigators who use rats in fields other than genetics.

Because rats and the data obtained through studying them are shared worldwide, the committee recognized the necessity of addressing those issues in an international forum. Accordingly, it organized an international workshop, which was held January 14-16, 1992, at the Arnold and Mabel Beckman Center of the National Academy of Sciences and National Academy of Engineering, Irvine, California. The committee expresses its thanks to the workshop participants for their information and insights, which form the basis of this report.

The committee also acknowledges the assistance of the staffs of ILAR, Washington, D.C., and the Central Institute for Experimental Animals, Kawasaki, Japan, in organizing the workshop and preparing this report.

Thomas J. Gill III, Cochairman
Committee on Rat Nomenclature

Tatsuji Nomura, Cochairman
Committee on Rat Nomenclature

1.1 Definition
1.2 Symbols
1.3 Indication of Inbreeding
1.4 Substrains
1.5 Laboratory Codes
1.6 Recombinant Inbred Strains
1.7 Coisogenic, Congenic, and Segregating Inbred Strains

2. Hybrid Strains
3. Genes

3.1 Names of Loci
3.2 Symbols for Loci
3.3 Loci That Are Members of a Series
3.4 Homology with Other Organisms
3.5 Alleles
3.6 Phenotype Symbols
3.7 Gene Complexes
3.8 Pseudogenes
3.9 Lethals
3.10 Viruses
3.11 Oncogenes
3.12 Mitochondrial Genome
3.13 Restriction-Fragment Length Polymorphisms
3.14 Biochemical Variants
3.15 The Major Histocompatibility Complex and Other Alloantigenic Systems
3.16 Immunoglobulin Complexes
3.17 Globin Gene Complexes
3.18 Homeobox-containing Genes
3.19 Cytochrome P450
3.20 Transgenes

4. Chromosomes
5. Outbred Stocks

5.1 Definition
5.2 Symbols
5.3 Widely Accepted Outbred-Stock Symbols

6. Resources
References
Appendix II: Summary: Important Laboratory Animal Resources: Selection Criteria and Funding Mechanisms for Their Preservation

To encourage genetic characterization and monitoring of stocks and strains of rats used in biomedical research by developing a set of recommendations, including recommendations for practical techniques for genetic characterization and monitoring.

To implement suitable genetic nomenclature for the rat, taking into account existing nomenclature used for humans, mice, and other relevant species.

To encourage the conservation of rat strains and stocks by recommending a set of criteria for determining which strains and stocks should be conserved and by what means and by promoting systematic, national efforts to conserve valuable strains and stocks.

To disseminate information on rat genetics to all appropriate scientific disciplines by publishing new genetic information in journals appropriate to various fields, encouraging journal editors to require the use of standardized nomenclature in submitted manuscripts, and establishing registries with widely available electronic data bases.

Rejection times of organs in transplantation research depend on the source of the rats used and their proximate environment.

Biological characteristics (e.g., the expression of diabetes, reproductive performance) frequently differ in supposedly identical strains held in different laboratories.

There is often considerable confusion in interpreting experimental results from different laboratories that are ostensibly using the same strain.

Characterization of a strain involves a detailed investigation of its genotype (the genetic endowment of the animal), its phenotype (manifestations of the genotype as influenced by the environment during gestation and the postnatal period), and its dramatype (manifestations of the phenotype as influenced by the proximate environment in which experiments are performed). The following are useful for genetically defining inbred strains:

Cytogenetic techniques (karyotyping) detect important polymorphic morphological markers of chromosomes, especially the C-banding pattern and the position of the nuclear organizer region. Most of the linkage groups have been assigned to specific chromosomes, and the rest should be identified shortly. The synteny groups of the mouse, rat, and human chromosomes will play an important role in gene mapping and disease associations in the three species.

Biochemical polymorphisms are important genetic markers. The panel of markers (generally 15-30) selected should represent a broad sampling of the genome and be reproducible over a long period. Useful protein and enzyme markers can be obtained from blood, tissues, and urine.

Immunological markers include the antigens encoded by the MHC (RT1) and by the blood-group loci RT2 and RT3. Skin grafting is an all-encompassing way in which to test histocompatibility, and it can be done whenever strains are compared or when a strain is tested for its degree of inbreeding.

Molecular genetic markers are powerful tools for characterizing the rat genome. The methods to be used and their interpretation are the subject of intensive research in a number of species. At the moment, the microsatellite DNA profile appears to be the most useful for strain characterization. So-called DNA fingerprinting and mitochondrial DNA restriction-fragment length polymorphism (RFLP) patterns are also useful.

Phenotypic traits remain important components of strain characterization. Useful phenotypic traits are coat color, eye color, reproductive performance, and behavioral patterns. Other unique traits are useful for characterizing strains that are models of human diseases (e.g., hypertension and diabetes).

Multiple sets of inbred strains independently derived from the same outbred stock have been given the same designation, although they are genetically different (e.g., there are several different BB, SHR, and WKY strains).

Some inbred strains (e.g., LOU/Iap and BDII/Cr) have become genetically contaminated but have retained the original strain name.

Substrains of several commonly used strains differ at several loci but have not officially been given substrain symbols (e.g., BN strains, which differ at the [Pep3 locus, and MNR strains, which differ at the RT1 locus).

Obsolete synonyms of inbred strains are still widely used (e.g., Brown Norway for BN and Fischer or Fischer 344 for F344).

2. Gene symbols and mutant loci

Several lists of gene symbols exist but are not in complete agreement.

Rules for loci identified by molecular genetic methods have not been established.

3. Outbred stocks. Outbred stocks have generally not been genetically characterized, and lists of these stocks have not been compiled.
4. Exclusivity. To maintain the exclusivity of certain animal models, there has been a recent trend toward trademarking the animal's name or patenting the animal.

A trademark is usually applied to a brand name, that differs from the standardized nomenclature. This leads to confusion about which of the two names is the proper one. If a trademark is applied to the standardized nomenclature, companies other than the trademark holder that supply the animal tend to change the name to avoid using the trademark, causing further confusion.

A patented animal model is generally called by some nickname that is thought to be descriptive of the model's main characteristic. That has resulted in several different models with the same nickname and makes it difficult to communicate information.

Rules of nomenclature and revisions thereof can be submitted for publication in various journals. especially journals that commonly publish articles on rat genetics and immunology, and the editors of those journals can be urged to require the use of standardized nomenclature in submitted manuscripts.

Commercial breeders can play an important part in educating those using rats by giving more prominence to the standardized nomenclature in their catalogs and less prominence to obsolete names and brand names. They can also be requested to distribute the rules for nomenclature of rats to their customers.

Data bases containing information on genetically defined rats now housed in individual institutions can be made widely available by linking to a single, publicly accessible data base such as GBASE, The Genomic Data Base of the Mouse, which is maintained at the Jackson Laboratory, Bar Harbor, Maine.

The committee recommends that responsibility for the appropriate dissemination of information be assigned to the international committee discussed below.

TABLE 1 Selected Markers Useful for Genetic Monitoring of Rats

The following rules have been adopted by the Committee on Rat Nomenclature of the National Research Council's Institute of Laboratory Animal Resources (ILAR). They are based on the rules adopted by the International Committee on Standardized Genetic Nomenclature for Mice (Lyon, 1989a, b). Although, some types of genes (e.g., recessive lethals and homeobox-containing genes) have not yet been described in rats, the rules for their nomenclature are presented because these genes are likely to be discovered in the foreseeable future. In these instances, examples for mice are used to illustrate the rules.

1. INBRED STRAINS

1.1 Definition

A strain is regarded as inbred when it has been mated brother x sister (hereafter called b x s) for 20 or more consecutive generations. To ensure isogenicity, as well as homozygosity, a single b x s pair must be selected in the twentieth or a subsequent generation to perpetuate the strain. Parent x offspring matings may be substituted for b x s matings, provided that in the case of consecutive parent x offspring matings, each mating is to the younger of the two parents; this will prevent repeated backcrossing to a single individual. Exceptionally, other breeding systems may be used, provided that the inbreeding coefficient achieved is at least equal to that at the twentieth generation, theoretically 0.99.

1.2 Symbols

Inbred strains should be designated by a capital letter or letters in Roman type. Brief symbols (four letters or fewer) are preferred (e.g., ACI, DA). An exception is allowed in the case of stocks already widely used and known by a designation that does not conform (e.g., F344, DONRYU). Strains with a common origin (i.e., from the same outbred base population or arising from the same cross but separated before the twentieth generation) should be regarded as related inbred strains and should be given symbols that indicate the relationship and that bring the strains together in alphabetical lists (e.g., the strain SR, which is resistant to sodium chloride-induced hypertension, and the strain SS, which is sensitive to sodium chloride-induced hypertension).

To avoid duplication in strain designations, anyone naming a new strain should consult the Registry of Inbred Strains (see Sec. 6, Resources). If two inbred strains are assigned the same symbol, the strain to retain the symbol will be determined by priority in publication. For this purpose, listing in Rat Newsletter will be regarded as publication. A list of inbred strains is published periodically in Rat Newsletter (see Sec. 6, Resources).

1.3. Indication of Inbreeding

When it is desired to indicate the number of generations of b x s inbreeding, this should be done by appending in parentheses an F followed by the number of inbred generations (e.g., F87). If only part of the total inbreeding is known, this should be indicated with a question mark and a plus sign (e.g., F? + 10).

1.4 Substrains

An established inbred strain is considered to have divided into substrains when known or probable genetic differences become established in separate branches. Such differences could arise by residual heterozygosity at the time of branching or by new mutation. Hence, substrains should be considered to be formed as follows:

· When branches are separated before F40 (i.e., after 20 and before 40 generations of b x s matings). In such cases, residual heterozygosity might be present.

· When genetic differences from other branches are discovered. Such differences could arise either by residual heterozygosity or mutation. Contamination is likely to lead to numerous genetic differences and might thus be distinguishable from mutation. If contamination is thought likely, the strain should be renamed.

· When a branch is known to have been maintained separately from other branches for 100 generations, even if neither of the above applies. In accordance with the rules of standardized nomenclature for inbred mice, the separate branch is considered a new substrain because the existence of differences arising by mutation is highly probable.

A substrain should be known by the name of the parent strain followed by a slanted line (slash) and, in the case of identifiable genetic differences, a number (e.g., BN/l, BN/2). The founding strain is considered the first substrain; the use of /1 for it is optional (e.g., KGH or KGH/1) In the case of established strains, the first substrain will be the one maintained in the greatest number of laboratories or so determined by the registrar of inbred strains (see Sec. 6, Resources).

When genetic differences are probable but not demonstrated, a laboratory code (e.g., Pit for the University of Pittsburgh Department of Pathology, and N for the NIH Genetic Resource (see Sec. 1.5) is used to designate a substrain (e.g., BN/lPitN becomes BN/1N after 100 generations at the NIH Genetic Resource).

1.5 Laboratory Codes

Each laboratory or institution that breeds rats should obtain a laboratory code from ILAR (see Sec. 6, Resources). This code, which can be used for all species, consists of either a single Roman capital letter or an initial Roman capital letter and one to three lower-case letters. Normally, a strain is designated by the strain name followed by a slanted line (slash), the substrain designation (if any), and the laboratory code (e.g., BN/ lPit). When the strain or substrain is established in another laboratory, the new laboratory code is appended (e.g., BN/lPitN). The first laboratory code should be retained until a genetic difference is demonstrated or a branch has been maintained separately from other branches for 100 generations (e.g., BN/lPitN becomes BN/1N after 100 generations at the NIH Genetic Resource). Intermediate laboratory codes should be dropped to avoid excessively long designations. It is the responsibility of the holder to maintain a history of the strain.

1.6 Recombinant Inbred Strains

Strains formed by crossing two inbred strains, followed by 20 or more generations of b x s mating are called recombinant inbred (RI) strains. The symbol of an RI strain should consist of an abbreviation of both parental strain names separated by a capital X with no intervening spaces (e.g., LXB for an RI strain developed from a cross of LEW and BN). Different RI strains in a series should be distinguished by numbers (e.g., LXB I, LXB2).

1.7 Coisogenic, Congenic and Segregating Inbred Strains

Two strains that are genetically identical except for a difference at a single locus are called coisogenic. True coisogencity can probably be achieved only by mutation within an existing inbred strain, whereas lines obtained by inbreeding with forced heterozygosis (segregating inbred strains) or by crossing onto an inbred strain (congenic strains) usually differ in a short chromosomal segment, rather than in a single gene.

Coisogenic and congenic strains (except for alloantigenic systems see Sec. 3.15) should be designated by the strain symbol, a slash, the substrain symbol (if any), and the laboratory code, followed by a hyphen and the gene symbol in italics (e.g., LEW/Han-ci, a coisogenic strain; LEW/N-rni, a congenic strain). When the mutant or introduced gene is maintained in the heterozygous condition, this may be indicated by including a slanted line and a plus sign in the gene symbol (e.g., LEW/N-rnu/+).

A strain developed by repeated backcrossing should be regarded as congenic when a minimum of 10 backcross generations to the background strain have been made, counting the first hybrid or Fl generation as generation 1. The number of backcross generations should be indicated by N followed by a number. If it is necessary to use more complex mating systems, the generations should be expressed as N equivalents (NE) and the strain regarded as congenic at a minimum of NE10.

For segregating inbred strains developed by inbreeding with forced heterozygosis, indication of the segregating locus is optional. The number of generations of such breeding should be indicated by FH followed by a number.

2. HYBRID STRAINS

The first filial generation of a cross between two inbred strains is called an Fl hybrid. It is designated by the full strain designation of the female parent, followed by a multiplication sign and the full strain designation of the male parent, followed by Fl (e.g., F344/NNia x BN/ RijNia F1). If there is any chance of confusion, parentheses should be used to enclose the parental strain names [e.g., (F344/NNia x BN/RijNia)F1]. The correct formal name should be given the first time the hybrid is mentioned in a publication; an abbreviated name can be used subsequently [e.g., F344/NNia x BN/RijNia F1 (hereafter called FBNF1)].

Hybrids from backcrosses and three- or four-way crosses are designated on the same basis, that is, by giving in parentheses the designation of the female parent first, followed by a multiplication sign and the designation of the male parent, followed by the generation number, for example, [(F344/NNia x BN/Rij/NNia)Fl x LEW/NHsd]Fl.

3. GENES

3.1 Names of Loci

Names of loci should be brief and should be chosen to convey as accurately as possible the characteristic by which the gene is usually recognized, including coat color, a morphological effect, a change in an enzyme or other protein, disease susceptibility or resistance, resemblance to a human syndrome, or a DNA sequence identified by a DNA probe for the gene or by sequence analysis.

3.2 Symbols for Loci

Symbols for loci should typically be two-, three-, or four-letter abbreviations of the name in italics. For ease in finding loci in alphabetical listings, the initial letters of names and symbols should, where possible, be the same. A number may be included for a protein in which a number is part of the recognized name or abbreviation, but the symbol should always begin with a letter (e.g., C4 and C6 for the fourth and sixth components of complement). Roman numbers, Greek letters, names of people, and names of places should not be used for gene names or symbols. Except in the case of loci first discovered because of a recessive mutation (see Sec. 3.5), the initial letter of the locus symbol should be a capital, and all others should be in lower case (e.g., di for diabetes insipidus; Hbb for hemoglobin ß-chain).

The discovery of a morphological, biochemical, or antigenic variant does not necessarily indicate the discovery of a new locus. Appropriate genetic tests should be conducted to show Mendelian segregation, and identity or lack of identity with known loci should be established as far as possible by mapping or by testing for allelism. Loci can also be identified by somatic cell genetics or studies of DNA.

A proposed new symbol must not duplicate one already used for another locus, even if the gene effect is very different. Listing of a gene symbol in Rat Newsletter establishes priority (see Sec. 6, Resources).

3.3 Loci That Are Members of a Series

Loci that are members of a series specifying similar proteins or other characteristics (e.g., isoenzymes and alloantigenic loci) should be designated by the same letter symbol and a distinguishing number without a hyphen (e.g., Es1, Es2, and Es3 for esterase loci; RT1, RT2, and RT3 for alloantigenic loci).

For morphological or "visible" loci with similar effects (e.g., genes that cause hairlessness), distinctive names should be given because the gene actions and gene products might prove to be very different (e.g., fz for fuzzy and rnu for Rowett nude).

3.4 Homology with Other Organisms

It is highly desirable that terminology for homologous genes be standardized among species. Therefore, for a rat gene that is homologous with a gene in another species, the symbol selected should be that already adopted for the other species, provided that it does not duplicate a symbol already in use for a different locus in the rat. To avoid such duplication, the symbol should be modified to one that resembles that used in the other species but does not duplicate one already in use for a different locus either in the rat or in the other species.

Where possible, the numbering of homologous loci in a series should be made concordant in various species, with locus 1 in the rat corresponding to the locus A in other species, locus 2 with locus B, and so on.

3.5 Alleles

Alleles should be designated by the locus symbol and a superscript. In computerized symbols the superscript may be denoted by prefixing an asterisk (e.g., Hbb^b or Hbb*b). Allele superscripts should typically be one or two lower-case letters and, if possible, should convey additional information about the allele (e.g., c^h for Himalayan allele of c or albino). If information is too complex to be conveyed conveniently in the symbol (e.g., biochemical properties or antigenic specificities), the alleles are still given superscripts (e.g., Pgm1^a, [Pgm1^b), but the information concerning the allelic properties is shown in catalogs or tables.

For the first discovered allele in cases in which there is clearly a wild type, no superscript is used (e.g., fa for fatty). When further alleles are discovered, the first mutant allele may still be written without a superscript (e.g., fa for fatty, fa^cp for corpulent).

Recessive alleles of a mutant gene should be indicated by a lower-case initial letter (e.g., a for nonagouti; rnu for Rowett nude). All other alleles--whether dominant, codominant, or having dominance relationships that vary with the method of assessment--should be indicated, as for the locus symbol, by a capital initial letter followed by lower-case letters (e.g., Ca for hereditary cataract).

Wild-type alleles should be designated by a plus sign with the locus symbol as a superscript (e.g., +^d, +^c). Reversions from a mutant allele to the wild type should be distinguished from the original wild-type allele by the locus symbol with a plus sign as a superscript (e.g., d⁺, c⁺). A plus sign may be used alone when the context leaves no doubt as to the locus represented (e.g., in genetic formulas).

Indistinguishable alleles of independent origin (e.g., recurrences and reversions to wild type) should be designated by the existing gene symbol with a series symbol appended as a superscript. The series symbol should consist of a number corresponding to the serial number of the recurring allele in the laboratory of origin plus the laboratory code. To avoid confusing the number 1 and the letter l, the first-discovered recurring allele may be left unnumbered and the second recurring, allele numbered 2 (e.g., in mice, bg for beige; bg^J for a recurrence of the mutation bg at the Jackson Laboratory; bg^2J for a second recurrence of the mutation bg at the Jackson Laboratory).

Mutations or other variations that occur in known alleles (except for alloantigenic systems-see Sec. 3.15.2) are designated by a superscript m and an appropriate series symbol, which consists of a number corresponding to the serial number of the mutant allele in the laboratory of origin plus the laboratory code. The symbol is separated from the original allele symbol by a hyphen (e.g., Mup1^a-m1Pit for the first mutant allele of Mup1^a found by the University of Pittsburgh Department of Pathology). For known deletions of all or part of an allele, the superscript m may be replaced with the superscript dl. This nomenclature is used for naming targeted mutations (often called "knockout" mutations), as well as spontaneously occurring ones (see also Sec. 3.20, Transgenes).

3.6 Phenotype Symbols

Phenotype symbols, if they are necessary (e.g., antigen loci, enzyme loci), should be the same as genotype symbols but in capital letters, not italicized, and with superscript characters lowered to the line. The phenotypes of heterozygotes should be written as in the following examples: ES1A, ES1C, and ES1AC for phenotypes associated with the Es1 locus and RT6A and RT6B for phenotypes associated with the RT6 locus.

3.7 Gene Complexes

Gene complexes are considered to exist when a number of apparently functionally related loci are closely linked. Alternative states of complexes are referred to as haplotypes, rather than as alleles. Known complexes are of two main types: less extensive complexes that involve duplicated loci or in which operators or cis-acting regulators of structural genes for protein show little or no recombination with the loci on which they act, and very extensive complexes that might involve hundreds of related loci and for which special rules might be necessary.

The existence of a gene complex, as opposed to the presence of multiple types of variation in a structural gene, should not be postulated without good evidence. Different mutations in a structural gene can affect not only electrophoretic mobility but also activity and stability, and chances in 5' or 3' regulatory sequences can cause apparent changes in tissue specificity or inducibility. Thus, such changes should be attributed to mutations in the structural gene unless there is good evidence otherwise.

To distinguish different loci of a complex, the basic symbol should have appended a single lower-case letter in italics designating the presumed function or means of identification of the locus, such as [s (structural), e (electrophoretic), r (regulatory), t (temporal), or m (mitochondrial). This letter should be set off by a hyphen (e.g., Bgl-e, ß-galactosidase electrophoretic), except for numbered unlinked loci in a series, in which case the letter should follow the number without a hyphen (e.g., Adh1t for alcohol dehydrogenase-2 temporal). When it is discovered that a previously described locus is part of a complex, a letter indicative of its function or means of identification should be added to the basic symbol to form the new symbol for the already known locus, and a different letter should be added to form the symbol for the newly discovered locus. For example, hypothetically, the electrophoretically detected Adh2
locus, after discovery of a temporal regulator, becomes Adh2e (i.e., Adh2 electrophoretic), and the regulator is called Adh2t (i.e, Adh2[ temporal). The basic symbol (e.g., Adh2) then represents the entire complex. If necessary for clarity, the complex may be additionally indicated by enclosing the basic symbol in parentheses or in brackets.

Haplotypes are designated by the symbol for the complex with a superscript lower-case letter. The components of the haplotype can be briefly indicated as in the following hypothetical example: Adh2^a or (Adh2) = Adh2e^a Adh2t^a = Adh2e^at^a. If two or more closely linked and functionally related structural loci have been given serial numbers, the complex, loci, and haplotypes should be indicated as in the following hypothetical example: complex, Amy or (Amy); loci, Amy1 and Amy2; haplotypes, Amy^a or (Amy)^a = Amy1^a Amy2^a = Amy1^a2^a.

Distantly acting regulators should be given locus symbols different from but related to the locus they regulate and preferably with the same initial letter (e.g., hypothetically, Gdr1 for a regulator of the glucose-6-phosphate dehydrogenase locus Gpd).

The list of extensive complexes with special rules continually increases. Special rules are needed because the various complexes differ widely in their structure, and no suitable single nomenclature system has yet been found that is adequate for all the complexes. Complexes with special rules are the following:

· the major histocompatibility complex and other alloantigenic systems (see Sec. 3.15)

· immunoglobulin complexes (see Sec. 3.16)

· globin gene complexes (see Sec. 3.17)

· homeobox-containing gene complexes (see Sec. 3.18)

· cytochrome P450 (see Sec. 3.19)

In some cases, the rules for these gene complexes might be formulated by a separate committee that covers more than one species.

3.8 Pseudogenes

The symbol for a pseudogene located away from the main gene complex should consist of the locus symbol followed by a hyphen, the suffix ps, and an appropriate serial number (e.g., cytc-psl for the first of approximately 30 known pseudogenes of cytochrome C located away from the structural gene locus).

3.9 Lethals

The symbol for a recessive lethal with no known heterozygous effect and an unidentified function consists of a lower-case letter l followed by the chromosome number of location in parentheses and a series symbol that indicates the serial number of the lethal in the laboratory of origin. No examples have yet been described in the rat; in the mouse, l(17)2Pas is the second lethal on chromosome 17 found at the Pasteur Institute.

Such symbols should be considered as provisional. The lethal should be renamed if it is found to be allelic with a known gene or if the underlying defect becomes understood.

3.10 Viruses

Nomenclature for genes related to the expression of viral antigens or to sensitivity or resistance to viruses should follow the standard rules for gene nomenclature, i.e., symbols should be italicized with the initial letter a capital and all others in lower case. Where possible and appropriate, the letters of the symbol should be those by which the virus is usually known. Successive loci concerned with the same virus should be distinguished by appending a number. Locus symbols ending in v should be reserved for viral loci. Little is known about viral loci in the rat; however, in the mouse, Mtv-l is a locus concerned with induction of mammary tumor virus, MTV, and Fv-1 and Fv-2 are loci concerned with resistance to Friend virus.

3.11 Oncogenes

Nomenclature for cellular oncogene sequences should follow the standard nomenclature for oncogenes. However, in lists of symbols and maps, the prefix c- denoting cellular sequence should be omitted and the initial letter of the symbol should be capitalized if it is not already (e.g., c-myc becomes Myc for the myelocytoma oncogene, and c-Hras1 becomes Hras1 for the Harvey rat sarcoma-1 oncogene).

The names and symbols of oncogenes should be regarded as provisional until the true functions of the genes become known, when they should be renamed (e.g., Erbb becomes Egfr for the epidermal growth factor receptor, and Sis becomes Pdgfb for the platelet-derived growth factor, ß polypeptide).

3.12 Mitochondrial Genome

The symbol for a locus in the mitochondrial genome should consist of the prefix mt followed by a hyphen and the main symbol.

3.13 Restriction-Fragment Length Polymorphisms

Restriction-fragment length polymorphism (commonly known as RFLP) can occur as

· Variation in DNA sequence within exons of a known gene.

· Variation in DNA sequence within introns or within flanking sequences of a known gene.

· Variation in DNA sequence outside exons or introns but detected by a probe for the known gene (e.g., the Hpa site variant 5 kb from the 3' end of the human ß-globin structural gene).

· Variation in DNA sequence detected using an arbitrary DNA sequence as a probe.

The first two types of variation should be described according to current rules for nomenclature of gene loci and alleles so that these variants can be listed both in a compilation of restriction-fragment length variants and in lists of gene loci.

For the third type, symbols for the restriction fragments should consist of the capital letter D (for DNA), the gene symbol, and a number (e.g., the Hpa site variant cited above would be symbolized DHbb1, the 1 indicating that this was the first probe found that detected a polymorphism). The variation in possession of the Hpa site can be described in terms of alleles. Thus, the presence of the site would be designated DHbbl^a and the absence DHbb1^b. If the allele in which the variation occurs is known, it should be indicated in the symbol (e.g., DHbb^d1a).

For the fourth type, it is not possible to ascertain whether the variation fits into any of the first three categories. The nomenclature should follow that in human gene mapping for provisional nomenclature (Skolnick and Francke, 1981).

An arbitrary probe is given a name composed of four parts: D for DNA, the chromosome number or 0 for unassigned segments, the laboratory code, and a number to give uniqueness to the probe (e.g., in mice, D1Pas5 is the fifth chromosome 1 probe developed at the Pasteur Institute and D17Leh48 is a chromosome 17 probe designated number 48 by Lehrach). Again, D1Pas5^a could indicate possession of a restriction site for a particular enzyme and D1Pas5l^b its absence. If the arbitrary sequence is later shown to be at a known locus, the nomenclature should be altered to take this into account.

Anonymous DNA segments from the human genome that hybridize with rat DNA and are mapped to a rat chromosome should retain their human symbol, and this should be followed by a lower case h to denote the human origin (e.g., D21S56h for a DNA segment from human chromosome 21).

3.14 Biochemical Variants

Biochemical nomenclature should be in accord with the rules of the International Union of Biochemistry's Commission on Biochemical Nomenclature. The nomenclature recommended by the commission is published periodically in major international biochemical journals, such as the Journal of Biological Chemistry and the Biochemical Journal[. Enzymes and other biochemicals have both formal and trivial names. The correct formal name should be given the first time a substance is mentioned in a publication [e.g., D-glucose-6-phosphate:NADP⁺ 1-oxidoreductase (E.C. 1.1.1.49)]; trivial names (e.g., glucose-6-phosphate dehydrogenase) or abbreviations (e.g., G6PD or GPD) can be used subsequently. The commission's nomenclature is used in periodicals, reference works, and textbooks of biochemistry.

3.14.1 Symbols for structural loci. Symbols for structural loci should typically be two-, three-, or four-letter abbreviations of the official commission name of the enzyme, protein, or other entity. The initial letter of the symbol should be capitalized [e.g., Gpd1 for the first identified structural locus of GPD). In the case of biochemical variants, beginning the locus symbol with a lower case letter to indicate a recessive mutant gene or a capital letter to indicate a dominant mutant gene should generally be avoided. Such nomenclature is not suited to polymorphic systems of alleles, and the dominant-recessive relationship usually varies and depends on the method used to assess it.

A Greek letter preceding the name of an enzyme or other protein should be changed to an appropriate English letter and placed at the end of the locus symbol (e.g., in mice, Fuca for a-fucosidase). That permits a rational alphabetic ordering of locus symbols. Similarly, an adjective describing tissue specificity or another property of an enzyme or protein should be placed after the noun to allow appropriate alphabetic ordering (e.g., in mice, Actc for actin, cardiac, and Acts for actin, skeletal).

3.14.2 Symbols for loci specifying isoenzyme structure or polypeptide chains. A series of loci specifying structurally different isoenzymes that catalyze the same or similar reactions or different potypeptide chains of a protein should be designated by the same letter symbol for the structural locus with the addition of a distinguishing number [e.g., Acp1 and Acp2 for loci of structurally different isoenzymes of orthophosphoric-monoester phosphohydrolase, acid optimum (E.C. 3.1.3.2, acid phosphatase- 1)].

3.14.3 Homology with other organisms. It is highly desirable that terminology for homologous genes be standardized among species. Therefore, as in the standard rules, in choosing a gene symbol an attempt should first be made to discover and use any symbols already adopted for the same locus in other species. However, care should be taken not to duplicate symbols already in use in the rat for other loci. If duplication would occur, the symbol should be modified to resemble that used in the other species without duplicating the symbol used for a different gene in that or another species (e.g., CA is the symbol for carbonic anhydrase, in humans, but it is used in the rat for hereditary cataract, so the symbol used for carbonic anhydrase in the rat should be that used in the mouse, Car). Where possible, the numbering of homologous loci in a series should be made concordant in various species, with locus 1[ in the mouse and rat corresponding to the locus A in other species, locus 2 with locus B, and so on (e.g., Car1, Car2).

It is not appropriate to insert the letter r or R (for rat) as the first letter of the symbol for a locus with homologues in other species because all rat locus symbols would then begin with the same letter.

3.14.4 Alleles. An allele should be designated by the locus symbol with an added superscript, as in the standard rules. In describing alleles, whether found in inbred strains or in the wild, it is desirable to report the phenotype of a number of widely used inbred strains. One strain should arbitrarily be designated the prototype strain for each allele, because variation that has not been detected by the methods used might be present in each allelic class. If an apparently identical allele in another strain is found by new methods to differ from that in the prototype strain, it should be assigned a new alphabetical symbol as a superscript and a prototype strain for the new allele should be designated. This system permits the orderly assignment of symbols to newly identified alleles and allows ready comparisons of new variants with previously reported variants.

Locus and allele symbols are necessarily brief and cannot contain more than a small fraction of the known information. Additional information can be contained in gene descriptions, which in some cases, can be collected in catalogs or tables. For example, haplotypes or alleles of the mouse hemoglobin a-chain locus Hba specify at least five polypeptides. In general, each strain produces a single polypeptide, but in some strains, two polypeptides are produced. The loci encoding the polypeptides of an allele can be assigned letter designations corresponding to the allele, and information about the amino acid composition of the chains produced by the alleles can be shown in tables.

3.14.5 Proteins detected as spots on 2D-gels but not identified. Locus symbols for proteins detected as spots on 2D-gels should be given only if genetic variation or gene location is established, if the gene behaves in a Mendelian fashion, and if the protein is known (or strongly believed) to be distinct from those already named. Such a symbol should consist of four parts: the capital letter P for protein, a number indicating the chromosome that holds the coding gene (using the number 0 to indicate unknown location), a laboratory code, and a number distinguishing the protein from others found in the same laboratory (e.g., P0Pas1 for the first 2D protein in a Pasteur Institute series). The number of digits in the distinguishing number should be kept as low as possible for convenience in listing. When the protein is identified, the locus should be given a new and appropriate symbol.

3.14.6 Phenotype symbols. Phenotype symbols, if they are necessary, should be the same as genotype symbols but capital letters, not italicized, and with superscript characters lowered to the line (e.g., GST1A and GST1B for phenotypes associated with the Gst1 locus).

When information concerning subunit structure is available, phenotype symbols should reflect the subunit composition, according to the rules of the International Union of Biochemistry, by use of capital letters (Green, 1979). Details are given in rules for gene nomenclature (see Sec. 3.6).

Identification of loci should not be assumed from the discovery of phenotypic structural variation; crosses should be made to show Mendelian segregation of the alleles. Official gene symbols should not be assigned to variants found in wild rats unless appropriate genetic tests for allelism with known similar variants are carried out. In the absence of genetic tests, phenotypic symbols (as in the standard rules) should be used with a description of the criteria for establishing identity with phenotypes of inbred strains.

3.14.7 Genetic variants affecting enzyme activity. Genetic variants that affect enzymes can do so for reasons other than a direct change in the catalytic activity per molecule of the enzyme under study. Presumptive mutations in this group include those affecting enzymatic activity with no discernible alteration in physical or chemical properties of the enzyme and those producing tissue-specific differences in activity. Mutations producing this type of quantitative variation might or might not prove to be allelic or to form a gene complex with the structural locus of the enzyme in question. When allelic with the structural locus, they should be designated according to the standard rules. Even when not allelic, or when the structural locus has not been identified, the new locus should be named on the basis of its discernible phenotype, following the above rules (e.g.,Ak1 for adenylate kinase-1, a locus in rats that controls the level of the enzyme).

3.15 The Major Histocompatibility Complex (MHC) and Other Alloantigenic Systems

3.15.1 Symbols. The locus of an alloantigenic system should be designated by RT followed by a number (e.g, RT1, RT2, RT3). The numbers should be assigned in the order of discovery of the loci. The MHC is designated RT1.

3.15.2 Haplotypes. Haplotypes should be given superscript letters as follows:

· Haplotypes of inbred strains of rats should be designated by lower-case letters from a to a to u omitting r (e.g., RT1^a). Used alone, m indicates the haplotype of the MNR strain (RT1^m). When used with another haplotype symbol, m indicates a mutant form of that haplotype (e.g., RT1^lm1-see below).

· A haplotype of a laboratory recombinant should be designated by the superscript haplotype symbol r followed by a series number (e.g., RT1^r1, RT1^r2).

· A variant haplotype should be designated by adding the letter v, and a series number to the haplotype superscript symbol (e.g., LEW = RT1^l, F344 = RT^lv1).

· A mutant haplotype should be designated by adding the letter m and a series number to the haplotype superscript symbol (e.g., RT1^lm1).

· A haplotype of a wild rat should be designated by a superscript w, followed by a series number (e.g., RT1^w1).

· The letters x, y, and z are reserved as generic designations of unknown haplotypes.

3.15.3 Congenic strains. A congenic strain involving an alloantigenic system should be designated by the name of the inbred background strain, either a hyphen and the differential locus or a period and an abbreviation of the differential locus, the name of the donor strain enclosed in parentheses, a slash, and the laboratory code of the strain's developer (e.g., BN-RT1^c(AUG)/Pit or BN.1C(AUG)/Pit). The name may be abbreviated after the first time it is used in a publication by leaving out the name of the donor strain [e.g., BN-RT1^c(AUG)/Pit is abbreviated BN-RT1^c/Pit, and BN.1C(AUG)/Pit is abbreviated BN.1C/Pit].

A congenic strain involving an alloantigenic system with a recombinant haplotype should be designated by the name of the inbred background strain, either a hyphen and the differential locus or a period and an abbreviation of the differential locus, a slash, and the laboratory code of the strain's developer (e.g., PVG-RT1^r1/Ola or PVG.1R1/Ola).

3.15.4 Loci. Each locus should be designated by a capital letter. An allele is designated by a superscript denoting the haplotype from which the locus originated. The letters should be assigned in the order of discovery starting with A. The order in which the letters are written should indicate the sequence of loci on the chromosome, as determined by mapping studies (e.g., RT1.A^aB^aD^aE^aC^a). Although loci within the MHC should be designated on the basis of laboratory-derived recombinants, uncompromising adherence to this precept greatly reduces the utility of the nomenclature as a shorthand description of the information that is available on a given strain. A reasonable compromise is to restrict genetic diagrams showing the relative positions of the various loci to cases in which each locus is defined by a recombination and to allow the use of locus designations on an inferential basis in
other cases. For example, a recombination in a given strain may define two loci, A and B, which encode antigens defined by the appropriate serological test. Then it should be permissible to ascribe these functions to the same loci in other strains, even though they have not yet been defined by recombination in these strains, provided that the inferential nature of the assignment is clearly stated.

3.15.5 Reporting new systems. The report of a new antigenic system should include the following data: demonstration that it segregates independently of known systems; strain distribution pattern; tissue distribution pattern; and nomenclature assignment, using first the provisional (local laboratory) name and, after a period of usage and confirmation, the formal name.

3.16 Immunoglobulin Complexes

The following rules were developed for mice by Green (1979) and were adopted for rats at the Fourth International Workshop on Alloantigenic Systems in the Rat (reported by Gutman et al., 1983). The heavy-, kappa-, and lambda-chain regions are designated Igh, Igk, and Igl, respectively. The constant subregions are designated Igh-C, Igk-C, and Igl-C. Individual loci in these subregions are designated by numbers, which are assigned chronologically; however, the hyphen that originally appeared in the designation of an individual locus has been dropped. As a result, the kappa-chain locus in the rat is called Igk1, the alpha-chain locus is Igh1, the gamma-2b locus is Igh2, and the gamma-2c locus is Igh3. Although results of DNA cloning studies (Sheppard and Gutman, 1981) make it unlikely that new loci will be discovered for rat kappa chains, the number 1 in the Igk1 designation is kept for clarity. An allele of an individual locus is designated by the symbol for the locus and a superscript lower-case letter (e.g., Igh1^a, Igh1^b).

The variable subregions are designated Igh-V, Igk-V, and Igl-V. An individual locus in one of these subregions that encodes a specific immunoglobulin chain is designated by a hyphen and two or three letters or by a hyphen, two letters, and a number (e.g., in mice, Igh-Dex, Igh-Pc, Igk-Ef1). The symbol after the hyphen for a variable-region locus should be related to the antigen for which the immunoglobulin is specific or to the method used for recognizing the variant. Allelic symbols are superscript lower-case letters such as a and b when allelic markers are well established (e.g., in mice, Igk-Ef1^b, Igk-Ef1^a) or a and o when the allelic nature of markers is in doubt and the alleles are postulated to determine the presence or absence of a marker (e.g., in mice, Igh-Dex^a, Igh-Dex^o).

3.17 Globin Gene Complexes

3.17.1 Symbols. The a- and ß-globin genes should be considered as constituting gene complexes and should be given the names and symbols hemoglobin-alpha, Hba, and hemoglobin-beta, Hbb.

3.17.2 Haplotypes. The different forms of the complexes should be considered as haplotypes and designated by superscript lower-case letters (e.g., Hbb^a, Hbb^b). The letters m and o should be omitted as they might be confused with 'mutant' or 'null', and the letter w should be reserved for wild-derived haplotypes. If the alphabet becomes exhausted, a series of two-letter symbols should be used (e.g., Hbb^a, Hbb^b).

3.17.3 Loci within complexes. The individual loci in the Hba andHbb complexes should be denoted by lowercase letters, in some cases followed by numbers and set off from the main symbol by a hyphen (e.g., in mice, Hba-x, Hbb-y). The numbers should run from the 5' end.

3.17.4 Alleles. The alleles of genes in the complexes should be denoted by superscript lower-case letters indicating the haplotype of origin (e.g., in mice, Hbb-y^a and Hbb-y^b for the alleles of Hbb-y occurring in haplotypes Hbb^a and Hbb^b).

3.17.5 Variant haplotypes and alleles. A new haplotype or allele that arises in a known haplotype by mutation or another change should be denoted by appending a serial number to the haplotype superscript. If the change is known to be caused by mutation or deletion within a particular allele, this should be indicated by adding a hyphen and an appropriate letter symbol and serial number to the allele superscript (e.g., in mice, Hbb^a2 and Hbb^a3 for the first two variants of the haplotype Hbb^a, [Hbb-b1^d-m1 for the first mutant allele of the gene Hbb-b1[^d, and Hbb-b1^d-dl1 for the first deletion found in the allele Hbb-b1^d).

3.17.6 Pseudogenes. A pseudogene located at a distance from a main complex should be given a locus symbol consisting of the main haplotype symbol, a hyphen, the lower-case letters ps, and a serial number (e.g., in mice, Hba-ps3 and Hba-ps4 for a-globin pseudogenes located away from the main Hba complex).

3.18 Homeobox-containing Genes

The following is based on modifications made by the International Committee for Standardized Nomenclature for Mice to recommended nomenclature drawn up at a meeting on homeobox-containing genes and published by Martin (1987).

Any homeobox-containing gene or genomic fragment may be given the designation Hox provided that a substantial fraction of the amino acids that it encodes are identical with those of the homeobox in the Drosophila Antennapedia gene.

The criterion for designating a new Hox locus is that it occupies a different map position (i.e., it is physically distinct) from all other known Hox loci. Until this criterion is met, a new homeobox-containing gene or genomic sequence should be designated by a laboratory name. The designation of any new Hox locus or group of loci (complex), will be determined as follows:

· If the new locus is not apparently closely linked to any previously described Hox locus, a number should be appended. The numbers should be assigned sequentially (e.g., Hoxl, Hox2, Hox3). If two or more homeobox-containing loci are present, they will be designated by decimal numbers (e.g., Hox-2.1, Hox-2.2). Decimal subdesignations should, where possible, reflect the linear order of the Hox loci along the chromosome.

· If the new locus is known to be closely linked to a previously designated Hox locus, it should be given the numerical designation of that locus (or complex) and the next available decimal subdesignation in the series. Decimal subdesignations should, where possible, reflect the linear order of the Hox loci along the chromosome.

3.19 Cytochrome P450

The symbol Cyp is used to designate cytochrome P450 loci. The root symbol is followed by a number to indicate the P450 family, a lower-case letter to indicate the subfamily, and another number to indicate the individual gene within the family and subfamily (e.g., Cyp2a1, Cyp2b1). Numbers are assigned in the order in which genes are identified (e.g., Cyp2a1, Cyp2a2, Cyp2a3). Pseudogenes are designated by appending the lower-case letters ps (e.g., Cyp2c6ps). Additional details are given by Nebert et al. (1989).

3.20 Transgenes

Transgenes are named according to the following conventions. Examples given are for the mouse.

3.20.1 Symbols. A transgene symbol consists of three parts, all in Roman type, as follows:
TgX(YYYYYY)#####Zzz,
where TgX = mode,
(YYYYYY) = insert designation,
##### = laboratory-assigned number, and
Zzz = laboratory code.

3.20.1.1 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 (see Sec. 3.5). 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, Mbp^m1Dn, 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 gene, is incidental to "knocking out" or mutating, the targeted locus (see also Lyon, 1989a). 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 in Section 3.20.1.4.

3.20.1.2 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:

· Short symbols (six or fewer characters) are preferred. The total number of characters in the insert designation plus the laboratory-assigned number may not exceed 11 (see below); therefore, if seven or eight characters are used, the number of digits in the laboratory-assigned number will be limited to four or three, respectively.

· The insert designation should identify the inserted sequence and indicate important features. If the insertion uses sequences from a named gene, it is preferable that the insert designation contain the standard symbol for that gene. If the gene symbol would exceed the spaces available, its beginning letters should be used. Hyphens should be omitted when normally hyphenated gene symbols are used. For example, Ins1 should be used in the symbols of transgenes that contain either coding or regulatory sequences from the mouse insulin gene (Ins-1) as an important part of the insert designation. Resources are available to identify standard gene symbols (see Sec. 6).

· Symbols that are identical with other named genes in the same species should be avoided. For example, the use of Ins to designate "insertion" would be incorrect.

· For consistency, a series of transgenic animals produced with the same construct might be given the same insert designation. However, that is not required: some lines might manifest unique and important characteristics (e.g., insertional mutations) that would warrant a unique insert designation. If two different symbols are used for the same construct in different transgenic lines, the published descriptions should clearly identify the construct as being the same in both lines. Two different gene constructs used for transgenic animal production, either within a laboratory or in separate laboratories, should not be identified by identical insert designations. Designations can be checked through the available resources (see Sec. 6).

· A standard abbreviation can be used as part of the insert designation (see Sec. 3.20.1.4 for an example). If a standard abbreviation is used, it should be placed at the end of the insert. These now include
An (anonymous sequence),
Ge (genomic clone),
Im (insertional mutation),
Nc (noncoding sequence),
Rp (reporter sequence),
Sn (synthetic sequence),
Et (enhancer trap constuct), and
Pt (promoter trap construct).

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

· The insert designation should identify the inserted sequence, not its location or phenotype.

3.20.1.3 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 ILAR (see Secs. 1.5 and 6).

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.

3.20.1.4 Examples.

· C57BL/6J-TgN(CD8Ge)23Jwg. The human CD8 genomic clone (Ge) inserted into C57BL/6 mice from the Jackson Laboratory (J); the 23rd mouse screened in a series of microinjections in the laboratory of Jon W. Gordon (Jwg).

· Crl:ICR-TgN(SVDhfr)432Jwg. The SV40 early promoter driving a mouse dihydrofolate reductase (Dhfr) gene; 4 kilobase plasmid; the 32nd animal screened in the laboratory of Jon W. Gordon (Jwg). The ICR outbred mice were obtained from Charles River Laboratories (Crl).

· TgN(GPDHIm)1Bir. The human glycerol phosphate dehydrogenase (GPDH) gene inserted into zygotes retrieved from (C57BL/6J x SJL/J)F1 females; the insertion caused an insertional mutation (Im) and was the 1st transgenic mouse named by Edward H. Birkenmeier (Bir). No strain designation is provided because each zygote derived from such an Fl hybrid mouse has a different complement of alleles derived from the original inbred parental strains.

· 129/J-TgH(SV40Tk)65Rpw (hypothetical). An SV40-thymidine kinase (Tk) transgene targeted by homologous recombination to a specific but anonymous locus using embryonic stem cells derived from mouse strain 129/J. This was the 65th mouse of this series produced by Richard P. Woychik (Rpw).

3.20.2 Abbreviation. Transgene symbols can be abbreviated by omitting the insert. For example, the full symbol TgN(GPDHIm)1Bir 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.

3.20.3 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. The allele of the locus identified by the insertion can then be identified by the abbreviated transgene symbol (see Sec. 3.20.2) according to the conventions adopted for the species. Two examples follow.

· ho^TgN447Jwg. The insertion of a transgene into the hotfoot locus (ho).

· xxx^TgN21Jwg. The insertion of a transgene that leads to a recessive mutation in a previously unidentified gene. A gene symbol for xxx must be obtained from a species-genome data base or member of a nomenclature committee (see Sec. 6, Resources).

4. CHROMOSOMES

The rules for nomenclature of rat chromosomes follow the human system for cytogenetic nomenclature, which has been described in detail (Harnden and Klinger, 1985). A standardized system for the numbering of rat chromosomes has been published by the Committee for a Standardized Karyotype of Rattus norvegicus (1973). Levan (1974). described the chromosome banding pattern of the rat and assigned numbers to each band in accordance with the human nomenclature system. A high-resolution banded idiogram has been produced by Satoh et al. (1989). The most recent tabulation of rat chromosomes is given in Levan et al. (1992).

5. OUTBRED STOCKS

5.1 Definition

A stock is regarded as outbred when it has been maintained as a closed colony for at least four generations. To minimize changes caused by inbreeding and genetic drift, the population should be maintained in such numbers as to give less than 1 percent inbreeding per generation. Under these conditions, a heterozygous breeding population is expected to reach equilibrium and to produce a stock of stable genetic composition. Formerly inbred strains may be included after four generations of closed outbreeding, provided that continued outbreeding is intended. Outbred stocks are not necessarily highly variable genetically. The degree of genetic variability of any individual stock can only be determined by studying the appropriate genetic markers.

5.2 Symbols

The stock designation consists of a laboratory code, a colon, and two to four capital letters (e.g., Hsd:LE, Crl:WI). The transfer of an outbred stock between breeders is indicated by listing the laboratory codes in chronological order from left to right (e.g., BluHsd:LE for rats obtained by Harlan Sprague Dawley from Blue Spruce Farms). To avoid excessively long designations, only two laboratory codes should be used: that of the current holder preceded by that of the holder from whom the stock was obtained.

An outbred stock that contains a specified mutation is designated by the stock symbol, a hyphen, and the gene symbol (e.g., Crl:ZUC-fa).

An outbred stock designation must not be the same as that for an inbred strain of the same species. As an exception, a stock derived by outbreeding a formerly inbred strain mat continue to use the original symbol; in this case, the laboratory code preceding the stock symbol characterizes the stock as outbred. New stock symbols should be registered with Dr. M. F. W. Festing (see Sec. 6, Resources).

5.3 Widely Accepted Outbred-Stock Symbols

The following symbols for outbred rats have been widely accepted for more than 20 years (ILAR, 1970):

6. RESOURCES

Assistance in naming rat strains and stocks can be obtained from the following organizations:

· Institute of Laboratory Animal Resources (ILAR). Assigns laboratory codes; assists in naming rat strains and stocks; provides rules for naming rat strains and stocks. Contact: Dr. Dorothy D. Greenhouse, ILAR, National Research Council, 2101 Constitution Avenue, Washington, DC 20418, USA (telephone. 1-202-334-2590: fax, 1-202-334-1687; Bitnet, DGREENHO@NAS).

· PALM Institute. Assists in naming rat strains and stocks; provides rules for naming rat strains and stocks. Contact: Dr. Takashi Natori, Director, PALM Institute, N29 W4 2-1-215 Sapporo 001, Japan (telephone, 81-11-746-3988; fax, 81-11-746-6722).

· Registry of Inbred Strains. Maintains lists of inbred strains and outbred stocks of rats; assists in naming strains and stocks of rats; provides rules for naming rat strains and stocks. Contact: Dr. Michael F. W. Festing, Medical Research Council Toxicology Unit, Woodmansterne Road, Carshalton, Surrey SM5 4EF, UK (telephone, 44-81-643-8000: fax, 44-81-642-6583). As of June 1993, Dr. Festing's address will be IRC for Human Toxicity, Leicester University, University Road, Leicester LE2 7RH, UK.

· Rat News Letter. Publishes new inbred strain, gene, and other symbols for rats. Periodically publishes lists of strain and gene symbols, chromosome maps, and rules for rat nomenclature. Contact: Dr. Viktor Stolc, Editor, Rat News Letter, 2542 Hario Drive, Allison Park, Pittsburgh, PA 15101 (telephone and fax, 1-412-487-4289).

· 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 (telephone, 1-615-574-7776; fax, 1-615-574-9888; Bitnet, TUG@ORNLSTC; Internet, OWENSET@IRAVAX.HSR.ORNL.GOV).

· The Jackson Laboratory. Assists in naming transgenes; provides lists of named mouse genes. Contact: Dr. Muriel T. Davisson, The Jackson Laboratory, Bar Harbor, ME 04609 (telephone, 1-207-288-337 1; fax, 1-207-288-8982).

· 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 (telephone, 1-301-955-9705; fax, 301-955-0054).

References

Committee for a Standardized Karyotype of Rattus norvegicus. 1973. Standard karyotype of the Norway rat, Rattus norvegicus. Cytogenet. Cell Genet. 12:199-205.
Green, M. C. 1979. Genetic nomenclature for the immunoglobulin loci of the mouse. Immunogenetics 8:89-97.
Gutman, G. A., H. Bazin, O. V. Rokhlin, and R. S. Nezlin. 1983. A standard nomenclature for rat immunoglobulin allotypes. Transplant. Proc. 15:1685-1686.
Harnden, D. G., and H. P. Klinger, eds. 1985. An International System for Human Cytogenetic Nomenclature. Birth Defects: Original Article Series, vol. 21, no. 1. New York: March of Dimes Birth Defects Foundation.
ILAR (Institute of Laboratory Animal Resources) Committee on Nomenclature. 1970. A nomenclatural system for outbred animals. Lab. Anim. Care 20(5):903-906.
Levan, G. 1974. Nomenclature for G-bands in rat chromosomes. Hereditas 77:37-52.
Levan, G., C. Szpirer, K. K. Levan, J. Szpirer, and C. Hanson. 1992. The rat gene map 1992. Rat News Letter 27:10-34.
Lyon, M. F. 1989a. Rules and guidelines for gene nomenclature. Pp. 1-11 in Genetic Variants and Strains of the Laboratory Mouse. 2d ed., M. F. Lyon and A. G. Searle, eds. Oxford: Oxford University Press.
Lyon. M. F. 1989b. Rules for nomenclature of inbred strains. Pp. 632-635 in Genetic Variants and Strains of the Laboratory Mouse. 2d ed., M. F. Lyon and A. G. Searle, eds. Oxford: Oxford University Press.
Martin, G. R. 1987. Nomenclature for homeobox containing genes. Nature 325:21-22.
Nebert, D. W., D. R. Nelson, M. Adesnik, M. J. Coon, R. W. Estabrook. F. J. Gonzalez, F. P. Guengerich, I. C. Gunsalus, E. F. Johnson, B. Kemper, W. Levin, I. R. Phillips, R. Sato, and M. R. Waterman. 1989. The P450 superfamily: Updated listing of all genes and recommended nomenclature for the chromosomal loci. DNA 8:113.
Satoh, H., M. C. Yoshida, and M. Sasaki. 1989. High resolution chromosome banding in the Norway rat, Rattus norvegicus. Cell Genet. 50:151-154.
Sheppard, H. W., and G. A. Gutman. 1981. Complex allotypes of rat kappa chains are encoded by structural alleles. Nature 293:669-671.
Skolnick, M. H., and U. Francke. 1981. Report of the Committee on Human Gene Mapping by Recombinant DNA Techniques. Cytogenet. Cell Genet. 32:194-204.

In response to the perception of U.S. scientists that some genetically unique animal models have been lost or are at risk, partly because of financial problems but also for such other reasons as the death or retirement of scientists responsible for specific stocks, the Committee on Preservation of Laboratory Animal Resources was formed by the Institute of Laboratory Animal Resources. The committee was charged with documenting losses of animal models and resources resulting from funding inadequacies or other reasons, evaluating the long-term effects of such losses on biomedical research, assessing existing animal resources and the current mechanisms for maintaining them, and recommending cost-effective procedures for preserving genetic stocks. The committee identified the following important problems associated with preserving laboratory animal resources: lack of centralized planning, lack of standardized criteria for assessing the value of an animal model or resource, instability of funding, changes in government regulations and funding priorities, and complex maintenance requirements of many animal models.

Criteria for Preservation

To reduce the risk of losing valuable animal models, the committee recommended establishment of a long-term, stable, integrated program for safeguarding the nation's animal resources. The program should include mechanisms for identifying valuable animal resources, maintaining and preserving, them, and providing for their financial support. The following criteria were recommended rigorously evaluating, animal models considered for preservation:

· Importance of disease process or physiologic function. Animal models of severe or common human pathologic conditions or models used to study normal physiologic function are extremely valuable. Even models representing diseases not yet observed in humans are important. In all cases, the value of such models depends on the ability to maintain and to transmit reliably the relevant traits through breeding.

· Validity. The validity of many models depends on proper genetic management to preserve their unique traits and to ensure that the phenotype is predictable.

· Replaceability. The difficulty of replacing a model is a measure of its value. Models that are require years of selective breeding to develop or that arise as a consequence of spontaneous mutations (especially in animals with long generation times) must be considered relatively important.

· Versatility. The variety of problems that can be studied with a given animal model is a measure of its value.

· Use. If an animal model is used by a large number of laboratories, its value is high. The number of investigators using the model in research is a more important measure of use than is the number of animals used.

Dual Review of Requests for Support of Research Involving Investigator-Managed Animal Resources

Funds should be allocated specifically for developing and preserving important laboratory animal resources that are maintained in investigator-managed facilities. Such funds should be administered through a competitive grants program reviewed by an appropriately constituted group. In the case of the National Institutes of Health (NIH), these funds should be administered conjointly by all the institutes to provide a single focus of responsibility.

A Review Group for Laboratory Animal Preservation should be established to evaluate grant proposals that request funds to support investigator-managed resources. The group should be composed primarily of scientists who use animals in their own research. These scientists should represent a broad range of disciplines, including the study of pathogenesis of disease, basic physiologic processes, and fundamental genetics. In addition, there should be at least one geneticist who is capable of evaluating the genetic quality of the animals in a resource and at least one laboratory animal scientist who is capable of evaluating the health of the animals and the husbandry procedures for maintaining them. The responsibility of this group should be the uniform application of the criteria for evaluating animal resources described previously. In addition to reviewing the merits of a resource application, the review group could, if it were deemed preferable, recommend that the proposed resource be maintained at some other established facility.

Applications for support of investigator-managed animal resources, whether or not they are submitted in conjunction with applications for associated research, should be reviewed by the proposed group. Applications seeking support for both research and resource components would also be reviewed by the appropriate study section. Applicants preparing proposals with a resource component should describe and document the resource according to the criteria outlined above. To provide stability to resource colonies, grants should generally be made for a period of 5 years between competing renewals, irrespective of the duration of funding for the research component.

National Center for Laboratory Animal Resources

Many animal models are not used consistently in large numbers, so commercial breeders do not maintain them. They also might not be used continuously enough by any one investigator to warrant maintaining them as an investigator-managed resource. It is in such situations that a national center would meet a major need. A National Center for Laboratory Animal Resources would provide a source of genetically defined and appropriately monitored animals to ensure quality control and cost-effective maintenance. It could also hold duplicates of valuable animal resources, so that if individual colonies housing such animals were lost, the resource would survive. The center could distribute these animals for experimental purposes or as breeding nuclei.

In addition to distributing animals, the center would be a source of information about the various strains and stocks and would work actively to develop new and useful animal resources and unique methods of preserving them (e.g., cryopreservation). The center could form the core of a network of resource colonies, both commercial and investigator-based, to provide extensive national coordination of laboratory animal resources.

A critical part of the structure of the national center should be an advisory committee to set policy and make decisions about which species and which strains and stocks within a species should be maintained and what new animal resources should be developed. The advisory committee should be distinct from the Review Group for Laboratory Animal Preservation, although it should be composed of scientists with a similar scope of expertise. A committee with such a composition is critical to the success of the National Center for Laboratory Animal Resources. The advisory committee would represent the scientific community and ensure appropriate oversight of the hard decisions that are essential in allocating limited resources.

Conclusions

The system recommended in this report should not greatly increase the overall amount spent for animal resources, in as much as the present system is inefficient and has large hidden costs that result in duplication of support for maintaining animal models and animal colonies. An important cost-effective aspect of the system proposed by the committee is that only animal resources that merit support, as determined by an appropriate group using objective criteria, will receive such support.

It was the consensus of the committee members that these recommendations are realistic and cost-effective and can provide the basis for many research initiatives. It is believed that the necessary investment, including the costs of operating the committees suggested in this report, will be offset in part by savings of funds currently committed. For example:

· Central facilities can maintain the very highest standards of animal husbandry and genetic management and provide the healthiest possible animals for research purposes. At the same time, the cost of producing animals will be considerably less than the combined cost of producing them at multiple independent facilities.

· The proposed program should eliminate duplication of stocks by several investigators, who might or might not be actively using the stocks.

· The proposed program will eliminate the necessity of having breeding colonies maintained by investigators who require animals of only one sex, animals of only one age class, only pregnant females, or animals with special requirements. Thus, a single breeding colony of the same size that would be required by each investigator can efficiently satisfy the needs of several investigators.

· The scientists and staff who maintain central facilities can provide critical advice and expertise on the maintenance and experimental manipulation of specialized animal models; such advice and expertise in many instances will lead to more efficient and more humane use of animals in research.


Copies of the full report Important Laboratory Animal Resources: Selection Criteria and Mechanisms for Their Preservation [ILAR News 32(4):A1-A32, 1990] are available from the Institute of Laboratory Animal Resources, National Research Council, 2101 Constitution Avenue, Washincton, DC 20418.

a This study was supported by the National Research Council Fund, a pool of private, discretionary, nonfederal funds that is used to support a program of Academy-initiated studies of national issues in which science and technology figure significantly.

b Members of the committee: Dorothea Bennett (Chairman), Department of Zoology, University of Texas, Austin. Texas (deceased); Linda C. Cork, Division of Comparative Medicine, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland; Thomas J. Gill III, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Jon W. Gordon, Department of Obstetrics and Gynecology, Mt. Sinai School of Medicine, New York, New York; Andrew G. Hendrickx, California Primate Research Center, University of California, Davis, California; Larry E. Mobraaten. The Jackson Laboratory, Bar Harbor, Maine; and John L. VandeBerg, Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas.

For additional information about ILAR Journal, please contact Susan Vaupel, ELS, Managing Editor, at (202)334-2592, email svaupel@nas.edu, or fax (202)334-1687.