Laboratory Codes in Nomenclature and Scientific Communication (Advancing Organism Nomenclature in Scientific Communication to Improve Research Reporting and Reproducibility)

Abstract

Laboratory registration codes, also known as laboratory codes or lab codes, are a key element in standardized laboratory animal and genetic nomenclature. As such they are critical to accurate scientific communication and to research reproducibility and integrity. The original committee on Mouse Genetic Nomenclature published nomenclature conventions for mice genetics in 1940, and then conventions for inbred strains in 1952. Unique designations were needed, and have been in use since the 1950s, for the sources of animals and substrains, for the laboratories that identified new alleles or mutations, and then for developers of transgenes and induced mutations. Current laboratory codes are typically a 2- to 4-letter acronym for an institution or an investigator. Unique codes are assigned from the International Laboratory Code Registry, which was developed and is maintained by ILAR in the National Academies (National Academies of Sciences Engineering and Medicine and previously National Academy of Sciences). As a resource for the global research community, the registry has been online since 1997. Since 2003 mouse and rat genetic and strain nomenclature rules have been reviewed and updated annually as a joint effort of the International Committee on Standardized Genetic Nomenclature for Mice and the Rat Genome and Nomenclature Committee. The current nomenclature conventions (particularly conventions for non-inbred animals) are applicable beyond rodents, although not widely adopted. Ongoing recognition, since at least the 1930s, of the research relevance of genetic backgrounds and origins of animals, and of spontaneous and induced genetic variants speaks to the need for broader application of standardized nomenclature for animals in research, particularly given the increasing numbers and complexities of genetically modified swine, nonhuman primates, fish, and other species.

INTRODUCTION

In the current Guidelines for Nomenclature of Genes, Genetic Markers, Alleles, and Mutations in Mouse and Rat, published at the MGI and RGD websites respectively, the Laboratory Registration Code or Laboratory code “…identifies a particular institute, laboratory, or investigator that produced, and may hold stocks of, for example, a DNA marker, a mouse or rat strain, or were [sic] the creator of a new mutation. Laboratory codes are also used in naming chromosomal aberrations, transgenes, and genetically engineered mutations. Because Laboratory codes are key to identifying original sources, they are not assigned to ‘projects,’ but rather to the actual producer/creator individual or site …” (emphasis mine). Until the “laboratory code” registry and database were formalized online by ILAR in the 1990s, the terms “code,” “abbreviation,” and “symbol” were variably used to refer to an abbreviated designation for the source (holder, breeder, supplier, laboratory) of a mutant allele or substrain or of an outbred stock.

BRIEF HISTORY OF NOMENCLATURE AND DEVELOPMENT OF LABORATORY CODES

The term “gen” or “gene” was introduced to the scientific community in 1909 by the Danish botanist Wilhelm Johannsen, some time after Mendel’s, Darwin’s, and other’s discussions of principles of heredity.^1,2 By 1919 there was a “Committee on Genetic Form and Nomenclature” (Wright, Shull, White, Sturtevant, chaired by C.C. Little). Their charge was to “…consider the matter of genetic nomenclature and submit constructive suggestions for standardizing descriptive terms in this subject.”³

MICE: Genetic and Inbred Strain Nomenclature

In 1940 genetic nomenclature “rules for assigning symbols to mutations” were established for laboratory mice by the Committee on Mouse Genetic Nomenclature (Dunn, Gruneberg, and Snell).⁴ The committee recognized the problem of multiple alleles and suggested that the novel or next allele be named the initial letter of the name of the mutation (useful for only 1 additional allele) or the initial letter of the name of the discoverer (also useful for only 1 additional allele). A variant of this suggestion persists in the current application of laboratory codes in naming alleles, mutations, chromosome aberrations, transgenes, and other genetic modifications or constructs.

In 1952 “Standardized Nomenclature for Inbred Strains of Mice” was published by the Committee on Standardized Nomenclature for Mice (Carter, Dunn, Falconer, Gruneburg, Heston, and Snell),⁵ noting then that the “multiplicity of strains and substrains has created a need for a standard system of nomenclature.” Aligning with today’s rules, substrains

• “. . . shall be known by the name of the parent strain followed by a slant line and the name of the person or laboratory maintaining it. Abbreviations [ie, for the name of the person or laboratory maintaining it] with the initial letter set in Roman capitals may be substituted for the full name.”

• “Abbreviations should be brief, should as far as possible be standardized, and should be checked with published information or with some designated central agency to avoid duplication.”Example: A/He is the Heston substrain of the A strain. . .

• “Where a new substrain is created by transfer, the old substrain symbol shall be maintained and a new one added.

  Example: The A/He strain, on transfer from Heston to the Inbred Nucleus at the Jackson Laboratory, becomes A/HeJax.”

They noted that if substrain symbols become cumbersome after several transfers, it was permissible to abbreviate, and “such abbreviations should be made a matter of public record in some suitable publication” (eg, listings of inbred strains of mice; see tables 2 and 3). The 1952 listing recognized strain names that already included a slant line “/” and had standing in the literature, eg BALB/c, C57BL/6, DBA/1 and DBA/2.

Appendix 3 of the 1952 publication listed 1–3 letter “abbreviations for use in symbolizing substrains.” Many of these should be familiar to contemporary users of mice and rats as laboratory codes in strain and stock names, for example (as listed):

An  Dr H. B. Andervont, National Cancer Institute, Bethesda, MD.

Fe  Miss E. Fekete, Roscoe B. Jackson Memorial Laboratory, Bar Harbor, ME.

Fu  Dr J. Furth, Oak Ridge National Laboratory.

Ha  Dr T. S. Hauschka, Institute for Cancer Research, Philadelphia, PA.

He  Dr W. E. Heston, National Cancer Institute, Bethesda, MD.

J or Jax  Roscoe B. Jackson Memorial Laboratory, Bar Harbor, ME.

Ks  Dr N. Kaliss, Roscoe B. Jackson Memorial Laboratory, Bar Harbor, ME.

Li  Dr C. C. Little, Roscoe B. Jackson Memorial Laboratory, Bar Harbor, ME.

N   Dr G. Jay, National Institutes of Health, Bethesda, MD.

Sc  Dr J. P. Scott, Roscoe B. Jackson Memorial Laboratory, Bar Harbor, ME.

Sn  Dr G. D. Snell, Roscoe B. Jackson Memorial Laboratory, Bar Harbor, ME.

St  Dr L. C. Strong, Yale University School of Medicine, New Haven, CT.

The 1960 revision to “Standardized Nomenclature for Inbred Strains of Mice” again “stress[ed] the importance of using full strain and substrain symbols in published papers.”⁶ It added some clarifications and designations for manipulations of a strain, for example, by fostering or by introduction of a foreign gene (Tables 2 and 3). However, the definitions and nomenclature for inbred strains and substrains have remained remarkably stable since 1952.

Since at least the 1930s, the histories and evolution of mouse strains and substrains, as identified by their strain names and laboratory codes, and research-relevant variations among them have been studied and reported. Examples include skeletal variations,⁷ tumor susceptibility,^8–10 radiation sensitivity,^11–13 and disease susceptibility and immunity (reviewed in Radaelli et al, 2019).¹⁴ Induced mutations on different backgrounds yield different phenotypes and results. Genetically engineered mice bearing multiple induced mutations may have contributions from 4 (or more) inbred strains that can affect phenotypes under study or lead to unexpected phenotypes, with potential impacts on morbidity, mortality, and research noise.^14–18 Concerns regarding background genetics and accurate identification of stocks, strains, lines, and their research impacts are being recognized beyond mice, for example in zebrafish¹⁹ and nonhuman primates.^20–22

Substrain designations using laboratory codes have enabled genetic (forensic) approaches to identify and date the origins of important mutations, such as the Tlr4 mutation (Tlr4^lps) that confers endotoxin (LPS) nonresponsiveness in C3H/HeJ and derived substrains. In 1976 the LPS-responsive C3H strains and substrains (C3H/St, C3H/Cr, C3H/Bi, C3H/He, C3H/HeN, C3H/HeBFeJ, C3H/DiSn) could be usefully distinguished by their names (and associated histories) from closely related, nonresponsive substrains (C3H/HeJ, C3H/Bts), leading to important insights into endotoxin responses and susceptibilities to Gram-negative bacteria.²³

C57BL/6 J, C57BL/6JOlaHsd, C57BL/6JRccHsd, C57BL/6JBomTac, C57BL/6JRj, C57BL/6ByJ, C57BL/6NHsd, C57BL/6NRj, C57BL/6NCrl, C57BL/6NTac, C57BL/6NCr, and C57BL/6NJ are some of the commercially available B6 strains, nominally distinguished by the laboratory codes of their origins and sources, and increasingly recognized to have research-relevant genetic variations, for example in Dock2, Nlrp12, Nnt, Snca, Mmrn1, Rd8, Cyfip2.^24–29 Incomplete mouse nomenclature, particularly missing substrain designations (laboratory codes), is a recognized problem in accurate research reporting.^30–33

Revisions to the mouse and genetic nomenclature guidelines were published periodically by the International Committee for Standardized Genetic Nomenclature in Mice (1960,⁶ 1963,³⁴ 1973,³⁵ 1981,³⁶ 1989,³⁷ 1994,³⁸ 1996^39,40) before online publication by MGI in the 1990s.⁴¹

Periodic listings of inbred mice, their known (named) mutations, holders or sources of mice, histories, and periodic updates to nomenclature rules were published in the journal Cancer Research, in textbooks,^37,42–44 and in the Mouse News Letter 1949–1989⁴⁴ (continued as Mouse Genome, Mammalian Genome c1990),⁴⁵ and in other periodical publications, (Table 2) until internet distribution of this information via MGI, RGD, and ILAR’s laboratory code registry in the 1990s made the information accessible online (Table 3).

Beyond Inbred Mice

ILAR’s 1954 “Handbook of Laboratory Animals” (and first listing of “Animals for Research,” based on information from mailed surveys) aimed to address the diversity of species involved in research, resources for them, and research relevant information about them.⁴⁶ It included sections on genetics, diseases, nutrition, bibliography, and complex tables of “strains” of mice, rats, guinea pigs, rabbits, hamsters, as well as information on other commercially available species. A number of mice strains were listed according to 1952 standardized nomenclature,⁵ with substrain designations and laboratory codes that remain relevant today, eg BALB/cAnN, C3H/HeN, C57BL/6JN, DBA/2JN.

The 1954 tables include previous sources or origins (of the animals), current breeding systems and production information, animal descriptions, rations (diet), uses, susceptibility, and resistance information. The challenge of identifying and cataloguing non-inbred animals is evident in multiple sources distributing similarly designated Swiss-derived, “Swiss” or “Swiss Webster” mice, and Wistar-derived, “Wistar,” “Sprague–Dawley,” “Fischer-344,” and “Long-Evans” rats. These are indicated “Outbr.” or “Not inbr.” or lack breeding information. The authors recognized gaps in the information but hoped that the effort would illustrate the value of such a listing to the research community.

ILAR’s 1958 “Animals for Research”⁴⁷ was distributed as Issue 3 in Vol. l of ILAR’s publication then called “Information on Laboratory Animals for Research (ILAR)” (later ILAR News,⁴⁸ then ILAR Journal⁴⁹). This and subsequent versions of “Animals for Research” listed suppliers of animals with their 3-letter “codes.” The 1958 listing was expanded from 1954, with species listed in phylogenetic order from Protozoa to Chordata (including aquatic and avian species, livestock, alligators, and elephants). The tables are somewhat simplified compared to 1954, with rabbit, mouse, rat, hamster and guinea pig strains in alphanumeric order, listed with their breeding strategies, diets and 3-letter supplier “codes” (eg, Fig. 1).

The 1958 lists illustrate the continuing challenge of non-inbred animals. The mouse list includes almost 2 pages of mostly “random bred” mice, similarly designated “Swiss,” “Swiss Webster” and “Webster Swiss” from various suppliers, plus “strains” such as CFW, FRF-1, FRF-2, Ha/ICR and MF1, with their Swiss origin indicated (or not, depending on the information provided by the supplier). In the rat list, (Wistar origin) non-inbred “Wistar,” “Sprague Dawley” and “Long Evans” constitute the majority of rat strain names, also available from multiple suppliers.

In 1959 Billingham and Silvers published the first listing of inbred rat strains.⁵⁰ Second and third listings were published in textbooks in 1963⁵¹ and 1965.⁵² In 1973 Festing and Staats published “Standardized Nomenclature for inbred Rat Strains” based on the rules for inbred mice, along with the fourth listing of inbred rat strains.⁵³ Updated lists were published in 1979⁵⁴ and 1981.⁵⁵ Rat genetic nomenclature revisions were published in 1992⁵⁶ and 1995,⁵⁷ again following conventions for mice. The rat and mouse committees unified their efforts in 2003, with online publication of nomenclature rules in MGI and RGD.

Beyond mice and rats, vertebrate gene nomenclature is addressed by the Vertebrate Gene Nomenclature Committee (VGNC at https://vertebrate.genenames.org/). VGNC is an extension of the HUGO Gene Nomenclature Committee project that names human genes, and it coordinates with the 5 existing vertebrate nomenclature committees, MGNC (mouse), RGNC (rat), CGNC (chicken), XNC (Xenopus frog) and ZNC (zebrafish), to ensure that gene names align with their human homologs.^58,59

The Alliance of Genome Resources currently includes 7 projects—Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database (MGD), the Zebrafish Information Network, Rat Genome Database (RGD), and the Gene Ontology Resource—in an effort to harmonize “…cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance.”⁶⁰

Standardized nomenclature for the human major histocompatibility complex (MHC) or human leukocyte antigen (HLA) genes was first established in 1968 by the HLA Nomenclature Committee under the auspices of the World Health Organization. Standardized HLA nomenclature is critical in clinical (eg, solid-organ and hematopoietic stem cell transplantation, transfusion support, disease association, etc) and in research settings worldwide. The success of the HLA nomenclature can be attributed in part to enforcement by regulatory and accreditation agencies such as the World Health Organization, US Center for Medicare and Medicaid Services, American Society for Histocompatibility and Immunogenetics, National Marrow Donor Program, and European Federation for Immunogenetics, as well as various scientific journals.

The Immuno Polymorphism Database (IPD) (https://www.ebi.ac.uk/ipd/imgt/hla/) was developed in 2003 as a centralized resource for immune-relevant genetic polymorphisms. All officially designated HLA alleles and sequences are deposited in the IPD. IPD also serves as a centralized repository for human Killer-cell Immunoglobulin-like Receptors sequence, and for nonhuman MHC sequences,^61–64 including MHC information for cattle, Bovine Leukocyte Antigen; chickens⁶⁵; dogs, Dog Leukocyte Antigen; fish (salmonids); sheep, Ovine Leukocyte Antigen; goats, Caprine Leukocyte Antigen; horses, Equine Leukocyte Antigen; nonhuman primates, NHP MHC (great and small ape, and Old and New World monkey species)⁶⁶; rat, RT1 complex⁶⁷; and swine, Swine Leukocyte Antigen.^68,69 Mouse histocompatibility genetics information is curated at MGD; Zebrafish histocompatibility genetics information is curated at Zebrafish Information Network.

However, strain/stock/line and induced mutation nomenclature for many species involved in research remains in varying stages of development and adoption, or neglect. Examples of (genus/species specific) genome, genetic, and nomenclature resources include the following:

Flybase  https://wiki.flybase.org/wiki/FlyBase:Drosophila_Online_Resources.^70,71

Species: Drosophila melanogaster etc, Drosophila species

Includes: Genome/gene information; genetic nomenclature

Mouse Genome Informatics (MGI) (MGD)  http://www. informatics.jax.org/.^72,73

Species: Laboratory mice, Mus musculus

Includes: Genome/gene information; genetic nomenclature; strain/line names/nomenclature (strain, line construct nomenclature uses ILAR laboratory codes); phenotype/phenome resources; IMSR online database of mouse strains, stocks, and mutant ES cell lines worldwide; etc resources.

Rat Genome Database (RGD)  https://rgd.mcw.edu/rgdweb/homepage/.^74,75

Species: Laboratory rats; Rattus norvegicus ^*

Includes: Genome/gene information; genetic nomenclature; strain/line names/nomenclature (strain, line construct nomenclature uses ILAR laboratory codes); phenotype, disease, model, strain/stock resources.

(RGD includes/integrates data from rat, mouse, human, chinchilla, bonobo, 13-lined ground squirrel, dog, pig, green monkey/vervet, and naked mole-rat).

Sal-Site  https://ambystoma. uky. edu/.^76,77

Species: Ambystoma mexicanum, etc Ambystoma species

Includes: Genome/gene information; stocks; (genetic nomenclature proposed).⁷⁸

Wormbase  https://wormbase. org/.^79,80

Species: Caenorhabditis elegans, several Caenorhabditis species, Brugia malayi, etc.

Includes: Genome/gene information; genetic nomenclature; strain/line names/nomenclature; “Laboratory code database” maintained at the Caenorhabditis Genetics Center https://cgc. umn. edu.

Xenbase  https://www.xenbase.org/.^81,82

Species: Xenopus laevis; X tropicalis (X borealis, X gilli)

Includes: Genome/gene information; genetic nomenclature; strain/line names/nomenclature;

Xenopus lines and strains are given Research Resource Identifiers; strain, line construct nomenclature uses ILAR laboratory codes.⁸³  https://www. xenbase. org/gene/static/tgNomenclature. jsp.

Zfin Zebrafish Information Network  https://zfin. org/.^19,84,85

Species: Danio rerio.

Includes: Genome/gene information; genetic nomenclature; stocks/mutants; strain/line names/nomenclature; https://zfin.org/action/feature/line-designations institutional line designations, institution identifier, nomenclature guidelines.

Non-Inbred (aka “Outbred”) Nomenclature

In 1968 “suggested nomenclature for non inbred rats and mice,” was published by ILAR’s Committee on Nomenclature (Poiley, [chair], Bogden, Foster, Norton, Root, Staats, Kile) in ILAR News.⁸⁶ They cite concerns that resonate today regarding the “…failure of the investigators to obtain pertinent information concerning their experimental animals; inadequate and inaccurate symbolization noted in many reports; and the fact that many reviewers are unfamiliar with nomenclature systems.…” They proposed “…stock” should be used rather than “strain,” and “non-inbred” would be more precisely descriptive than “random­ bred.” To distinguish non-inbred stocks from inbred strains:

• “The producer’s ‘code’ would appear first in the stock designation.

  The use of the producer’s code first would distinguish non-inbred stocks from inbred strain designations....

• “This would be followed by a colon ‘:’

  The colon again would identify the stock as being non-inbred....

• “The producer’s designation for his stock would follow the colon.

• Finally, a code for the basic origin of the stock would appear in parenthesis.”

  Eg, for rats: Long-Evans (LE), Osborne-Mendel (OM), Sherman (S), Sprague–Dawley (SD), and Wistar (W); for Mice: Swiss (S), Swiss-Webster (SW), ICR (ICR).

• Example: rats—ARC:Type 3 (LE); mice—ARC:XYZ (S)

Where ARC is the code for “American Rodent Corporation”; Type 3 and XYZ are examples of producer’s designations (for these stocks).

In 1970 ILAR’s Committee on Nomenclature published “a nomenclatural system for outbred animals” with similar recommendations and notably not limited to rats and mice.⁸⁷ The authors’ stated aim was for the recommendations to “…be adopted as standard terminology by the scientific community, ending the confusion presently existing in animal identification.”

ILAR’s 1971 publication Animals for Research: Eighth Edition⁸⁸ incorporated inbred and outbred nomenclature conventions for mice, rats, rabbits, hamsters, gerbils (1 inbred strain), and guinea pigs (abandoning the effort to implement the term “non-inbred”). Table 1 (below) includes a few examples (in species other than mice and rats) that illustrate the differences between inbred and outbred nomenclature, consistent with the 1968 ILAR proposal and 1970 publication, and the use of codes for suppliers.

In 1972 an ICLA Working Party for “International Nomenclature System for Outbred Animals” (Spiegel [chair], Festing, Kondo, Loosli, and Poiley) published “International Standardized Nomenclature for Outbred Stocks of Laboratory Animals” in ICLA Bulletin (No 30),⁸⁹ Zeitschrift fur Versuchstierkunde,⁹⁰ and ILAR News,⁹¹ aiming to reach breeders and users, and “editors of scientific journals, catalogues, and indices all over the world are also encouraged to require and use animal stock identification by this system for outbred animals used in experimentation.”^89–91 Again, the recommendations were not limited to mice and rats. They were similar to ILAR’s 1968 recommendation⁸⁶ but dropped the parenthesized references to original stocks (as in⁸⁷).

• Example: F344/Tif and Tif:344 are inbred and outbred rats, respectively, from Ciba Geigy (“breeder code”Tif).

They updated designations for breeding information and hygienic status. The authors further suggested (successfully) that periodic listings of stocks and breeders would be disseminated to the research community, eg, in “Animals for Research” (published by the U.S. National Academy of Sciences) and “International Index of Laboratory Animals” (published by the British Medical Research Council)” because these publications were key resources for the research community at that time (see Tables 2 and 3).

In 1974 ICLA Bulletin (No 35) included the first European list of outbred stocks of laboratory animals, including nonrodent species.

• Example: Tif:CAB for stock name CAB (Canine Beagle) from Ciba Geigy (“breeder code”Tif).

This bulletin also included an outbred nomenclature update to indicate transfer of stocks between breeders by successive addition of breeder “symbols” in front of the colon and stock name.

Per MGI and RGD nomenclature sites, outbred nomenclature remains very similar to the original recommendations but with options for the addition of genetic information (spontaneous and induced), and information about breeding strategies or other relevant data.

International Participation and Impact of Online Databases and Dissemination

Prior to free online access to Medline (via PubMed) in 1996,⁹² to mouse strain and nomenclature data in MGD and MGI in 1996,⁹³ to ILAR’s online laboratory code registry database in 1997 (announced in ILAR Journal 38(2)), and to RGD in 1999,^74,94,95 international organizations and committees cooperated to develop useful gene and nomenclature conventions and publish lists of inbred and non-inbred animals. Table 2 summarizes key periodicals and texts that illustrate the challenge and importance to the international scientific community of distributing this information.

Table 3 illustrates the longstanding efforts to support science and the informed use of appropriate models via standardized nomenclature and laboratory codes, well in advance of NIH’s 2016 research resource identification initiative.⁹⁶ Details in Table 3 are included as a resource on the origins and provenance of strains, stocks, and laboratory codes in historical literature as well as in use today. Not emphasized here but included in many of the publications is information on the care and welfare of animals in research.

CONCLUSIONS

More than 70 years after the publication of nomenclature conventions for animals and genetics to address research needs, the current reproducibility crisis again decries poor reporting and inadequate identification of research resources, including animal subjects. Existing nomenclature conventions accommodate a diversity of species and are a solid foundation on which to improve research reporting, reproducibility and integrity, scientific communication, and science. Appreciating the concerns for “future proofing” nomenclature, databases, and other publications, contemporary science requires broader application of accurate and useful nomenclature for animals in research.

ACKNOWLEDGMENTS

The author is very grateful to the USDA National Agricultural Library for providing resources that were not available elsewhere, and is also very grateful to the reviewers who provided valuable information and suggestions.

ABBREVIATIONS/ACRONYMS

GEM, Genetically Engineered Mice; ICLAS (ICLA), International Council for Laboratory Animal Science https://iclas.org/ (formerly International Council for Laboratory Animals); ILAR (IAR), Institute for Laboratory Animal Research https://www.nationalacademies.org/ilar/institute-for-laboratory-animal-research (Formerly Institute for Laboratory Animal Resources, and previously IAR, Institute for Animal Resources, which was founded 1953, as a division in the National Academy of Sciences); IMGS, International Mammalian Genome Society https://www.imgs.org/; MGD, Mouse Genome Database http://www.informatics.jax.org/; MGI, Mouse Genome Informatics http://www.informatics.jax.org/; MHC, Major histocompatibility complex; MRC, Medical Research Council (UK); NHP, Non Human Primates; RGD, Rat Genome Database https://rgd.mcw.edu/rgdweb/homepage/.

REFERENCES

Author notes