Guidelines For Human Gene Nomenclature Research Articles

Proposed standard nomenclature for the .ALPHA.- and .BETA.-globin gene families

The globin family of genes and proteins has been a recurrent object of study for many decades. This interest has generated a vast amount of knowledge. However it has also created an inconsistent and confusing nomenclature, due to the lack of a systematic approach to naming genes and failure to reflect the phylogenetic relationships among genes of the gene family. To alleviate the problems with the existing system, here we propose a standardized nomenclature for the alpha and beta globin family of genes, based on a phylogenetic analysis of vertebrate alpha and beta globins, and following the Guidelines for Human Gene Nomenclature.

Nomenclature for human DPYD alleles.

To standardize DPYD allele nomenclature and to conform with international human gene nomenclature guidelines, an alternative to the current arbitrary system is described. Based on recommendations for human genome nomenclature, we propose that each distinct allele be designed by DPYD followed by an asterisk and an Arabic numeral. The number specifies the key mutation and, where appropriate, a letter following the number indicates an additional mutation on the mutant allele. Criteria for classification as a distinct allele are also presented.

The Cattle Gene Map.

Cave paintings in Europe and North Africa depict wild cattle, the aurochs (Bos primigenius), among the prized prey of Stone Age hunters. These majestic animals stood nearly 2 M at the withers and had horns up to 1 M long. Bulls are usually shown as dark brown or black with cows and calves reddish brown, although white and speckled animals also appear in the paintings (Felius 1985). The aurochs spread out of western Asia after the Ice Age (250,000 yr ago) and are believed to have survived in Europe until early in the 17th century. Sometime before their extinction, probably 7000 to 10,000 yr ago, aurochs were domesticated. At least 2 domestications are likely represented in breeds of at the time of this writing. Bos primigenius primigenius, a European auroch subtype evidenced by the fossil record, is thought to be the ancestor to today's humpless breeds of given the species designation Bos taurus. An Asian auroch subtype, Bos primigenius namadicus, probably gave rise to today's humped zebu breeds classified as Bos indicus. Although domestic breeds of are divided into 2 species, they are totally interfertile; in fact, several synthetic breeds have arisen in this century from intercrosses of taurus and indicus breeds. Chromosome numbers are identical: 29 autosomes, all of which are acrocentric, and a submetacentric X. Morphology of the Y chromosomes is the only recognized structural difference in B. taurus and B. indicus karyotypes. Thus, the cattle gene map developed to date and discussed in this article is for 2 species that many people, including myself, believe should be reclassified as 1. Cattle are members of the subfamily Bovinae, the family Bovidae, the suborder Ruminantia, and the order Artiodactyla. A standard karyotype for was resolved by Popescu and others (1996), with gene nomenclature following the guidelines for human gene nomenclature as recommended by the International Society for Animal Genetics (ISAG). Loci without human equivalents are named according to the recommendations of the Committee on Genetic Nomenclature of Sheep and Goats (COGNOSAG 1995).

The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence.

This review represents an update of the nomenclature system for the UDP glucuronosyltransferase gene superfamily, which is based on divergent evolution. Since the previous review in 1991, sequences of many related UDP glycosyltransferases from lower organisms have appeared in the database, which expand our database considerably. At latest count, in animals, yeast, plants and bacteria there are 110 distinct cDNAs/genes whose protein products all contain a characteristic 'signature sequence' and, thus, are regarded as members of the same superfamily. Comparison of a relatedness tree of proteins leads to the definition of 33 families. It should be emphasized that at least six cloned UDP-GlcNAc N-acetylglucosaminyltransferases are not sufficiently homologous to be included as members of this superfamily and may represent an example of convergent evolution. For naming each gene, it is recommended that the root symbol UGT for human (Ugt for mouse and Drosophila), denoting 'UDP glycosyltransferase,' be followed by an Arabic number representing the family, a letter designating the subfamily, and an Arabic numeral denoting the individual gene within the family or subfamily, e.g. 'human UGT2B4' and 'mouse Ugt2b5'. We recommend the name 'UDP glycosyltransferase' because many of the proteins do not preferentially use UDP glucuronic acid, or their nucleotide sugar preference is unknown. Whereas the gene is italicized, the corresponding cDNA, transcript, protein and enzyme activity should be written with upper-case letters and without italics, e.g. 'human or mouse UGT1A1.' The UGT1 gene (spanning > 500 kb) contains at least 12 promoters/first exons, which can be spliced and joined with common exons 2 through 5, leading to different N-terminal halves but identical C-terminal halves of the gene products; in this scheme each first exon is regarded as a distinct gene (e.g. UGT1A1, UGT1A2, ... UGT1A12). When an orthologous gene between species cannot be identified with certainty, as occurs in the UGT2B subfamily, sequential naming of the genes is being carried out chronologically as they become characterized. We suggest that the Human Gene Nomenclature Guidelines (http://www.gene.acl.ac.uk/nomenclature/guidelines.html++ +) be used for all species other than the mouse and Drosophila. Thirty published human UGT1A1 mutant alleles responsible for clinical hyperbilirubinemias are listed herein, and given numbers following an asterisk (e.g. UGT1A1*30) consistent with the Human Gene Nomenclature Guidelines. It is anticipated that this UGT gene nomenclature system will require updating on a regular basis.

Extensive polymorphism of ABO blood group gene: three major lineages of the alleles for the common ABO phenotypes.

Polymorphism of the ABO blood group gene was investigated in 262 healthy Japanese donors by a polymerase chain reactions-single-strand conformation polymorphism (PCR-SSCP) method, and 13 different alleles were identified. The number of alleles identified in each group was 4 for A1 (provisionally called ABO*A101, *A102, *A103 and *A104 according to the guidelines for human gene nomenclature), 3 for B (ABO*B101, *B102 and *B103), and 6 for O (ABO*O101, *O102, *O103, *O201, *O202 and *O203). Nucleotide sequences of the amplified fragments with different SSCP patterns were determined by direct sequencing. Phylogenetic network analysis revealed that these alleles could be classified into three major lineages, *A/*O1, *B and *O2. In Japanese, *A102 and *B101 were the predominant alleles with frequencies of 83% and 97% in each group, respectively, whereas in group O, two common alleles, *O101 (43%) and *O201 (53%), were observed. These results may be useful for the establishment of ABO genotyping, and these newly described ABO alleles would be advantageous indicators for population studies.

Nomenclature for human CYP2D6 alleles.

To standardize CYP2D6 allele nomenclature, and to conform with international human gene nomenclature guidelines, an alternative to the current arbitrary system is described. Based on recommendations for human genome nomenclature, we propose that alleles be designated by CYP2D6 followed by an asterisk and a combination of roman letters and arabic numerals distinct for each allele with the number specifying the key mutation and, where appropriate, a letter specifying additional mutations. Criteria for classification as a separate allele and protein nomenclature are also presented.

Nomenclature for naming loci, alleles, linkage groups and chromosomes to be used in poultry genome publications and databases

The Second International Workshop on Poultry Genome Mapping, meeting at the 1994 Conference of the International Society for Animal Genetics, and the Poultry Committee of the USDA National Animal Genome Research Program have approved a new set of guidelines for poultry gene and allele symbols to replace the guidelines published previously. The new guidelines are a modification of the human gene nomenclature guidelines and are designed to facilitate the naming of loci detected by molecular probes and electronic publication in on-line databases. Authors and journal editors are strongly encouraged to adopt the new nomenclature guidelines. Comments and suggestions are welcome. The complete text of the guidelines can be accessed on the World Wide Web. The home page addresses are: http://www.ri.bbsrc.ac.uk/chickmap/ChickMapHomePage.html for the ChickMap home page, Roslin Institute, UK and http://poultry.mph.msu.edu/ for the Department of Microbiology, Michigan State University, USA. The home pages will contain updates and changes in the guidelines. The home pages also provide access to CHICKBASE, a chicken genome database, which will have a listing of old and new gene symbols. A World Wide Web browser is required for access. The guidelines can also be obtained from LB Crittenden (e-mail: slcritte@facstaff.wisc.edu). The International Poultry Gene Nomenclature Committee comprises the authors of this letter to the editor.

C4 Nomenclature Statement (1990)

A common and revised nomenclature of the allotypes of the fourth component (C4) of human complement has been proposed. It is based on the results of the C4 Reference Typing of the VIth Complement Genetics Workshop and Conference, Mainz, FRG, 1989, the previous C4 nomenclature and the guidelines for human gene nomenclature (ISGN). The designation of allotypes derives from their relative electrophoretic mobility, the distinction between C4A and C4B proteins from their relative hemolytic activity. Common alleles retain their single digit numeric designation, intermediate variants their two- or three-digit designations; newly discovered alleles should not interfere with already described variants. At least 13 C4A alleles, 16 C4B alleles as well as non-expressed genes at each C4 locus are presently known. There are also duplicated loci of each C4 gene; they should be designated by repetition of the locus symbol at the haplotype or genotype level. As a phenotype they will be placed in parenthesis without repetition of the locus symbol. Aberrant allotypes or hybrid genes should be explained by a special suffix. No special nomenclature is recommended for restriction fragment length polymorphisms. Their designation should follow the general rules of the ISGN.