Allele Nomenclature Research Articles

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease

The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse–human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human–Mouse: Disease Connection, allows users to explore gene–phenotype–disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community.

A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers.

The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation.

Functional gene variants of CYP3A4.

Cytochrome P450 3A4 (CYP3A4) is involved in the metabolism of more drugs in clinical use than any other foreign compound-metabolizing enzyme in humans. Recently, increasing evidence has been found showing that variants in the CYP3A4 gene have functional significance and--in rare cases--lead to loss of activity, implying tremendous consequences for patients. This review article highlights the functional consequences of all CYP3A4 variants recognized by the Human Cytochrome P450 (CYP) Allele Nomenclature Database.

Forensic animal DNA typing: Allele nomenclature and standardization of 14 feline STR markers.

Since the domestic cat (Felis catus) has become one of the most popular pets and owners usually develop a close relationship to their cats, it is necessary to take traces of cats into account for forensic casework. For this purpose feline short tandem (STR) repeat markers have been investigated in several earlier studies, but no detailed description of sequence data, allelic variations or a repeat-based nomenclature is available. The aim of the study was to provide a suggestion for the allele nomenclature of 14 cat STR markers according to the recommendations of the International Society for Forensic Genetics (ISFG) for human DNA typing and to present a standardized system for a secure DNA typing of samples. Samples of 122 unrelated cats from a local animal shelter and private owners in Germany were used to generate a population database with allele frequencies and to analyze the tandemly repeated sequence variations within the alleles of each STR marker. These markers could be grouped into two STR classes: simple repeat STRs and complex STRs (some with the supplement highly complex), consisting of di- and tetranucleotide repeat motifs. After analyzing the repeat structure and elaborating a repeat based nomenclature, allelic ladders of common and rarely occurring alleles for each marker were designed to enable accurate typing of alleles that differ in fragment length and to facilitate data exchange.

Inter-laboratory comparison of multi-locus variable-number tandem repeat analysis (MLVA) for verocytotoxin-producingEscherichia coliO157 to facilitate data sharing

Multi-locus variable number tandem repeat analysis (MLVA) is used in clinical and reference laboratories for subtyping verocytotoxin-producing Escherichia coli O157 (VTEC O157). However, as yet there is no common allelic or profile nomenclature to enable laboratories to easily compare data. In this study, we carried out an inter-laboratory comparison of an eight-loci MLVA scheme using a set of 67 isolates of VTEC O157. We found all but two isolates were identical in profile in the two laboratories, and repeat units were homogeneous in size but some were incomplete. A subset of the isolates (n = 17) were sequenced to determine the actual copy number of representative alleles, thereby enabling alleles to be named according to international consensus guidelines. This work has enabled us to realize the potential of MLVA as a portable, highly discriminatory and convenient subtyping method.

Antibody Informatics: IMGT, the International ImMunoGeneTics Information System.

Antibody informatics, a part of immunoinformatics, refers to the concepts, databases, and tools developed and used to explore and to analyze the particular properties of the immunoglobulins (IG) or antibodies, compared with conventional genes and proteins. Antibody informatics is based on a unique ontology, IMGT-ONTOLOGY, created in 1989 by IMGT, the international ImMunoGeneTics information system (http://www.imgt.org). IMGT-ONTOLOGY defined, for the first time, the concept of 'genes' for the IG and the T cell receptors (TR), which led to their gene and allele nomenclature and allowed their entry in databases and tools. A second IMGT-ONTOLOGY revolutionizing and definitive concept was the IMGT unique numbering that bridged the gap between sequences and structures for the variable (V) and constant (C) domains of the IG and TR, and for the groove (G) domains of the major histocompatibility (MH). These breakthroughs contributed to the development of IMGT databases and tools for antibody informatics and its diverse applications, such as repertoire analysis in infectious diseases, antibody engineering and humanization, and study of antibody/antigen interactions. Nucleotide sequences of antibody V domains from deep sequencing (Next Generation Sequencing or High Throughput Sequencing) are analyzed with IMGT/HighV-QUEST, the high-throughput version of IMGT/V-QUEST and IMGT/JunctionAnalysis. Amino acid sequences of V and C domains are represented with the IMGT/Collier-de-Perles tool and analyzed with IMGT/DomainGapAlign. Three-dimensional (3D) structures (including contact analysis and paratope/epitope) are described in IMGT/3Dstructure-DB. Based on a friendly interface, IMGT/mAb-DB contains therapeutic monoclonal antibodies (INN suffix-mab) that can be queried on their specificity, for example, in infectious diseases, on bacterial or viral targets.

Constructing STR Multiplexes for Individual Identification of Hungarian Red Deer

Red deer is the most valuable game of the fauna in Hungary, and there is a strong need for genetic identification of individuals. For this purpose, 10 tetranucleotide STR markers were developed and amplified in two 5-plex systems. The study presented here includes the flanking region sequence analysis and the allele nomenclature of the 10 loci as well as the PCR optimization of the DeerPlex I and II. LD pairwise tests and cross-species similarity analyses showed the 10 loci to be independently inherited. Considerable levels of genetic differences between two subpopulations were recorded, and F(ST) was 0.034 using AMOVA. The average probability of identity (PI(ave)) was at the value of 2.6736 × 10(-15). This low value for PI(ave) nearly eliminates false identification. An illegal hunting case solved by DeerPlex is described herein. The calculated likelihood ratio (LR) illustrates the potential of the 10 red deer microsatellite markers for forensic investigations.

Immunoinformatics of the V, C, and G domains: IMGT® definitive system for IG, TR and IgSF, MH, and MhSF.

By its creation in 1989, IMGT(®), the international ImMunoGeneTics information system(®) ( http://www.imgt.org , CNRS and Université Montpellier 2), marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT(®) is the global reference in immunogenetics and immunoinformatics. The accuracy and the consistency of the IMGT(®) data are based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts, which comprise IMGT standardized labels (DESCRIPTION), IMGT gene and allele nomenclature (CLASSIFICATION), IMGT unique numbering, and IMGT Collier de Perles (NUMEROTATION). The IMGT(®) standards have bridged the gap between genes, sequences, and three-dimensional (3D) structures for the receptors, chains, and domains. Started specifically for the immunoglobulins (IG) or antibodies and T cell receptors (TR), the IMGT-ONTOLOGY concepts have been extended to conventional genes of the immunoglobulin superfamily (IgSF) and major histocompatibility (MH) superfamily (MhSF), members of which are defined by the presence of at least one variable (V) or constant (C) domain, or two groove (G) domains, respectively. In this chapter, we review the IMGT(®) definitive system for the V, C, and G domains, based on the IMGT-ONTOLOGY concepts of IMGT unique numbering and IMGT Collier de Perles.

Genetic polymorphisms associated with antiepileptic metabolism.

Several factors, including pharmacogenetics, contribute to inter-individual variability in drug response. Many antiepileptic drugs (AEDs) are metabolized by a variety of enzymatic reactions, and the cytochrome P450 (CYP) family has attracted considerable attention. Some of the CYPs exist as genetic (allelic) variants, which may also affect the plasma concentrations or drug exposure. Regarding the metabolism of AEDs, the polymorphic CYP2C9 and CYP2C19 are of particular interest. There have been recent advances in discovering factors such as these, especially those underlying the risk of medication toxicity. This review summarizes the evidence about whether such polymorphisms affect the clinical action of AEDs to facilitate future studies on the pharmacogenetics of epilepsy. We performed Key Words searches in the public databases PubMed, Medscape, and Rxlisty, Pharm GKB for genetic polymorphisms and the NCBI website for the nomenclature of alleles of CYP450, finding that CYP2D6, CYP2C9, CYP3A4, and CYP2D19 were involved in the metabolism of most antiepileptic drugs, given the allele frequency in the population and the associated variability in the clinical response.

Genetic Variations of Human CYP2D6 in the Chinese Han Population

The purpose of this study was to determine the genetic polymorphisms of the CYP2D6 gene and to elucidate the allele distribution pattern in the Chinese Han population. We used PCR and bidirectional sequencing methods to analyze all nine exons of the CYP2D6 gene in 2129 unrelated, healthy Chinese Han subjects from two geographical locations in China: the northern and southern regions. In total, 165 mutated sites were detected in 2129 participants, of which 67 sites were reported for the first time. Among these novel mutation sites, 22 were nonsynonymous and 12 were named as novel alleles (*87-*93, *94A, *94B and *95-*98) by the Human CYP Allele Nomenclature Committee. In addition, 29 previously reported alleles and 84 genotypes were also detected in 1954 volunteers. Functional prediction of novel variants revealed that eight variants might have a deleterious effect on CYP2D6. Linkage disequilibrium analysis and tagSNP selection were performed separately. By using these methods, distinct differences were found between the two regions. This study provides the most comprehensive data concerning CYP2D6 polymorphisms in the Chinese Han population to date and increases the number of known alleles; these findings may greatly contribute to the development of personalized medicine for the Chinese Han population.

Erratum: Polymorphisms in xenobiotic transporters ABCB1, ABCG2, ABCC2, ABCC1, ABCC3 and multiple myeloma risk: a case—control study in the context of the International Multiple Myeloma rESEarch (IMMEnSE) consortium

Correction to: Leukemia (2012) 26, 1419–1422; doi:10.1038/leu.2011.352 Since the publication of this article the authors have noticed errors within the original text of the manuscript. Allele nomenclature of some SNP have been wrongly reported with the name of the two homozygous group inverted, as illustrated in the example below:

Frequent LOH of CYP2D6 in ER+ breast cancer determined by next-generation sequencing (NGS).

534 Background: The role of CYP2D6 genetic variation in predicting response to tamoxifen in ER+ breast cancer is a subject of ongoing debate. There has been great variability in approaches to both genotyping and phenotyping, and in particular many investigators have extracted DNA from breast cancer samples rather than peripheral blood. We hypothesized that CYP2D6 gene copy number alterations are common in ER+ breast cancer, affecting genotype results, and used NGS to characterize CYP2D6 in patients with ER+ disease. Methods: CYP2D6 sequencing was performed as part of a comprehensive NGS profile of cancer-related genes for 261 predominantly relapsed and metastatic ER+ breast cancer FFPE specimens. Sequence data were resolved into genotypes according to the * allele nomenclature. Tumor LOH was determined at CYP2D6, and its error impact on genotyping methods was estimated. To assess biological significance, the prevalence of CYP2D6 alleles and LOH in ER+ disease was compared against a control set of 99 ER- tumors. Results: CYP2D6 allele frequencies in our full cohort (ER+, 261; ER-, 99) were consistent with prior studies; 64.4%, 16.8%, 9.0% vs. 63.1%, 17.2%, 7.0% for *1/*2, *4, and *41 respectively, and 1%-2% for the rarer alleles *9, *10, and *5. The rate of CYP2D6 LOH was higher in ER+ disease (41% vs. 26%, p<0.01), with all excess arising from copy-loss (as opposed to copy-neutral) changes (22% vs. 7%, p<0.002). The estimated impact of LOH on germline genotype assessment from tumor was considerable; an assay sensitive at >20% minor allele frequency (e.g., Sanger sequencing) can misclassify >10% of heterozygotes, leading to significant Hardy-Weinberg disequilibrium (e.g., p=8.3x10-8 for *4). Interestingly, an enrichment of reduced or non-functional CYP2D6 alleles in ER+ samples was observed (61% vs. 47%, p<0.03). Conclusions: Our results demonstrate the distorting effect of extensive LOH on genotype assessment of CYP2D6 in breast cancer. Therefore, tumor DNA should not be routinely used for determination of germline 2D6 genotype, although it appears possible to use NGS. The apparent association between reduced function CYP2D6 alleles and ER+ breast cancer in our dataset requires further investigation.

High susceptibility to pemphigus vulgaris due to HLA‐DRB1*14:54 in the Slovak population

The current work describes an association between pemphigus vulgaris (PV) and class II HLA alleles in the Slovak population, the first such study in Slovakia on the 'high-resolution level'. This work takes into account the new HLA allele nomenclature, officially adopted in 2010. In particular, we have focused on the associations between PV and DRB1*14:54 and DRB1*14:01. This case-control study was performed in a cohort of 43 PV Caucasian patients and 113 Caucasian control subjects from Slovakia. HLA typing was performed using PCR-SSP (polymerase chain reaction with sequence-specific primers). We found significantly positive associations between PV and the HLA alleles DRB1*04:02, DRB1*04:04, DRB1*14:54, DRB1*14:04, DRB1*14:05, DQB1*03:02 and DQB1*05:03. In contrast, HLA-DQB1*06, DRB1*07 and DRB1*13 were negatively associated with PV. Importantly, 93% of PV patients possessed at least one of two HLA haplotypes, DRB1*04-DQB1*03 or HLA-DRB1*14-DQB1*05. We confirmed the previously reported associations between HLA class II alleles and PV and described a new association between PV and DRB1*14:54. This allele was first described in 2005, and there has been only one report of its association with PV to date.

Nomenclature for alleles of the thiopurine methyltransferase gene

The drug-metabolizing enzyme thiopurine methyltransferase (TPMT) has become one of the best examples of pharmacogenomics to be translated into routine clinical practice. TPMT metabolizes the thiopurines 6-mercaptopurine, 6-thioguanine, and azathioprine, drugs that are widely used for treatment of acute leukemias, inflammatory bowel diseases, and other disorders of immune regulation. Since the discovery of genetic polymorphisms in the TPMT gene, many sequence variants that cause a decreased enzyme activity have been identified and characterized. Increasingly, to optimize dose, pretreatment determination of TPMT status before commencing thiopurine therapy is now routine in many countries. Novel TPMT sequence variants are currently numbered sequentially using PubMed as a source of information; however, this has caused some problems as exemplified by two instances in which authors' articles appeared on PubMed at the same time, resulting in the same allele numbers given to different polymorphisms. Hence, there is an urgent need to establish an order and consensus to the numbering of known and novel TPMT sequence variants. To address this problem, a TPMT nomenclature committee was formed in 2010, to define the nomenclature and numbering of novel variants for the TPMT gene. A website (http://www.imh.liu.se/tpmtalleles) serves as a platform for this work. Researchers are encouraged to submit novel TPMT alleles to the committee for designation and reservation of unique allele numbers. The committee has decided to renumber two alleles: nucleotide position 106 (G>A) from TPMT*24 to TPMT*30 and position 611 (T>C, rs79901429) from TPMT*28 to TPMT*31. Nomenclature for all other known alleles remains unchanged.

CYP21A2 p.E238 Deletion as Result of Multiple Microconversion Events

More than 90% of congenital adrenal hyperplasia (CAH) cases are associated with mutations in the 21-hydroxylase gene (CYP21A2) in the HLA class III area on the short arm of chromosome 6p21.3. The major part of disease-causing mutations in CYP21A2 alleles are CYP21A1P-derived sequence transferred to the active gene by macroconversion or microconversion events. Only around 5% of all disease-causing CYP21A2 alleles harbor rare mutations that do not originate from the pseudogene. A complete list of all reported CYP21A2 mutations can be found in the CYP21A2 database created by the Human Cytochrome P450 (CYP) Allele Nomenclature Committee (http://www.imm.Ki.se/CYPalleles/cyp21.htm). In this report, we describe clinical and genetic findings regarding an Italian woman suffering from a classic salt-wasting form of CAH due to a severe 21-hydroxylase deficiency. A complex genetic family study was performed including a prenatal diagnosis. The patient was found to be heterozygous for p.I172N (exon 4), p.E238del (exon 6), p.M239K (exon 6), and p.F306insT (exon 7) mutations and homozygous for p.I236N (exon 6) and p.V237E (exon 6) mutations. The deletion of glutamic acid 238 is a new mutation not reported before in the literature. CYP21A2 genotyping has become a valuable complement to biochemical CAH investigation. We highlight the contribution of molecular genetic advancements to the clinical management of patients with 21-hydroxylase deficiency.

CYP2C9 polymorphism analysis in Han Chinese populations: building the largest allele frequency database

Genetic polymorphisms of CYP2C9 significantly influence the pharmacokinetics and pharmacodynamics of some drugs, which might result in adverse drug effects and therapeutic failure. Several studies have been performed on CYP2C9 genetic polymorphisms in Han Chinese populations. However, these studies only focused on two commonly investigated alleles, *2 and *3, in relatively small sample sizes. To scale up the gene-scanning region and determine relatively precise data on the genetic distribution pattern in Chinese populations, unrelated healthy Han Chinese volunteers from Zhejiang Province (n=1127) and Hebei (n=1000) Province were recruited as subjects for the direct sequencing of all exons of CYP2C9. As a result, 14 previously reported alleles were detected in this work, and 8 of these alleles (*14, *16, *19, *23, *27, *29, *33 and *34) were described for the first time in Chinese populations. In addition, 37 novel mutations were also detected, of which 22 variants were non-synonymous, and 21 new alleles, *36-*56, were designated by the Human CYP Allele Nomenclature Committee. In vitro functional analysis of these 22 novel CYP2C9 variants revealed that 17 mutations had a significant influence on the protein's catalytic activity. Our study provides the most accurate data on CYP2C9 polymorphisms in Han Chinese populations and detects the largest number of novel allelic variants existing to date. These new alleles will greatly enrich the current knowledge of naturally occurring CYP2C9 variants in Chinese populations.

Efficient multiplex simple sequence repeat genotyping of the oomycete plant pathogen Phytophthora infestans

Genotyping is fundamental to population analysis. To accommodate fast, accurate and cost-effective genotyping, a one-step multiplex PCR method employing twelve simple sequence repeat (SSR) markers was developed for high-throughput screening of Phytophthora infestans populations worldwide. The SSR markers reported for this species were evaluated and the twelve most informative and easily scored were selected. To accomplish a single step genotyping procedure, we optimized primers, fluorescent labels and PCR conditions to genotype using a capillary electrophoresis system with four fluorescent labels (FAM, NED, PET and VIC) and a labeled LIZ standard for sizing of the SSR fragments. The results obtained using commercially available multiplex PCR kits on a set of reference isolates were in agreement with that obtained using primer pairs in simplex reactions. In testing on many thousands of isolates, we have found the markers appropriate for resolving distinct multilocus genotypes (MLGs) of isolates of European and wider populations. Here we demonstrate the utility of the assay on a set of 19 reference isolates plus 77 others sampled from The Netherlands and Great Britain. In most isolates one to two alleles were observed at each locus but the presence of three alleles at a single locus in some isolates was consistent with increased ploidy. Methods are presented that are appropriate for the analysis of datasets comprising isolates of mixed ploidy levels. We also report on the direct P. infestans genotyping from infected field material to collect, store and extract pathogen DNA. A critical step in this multiplex method was the standardization of the protocol between two laboratories in The Netherlands and Great Britain. Reference isolates were exchanged and an allele nomenclature and scoring system agreed. Such co-operation is facilitating the genotyping of international collections of P. infestans isolates in wider networks of laboratories and providing the data required to expand an existing international database of pathogen diversity.

Nomenclature for alleles of the thiopurine methyltransferase gene

Nomenclature for alleles of the thiopurine methyltransferase gene

Developmental validation of 15 X chromosomal short tandem repeat markers

The use of X chromosomal short tandem repeat (STR) markers has been greatly increasing in the forensic setting. Using guidelines set forth previously for the validation of autosomal and Y STRs, aspects of the feasibility of routine X chromosomal STR use were evaluated. Two mini-X chromosomal STR multiplexes capable of amplifying 15 total markers were developed and utilized to determine allele nomenclature, allele/genotype frequencies, mutation rates, and linkage between markers. Additionally, a concordance study between these multiplexes and a commercially available kit was performed. Here, the authors present an overview of this extensive developmental validation study.

CYP2D6*11 and Challenges in Clinical Genotyping of the Highly Polymorphic CYP2D6 Gene

CYP2D6 is genotyped clinically for prediction of response to tamoxifen, psychotropic drugs and other medications. Phenotype prediction is dependent upon accurate genotyping. The CYP Allele Nomenclature Committee maintains the allelic nomenclature for CYP2D6; however, in some cases, the list of polymorphisms associated with a given allele is incomplete. Clinical laboratories and in vitro diagnostic manufacturers rely upon this nomenclature, in addition to the literature, to infer allelic function and haplotypes and when they design CYP2D6-testing platforms. This article provides more complete sequencing data for the CYP2D6*11 allele and describes the difficulties encountered in genotyping CYP2D6 when incomplete data are available. The CYP Allele Nomenclature Committee should provide clear information about the completeness of the original data used to define each allele.