HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update

Abstract

Communicated by Stylianos E. AntonarakisHbVar (http://globin.bx.psu.edu/hbvar) is a locus-specific database (LSDB) developed in 2001 by a multi-center academic effort to provide timely information on the genomic sequence changes leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology, and ethnic occurrence, accompanied by mutation frequencies and references. In addition to the regular updates to entries, we report significant advances and updates, which can be useful not only for HbVar users but also for other LSDB development and curation in general. The query page provides more functionality but in a simpler, more user-friendly format and known single nucleotide polymorphisms in the human α-and β-globin loci are provided automatically. Populationspecific β-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported δ-and α-thalassemia mutation frequency data from 10 population groups have also been incorporated. In addition, an independent flat-file database, named XPRbase (http://www.goldenhelix.org/xprbase), has been developed and linked to the main HbVar web page to provide a succinct listing of 51 experimental protocols available for globin gene mutation screening. These updates significantly augment the database profile and quality of information provided, which should increase the already high impact of the HbVar database, while its combination with the UCSC powerful genome browser and the ITHANET web portal paves the way for drawing connections of clinical importance, that is from genome to function to phenotype.

Hemoglobin βCys93 is essential for cardiovascular function and integrated response to hypoxia

“…It should be noted that, despite a long list of human Hb mutants (55), which include mutations that markedly affect Hb O 2 affinity, function, and stability, , T-wave amplitude is significantly reduced in βC93A and γβC93A mice versus γβC93 mice, indicative of myocardial ischemia. In B and C data are presented as mean ± SEM; n = 13-21 mice; *P < 0.05 by one-way ANOVA for differences between βC93A and γβC93A mice versus γβC93 mice; † P < 0.05 by one-way ANOVA for differences between βC93A mice versus γβC93 mice.…”

A1ATVar: a relational database of humanSERPINA1gene variants leading to α1-antitrypsin deficiency and application of the VariVis software

“…They are built using a custom-made PHP script that comprises the archive's core engine, not only for menus and basic screens that display and parse files, but also for handling data queries. Although the structure of this database resembles the XPRbase database for human globin gene experimental protocols (www.goldenhelix.org/ xprbase) [Giardine et al, 2007], protocol querying is done on a different and much simpler way, i.e., keyword-based rather than gene-based querying.…”

Top-Down Proteomics and Direct Surface Sampling of Neonatal Dried Blood Spots: Diagnosis of Unknown Hemoglobin Variants

“…Hemoglobinopathies are classified into two types: thalassemias, which are characterized by a reduction in the synthesis of the globin chains, and structural hemoglobin variants which are caused by a point mutation in the globin gene typically leading to a single amino acid substitution in the globin chain. There are over 1000 Hb variants classified [3] and in the majority of cases the variants are not clinically significant. The most well-known clinically significant structural Hb variant is the sickle variant (HbS) (β6 Glu→Val Δm -29.97 Da) [4].…”