HbVar database of human hemoglobin variants and thalassemia mutations: 2007 update.
HbVar (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 alpha- and beta-globin loci are provided automatically. Population-specific beta-thalassemia mutation frequencies for 31 population groups have been added and/or modified and the previously reported delta- and alpha-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.
Giardine
Belinda
B
The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, University Park, Pennsylvania, USA.
van Baal
Sjozef
S
Kaimakis
Polynikis
P
Riemer
Cathy
C
Miller
Webb
W
Samara
Maria
M
Kollia
Panagoula
P
Anagnou
Nicholas P
NP
Chui
David H K
DH
Wajcman
Henri
H
Hardison
Ross C
RC
Patrinos
George P
GP
D004252:DNA Mutational Analysis / Q000379:methods; D030561:Databases, Nucleic Acid; D005820:Genetic Testing / Q000379:methods; D014644:Genetic Variation; D006454:Hemoglobins / Q000235:genetics*; D006801:Humans; D005810:Multigene Family; D009154:Mutation; D013789:Thalassemia / Q000235:genetics*
D006454:Hemoglobins