Wolfgang Helmberg

Database resources of the National Center for Biotechnology Information.

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website. NCBI resources include Entrez, PubMed, PubMed Central, LocusLink, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SARS Coronavirus Resource, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

Novel Sequence Feature Variant Type Analysis of the HLA Genetic Association in Systemic Sclerosis

We describe a novel approach to genetic association analyses with proteins sub-divided into biologically relevant smaller sequence features (SFs), and their variant types (VTs). SFVT analyses are particularly informative for study of highly polymorphic proteins such as the human leukocyte antigen (HLA), given the nature of its genetic variation: the high level of polymorphism, the pattern of amino acid variability, and that most HLA variation occurs at functionally important sites, as well as its known role in organ transplant rejection, autoimmune disease development and response to infection. Further, combinations of variable amino acid sites shared by several HLA alleles (shared epitopes) are most likely better descriptors of the actual causative genetic variants. In a cohort of systemic sclerosis patients/controls, SFVT analysis shows that a combination of SFs implicating specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk.

The sequencing-based typing tool of dbMHC: typing highly polymorphic gene sequences

The dbMHC resource (http://www.ncbi.nlm.nih.gov/mhc/sbt.cgi?cmd=main) at the National Center for Biotechnology Information (NCBI) has developed an online tool for evaluating the allelic composition of sequencing-based typing (SBT) results of cDNA or genomic sequences. Whether the samples are heterozygous, haploid or a combination of the two, they can be compared with two up-to-date databases of all known alleles of several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) loci. The results of the submission are returned as a table of potential allele hits, along with the respective base changes and an interactive sequence viewer for close examination of the alignment.

Ultrastructural changes and activation differences in platelet concentrates stored in plasma and additive solution

BACKGROUND : The aim of this study was to demonstrate how ultrastructural morphology of platelets stored in different media correlate with the appearance of particular activation markers on their cell surface.

BGMUT Database of Allelic Variants of Genes Encoding Human Blood Group Antigens.

The Blood group antigen Gene MUTation (BGMUT) database documents variations in genes of human blood group systems. In March 2014, the database, accessible at www.ncbi.nlm.nih.gov/gv/mhc/xslcgi.cgi?cmd=bgmut, listed 1,545 alleles of 44 genes of 34 blood group systems. Besides allelic information, the BGMUT resource also presents comprehensive and current information on blood group systems. This review describes the database and notes its utility for the transfusion medicine and human genetics communities.

A new h allele detected in Europe has a missense mutationin alpha(1,2)-fucosyltransferase motif II.

BACKGROUND: The FUT1 gene encodes an α(1,2)‐fucosyltransferase (H transferase), which determines the blood group H. Nonfunctional alleles of this gene, called h alleles and carrying loss‐of‐function mutations, are observed in the exceedingly rare Bombay phenotype. Twenty‐three distinct h alleles have been characterized at the molecular level in various populations. The FUT2 (SE) gene is highly homologous to FUT1 (H).

Identification of 14 new alleles at the fucosyltransferase 1, 2, and 3 loci in Styrian blood donors, Austria

BACKGROUND: Genes for fucosyltransferases 1 (FUT1:H), 2 (FUT2:Secretor), and 3 (FUT3:Lewis) encode enzymes crucial for ABH and Lewis blood group antigen synthesis. They are highly polymorphic and ethnically and geographically specific.

Detection and differentiation of platelet‐specific antibodies by flow cytometry: the bead‐mediated platelet assay

BACKGROUND: Platelet‐reactive antibodies cause a number of clinical disorders. The detection and differentiation of these antibodies are prerequisites for the adequate treatment of these disorders. The bead‐ mediated platelet assay described here enables the detection and differentiation of platelet‐bound antibodies by the use of flow cytometry.

HLA-DRB3*02:61Q , a novel HLA-DRB3 allele identified in a volunteer bone marrow donor

HLA‐DRB3*02:61Q , a novel HLA‐DRB3 allele identified in a volunteer bone marrow donor.

HLA-A*68:02:11, a new HLA-A*68 allele identified during family HLA typing.

A*68:02:11 differs from A*68:02:01 by a silent mutation in codon 122.