In this issue

Transitioning from LocusLink to Entrez Gene

Cancer Chromosomes: a New Entrez Database

HomoloGene: An Entrez Database with a New Look

BLAST Link (BLink) to Protein Alignments and Structures

Debut of the HCT Database and Anthropology/Allele Frequencies in dbMHC

350kb Sequence Length Limit Removed by Sequence Database Collaboration

New Eukaryotic Genomes at NCBI

Environmental Samples Make Big Splash

HIV Protein-Interaction Database

e-PCR and Reverse e-PCR: Greater Sensitivity, More Options

New Organisms in UniGene

RefSeq Accession Numbers Get Longer as Rat Gets Last 6-digit Accession

Slots available for FieldGuidePlus Training Course Onsite at NCBI

RefSeq Release 6 on FTP Site

Exponential Growth of GenBank Continues with Release 142

Entrez Tools is a 'Hot Spot'

BLAST Lab: Using BLASTClust

New Microbial Genomes in GenBank

Entrez Quiz


Debut of the HCT Database and Anthropology/Allele Frequencies in dbMHC

The International Histocompatibility Working Group (IHWG) in Hematopoietic Cell Transplantation (HCT) is a worldwide scientific collaborative effort to support the use of information on the properties of the HLA barrier to allogeneic transplantation to improve the safety, efficacy and availability of HCT. The IHWG HCT studies are designed to determine whether complete allele matching for HLA-A, B, C DRB1, DQB1 and DPB1 is necessary for successful transplantation. Data generated from the study are anticipated to offer new approaches to the selection of suitable donors for HCT.

The IHWG and the NCBI at the National Institutes of Health, have collaborated to create a public database, dbMHC, to store genotype and clinical data, including up-to-date information on matching and transplant outcomes, and to provide online tools for data analysis. The new database contains anonymous data for selected unrelated donor transplants performed worldwide for the treatment of both malignant and non-malignant blood disorders. More information and a link to a list of contributors to dbMHC is found on the home page at:

A powerful way to view the data in dbMHC is to compute Kaplan-Meier survival plots using the HCT online plotting tool. Many default parameters for the plots can be adjusted in order to customize the data displayed. Help and FAQ documents are available for most plots. As an example, consider the Kaplan-Meier survival plot shown in Figure 1.

Click on image to view larger

Figure 1: Kaplan-Meier survival plot generated on the Web using analysis tools available from dbMHC. A summary of the parameters used to created the plot is displayed to the right.

The plot uses tick marks for censored data and shading to indicate the confidence intervals. To produce the plot, the Advanced Query Form is initialized with default parameters and one curve is plotted which allows no mismatches at HLA A, B, C, DRB1 and DQB1 loci and ignores HLA DPB1 locus. The parameters which affect the entire plot can be specified and a summary is displayed for each curve. A user may add a curve, modify a curve, delete a curve, view the plot, view plot data, view individual data, save the curve parameters, or restore saved parameters. When adding or modifying a curve, another form is displayed for entering the parameters for the curve and upon completion the user will return to the original page to view the updated selections.

Another important resource stemming from the efforts of the IHWG is the Antrhopology/Allele Frequencies databank, created in an effort to determine HLA class I and class II allele and haplotype frequencies in various human populations. Studies of allelic diversity in different populations can shed light on the evolution of HLA polymorphism as well as on the evolution and migration of human populations. In a clinical context, knowledge of the allele frequency distributions in various populations is critical to the strategy of establishing and searching bone marrow donor registries as well as for studies of HLA-associated disease susceptibility.

Users of the resource can choose to view allelic frequencies found in individuals from certain regions of the world, or view data submitted by a particular group. Users can also specify the loci to be displayed in the output table. Additional information about the project from the links to project overview and data contributors is found at:

The HCT and Anthropology/Allele Frequencies resources are available from the dbMHC home page via links from the blue sidebar menu.
Questions and comments can be addressed to the NCBI Service Desk at:


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NCBI News | Fall/Winter 2002 NCBI News: Spring 2003