Jove
Visualize
Contact Us

Related Experiment Videos

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

Wolfgang Helmberg1, Raymond Dunivin, Michael Feolo

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, 8600 Rockville Pike, Bethesda, MD 20894, USA. helmberg@ncbi.nlm.nih.gov

Nucleic Acids Research
|June 25, 2004
PubMed
Summary

The dbMHC resource offers an online tool to analyze sequencing-based typing (SBT) results for human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) alleles. This tool aids in determining sample composition and identifying specific allele variations.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Allele-specific long-range sequencing as a method for ABO haplotyping in clinical blood group diagnosis and immunohematology research.

Molecular genetics & genomic medicine·2023
Same author

Pilot Study to Gain First Indications for the Impact of a 3-Month's Oral Intake of a Sucrosomial Iron Supplement on Hemoglobin in Iron-Deficient Blood Donors.

Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie·2023
Same author

Whole genome DNA and RNA sequencing of whole blood elucidates the genetic architecture of gene expression underlying a wide range of diseases.

Scientific reports·2022
Same author

Identifying Datasets for Cross-Study Analysis in dbGaP using PhenX.

Scientific data·2022
Same author

Impact of allogeneic red blood cell transfusion on prognosis in soft tissue sarcoma patients. A single-centre study.

Cancer medicine·2022
Same author

Whole Genome DNA and RNA Sequencing of Whole Blood Elucidates the Genetic Architecture of Gene Expression Underlying a Wide Range of Diseases.

Research square·2022
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Area of Science:

  • Immunogenetics
  • Bioinformatics
  • Molecular Biology

Background:

  • Accurate typing of human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptor (KIR) genes is crucial for transplantation and disease research.
  • Existing methods for analyzing sequencing-based typing (SBT) data can be complex and time-consuming.
  • The National Center for Biotechnology Information (NCBI) hosts the dbMHC resource, a valuable platform for MHC and KIR-related data.

Purpose of the Study:

  • To introduce and describe the functionalities of the dbMHC online tool for evaluating SBT results.
  • To provide a user-friendly platform for analyzing the allelic composition of cDNA or genomic sequences for HLA and KIR loci.
  • To facilitate the identification of specific allele variants and base changes within sequencing data.

Main Methods:

Related Experiment Videos

  • Development of an online tool integrated within the dbMHC resource at NCBI.
  • Comparison of submitted SBT sequences (heterozygous, haploid, or mixed) against comprehensive, up-to-date databases of known HLA and KIR alleles.
  • Utilizing an interactive sequence viewer for detailed examination of sequence alignments and base changes.

Main Results:

  • The tool successfully evaluates the allelic composition of SBT results for HLA and KIR loci.
  • It provides a table of potential allele hits, detailing specific base changes for each identified allele.
  • An interactive sequence viewer allows for in-depth analysis of sequence alignments, aiding in accurate interpretation.

Conclusions:

  • The dbMHC online tool offers an efficient and accessible method for analyzing SBT data for HLA and KIR typing.
  • This resource simplifies the process of identifying allele variants and understanding sample composition.
  • The tool enhances the utility of SBT for researchers and clinicians working with immunogenetic data.