IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

Abstract

The IPD-MHC Database project (http://www.ebi.ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and tools to enable accurate analysis. Since the first release of the database in 2003, IPD-MHC has grown and currently hosts a number of specific sections, with more than 7000 alleles from 70 species, including non-human primates, canines, felines, equids, ovids, suids, bovins, salmonids and murids. These sequences are expertly curated and made publicly available through an open access website. The IPD-MHC Database is a key resource in its field, and this has led to an average of 1500 unique visitors and more than 5000 viewed pages per month. As the database has grown in size and complexity, it has created a number of challenges in maintaining and organizing information, particularly the need to standardize nomenclature and taxonomic classification, while incorporating new allele submissions. Here, we describe the latest database release, the IPD-MHC 2.0 and discuss planned developments. This release incorporates sequence updates and new tools that enhance database queries and improve the submission procedure by utilizing common tools that are able to handle the varied requirements of each MHC-group.

The desirable donor pig to eliminate all xenoreactive antigens

“…Changing 55R to a proline (which is present in non‐HLA‐DQ 4,5,6) reduced, or completely eliminated, the xenoantigenicity of a SLA‐DQ molecule recognized by antibodies in human sera. 51 of 52 known SLA‐DQβ chains contain the 55R residue . Consequently, patients with antibodies to this epitope will likely have antibodies towards every pig.…”

“…51 of 52 known SLA-DQβ chains contain the 55R residue. 21 Consequently, patients with antibodies to this epitope will likely have antibodies towards every pig.…”

Identification of MHC‐DMA and ‐DMB alleles in Tibetan macaques (Macaca thibetana)

“…The PCR amplification was performed using Premix Taq (LA Taq Version 2.0, Takara, China) and the products were cloned into the pUCm‐T Vector (Sangon Biotech, China) and sequenced on the ABI3730 platform (Applied Biosystems). The sequences were analyzed and novel alleles were submitted to the GenBank database and officially assigned allele‐names by the Nonhuman Primate (NHP) MHC committee of the Immuno Polymorphism Database (IPD) …”

First identification of the MHC‐DPB2 alleles in the rhesus macaques (Macaca mulatta)

“…Polymerase chain reaction (PCR) products were purified, cloned, and sequenced. As a result, three novel DPB2 alleles were identified, which have been submitted to the National Center for Biotechnology Information (NCBI) and were officially named by the nonhuman primate MHC committee of the Immuno Polymorphism Database (IPD): Mamu‐DPB2*01:01 (MG572767), Mamu‐DPB2*01:02 (MG585350), and Mamu‐DPB2*01:03 (MG572768) . In the previous publications on the rhesus macaque DPB gene, some DPB1 alleles have been identified, but not DPB2 gene.…”