Search tips
Search criteria 


Logo of nihpaAbout Author manuscripts
Tissue Antigens. Author manuscript; available in PMC 2011 February 1.
Published in final edited form as:
PMCID: PMC2871286

Identification of a new Patr-B*01 variant, Patr-B*0102, by sequence-based typing in a chimpanzee (Pan troglodytes)


Description of one new non-human primate MHC-B (Patr-B) allele.

Keywords: Patr-B, Pan troglodytes, polymerase chain reaction-sequencing based typing

Chimpanzees (Pan troglodytes), humans' closest living relative, are not only genetically similar to humans but also share susceptibility to some infectious diseases. Because the chimpanzees are used in biomedical research, investigation of their genetic background becomes important to extrapolated results for human.

This report describes the identification of a novel Patr-B*01 allele found in a chimpanzee studied under Institutional Animal Care and Use Committee-approved protocols. The determination of nucleotide sequence of the polymorphic exons 2 and 3 of Patr-B was performed by sequences-based typing (SBT) techniques as previously described (1). The electropherogram of directed sequencing showed the presence of two superimposed peaks in exon 2 of aligned Patr-B*0101.

To confirm the presence of two Patr-B alleles, one Patr-B*0101 and one new allele, the PCR product from two different reactions was cloned in Topo Ta Cloning Kit for sequencing (Invitrogen). Many clones for the allele of interest were obtained, from which 10 clones were sequenced. The consensus sequence has been submitted to GenBank, accession number GQ470394, and to the IPD-MHC Database receiving the official name Patr-B*0102 (2).

The new allele differs from the sequence of Patr-B*0101 by a non-synonymous nucleotide exchange at first and third position in codon 57 in exon 2 (CCG → TCA) (Figure 1A). This substitution changes the amino acid from proline to serine (P → S) (Figure 1B). Codon 57 is located outside of the antigen-binding cleft (3).

Figure 1
Alignment of the nucleotide sequence of exon 2 (A) and the partial deduced amino acid sequence (B) of Patr-B*0102 with that of Patr-B*0101. Dashes (−) indicate identity with the Patr-B*0101 sequence. Numbers above correspond to the codon position ...


The authors thank Dr Natasja de Groot, Dr Nel Otting and the IMGT Non-human Primate Nomenclature Committee for registering the Patr-B allele. This work was supported in part by : “Associazione Italiana per la Ricerca sul Cancro” (AIRC), Isituto Superiore Sanità-ACC4 and Direzione Centrale del Lavoro, Formazione, Università e Ricerca Della Regione Autonoma Friuli Venezia Giulia Codice Progetto 200502027001.


1. Caggiari L, Simula MP, Marzotto A, Shiina M, Rehermann B, De Re V. Identification of novel chimpanzee MHC class I and II alleles using an improved sequence-based typing strategy. Hum Immunol. 2006;67:63–72. [PubMed]
2. Robinson J, Waller MJ, Parham P, et al. IMGT/HLA and IMGT/MHC: databases for the study of the major histocompatibility complex. Nucleic Acids Res. 2003;31:311–314. [PMC free article] [PubMed]
3. Bjorkman PJ, Saper MA, Samroui B, Bennett WS, Strominger JL, Wiley DC. The foreign antigen binding site and T cell recognition regions of class I histocompatibility antigens. Nature. 1987;329:512–518. [PubMed]