Polymorphism of HLA‐DRw52‐associated DRB1 genes as defined by sequence‐specific oligonucleotide probe hybridization and sequencing

Abstract

We have used group-specific DNA amplification and sequence-specific oligonucleotide probe (SSOP) hybridization to study DRB1 sequence polymorphisms associated with DR3, DRw11(5), DRw12(5), DRw13(w6), DRw14(w6) and DRw8 alleles. Group-specific amplification of DRw52-associated DRB1 alleles was achieved using a 5' amplification primer designed to hybridize with a first hypervariable region (HVR) sequence common to all known alleles in this group, together with a 3' intron primer. Prospective SSOP typing of DR3, DRw11, DRw12, DRw13, DRw14 and DRw8 alleles was performed in 318 individuals, including 124 patients, 46 family members and 148 unrelated marrow donors. Among the 395 DRw52-associated DRB1 alleles tested in our study, a subtype corresponding to the previously defined alleles DRB1*0301-2 (DR3), DRB1*1101-4 (DR5), DRB1*1201-2 (DR5), DRB1*1301-5 (DRw6), DRB1*1401-2 and 1404 (DRw6), and DRB1*0801-4 (DRw8) could be assigned in all but 6 individuals (1.9%) tested. In addition to the 22 known alleles, we identified two new DRw6-associated alleles, DRB1*13.MW(1) and DRB1*14.GB(1). DRB1*13.MW typed serologically as DRw13 and was identical to DRB1*1301 except at codon 71 where AGG encodes arginine instead of GAG encoding glutamic acid. DRB1*14.GB represents a DRB1*1402 variant whose sequence at codon 86 encodes valine (GTG) instead of glycine (GGT). These results demonstrate that SSOP methods represent an efficient and precise approach for typing DRB1 alleles and for identifying potential novel variants previously unrecognized by conventional typing methods.

An Analysis of HLA-A, -B, and -DRB1 Allele and Haplotype Frequencies of 21,918 Residents Living in Liaoning, China

“…Nowadays, there are several kinds of PCR-based HLA typing being used: DNA amplification with sequence specific primers (SSP) [18], sequence specific oligonucleotide probes (SSO) [19], single-stranded conformation polymorphism (SSCP) [20], sequence-based typing (SBT) [21], and DNA chip technology [22]. These HLA typing techniques are of much higher accuracy as well as reliability than the conventional serologic typing method, and also may facilitate the standardization of HLA typing processes [23].…”

Distributions of HLA-A and -B alleles and haplotypes in the Yi ethnic minority of Yunnan, China: relationship to other populations

“…The technology of HLA typing has significantly evolved since the PCR method was introduced by Mullis and Faloona (1987). Nowadays, there are several kinds of PCR-based HLA typing being used: DNA amplification with sequence specific primers (SSP) (Zetterquist and Olerup, 1992), sequencespecific oligonucleotide probes (SSOP) (Petersdorf et al, 1991), single-stranded conformation polymorphism (SSCP) (Lo et al, 1992), sequence-based typing (SBT) (Santamaria et al, 1993), and DNA chip technology (Jiang et al, 2006). These HLA typing techniques have much higher accuracy as well as reliability than the classical serologic typing method, and also facilitate the standardization of HLA typing processes.…”

HLA‐B*15 subtypes distribution in Han population in Beijing, China, as compared with those of other populations

“…The development of molecular biology techniques based on PCR (polymerase chain reaction) has greatly improved the accuracy and practicability of HLA typing (Hao & Xiao, 2002). There are several kinds of PCR‐based HLA typing: DNA amplification with sequence specific primers (SSP) (Zetterquist & Olerup, 1992), sequence specific oligonucleotide probes (SSOP) (Petersdorf et al. , 1991), single‐stranded conformation polymorphism (SSCP) (Lo et al.…”