HLA-DQB1 sequencing-based typing using newly identified conserved nucleotide sequences in introns 1 and 2

Characterizing alleles with large deletions using region specific extraction

Two novel HLA class II alleles, DRB4*03:01N and DQB1*03:276N, containing large deletions were identified during routine typing. Extraction of DNA encompassing the deletions was carried out with a panel of capture oligonucleotides followed by whole genome amplification. Next generation DNA sequencing was then used to characterize the sequences. DRB4*03:01N has a 16 kilobase pair deletion stretching upstream from intron 2 toward centromeric DRB8. DQB1*03:276N has two deletions separated by 844 nucleotides. The first deletion (3.7 kilobase pairs) is upstream of intron 1 and the second deletion removes 3.3 kilobase pairs further upstream towards centromeric DQA2.

Unambiguous high resolution genotyping of human leukocyte antigens

We have developed a high resolution sequencing based typing method for genotyping Human Leukocyte Antigens (HLA) over a period of twenty years. The methods are based upon the separation of HLA alleles per locus at the initial amplification to simplify the analysis post-sequencing. The increasing discovery of polymorphism in HLA, manifested in new alleles, has necessitated the continuing development of this method. Here we present methods for the high resolution Sequence Based Typing of HLA-A, B, C (class I) and HLA-DQB1 and DRB1 (class II). The purpose of this article is to provide a valuable resource of methods and primers for other laboratories engaged in HLA typing.

Immunogenetic Markers Definition in Latvian Patients with Lyme Borreliosis and Lyme Neuroborreliosis

The aim of this study was to determine the human leukocyte antigen (HLA)-DRB1 alleles in two groups of patients in Latvia: patients with Lyme borreliosis and patients with Lyme neuroborreliosis. The study included 216 patients with Lyme borreliosis, 29 patients with Lyme neuroborreliosis and 282 control persons. All surveyed persons were residents of Latvia. The HLA-DR genotyping was performed by polymerase chain reaction- sequence specific primer (PCR-SSP). The predisposition to the Lyme borreliosis is associated with the HLA-DRB1*07, -DRB1*17(03), -DRB1*04, -DRB1*15(02) alleles. The allele -DRB1*11(05), -DRB1*14(06) and -DRB1*13(06) were significantly more frequent in controls. In-group with Lyme neuroborreliosis differences were found for the -DRB1*07 and -DRB1*04 alleles, but only HLA-DRB1*07 allele was statistically significant after Bonferroni correction and associated with Lyme neuroborreliosis in Latvian patients.

Polymorphisms of HLA-DRB1, -DQA1 and -DQB1 in inhabitants of Astana, the capital city of Kazakhstan

BACKGROUND

Kazakhstan has been inhabited by different populations, such as the Kazakh, Kyrgyz, Uzbek and others. Here we investigate allelic and haplotypic polymorphisms of human leukocyte antigen (HLA) genes at DRB1, DQA1 and DQB1 loci in the Kazakh ethnic group, and their genetic relationship between world populations.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 157 unrelated Kazakh ethnic individuals from Astana were genotyped using sequence based typing (SBT-Method) for HLA-DRB1, -DQA1 and -DQB1 loci. Allele frequencies, neighbor-joining method, and multidimensional scaling analysis have been obtained for comparison with other world populations. Statistical analyses were performed using Arlequin v3.11. Applying the software PAST v. 2.17 the resulting genetic distance matrix was used for a multidimensional scaling analysis (MDS). Respectively 37, 17 and 19 alleles were observed at HLA-DRB1, -DQA1 and -DQB1 loci. The most frequent alleles were HLA-DRB1*07:01 (13.1%), HLA-DQA1*03:01 (13.1%) and HLA-DQB1*03:01 (17.6%). In the observed group of Kazakhs DRB1*07:01-DQA1*02:01-DQB1*02:01 (8.0%) was the most common three loci haplotype. DRB1*10:01-DQB1*05:01 showed the strongest linkage disequilibrium. The Kazakh population shows genetic kinship with the Kazakhs from China, Uyghurs, Mongolians, Todzhinians, Tuvinians and as well as with other Siberians and Asians.

CONCLUSIONS/SIGNIFICANCE

The HLA-DRB1, -DQA1 and -DQB1 loci are highly polymorphic in the Kazakh population, and this population has the closest relationship with other Asian and Siberian populations.

HLA-class II alleles in patients with drug-resistant pulmonary tuberculosis in Kazakhstan

The human leukocyte antigen (HLA) system has a major role in the regulation of the immune response as it is involved in the defense against pathogens. Some studies have reported that HLA class II genes play a strong role in severe cases of pulmonary tuberculosis (PTB) in several populations. Thus the aim of the study was to compare the HLA-class II alleles of patients with drug resistant tuberculosis with those of healthy controls from the same ethnic group in Kazakhstan. The aim of the present study was to evaluate the correlation of HLA-class II alleles by patients with drug resistant tuberculosis and the healthy controls of the same ethnic group in Kazakhstan. The HLA-class II alleles of 76 patients with tuberculosis (TB) and 157 healthy volunteers were investigated using sequence-based typing (SBT)-method. HLA-DQA1*03:02 HLA-DRB1*08:01 and DRB1*08:03 occurred more frequently (P = 0.05) in patients with drug resistant tuberculosis than in controls. We observed a possible association between certain HLA alleles and TB that are specific for the Kazakh population. Further studies are needed to confirm our findings using a larger number of patients with drug resistant tuberculosis.

Human leukocyte antigen (HLA) typing by DNA sequencing

DNA sequencing is a powerful technique for identifying allelic variation within the human leukocyte antigen (HLA) genes. Sequencing is usually focused on the most polymorphic exons of the class I (HLA-A, -B, -C) and class II (HLA-DR, -DQ, and -DP) genes. These exons encode the antigen recognition site, the region of the HLA molecule that binds peptides and interacts with the T cell receptor for antigen and natural killer cell immunoglobulin-like receptors (KIR). Sanger sequencing of amplified DNA from each HLA gene from a preparation containing one or two alleles yields a sequence that is used to identify the alleles by comparison with a reference database.

Human leucocyte antigen typing: techniques and technology, a critical appraisal

Methods for the identification of Human Leukocyte Antigens (HLA) have changed significantly since this group of polymorphic proteins were first characterized by serological reagents in the 1960s and 1970s. The invention and development of the Polymerase Chain Reaction (PCR) has been key in the progress of methods for HLA genotyping. As the complexity of HLA polymorphism has unravelled so it has exposed the weaknesses in techniques such as PCR - Restriction Fragment Length Polymorphism (RFLP) and Reference Strand Mediated Conformation Analysis (RSCA), which are no longer in use today. Methods which have been considered routine laboratory tools in recent years, such as Sequence-Specific Primer - PCR and Sequencing Based Typing (SBT) are now also threatened with extinction, not only because of the depth of HLA variation but also because of the rapid development of Next Generation Sequencing and technologies which will follow this. This review describes the merits and disadvantages of current technologies available to HLA Typing laboratories, future trends and the problems posed by new alleles.

HLA typing by direct DNA sequencing

Sequencing-based typing is a high resolution method for the identification of HLA polymorphisms. The majority of HLA Class I alleles can be discriminated by their exon 2 and 3 sequence, and for Class II alleles, exon 2 is generally sufficient. There are polymorphic positions in other exons which may require additional sequencing to exclude certain alleles with differences outside exon 2 and 3, depending on the clinical requirement and relevant accredition guidelines. The process involves selective amplification of target alleles by PCR, agarose gel electrophoresis of the PCR products to assess the quantity and quality, followed by purification of PCR amplicons to remove excess primer and dNTPs. Cycle sequencing reactions using Applied Biosystems™ BigDye(®) Terminator Ready Reaction v1.1 or v3.1 Kit are performed, then purification of sequence reactions before electrophoresing using Applied Biosystems™ 3730 or 3730XL Genetic Analyser (or similar). Data is processed by specialised software packages, which compare the sample sequence to the sequences of all possible theoretical allele combinations to assign an accurate genotype. Examination of all nucleotides, both at conserved and polymorphic positions enables the direct identification of new alleles, which may not be possible with techniques such as SSP and SSO typing.

Methods for diagnostic HLA typing in disease association and drug hypersensitivity

This chapter describes the application of diagnostic HLA typing for disease association and five methods used for specific HLA genotypes. The methods utilise a combination of polymerase chain reaction (PCR) amplification to detect sequence polymorphism by the presence or absence of amplification, nucleotide sequencing of the PCR product, and hybridisation of the PCR product with labelled probes. The probes are specific for sequence polymorphism associated with the genotype and are attached to either a Micro Bead or a Solid Phase. In addition, the detection of single nucleotide polymorphism(s) which "tag" for the genotype using a real-time PCR is described.

Allelic and haplotypic HLA frequency distribution in Spanish hematopoietic patients. Implications for unrelated donor searching

Histocompatibility criteria for unrelated donor selection are based on high-resolution definition of HLA genes. In spite of the expansion of the unrelated donor registries, HLA matching remains a problem for many patients because of the great diversity of HLA alleles and haplotypes. The availability of matched donors at an allelic level depends on the frequency of the patient's alleles and haplotypes. Therefore, data regarding HLA distribution for each population are needed in order to evaluate the donor searching approach and, may be, even the therapeutic strategy. In the present report, we have analyzed 253 haematological Spanish patients awaiting unrelated haematopoietic stem cell (HSC) donors. HLA allele and haplotype frequencies have been defined at high resolution for the first time in this population. Significant differences in HLA distribution have been reported when comparing two patient groups, one that received full-match (10/10) unrelated donors and one that did not. Factors like rare alleles, presence of B*510101 (because of the association with multiple HLA-C alleles), as well as infrequent B-C and DRB1-DQB1 associations, showed a negative value for finding a suitable donor, whereas the presence of one of the six-gene haplotypes with a frequency ≥ 0.9% in our sample was a positive factor influencing donor searching. These differences will be useful in donor searching advising and in the use of different therapeutic strategies.

Identification of a novel HLA-DQB1 allele, DQB1*0326, in a College of American Pathologists 2009 survey specimen

We identified a novel DQB1*0326 allele from a proficiency test sample provided by the College of American Pathologists (CAP) medical society. This novel DQB1 allele was unexpectedly discovered by sequence-based typing method in an attempt to resolve a discrepant typing result between the CAP survey report and our laboratory report. This novel DQB1 allele is most similar to DQB1*030302 and DQB1*0311. DQB1*0326 has a nucleotide substitution resulting an amino acid change when compared with DQB1*030302 (M to L) and it differs from DQB1*0311 by one nucleotide variation causing an amino acid replacement (A to D).

Two novel HLA class II alleles, DRB1*11:96 and DQB1*02:01:03, identified in Koreans

DRB1*11:96 and DQB1*02:01:03 differ from DRB1*11: 01:01 and DQB1*02:01:01 by one nucleotide in exon 2, respectively.

DQB1 intron 3 sequences provide an insight into the evolution of DQB1 alleles and form the basis for intron-based sequencing

The goal of this project was to obtain sequences of intron 3 of DQB1 in order to develop a sequencing-based typing protocol that provides a complete DQB1 exon 3 sequence. Current protocols do not provide complete sequences of exon 3, thus not allowing to differentiate common and well-documented alleles DQB1*0301 and *0319 and resolve some common trans-ambiguities with group-specific sequencing primer (GSSP) sequencing using positions 641 and 650. Samples homozygous for the most common DQB1 alleles were used to obtain intron 3 sequences, which were used to design intron-based primers for exon 3 amplification. The protocol was extensively validated; no allele dropouts were observed. The presented protocol allows differential typing of DQB1*0301 and *0319 and resolves some common trans-ambiguities.

Novel alleles at the HLA-DRB1 and -DQB1 loci

Twelve novel human leukocyte antigen class II alleles are described; eight DRB1 alleles and four DQB1 alleles. Nine of the variants are single nucleotide substitutions from their most homologous allele, of which six result in amino acid changes (DRB1*0459, *1156 and *1522; DQB1*0205, *0320 and *0321) and three are silent substitutions (DRB1*030105 and *040304, and DQB1*030104). The remaining alleles (DRB1*0906, *1464 and *1468) differ from their most similar alleles by two to three nucleotide substitutions which alter one to two amino acids.

Group-specific amplification of cDNA from DRB1 genes. Complete coding sequences of partially defined alleles and identification of the new alleles DRB1*040602, DRB1*111102, DRB1*080103, and DRB1*0113

We present here the complete coding sequences, previously unavailable, of the DRB1 alleles DRB1*030102, *0306, *040701, *0408, *1327, *1356, *1411, *1446, *1503, *1504, *0806, *0813, and *0818. For cDNA isolation, new group-specific primers located at the 5'UT and 3'UT regions were used to carry out allele-specific amplification and a convenient method for determining full-length sequences for DRB1 alleles. Complete coding sequencing of samples previously typed as DRB1*0406, DRB1*080101, and DRB1*1111 revealed new alleles with noncoding nucleotide changes at exons 1 and 3. In addition, we found a novel allele, DRB1*0113, whose second exon carries a sequence motif characteristic of DRB1*07 alleles. The predicted class II haplotypic associations of all alleles are reported and discussed.

KIR3DL3 allelic diversity: six new alleles exhibit both conservative and non-conservative substitutions

KIR3DL3 alleles were characterized in two families and one unrelated individual. Based on exon 2-9 nucleotide sequences, six novel alleles, 3DL3*00402, *005, *006, *007, *00801, *00802, were identified bringing the total number of known alleles to 11. Compared with 3DL3*001, the six new alleles differ by from three to nine nucleotides and from three to four amino acids. The new alleles double the number of known polymorphic positions to 18 with variation in exons encoding the extracellular domains, transmembrane region, and a portion of the cytoplasmic tail. Many of the nucleotide substitutions are shared among alleles of 3DL3 or other KIR loci, but five were found only in single 3DL3 alleles. Comparison of intron sequences among individuals carrying the same allele showed a modest number of substitutions with the exception of 3DL3*001 which differed substantially in its intron sequences. Two alleles sharing coding region sequences, 3DL3*00201 and 3DL3*00202, were also substantially different in intron sequences.