Fluorotyping of HLA-C: differential detection of amplicons by sequence-specific priming and fluorogenic probing

High-throughput high-resolution class I HLA genotyping in East Africa

HLA, the most genetically diverse loci in the human genome, play a crucial role in host-pathogen interaction by mediating innate and adaptive cellular immune responses. A vast number of infectious diseases affect East Africa, including HIV/AIDS, malaria, and tuberculosis, but the HLA genetic diversity in this region remains incompletely described. This is a major obstacle for the design and evaluation of preventive vaccines. Available HLA typing techniques, that provide the 4-digit level resolution needed to interpret immune responses, lack sufficient throughput for large immunoepidemiological studies. Here we present a novel HLA typing assay bridging the gap between high resolution and high throughput. The assay is based on real-time PCR using sequence-specific primers (SSP) and can genotype carriers of the 49 most common East African class I HLA-A, -B, and -C alleles, at the 4-digit level. Using a validation panel of 175 samples from Kampala, Uganda, previously defined by sequence-based typing, the new assay performed with 100% sensitivity and specificity. The assay was also implemented to define the HLA genetic complexity of a previously uncharacterized Tanzanian population, demonstrating its inclusion in the major East African genetic cluster. The availability of genotyping tools with this capacity will be extremely useful in the identification of correlates of immune protection and the evaluation of candidate vaccine efficacy.

Development of a new HLA-DRB real-time PCR typing method

Polymerase chain reaction (PCR)-based human leukocyte antigen (HLA) typing methods currently used in most histocompatibility laboratories, such as PCR-sequence-specific primers (PCR-SSP) and PCR-sequence-specific oligonucleotide probes (PCR-SSO), are time-consuming and are at risk of contamination during the post-PCR process. The aim of this study was to develop a real-time PCR (rtPCR)-based HLA-DRB1 and -DRB3/4/5 low-medium resolution typing method to avoid these problems. This new method combined the use of specific primers and probes for HLA-DRB alleles. One pair of DRB gene primers and two DRB-specific probes (FAM and VIC) were used per reaction in each of a set of 16 PCR reaction tubes. To provide an internal positive control, each tube also contained a pair of primers and a TET probe for glyceraldehyde phosphate dehydrogenase. This allowed a very significant reduction in the number of reactions and the processing time, whereas typing resolution increased. After successful testing on 100 samples, the technique was validated in 200 clinical samples that had previously been typed for HLA-DRB using a standard PCR-based method. Identical results were obtained with all samples. This new method also reduced ambiguous results and was faster and less cumbersome than currently used PCR-SSP or PCR-SSO techniques.

DNA Pooling: a tool for large-scale association studies

DNA pooling is a practical way to reduce the cost of large-scale association studies to identify susceptibility loci for common diseases. Pooling allows allele frequencies in groups of individuals to be measured using far fewer PCR reactions and genotyping assays than are used when genotyping individuals. Here, we discuss recent developments in quantitative genotyping assays and in the design and analysis of pooling studies. Sophisticated pooling designs are being developed that can take account of hidden population stratification, confounders and inter-loci interactions, and that allow the analysis of haplotypes.

Rapid and simultaneous HLA class I (-A, -B and -C loci) DNA typing using the microtitre plate-reverse hybridization assay (MRHA)

We have established a precise, rapid, simple and practical HLA class I DNA typing method using the microtitre plate-reverse hybridization assay (MRHA), which enables us to perform simultaneous DNA typing of the HLA-A, -B and -C loci using the same PCR parameters and hybridization conditions. PCR-amplified products for the HLA-A, -B and -C loci were hybridized, respectively, with sequence-specific oligonucleotide (SSO) probes, which were immobilized covalently onto a microtitre plate, in hybridization buffer containing formamide at 37 degrees C. After washing at room temperature, the bound PCR products were detected by peroxidase-conjugate streptavidine followed by colour development such as enzyme immunoassay (EIA). In addition to the simple thermoregulation for hybridization and postwashing, strong positive signals, low background and high reproducibility, this DNA typing method enabled simultaneous typing of the HLA-A, -B and -C loci using a single microtitre plate as in HLA serotyping. The assignment of the HLA genotype was easily achieved by automated colorimetric reading and computer software, based on the cut-off value (threshold) established for each probe. For routine HLA class I typing, it may be possible to replace serological typing with the HLA class I DNA typing system using our MRHA method.

A commented dictionary of techniques for genotyping

Several tools, differing in their technical and practical parameters, are available for the detection of point mutations as well as small deletions and insertions. In this article, a dictionary featuring over fifty methods for detection of mutation is presented. The distinguishing principle for each method is briefly explained. Sorting of and discussion on the methods give the reader a brief introduction to the field of genotyping.

Alkaline-mediated differential interaction (AMDI): a simple automatable single-nucleotide polymorphism assay

The key requirements for high-throughput single-nucleotide polymorphism (SNP) typing of DNA samples in large-scale disease case-control studies are automatability, simplicity, and robustness, coupled with minimal cost. In this paper we describe a fluorescence technique for the detection of SNPs that have been amplified by using the amplification refractory mutation system (ARMS)-PCR procedure. Its performance was evaluated using 32 sequence-specific primer mixes to assign the HLA-DRB alleles to 80 lymphoblastoid cell line DNAs chosen from our database for their diversity. All had been typed previously by alternative methods, either direct sequencing or gel electrophoresis. We believe the detection system that we call AMDI (alkaline-mediated differential interaction) satisfies the above criteria and is suitable for general high-throughput SNP typing.

Donor-type chimerism determination by competitive polymerase chain reaction (PCR) in a primate model for bone marrow transplantation

BACKGROUND

Evaluation of the outcome of successful bone marrow transplantation (BMT) and in-depth studies of transplantation biology rely increasingly on accurate detection of donor origin cells in the transplanted recipients. This study describes a quantitative competitive polymerase chain reaction (PCR) assay for accurate evaluation of chimerism after allogeneic BMT in a cynomologous primate model, based on detection of monkey Y-specific DNA.

METHODS

A competitor standard was generated via PCR using a mutagenic primer that makes the competitor DNA 22 bp less than the wild type monkey Y-specific DNA. The mutated form can still be amplified by the primer pair for the detection of monkey Y-specific DNA. A fixed amount of sample subjected to chimerism detection was co-amplified with a range of competitor DNA using a touch down program and hot start PCR technique. The PCR products were analyzed by computing densitometry. The ratio of competitor/target (Y-specific) DNA for each sample pair was calculated.

RESULTS

Using DNAs prepared from an artificial mixture of male and female cells, a set of standard curves has been obtained and the sensitivity of the established quantitative PCR was found to be 25 pg of male DNA, which corresponds approximately to 0.005 fg competitor DNA. A DNA sample taken from a female monkey, transplanted with purified CD34+ stem cells from a male monkey donor 26 days after BMT, was subjected to the competitive PCR with 10% male DNA as a control; the level of male DNA in this sample was calculated to be around 50%.

CONCLUSIONS

This quantitative PCR assay offers both a high degree of specificity as well as a very accurate and sensitive evaluation of chimerism in a sex-mismatched monkey BMT model.

High-resolution typing for HLA-DRB1*15 amd -DRB1*16 by fluorescence-marked sequence-specific priming (TaqMan assay)

Sequence-specific primed polymerase chain reaction (PCR-SSP) is widely used in HLA laboratories. The TaqMan method, which is described here for high-resolution typing of HLA-DRB1*15 and -DRB1*16, does not require elaborate and time-consuming post-PCR detection steps. In this one-tube assay, conventional PCR-SSP and fluorescence detection of the amplicon with a doubly labeled fluorescent probe are combined: a fluorogenic hybridization probe (FHP) labeled with a spectral resolvable fluorescent reporter dye (FAM or TET) at its 5' terminus and a common quencher dye (TAMRA) at its 3' terminus is cleaved by the 5' nuclease activity of Taq DNA polymerase only if the target sequence is amplified. An increase of fluorescence intensity indicates a successful amplification. For high-resolution typing of HLA-DRB1*15 and -DRB1*16 alleles we designed two FHPs and 14 specific primer mixes (7 for DR15 and 7 for DR16). Amplification of the specific sequence was detected by a FAM-labeled FHP, whereas amplification of the internal control was detected by a TET-labeled FHP. We were able to type all heterozygous DRB1*15/DRB1*16 subtype combinations. For evaluation, 60 HLA-DRB1*15-positive and 40 HLA-DRB1*16-positive individuals were typed and the results were compared with conventional PCR-SSP DR15/16 subtyping. There were no discrepancies between the two methods. The TaqMan method is an alternative to conventional PCR-SSP typing which is suitable for routine use in HLA laboratories.

Fluorotyping of HLA-DRB by sequence-specific priming and fluorogenic probing

Similar to our recently described HLA-A and -C fluorotyping strategies, the aim of this study was to develop a sequence-specific primed polymerase chain reaction (PCR-SSP)-based fluorotyping method for HLA-DRB. Applying the fluorogenic 5' nuclease assay, it is possible to increase the sample throughput rate by abolishing all labor-intensive post-amplification steps. Additionally, problems related to contamination are eliminated. The method relies on the 5'-3' exonuclease activity of the Taq-DNA Polymerase which cleaves a target-specific and individually labelled fluorogenic probe during successful PCR. Different labelled probes specific for different targets can be applied in a single PCR, allowing independent detection of the specific HLA and the internal control product. The probe used to detect the HLA-DRB specific amplicons was labeled at its 5' end with FAM as the reporter and further 3' with TAMRA as the quencher. The probe hybridized within the 2nd exon to a conserved region which was covered by all primer mixes. In case of amplification, the cleavage of the fluorogenic probe led to an interruption of the TAMRA-mediated quenching effect and generated a significant increase of the FAM fluorescence. The HLA-DRB fluorotyping information was based on the FAM fluorescence released by 24 individual primer mixes. A TET-TAMRA-labelled probe was used to indicate amplification of the internal control sequence in each PCR reaction. So far, 170 PCR typed clinical samples representing all serologically defined HLA-DRB specificities were analyzed using this fluorotyping method. The results were 100% concordant with those obtained by conventional agarose gel detection.

Fluorotyping of HLA-A by sequence-specific priming and fluorogenic probing

The aim of our study was to develop a fluorotyping strategy for the HLA-A locus. In contrast to conventional sequence-specific primed PCR (PCR-SSP), which is based on an agarose gel electrophoresis, fluorotyping eliminates the drawback of low sample throughput, low potential for automation and problems related to contamination. Additionally, fluorotyping is capable of delivering quantitative results depending on the system set-up. The fluorescence-based PCR-SSP assay relies on target-specific and individually labeled fluorogenic probes allowing a simultaneous and differential detection of the specific HLA and the internal control product. The probe used to detect the HLA-A specific amplicons was labeled at its 5' end with 6-carboxyfluorescein (FAM) as the reporter and at its 3' end with 6-carboxy-tetramethylrhodamine (TAMRA) as the quencher. The probe hybridized within the 2nd intron to a conserved region which was found to be identical in all HLA-A alleles and was covered by all primer mixes. During successful PCR the cleavage of the FAM-labeled probe through the 5'-3' exonuclease activity of the Taq DNA-polymerase led to an interruption of the TAMRA-mediated quenching effect and generated a significant increase of the FAM fluorescence. The specific HLA-A typing information was based on the FAM fluorescence released by 24 individual PCR primer mixes. The internal control amplicon was detected with a tetrachloro-6-carboxyfluorescein-TAMRA-labeled fluorogenic probe. Since the HLA-A amplicons had to include the 2nd intron as the target for the fluorogenic probe, the sequence motifs which could be used as priming sites were limited. Therefore, some primer mixes covered more than one specificity resulting in ambiguous amplification patterns in 31 of 231 possible allele or group combinations of HLA-A1-A80. These ambiguities, which all involved the inability to discriminate a particular heterozygous genotype from a homozygous genotype, may be resolved by the quantitative data revealed by fluorotyping. This feature is also helpful to detect new alleles which are not amplified by the current primer mixes.

HLA-C high resolution typing: analysis of exons 2 and 3 by sequence based typing and detection of polymorphisms in exons 1-5 by sequence specific primers

HLA-C high resolution sequence based typing developed in this study involves a unique DNA amplification encompassing exon 1 to intron 3 and four fluorescent sequencing reactions covering exon 2 and 3. Both dye primer and dye terminator sequencing techniques were performed and results compared. This approach allowed the identification of all of the 50 HLA-C allelic variants so far described, except for two allele pairs that are distinguished by non-coding nucleotide changes (Cw*12021 = 12022, Cw*15051 = 15052) and three allele pairs (Cw*0701 = 706, Cw*1701 = 1702 and Cw*1801 = 1802) that share the same nucleotide sequence in exon 2 and 3. For complete subtyping of these allelic variants, an amplification based on sequence specific primers (PCR-SSP) was used. No ambiguous heterozygous combinations of alleles were detected in our panel so far. HLA-C typing data obtained by this method were compared with data from serological and low resolution PCR-SSP typing, which had been performed previously on the samples sequenced.