Reference Strand Mediated Conformation Analysis Research Articles

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.

Risk of canine cranial cruciate ligament rupture is not associated with the major histocompatibility complex

To investigate the association of the major histocompatability (MHC) class II allele haplotype frequencies with the diagnosis of cranial cruciate ligament (CCL) rupture in two breeds of dog. DNA samples from populations of Labrador Retrievers and Golden Retrievers with CCL rupture and general populations of the same breeds were characterised for three DLA class II loci (DRB1*, DQA1* and DQB1*) alleles using sequence-based typing or reference strand-mediated conformation analysis. Although distinct differences in haplotype types, frequencies and homozygozity were observed between the two breeds, no disease specific association could be identified for the development of the CCL rupture within either population. The risk for developing CCL rupture was not associated with DLA haplotype group(s) in Labrador Retrievers or Golden Retrievers, thus the hypothesis that there is an autoimmune basis to CCL rupture was not supported.

MICA polymorphisms and decreased expression of the MICA receptor NKG2D contribute to idiopathic pulmonary fibrosis susceptibility

Idiopathic pulmonary fibrosis (IPF) is a progressive and lethal lung disorder of unknown etiology. IPF is likely the result of complex interrelationships between environmental and host factors, although the genetic risk factors are presently uncertain. Because we have found that some MHC polymorphisms confer susceptibility to IPF, in the present study we aimed to evaluate the role of the MHC class I chain-related gene A (MICA) in the risk of developing the disease. MICA molecular typing was done by reference strand mediated conformation analysis in a cohort of 80 IPF patients and 201 controls. In addition, the lung cellular source of the protein was examined by immunohistochemistry, the expression of the MICA receptor NKG2D in lung cells by flow cytometry and soluble MICA by ELISA. A significant increase of MICA*001 was observed in the IPF cohort (OR = 2.91, 95% CI = 1.04-8.25; pC = 0.03). Likewise, the frequency of the MICA*001/*00201 genotype was significantly increased in patients with IPF compared with the healthy controls (OR = 4.72, 95% CI = 1.15-22.51; pC = 0.01). Strong immunoreactive MICA staining was localized in alveolar epithelial cells and fibroblasts from IPF lungs while control lungs were negative. Soluble MICA was detected in 35% of IPF patients compared with 12% of control subjects (P = 0.0007). The expression of NKG2D was significantly decreased in gammadelta T cells and natural killer cells obtained from IPF lungs. These findings indicate that MICA polymorphisms and abnormal expression of the MICA receptor NKG2D might contribute to IPF susceptibility.

RSCA genotyping of MHC for high-throughput evolutionary studies in the model organism three-spined stickleback Gasterosteus aculeatus

BackgroundIn all jawed vertebrates, highly polymorphic genes of the major histocompatibility complex (MHC) encode antigen presenting molecules that play a key role in the adaptive immune response. Their polymorphism is composed of multiple copies of recently duplicated genes, each possessing many alleles within populations, as well as high nucleotide divergence between alleles of the same species. Experimental evidence is accumulating that MHC polymorphism is a result of balancing selection by parasites and pathogens. In order to describe MHC diversity and analyse the underlying mechanisms that maintain it, a reliable genotyping technique is required that is suitable for such highly variable genes.ResultsWe present a genotyping protocol that uses Reference Strand-mediated Conformation Analysis (RSCA), optimised for recently duplicated MHC class IIB genes that are typical for many fish and bird species, including the three-spined stickleback, Gasterosteus aculeatus. In addition we use a comprehensive plasmid library of MHC class IIB alleles to determine the nucleotide sequence of alleles represented by RSCA allele peaks. Verification of the RSCA typing by cloning and sequencing demonstrates high congruency between both methods and provides new insight into the polymorphism of classical stickleback MHC genes. Analysis of the plasmid library additionally reveals the high resolution and reproducibility of the RSCA technique.ConclusionThis new RSCA genotyping protocol offers a fast, but sensitive and reliable way to determine the MHC allele repertoire of three-spined sticklebacks. It therefore provides a valuable tool to employ this highly polymorphic and adaptive marker in future high-throughput studies of host-parasite co-evolution and ecological speciation in this emerging model organism.

Development of anELA-DRAgene typing method based on pyrosequencing technology

The polymorphism of equine lymphocyte antigen (ELA) class II DRA gene had been detected by polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) and reference strand-mediated conformation analysis. These methodologies allowed to identify 11 ELA-DRA exon 2 sequences, three of which are widely distributed among domestic horse breeds. Herein, we describe the development of a pyrosequencing-based method applicable to ELA-DRA typing, by screening samples from eight different horse breeds previously typed by PCR-SSCP. This sequence-based method would be useful in high-throughput genotyping of major histocompatibility complex genes in horses and other animal species, making this system interesting as a rapid screening method for animal genotyping of immune-related genes.

Single locus typing of MHC class I and class II B loci in a population of red jungle fowl

In species with duplicated major histocompatibility complex (MHC) genes, estimates of genetic variation often rely on multilocus measures of diversity. It is possible that such measures might not always detect more detailed patterns of selection at individual loci. Here, we describe a method that allows us to investigate classical MHC diversity in red jungle fowl (Gallus gallus), the wild ancestor of the domestic chicken, using a single locus approach. This is possible due to the well-characterised gene organisation of the 'minimal essential' MHC (BF/BL region) of the domestic chicken, which comprises two differentially expressed duplicated class I (BF) and two class II B (BLB) genes. Using a combination of reference strand-mediated conformation analysis, cloning and sequencing, we identify nine BF and ten BLB alleles in a captive population of jungle fowl. We show that six BF and five BLB alleles are from the more highly expressed locus of each gene, BF2 and BLB2, respectively. An excess of non-synonymous substitutions across the jungle fowl BF/BL region suggests that diversifying selection has acted on this population. Importantly, single locus screening reveals that the strength of selection is greatest on the highly expressed BF2 locus. This is the first time that a population of red jungle fowl has been typed at the MHC region, laying the basis for further research into the underlying processes acting to maintain MHC diversity in this and other species.

Immunogenetic factors in donors and patients that affect the outcome of hematopoietic stem cell transplantation

We have correlated the clinical outcome with the level of HLA matching in 423 patients who received a transplant from a volunteer unrelated donor in the United Kingdom. HLA matching was performed at the allelic level (i.e. high-resolution) using reference strand mediated conformation analysis (RSCA) at HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1. The three-year probability of overall survival (OS) was 45% (median survival of 593 days; six-year overall survival probability was 40%). The mean follow-up was 1013 days (range 89–2697). Those matched for their HLA loci had a significantly better overall survival than the mismatched pairs (47% versus 40%, p = 0.040). This result could be refined based on the number of alleles that were mismatched. In patients with a single HLA mismatch, the overall survival was 43%, compared to 30% in those with multiple mismatches; however, there was no statistically significant difference between matched pairs or those with one mismatch. Although there was no significant difference in the overall survival dependent on DPB1 matching in the group overall, in acute lymphocytic leukemia, DPB1-matched pairs had a significantly worse overall survival (log rank; p = 0.025). Thus, a match for DPB1 is associated with a significantly increased risk of disease relapse, irrespective of the matching status for the other HLA molecules. In a multivariate analysis, a high pre-transplant levels of Tregs resulted in worse overall survival (relative risk (RR), 2.74; p = 0.01), a trend to reduce disease-free survival (RR, 2.05; p = 0.060) and to increase disease relapse (RR, 3.36; p = 0.006). Residual patient CD4 +CD25 hi regulatory T cells may suppress graft-versus-tumour responses, decreasing the overall survival by increasing the rates of relapse. In acute leukemia, the presence of NOD2/CARD15 SNPs in the genotype of unrelated donor hematopoietic stem cell transplant pairs results in significant increases in disease relapse and consequently in death. These data show an important role for NOD2/CARD15 genotyping in transplantation and suggest a possible effect of the NOD2 protein in alloreactivity and tumour surveillance. Genotyping recipients and donors prior to transplant may present valuable information for planning and management of pre-transplant conditioning regimens, and for prognosis of the outcome.

Placental Expression of Major Histocompatibility Complex Class I in Bovine Somatic Clones

Abnormally increased placental expression of major histocompatibility complex class I (MHC-I) molecules at the trophoblastic surface has been suggested previously to be the cause of early fetal loss in nuclear transfer (NT) bovine pregnancies. Here, we report the lack of expression of MHC-I at the trophoblastic surface at D30 and D60 and in placentomes from D60 to term in placentas obtained by NT from three different genotypes and by artificial insemination, whatever the outcome of the pregnancy. MHC-I expression was assessed by immunohistochemistry using four different antibodies, including a novel beta2-microglobulin antibody. The MHC-I type of the clones was established using reference strand-mediated conformation analysis (RSCA); however, since it proved problematic to type the recipient animals in the same way, outcome of pregnancy could not be related to MHC compatibility. In conclusion, the present study provides no evidence to support abnormal expression of MHC-I on the trophoblastic surface in clones as a major cause of fetal loss during pregnancy after NT.

Human Leukocyte Antigens A and B Loci Genotyping by Reference Strand-Mediated Conformation Analysis in Hematopoietic Stem Cell Transplantation Donor Selection

Research has been carried out to evaluate the reference strand-mediated conformation analysis (RSCA) typing method on human leukocyte antigen (HLA)-A and -B loci matching in donor selection for hematopoietic stem cell transplantation (HSCT). Twenty standard DNA samples from the RSCA program of the 13th International Histocompatibiliy Working Group, and 124 DNA samples extracted from peripheral blood cells of 39 patients and 85 related potential donors were typed both by RSCA and polymerase chain reaction sequence-specific primer (PCR-SSP) for their HLA-A and -B genes. The ambiguous results were further confirmed by sequence-based typing (SBT). HLA-A and -B genotypes assigned by RSCA correlated well with PCR-SSP and the repetitive rate of RSCA was 100%. In our study, 33/84 (39%) and 67/90 (72.8%) RSCA genotyping results of HLA-A and -B loci could be typed to allelic level, respectively. RSCA can detect mismatches that are not routinely identified by the PCR-SSP method and can detect the chimerism status after patients have gone through HLA-mismatched HSCT. Eight ambiguous samples were confirmed by SBT and the results indicated that RSCA was more accurate than low-resolution PCR-SSP and its database should be improved. RSCA is reproducible, has a high resolution, is able to detect chimerism follow-up after HLA-mismatched HSCT, and is a useful approach for donor selection with some insufficiencies to be improved.

Reference strand‐mediated conformation analysis‐based typing of multiple alleles in the rhesus macaque MHC class I Mamu‐A and Mamu‐B loci

The rhesus macaque exhibits individual differences in susceptibility and resistance to infectious agents such as simian immunodeficiency virus (SIV) under experimental conditions, and these may be genetically determined at least in part by major histocompatibility complex (MHC) class I polymorphism. Although the importance of defining MHC class I polymorphism is well recognized, development of a generic and comprehensive molecular typing method of MHC class I alleles of the rhesus macaque has been hampered because, during the evolution of this species, multiple copies of similar DNA sequences have been generated by duplication events including the coding sequences of Mamu-A and Mamu-B loci. We report here a newly developed reference strand-mediated conformation analysis (RSCA)-based typing method of multiple Mamu-A and Mamu-B cDNAs that allowed us to estimate the number of expressed alleles. This technique detected 1-7 Mamu-A signals and 2-12 Mamu-B signals in a single sample, indicating that the number of functional alleles may vary. By comparing the data from the parents with those from the descendants in the breeding colony, several MHC class I haplotypes consisting of variable numbers of functional Mamu-A and Mamu-B alleles could be assigned.

Direct Determination of Single Nucleotide Polymorphism Haplotype of NFKBIL1 Promoter Polymorphism by DNA Conformation Analysis and Its Application to Association Study of Chronic Inflammatory Diseases

We previously revealed that one of the human leukocyte antigen-linked susceptibility genes for Takayasu’s arteritis (TA) was mapped between TNFA and MICB loci and that −63T allele of NFKBIL1, which is between TNFA and MICB loci, was associated with rheumatoid arthritis (RA) in the Japanese population. We have developed a novel typing method based on reference strand-mediated conformation analysis for the upstream sequence of the NFKBIL1 gene, where −422 (T) 8/(T) 9, −325 C/G, −263 A/G, and −63 T/A polymorphisms were found. Upon the analysis of the patients with TA ( n = 84), those with RA ( n = 120), and healthy control subjects ( n = 217), five common haplotypes named IKBLp*01 through IKBLp*05 were found in the Japanese population. The frequency of IKBLp*03 was significantly increased in the patient with TA (57.1% vs 35.0%, giving an odds ratio of 2.47). In addition, the frequency of IKBLp*01, but not that of other −63T-bearing alleles, was increased in the patients with RA (73.3% vs 58.1%, giving an odds ratio of 1.99), suggesting that the susceptibility to RA was conferred not by −63T alone but by combination of single nucleotide polymorphisms in the NFKBIL1 promoter. A higher promoter activity associated with IKBLp*03 and a lower activity associated with IKBLp*01 may contribute to the susceptibility to TA and RA, respectively.

Canine DNA Subjected to Whole Genome Amplification is Suitable for a Wide Range of Molecular Applications

Molecular and genetic studies of canine disease phenotypes can be limited by the amount of DNA available for analysis. New methods have been developed to amplify the genomic DNA of a species producing large quantities of DNA from small starting amounts. Whole genome amplification (WGA) of DNA is now being used in human studies, although this technique has not been applied extensively in veterinary research. We evaluated WGA of canine DNA for suitability in a range of molecular tests. DNA from 93 canine blood extracted and 18 buccal swab samples was subjected to WGA using the GenomiPhi kit (Amersham). Genomic DNA was compared with WGA product using a range of techniques, including reference strand-mediated conformation analysis, denaturing high-performance liquid chromatography analysis, microsatellite genotyping, direct DNA sequencing, and single nucleotide polymorphism allelic discrimination. All samples amplified well, giving an average yield of 3 mug of DNA from 2.5 ng of starting material. Extremely high levels of experimental reproducibility and concordance were observed between source and WGA DNA samples for all analyses used: greater than 95% for blood extracted DNA and greater than 80% for buccal swab DNA. These studies clearly demonstrate the usefulness of WGA of canine DNA as a means of increasing DNA quantities for canine studies. This technique will have major implications for future veterinary research.

High-Resolution Characterization of the Canine DLA-DRB1 Locus Using Reference Strand-Mediated Conformational Analysis

Several methods exist for genotyping class II DLA gene polymorphisms in the dog. The most accurate method is sequence-based typing, which involves direct sequencing of polymerase chain reaction products. However, this method is expensive and unsuitable for large-scale studies. Recently, reference strand-mediated conformation analysis (RSCA) has been shown to be effective for characterizing major histocompatibility complex genes in humans, sheep, horse, and cats. RSCA is a cheap and rapid method, ideal for large epidemiological studies. We have developed RSCA for typing DLA-DRB1 in the dog. Control panels including dogs typed by sequence-based typing and cloned major histocompatibility complex class II alleles in plasmids were used to establish migration patterns for each allele using 20 different fluorescent labeled references, of which 5 were selected to allow for clear identification and discrimination of all known DLA-DRB1 alleles. We have compared 168 dogs typed by RSCA for DLA-DRB1 and characterized by sequence-based typing, with less than 1% discrepancy. These differences were due to missing alleles because of a weak polymerase chain reaction. To date, we have RSCA-typed 1,394 dogs. RSCA is likely to become the method of choice for characterizing DLA genes in the dog and will prove a useful tool for dissecting the immune response of dogs in clinical studies.

A novel HLA-A allele: A*0257.

A novel human leucocyte antigen-A*02 (HLA-A*02) allele was detected by reference strand-mediated conformation analysis (RSCA) of a DNA sample from a Tarahumara individual. Direct sequencing of HLA-A locus polymerase chain reaction products identified a mutation in one of the alleles. Cloning and sequencing confirmed the presence of a new allele, A*0257 which differed from A*0206 by two nucleotides at positions 355 and 362, inducing changes in residues 95 and 97, respectively, within the peptide-binding site. Those changes suggest that allele A*0257 may have resulted from an intralocus recombination event.

Clinical application for reference strand mediated conformation analysis system in HLA-A loci

Clinical application for reference strand mediated conformation analysis system in HLA-A loci

Deletion of HLA-A∗2402 allele confirmed by using reference strand-mediated conformation analysis (RSCA) in a healthy child

Deletion of HLA-A∗2402 allele confirmed by using reference strand-mediated conformation analysis (RSCA) in a healthy child

HLA typing with reference strand-mediated conformation analysis.

HLA typing with reference strand-mediated conformation analysis.

Frequency of HLA-DPB1 disparities detected by reference strand-mediated conformation analysis in HLA-A, -B, and -DRB1 matched siblings

The role of HLA-DPB1 as transplantation antigen is controversial. The frequency and relevance of HLA-DPB1 mismatch in hematopoietic stem cell transplantation are unknown. To ascertain the rate of HLA-DBP1 mismatch in siblings that had been matched for HLA-A, -B, and -DRB1, reference strand mediated conformation analysis (RSCA) a high resolution HLA typing method was used. Locus-specific primers were used to amplify the HLA-DPB1 locus. The PCR product was then hybridized with two fluorescein-labeled references and the duplexes were analyzed after electrophoresis in a short polyacrylamide gel. Among the 113 pairs of individuals tested, six HLA-DPB1 mismatches were identified, which corresponds to a frequency of 5.31 % (95% confidence interval 3.20%–7.42 %).

HLA-B typing by reference strand mediated conformation analysis using a capillary-Based semiautomated genetic analyzer

The application of reference strand conformation analysis (RSCA) to HLA-A typing using the ABI PRISM 310 capillary based genetic analyzer has recently been described. This study outlines the development and validation of capillary RSCA for HLA-B typing. Mobility values for 93 HLA-B alleles were defined following electrophoresis of known controls through the system. Three fluorescently labelled references, labelled with three different dyes can be electrophoresed simultaneously. The technique was validated by comparing results from 296 cord blood donors with those obtained using reverse SSO. Following capillary RSCA 14.5% of samples required confirmatory typing, compared with a repeat rate of 5.1% following reverse SSO. In samples where no other typing was necessary there was 100% correlation between the two methods. Capillary RSCA for HLA-B typing is quick, easy to implement, and with the introduction of new FLRs and gel matrices has the potential to evolve into a high resolution typing method.

Identification of HLA-A*2306.

We describe a novel allele encoding HLA-A23: A*2306, discovered in an African-American individual, whose DNA was HLA typed as part of a quality control exercise. Direct sequencing typing identified A*2301 and A*6601 with an unexpected heterozygous peak at position 331. As position 331 is at the end of exon 2, near the priming site for the B3.6 anti-sense sequencing primer, the sequencing data is not optimal in this region and sequencing from the sense primer is relied on. In addition the new polymorphism was not at an expected polymorphic position and could easily have been missed, leading to the assignment of A*2301. However, data from reference strand mediated conformation analysis showed distinct new mobilities from those expected for A*2301 with two different fluorescent-labelled references, leading to the conclusion that the heterozygous peak seen at position 331 was a true variant of the A*2301 allele. A*2306 is most similar to A*2301 with 1 nucleotide difference at position 331 in exon 2 which was previously a conserved position. This mutation results in an amino acid substitution of glutamine for glutamate at residue 87.