RhD genotyping by quantitative fluorescent polymerase chain reaction: a new approach

New RHCE variant alleles encoding the D- - phenotype

BACKGROUND

Variant alleles that do not produce RhCE antigens are rare. Consequently, they pose a challenge to transfusion when found in alloimmunized patients and make blood units valuable when found in donors.

STUDY DESIGN AND METHODS

Five index cases and their relatives were studied by both serologic and molecular techniques. Genomic DNA was subjected to microarray genotyping, sequencing, exon scanning, and/or copy number determination assays to identify the RHCE allele(s) responsible for their D+ C- c- E- e- (D- -) phenotype.

RESULTS

The five apparent D- - phenotypes were confirmed by molecular methods. Three of them contained unreported RHCE-null alleles, namely, RHCE*Ce-D(3-9)-Ce, RHCE*Ce87_93insT, and RHCE*cE221A.

CONCLUSION

Molecular analysis of D- - phenotypes allows the identification of new RHCE-null variants. Conversely, detection of described RHCE-null variants facilitates confirmation of D- - phenotypes in patients and donors, helping improve transfusion safety.

Comparison of PCR methods for detecting fetal RhDin maternal plasma

BACKGROUND

Aim of this study was to establish the method yielding the highest sensitivity routinely used to determine fetal RhD type and gender from maternal cell-free plasma DNA in different periods of gestation.

METHODS

Plasma DNA concentrations were measured from 46 pregnant women in different gestational periods and tested for RhD using three different PCR methods on exon 7: Thermal Cycler, Taqman method on LightCycler, and melting curve analysis on LightCycler. In addition, fetal gender was determined by PCR. Cell-free plasma DNA was measured in 100 healthy volunteers as a reference group.

RESULTS

The mean value of cell-free plasma DNA in the reference group was 10.9 pg/microL mean, (standard deviation (SD): 3.66) in 50 healthy women and 12.7 pg/microL (SD: 8.2) in 50 healthy men. In the first trimester of pregnancy cell-free plasma DNA was 14.9 pg/microL mean, (SD: 4.2), in the second trimester 15.4 pg/microL mean, (SD: 4.96), and the maximum was achieved in the third trimester of pregnancy 15.6 pg/microl mean, (SD: 6.49). TaqMan probes had the same accuracy, when compared with Thermal Cycler technology (46 samples, 6 failures). Using real-time PCR with melting curve analysis 12 of 17 samples were correctly tested. Gender determination was correctly in 41 of 46 samples.

CONCLUSION

RhD determinations with TaqMan and Thermal Cycler technology are useful methods for fetal RhD prediction. To increase the accuracy of RhD determination it is necessary to test on other exons in addition.

Workshop report on the extraction of foetal DNA from maternal plasma

OBJECTIVE

Cell free foetal DNA (cff DNA) extracted from maternal plasma is now recognized as a potential source for prenatal diagnosis but the methodology is currently not well standardized. To evaluate different manual and automated DNA extraction methods with a view to developing standards, an International Workshop was performed.

METHODS

Three plasma pools from RhD-negative pregnant women, a DNA standard, real-time-PCR protocol, primers and probes for RHD were sent to 12 laboratories and also to one company (Qiagen, Hilden, Germany). In pre-tests, pool 3 showed a low cff DNA concentration, pool 1 showed a higher concentration and pool 2 an intermediate concentration.

RESULTS

The QIAamp DSP Virus Kit, the High Pure PCR Template Preparation Kit, an in-house protocol using the QIAamp DNA Blood Mini Kit, the CST genomic DNA purification kit, the Magna Pure LC, the MDx, the M48, the EZ1 and an in-house protocol using magnetic beads for manual and automated extraction were the methods that were able to reliably detect foetal RHD. The best results were obtained with the QIAamp DSP Virus Kit. The QIAamp DNA Blood Mini Kit showed very comparable results in laboratories that followed the manufacturer's protocol and started with > or = 500 microL plasma. One participant using the QIAamp DNA Blood Midi Kit failed to detect reliably RHD in pool 3.

CONCLUSIONS

This workshop initiated a standardization process for extraction of cff DNA in maternal plasma. The highest yield was obtained by the QIAamp DSP Virus Kit, a result that will be evaluated in more detail in future studies.

Rapid Prenatal Diagnosis by QF-PCR: Evaluation of 30,000 Consecutive Clinical Samples and Future Applications

Rapid prenatal diagnoses of major chromosome abnormalities can be performed on a large scale using highly polymorphic short tandem repeats (STRs) amplified by the quantitative fluorescent polymerase chain reaction (QF-PCR). The assay was introduced as a preliminary investigation to remove the anxiety of the parents waiting for the results by conventional cytogenetic analysis using amniotic fluid or chorionic cells. However, recent studies, on the basis of the analyses of several thousand samples, have shown that this rapid approach has a very high rate of success and could reduce the need for cytogenetic investigations. Its high efficiency, for example, allows early interruption of affected fetuses without the need of waiting for completion of fetal karyotype. The main advantages of the QF-PCR are its accuracy, speed, automation, and low cost that allows very large number of samples to be analyzed by few operators. Here, we report the results of using QF-PCR in a large series of consecutive clinical cases and discuss the possibility that, in a near future, it may even replace conventional cytogenetic analyses on selected samples.

Outliers in RhD membrane integration are explained by variant RH haplotypes

BACKGROUND

Variations in a multipass transmembrane protein may affect its membrane integration. To study this effect, the systematic molecular characterization of variant D antigen density is a suitable model. Unlike most other membrane proteins, the expression of the D antigen is often determined by a single allele, because it occurs frequently in hemizygous form.

STUDY DESIGN AND METHODS

The D antigen density distribution of 530 CcDee, 475 ccDEe, and 514 ccDee random samples was established by flow cytometry. The molecular bases of samples with D antigen densities outside a bell-shaped peak was investigated.

RESULTS

The antigen densities of 499 CcDee, 437 ccDEe, and 480 ccDee samples formed bell-shaped peaks. Three, 10, and 12 samples, respectively, had decreased antigen densities and carried variant RHD alleles. Weak D type 19, RHD(I204T); weak D type 20, RHD(F417S); and the partial D DYU (also known as DQC), RHD(R234W) were new RHD alleles. Twenty-eight CcDee, 28 ccDEe, and 22 ccDee samples had increased antigen densities; 53 of them lacked a hybrid Rhesus box and were thus predicted to be RHD homozygous. Eight ccDee samples were predicted to be heterozygous despite a large relative dose of RHD to RHCE alleles in quantitative polymerase chain reaction. One of these samples was further investigated and carried an RHD-CE hybrid transcript characteristic for a -D- haplotype.

CONCLUSIONS

Unusual little and large RhD protein integration into the membrane could be traced to a host of distinct protein variants. Weak expression of D antigen was invariably associated with variant RHD alleles. Larger than normal D antigen density may often be caused by the presence of two D encoding alleles, which may be located in cis, and confounding zygosity testing that is solely based on gene copy number.

Genetic mechanisms of Rhesus box variation

BACKGROUND

The RHD gene is flanked by two highly homologous DNA segments of approximately 9000 bp, the upstream and downstream Rhesus boxes. In haplotypes with an RHD deletion, the fusion of the two Rhesus boxes generates the single-hybrid Rhesus box, the detection of which has been applied for RHD zygosity determination. Aberrant Rhesus boxes can confound this application and appear to be frequent among African individuals.

STUDY DESIGN AND METHODS

A total of 5850 bp of the upstream and of the downstream Rhesus boxes were sequenced in 18 samples that were representative for all four D clusters and of the hybrid Rhesus boxes in four samples that were mistyped in assays for the hybrid Rhesus box.

RESULTS

The known differences between upstream and downstream Rhesus boxes were in part restricted to subsets of RHD alleles. Forty-six additional polymorphisms were detected and caused by single-nucleotide substitutions, short insertions, or deletions. Gene conversions were found in the upstream Rhesus boxes of RHDpsi, DAU-1, and DAU-3 and in the downstream Rhesus boxes of Ccdes, weak D type 4.1, type 4.2 (DAR), and DAU-0. Recombinations between haplotypes were likely in several alleles like DIII type 4. Four nonstandard hybrid Rhesus boxes were suggestive of multiple RHD deletion events.

CONCLUSION

There is considerable variation of Rhesus box sequences associated with distinct RHD alleles. RHD zygosity diagnostics in African persons is best based on quantitative polymerase chain reaction or amplification of the full-length hybrid Rhesus box. Because aberrant Rhesus boxes were observed among European persons, use of more than one method for hybrid Rhesus box detection may even be advisable in European persons.

The highly variable RH locus in nonwhite persons hampers RHD zygosity determination but yields more insight into RH-related evolutionary events

BACKGROUND

Knowledge about paternal RHD hemi- or homozygosity is of clinical interest in alloimmunized pregnant women. D negativity in white persons is usually caused by deletion of the RHD gene. Recently, the physical structure of the RH locus and the mechanism causing the deletion of the RHD gene have been explored, enabling RHD zygosity determination in white persons by specific detection of a hybrid Rhesus box characteristic for the RHD- locus.

STUDY DESIGN AND METHODS

RHD zygosity was determined in 402 samples from five different ethnic groups by polymerase chain reaction (PCR)-restriction fragment length polymorphism and by a newly developed real-time quantitative PCR. The Rhesus boxes of samples showing discrepancies between both tests were cycle sequenced.

RESULTS

In nonwhite persons, several mutated Rhesus boxes exist that hamper zygosity determination by detection of the RHD- locus. Such mutated Rhesus boxes in D+RHD homozygous black persons have a frequency of 0.22. In white persons, no mutated Rhesus boxes were encountered so far.

CONCLUSIONS

Owing to the high frequency of the mutated Rhesus boxes, zygosity determination by detection of the RHD- locus is not feasible in nonwhite persons. The cosegregation of variant RHD genes (RHDpsi and (C)cdes) with specific mutated Rhesus boxes yields more insight into the evolutionary events concerning variant RHD genes and mutated Rhesus boxes.

Novel 3'Rhesus box sequences confound RHD zygosity assignment

BACKGROUND

Paternal RHD zygosity is required for genetic counseling and management of HDN caused by anti-D. The most common D- haplotype is due to the deletion of RHD, which results in the formation of a hybrid Rhesus box, theoretically through the recombination of 5' and 3'Rhesus boxes.

STUDY DESIGN AND METHODS

The validity of Rhesus box PstI analysis was assessed to determine RHD zygosity by correlating D phenotype, most probable genotype, and Rhesus box PCR-RFLP. RHD exons were examined, and a 501-bp Rhesus box fragment was sequenced that flanked the polymorphic PstI site.

RESULTS

Rhesus box analysis and the most probable genotype differed for 60 of 200 of the samples (30%). The incorrect zygosity assignment by the most probable genotype method is the likely reason for the difference. However, 8 of 328 samples showed Rhesus box copy numbers that were inconsistent with the D phenotype. Two D- samples with one hybrid Rhesus box had a nonfunctional RHD. Six D+ samples appeared to have two copies of the hybrid Rhesus box due to novel 3'Rhesus boxes that contained nucleotide polymorphisms previously assigned to the 5' and hybrid Rhesus boxes. All eight samples were from people of black descent, as determined by the GATA-1 silencing mutation at the FY locus.

CONCLUSION

Rhesus box PCR-RFLP analysis for RHD zygosity assignment is confounded by the presence of nonfunctional RHD+ (2.3% of D-) and novel, low frequency (0.9% of all alleles) 3'Rhesus box sequences.