QF-PCR: application, overview and review of the literature

CRISPR/Cas12 System-Based Assay for Rapid, Sensitive Detection of Rotavirus in Food Samples

Foodborne viruses have become an important threat to food safety and human health. Among the foodborne viruses, group A rotavirus is the most important pathogen of diarrhea in autumn and winter. The field detection of rotavirus is crucial for the early control of infection and patient management. Quantitative real-time reverse transcription-polymerase chain reaction is the most widely used in virus detection. However, the technique relies on high-cost instruments and trained personnel, which limit its use in field detection. In this study, we developed accurate, realizable, and simple detection methods by combining optimized CRISPR (clustered regularly interspaced short palindromic repeats) Cas12 and reverse transcription loop-mediated isothermal amplification (RT-LAMP) (reverse transcription loop-mediated isothermal amplification) to reduce the requirements for temperature control and costly real-time fluorescence polymerase chain reaction instruments. We investigated two nucleic acid detection systems combining RT-LAMP with CRISPR Cas12a and RT-LAMP with CRISPR Cas12b and compared them with reverse transcription-quantitative polymerase chain reaction. The resulting detection system only needs a reaction temperature and in single tube to react for 60 min with the detection sensitivity of 38 copies/μL. Overall, this study developed an innovative method for the rapid detection of rotavirus in food samples, which will help to effectively identify food contaminated by pathogens and prevent human infections and economic losses caused by disease outbreaks.

Morphology combined with HER2 D-DISH ploidy analysis to diagnose partial hydatidiform mole: an evaluation audit using molecular genotyping

AIMS

A hydatidiform mole (HM) is classified as complete (CHM) or partial (PHM) based on its morphology and genomic composition. Ancillary techniques are often required to confirm a morphologically suspected PHM diagnosis. This study sought to evaluate the clinical accuracy of PHM diagnosis using morphological assessment supported by HER2 dual-colour dual-hapten in situ hybridisation (D-DISH) ploidy determination.

METHODS

Over a 2-year period, our unit examined 1265 products of conception (POCs) from which 103 atypical POCs were diagnosed as PHM or non-molar conceptuses with the assistance of HER2 D-DISH ploidy analysis. We retrospectively audited a sample of 40 of these atypical POCs using short tandem repeat genotyping. DNA extracted from formalin-fixed paraffin-embedded tissue was genotyped using 24 polymorphic loci. Parental alleles in placental villi were identified by comparison to those in maternal decidua. To identify triploid PHM cases, we sought three alleles of equal peak height or two alleles with one allele peak twice the height of the other at each locus.

RESULTS

Thirty-six of the 40 cases (19 PHM and 17 non-molar) were successfully genotyped and demonstrated complete concordance with the original diagnosis. All PHMs were diandric triploid of dispermic origin. In two non-molar diploid cases, we identified suspected trisomies (13 and 18), which potentially explains the pregnancy loss in these cases.

CONCLUSIONS

This study validates the use of HER2 D-DISH ploidy analysis to support the diagnosis of a morphologically suspected PHM in our practice.

Development of a Quantitative Multiplex PCR to Detect Three Common Alpha Thalassemia Deletions

Alpha thalassemia is an autosomal recessive genetic disorder with a high prevalence in the Middle East. The severe form of alpha-thalassemia is incompatible with life and can cause significant obstetric complications in the mother. Therefore, it is important to determine the genotype in parents who have a chance of having a fetus with one of the severe forms of this disease. A total of 112 samples that were previously analyzed for common alpha thalassemia mutations in Iran were used in this study. A new multiplex PCR including quantitative polymerase chain reaction to amplify the homologous regions of the alpha-globin gene cluster and fluorescent gap PCR was designed to identify -α3.7, -α4.2, --MED deletions. The ROC curve was used to determine the optimum cutoff points. Statistical analysis showed that there is a significant difference between the peak height ratios for different genotypes. The peak corresponding to the 297 bp fragment resulting from the amplification of the allele with MED-I deletion was detected in all the samples with this deletion. Different cutoffs for a range of sensitivities and specificities were determined by the ROC curve. The suggested method can identify three common large deletions in the alpha-globin gene cluster. A study with a larger sample size can provide more accurate information about the sensitivity and specificity of this test.

CRISPR-Cas-Integrated LAMP

Pathogen-specific point-of-care (PoC) diagnostic tests have become an important need in the fight against infectious diseases and epidemics in recent years. PoC diagnostic tests are designed with the following parameters in mind: rapidity, accuracy, sensitivity, specificity, and ease of use. Molecular techniques are the gold standard for pathogen detection due to their accuracy and specificity. There are various limitations in adapting molecular diagnostic methods to PoC diagnostic tests. Efforts to overcome limitations are focused on the development of integrated molecular diagnostics by utilizing the latest technologies available to create the most successful PoC diagnostic platforms. With this point of view, a new generation technology was developed by combining loop-mediated isothermal amplification (LAMP) technology with clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) technology. This integrated approach benefits from the properties of LAMP technology, namely its high efficiency, short turnaround time, and the lack of need for a complex device. It also makes use of the programmable function of CRISPR-Cas technology and the collateral cleavage activity of certain Cas proteins that allow for convenient reporter detection. Thus, this combined technology enables the development of PoC diagnostic tests with high sensitivity, specificity, and ease of use without the need for complicated devices. In this review, we discuss the advantages and limitations of the CRISPR/Cas combined LAMP technology. We review current limitations to convert CRISPR combined LAMP into pathogen-specific PoC platforms. Furthermore, we point out the need to design more useful PoC platforms using microfabrication technologies by developing strategies that overcome the limitations of this new technology, reduce its complexity, and reduce the risk of contamination.

Pigmentary mosaicism as a recurrent clinical manifestation in three new patients with mosaic trisomy 12 diagnosed postnatally: cases report and literature review

Background

To date, only twenty-one cases diagnosed postnatally with mosaic trisomy 12 have been reported. The most frequent phenotypic manifestations are developmental delay, dysmorphic facial features, congenital heart defects, digital alterations, and pigmentary disorders. In the present report, detailed clinical and genetic profiles of three unrelated new patients with mosaic trisomy 12 are described and compared with previously reported cases.

Case presentation

In the present report, we include the clinical, cytogenetic, and molecular description of three Mexican patients diagnosed postnatally with mosaic trisomy 12. At phenotypic level, the three patients present with developmental delay, dysmorphic facial features, congenital heart defects and skin pigmentary anomalies. Particularly, patient 1 showed unique eye alterations as bilateral distichiasis, triple rows of upper lashes, and digital abnormalities. In patient 2 redundant skin, severe hearing loss, and hypotonia were observed, and patient 3 presented with hypertelorism and telecanthus. Hyperpigmentation with disseminated pigmentary anomalies is a common trait in all of them. The cytogenetic study was carried out under the strict criteria of analysis, screening 50–100 metaphases from three different tissues, showing trisomy 12 mosaicism in at least one of the three different tissues analyzed. With SNParray, the presence of low-level mosaic copy number variants not previously detected by cytogenetics, and uniparental disomy of chromosome 12, was excluded. STR markers allowed to confirm the absence of uniparental disomy as well as to know the parental origin of supernumerary chromosome 12.

Conclusions

The detailed clinical, cytogenetic, and molecular description of these three new patients, contributes with relevant information to delineate more accurately a group of patients that show a heterogeneous phenotype, although sharing the same chromosomal alteration. The possibility of detecting mosaic trisomy 12 is directly associated with the sensitivity of the methodology applied to reveal the low-level chromosomal mosaicism, as well as with the possibility to perform the analysis in a suitable tissue.

Molecular Genetic Techniques in Biomarker Analysis Relevant for Drugs Centrally Approved in Europe

On the basis of scientific evidence, information on the option, recommendation or requirement to test for pharmacogenetic or pharmacogenomic biomarkers is incorporated in the Summary of Product Characteristics of an increasing number of drugs in Europe. A screening of the Genetic Testing Registry (GTR) showed that a variety of molecular genetic testing methods is currently offered worldwide in testing services with regard to according drugs and biomarkers. Thereby, among the methodology indicated in the screened GTR category ‘Molecular Genetics’, next-generation sequencing is applied for identification of the largest proportion of evaluated biomarkers that are relevant for therapeutic management of centrally approved drugs in Europe. However, sufficient information on regulatory clearances, clinical utility, analytical and clinical validity of applied methods is rarely provided.

The Influence of Maternal Cell Contamination on Fetal Aneuploidy Detection Using Chip-Based Digital PCR Testing

Prenatal samples obtained by amniocentesis or chorionic villus sampling are at risk of maternal cell contamination (MCC). In traditional prenatal analysis, MCC is recommended to be assayed by special tests, such as the short tandem repeat analysis and, if detected at a high level, may result in failed analysis report. The objective of this study was to test the ability of chip-based digital PCR to detect fetal aneuploidies in the presence of MCC. To determine the level of accuracy of MCC detection, an aneuploid male sample was subjected to serial dilution with an euploid female sample. DNA was extracted from prenatal samples and analyzed with QuantStudio 3D Digital PCR. Digital PCR analysis allowed the detection of trisomy 21, trisomy 18, and X monosomy accurately in samples with 90%, 85%, and 92% of MCC, respectively. Moreover, our results indicated that digital PCR was able to accurately confirm the presence of Y chromosome at up to 95% contamination. The amniotic fluid and chorionic villus sampling (CVS) received in our clinical laboratory was subjected to further analysis of MCC based on the aneuploidy assessment algorithm, resulting in the identification of 10 contaminated samples and four cases of true fetal mosaicism. We conclude that chip-based digital PCR analysis enables the detection of fetal aneuploidy with high levels of accuracy, even in cases of significant MCC. Importantly, the algorithm eliminates the need for maternal DNA and additional MCC tests, which reduces costs and simplifies the diagnostic procedure. The method is easy to set up and suitable for routine clinical practice.

Discrepancy of QF-PCR, CMA and karyotyping on a de novo case of mosaic isodicentric Y chromosomes

Background

Isodicentric chromosomes are the most frequent structural aberrations of human Y chromosome, and usually present in mosaicism with a 45, X cell line. Several cytogenetic techniques have been used for diagnosing of uncommon abnormal sex chromosome abnormalities in prenatal cases.

Case presentation

A 26-year-old healthy woman was referred to our centre at 24 weeks of gestation age. Ultrasound examination indicated she was pregnant with imbalanced development of twins. Amniocentesis was referred to the patient for further genetic analyses. Quantitative Fluorescent Polymerase Chain Reaction (QF-PCR) indicated the existence of an extra Y chromosome or a structurally abnormal Y chromosome in primary amniotic cells. Chromosome microarray (CMA) analysis based on Comparative Genomic Hybridization (aCGH) platform was performed and identified a 10.1 Mb deletion on Y chromosome in 8-days cultured amniotic cells. Combined with the data of QF-PCR and aCGH, karyotyping and fluorescence in situ hybridization (FISH) revealed a mosaic cell line of 45,X[27]/46,X, idic(Y)(q11.22) [14] in fetus.The karyotyping analysis of cord blood sample was consistent with amniotic cells. The parental karyotypes were normal, which indicated this mosaic case of isodicentric Y (idicY) chromosomes of the fetus was a de novo case.

Conclusion

Several approaches have been used for the detection of numerical and structural chromosomal alterations of on prenatal cases. Our report supported the essential role of incorporating multiple genetic techniques in prenatal diagnosing and genetic counseling of potential complex sex chromosomal rearrangements.

The indications for early prenatal diagnosis of trisomy 18: a 7-year experience at mainland China

Objective: To report the experience with first-trimester prenatal detection of pregnancies complicated by trisomy 18.Study design: Proven cases of trisomy 18 identified between 11 and 14 weeks of gestation were retrospectively reviewed. Information on maternal demographics, prenatal sonographic findings, indications for prenatal diagnosis and chromosomal analysis results was obtained by reviewing medical records.Results: During the 7-year period from January 2011 to December 2017, 89 cases of full trisomy 18 had first-trimester indications for prenatal diagnosis at Guangzhou Women and Children's Medical Center. Eighty-five (95.5%) had abnormal sonographic findings in the first trimester. The most common finding was increased nuchal translucency (55.1%), followed by cystic hygroma (18.0%), omphalocele (14.6%), and fetalis hydrops (11.2%). Four cases (4.5%) were not associated with any abnormal first-trimester sonographic finding, and were diagnosed because of routine positive screening results for trisomy 18. A single case was diagnosed because of a positive cell-free DNA (cfDNA) result.Conclusion: These results demonstrate that a large number of fetuses with trisomy 18 have abnormal sonographic findings in the first trimester, and support the continued utility of first-trimester sonographic examination in the diagnosis of this trisomy even with the availability of cfDNA.

Validation of QF-PCR for prenatal diagnoses in a Brazilian population

OBJECTIVES:

Quantitative fluorescence polymerase chain reaction (QF-PCR) is a rapid and reliable method for screening aneuploidies, but in Brazil, it is not used in public services. We investigated the accuracy of QF-PCR for the prenatal recognition of common aneuploidies and compared these results with cytogenetic results in our laboratory.

METHOD:

A ChromoQuant QF-PCR kit containing 24 primer pairs targeting loci on chromosomes 21, 13, 18, X and Y was employed to identify aneuploidies of the referred chromosomes.

RESULTS:

A total of 162 amniotic fluid samples analyzed using multiplex QF-PCR were compared with karyotyping analysis. The QF-PCR results were consistent with the results of cytogenetic analysis in 95.4% of all samples.

CONCLUSION:

QF-PCR was demonstrated to be efficient and reliable for prenatal aneuploidy screening. This study suggests that QF-PCR can be used as a rapid diagnostic method. However, rearrangements and some mosaic samples cannot be detected with this test; thus, those exceptions must undergo cytogenetic analysis.

Quantitative fluorescent polymerase chain reaction for rapid prenatal diagnosis of fetal aneuploidies in chorionic villus sampling in a single institution

Objective

To validate quantitative fluorescent polymerase chain reaction (QF-PCR) via chorionic villus sampling (CVS) for the diagnosis of fetal aneuploidies.

Methods

We retrospectively reviewed the medical records of consecutive pregnant women who had undergone CVS at Cheil General Hospital between December 2009 and June 2014. Only cases with reported QF-PCR before long-term culture (LTC) for conventional cytogenetic analysis were included, and the results of these two methods were compared.

Results

A total of 383 pregnant women underwent QF-PCR and LTC via CVS during the study period and 403 CVS specimens were collected. The indications of CVS were as follows: abnormal first-trimester ultrasonographic findings, including increased fetal nuchal translucency (85.1%), advanced maternal age (6.8%), previous history of fetal anomalies (4.2%), and positive dual test results for trisomy 21 (3.9%). The results of QF-PCR via CVS were as follows: 76 (18.9%) cases were identified as trisomy 21 (36 cases), 18 (33 cases), or 13 (seven cases), and 4 (1.0%) cases were suspected to be mosaicism. All results of common autosomal trisomies by QF-PCR were consistent with those of LTC and there were no false-positive findings. Four cases suspected as mosaicism in QF-PCR were confirmed as non-mosaic trisomies of trisomy 21 (one case) or trisomy 18 (three cases) in LTC.

Conclusion

QF-PCR via CVS has the advantage of rapid prenatal screening at an earlier stage of pregnancy for common chromosomal trisomies and thus can reduce the anxiety of parents. In particular, it can be helpful for pregnant women with increased fetal nuchal translucency or abnormal first-trimester ultrasonographic findings.

Invasive prenatal diagnosis of fetal thalassemia

Thalassemia is the most common monogenic inherited disease worldwide, affecting individuals originating from many countries to various extents. As the disease requires long-term care, prevention of the homozygous state presents a substantial global disease burden. The comprehensively preventive programs involve carrier detections, molecular diagnostics, genetic counseling, and prenatal diagnosis. Invasive prenatal diagnosis refers to obtaining fetal material by chorionic villus sampling (CVS) at the first trimester, and by amniocentesis or cordocentesis at the second trimester. Molecular diagnosis, which includes multiple techniques that are aimed at the detection of mutations in the α- or β-globin genes, facilitates prenatal diagnosis and definitive diagnosis of the fetus. These are valuable procedures for couples at risk, so that they can be offered options to have healthy offspring. According to local practices and legislation, genetic counseling should accompany the invasive diagnostic procedures, DNA testing, and disclosure of the results. The most critical issue in any type of prenatal molecular testing is maternal cell contamination (MCC), especially when a fetus is found to inherit a particular mutation from the mother. The best practice is to perform MCC studies on all prenatal samples. The recent successful studies of fetal DNA in maternal plasma may allow future prenatal testing that is non-invasive for the fetus and result in significant reduction of invasive diagnostic procedures.

Prenatal diagnosis of fetuses with increased nuchal translucency using an approach based on quantitative fluorescent polymerase chain reaction and genomic microarray

OBJECTIVE

To assess the clinical value of prenatal diagnosis of fetuses with increased nuchal translucency (NT) using an approach based on quantitative fluorescent polymerase chain reaction (QF-PCR) and chromosomal microarray (CMA).

STUDY DESIGN

From January 2013 to October 2014, we included 175 pregnancies with fetal NT ≥ 3.5mm at 11-13 weeks' gestation who received chorionic villus sampling. QF-PCR was first used to rapidly detect common aneuploidies. The cases with a normal QF-PCR result were analyzed by CMA.

RESULTS

Of the 175 cases, common aneuploidies were detected by QF-PCR in 53 (30.2%) cases (30 cases of trisomy 21, 12 cases of monosomy X, 7 cases of trisomy 18, 3 cases of trisomy 13 and 1 case of 47, XXY). Among the 122 cases with a normal QF-PCR result, microarray detected additional pathogenic copy number variants (CNVs) in 5.7% (7/122) of cases. Four cases would have expected to be detectable by conventional karyotyping because of large deletions/duplications (>10 Mb), leaving three cases (2.5%; 3/118) with pathogenic CNVs only detectable by CMA.

CONCLUSION

It is rational to use a diagnostic strategy in which CMA is preceded by the less expensive, rapid, QF-PCR to detect common aneuploidies. CMA allows detection of a number of pathogenic chromosomal aberrations in fetuses with a high NT.

Detection of sex chromosome aneuploidies using quantitative fluorescent PCR in the Hungarian population

BACKGROUND

Aneuploidies are the most frequent chromosomal abnormalities at birth. Autosomal aneuploidies cause serious malformations like trisomy 21, trisomy 18 and trisomy 13. However sex chromosome aneuploidies are causing less severe syndromes. For the detection of these aneuploidies, the "gold standard" method is the cytogenetic analysis of fetal cells, karyograms show all numerical and structural abnormalities, but it takes 2-4 weeks to get the reports. Molecular biological methods were developed to overcome the long culture time, thus, FISH and quantitative fluorescent PCR were introduced. In this work we show our experience with a commercial kit for the detection of sex chromosome aneuploidies.

METHODS

We analyzed 20.173 amniotic fluid samples for the period of 2006-2013 in our department. A conventional cytogenetic analysis was performed on the samples. We checked the reliability of quantitative fluorescent PCR and DNA fragment analysis on those samples where sex chromosomal aneuploidy was diagnosed.

RESULTS

From the 20.173 amniotic fluid samples we found 50 samples with sex chromosome aneuploidy. There were 19 samples showing 46, XO, 17 samples with 46, XXY, 9 samples with 47, XXX and 5 samples with 47, XYY karyotypes. The applied quantitative fluorescent PCR and DNA fragment analyses method are suitable to detect all abnormal sex chromosome aneuploidies.

CONCLUSIONS

Quantitative fluorescent PCR is a fast and reliable method for detection of sex chromosome aneuploidies.

An Overview on Prenatal Screening for Chromosomal Aberrations

This article is a review of current and emerging methods used for prenatal detection of chromosomal aneuploidies. Chromosomal anomalies in the developing fetus can occur in any pregnancy and lead to death prior to or shortly after birth or to costly lifelong disabilities. Early detection of fetal chromosomal aneuploidies, an atypical number of certain chromosomes, can help parents evaluate their pregnancy options. Current diagnostic methods include maternal serum sampling or nuchal translucency testing, which are minimally invasive diagnostics, but lack sensitivity and specificity. The gold standard, karyotyping, requires amniocentesis or chorionic villus sampling, which are highly invasive and can cause abortions. In addition, many of these methods have long turnaround times, which can cause anxiety in mothers. Next-generation sequencing of fetal DNA in maternal blood enables minimally invasive, sensitive, and reasonably rapid analysis of fetal chromosomal anomalies and can be of clinical utility to parents. This review covers traditional methods and next-generation sequencing techniques for diagnosing aneuploidies in terms of clinical utility, technological characteristics, and market potential.

A fast-and-robust profiler for improving polymerase chain reaction diagnostics

Polymerase chain reaction (PCR) is an in vitro technology in molecular genetics that progressively amplifies minimal copies of short DNA sequences in a fast and inexpensive manner. However, PCR performance is sensitive to suboptimal processing conditions. Compromised PCR conditions lead to artifacts and bias that downgrade the discriminatory power and reproducibility of the results. Promising attempts to resolve the PCR performance optimization issue have been guided by quality improvement tactics adopted in the past for industrial trials. Thus, orthogonal arrays (OAs) have been employed to program quick-and-easy structured experiments. Profiling of influences facilitates the quantification of effects that may counteract the detectability of amplified DNA fragments. Nevertheless, the attractive feature of reducing greatly the amount of work and expenditures by planning trials with saturated-unreplicated OA schemes is known to be relinquished in the subsequent analysis phase. This is because of an inherent incompatibility of ordinary multi-factorial comparison techniques to convert small yet dense datasets. Treating unreplicated-saturated data with either the analysis of variance (ANOVA) or regression models destroys the information extraction process. Both of those mentioned approaches are rendered blind to error since the examined effects absorb all available degrees of freedom. Therefore, in lack of approximating an experimental uncertainty, any outcome interpretation is rendered subjective. We propose a profiling method that permits the non-linear maximization of amplicon resolution by eliminating the necessity for direct error estimation. Our approach is distribution-free, calibration-free, simulation-free and sparsity-free with well-known power properties. It is also user-friendly by promoting rudimentary analytics. Testing our method on published amplicon count data, we found that the preponderant effect is the concentration of MgCl2 (p<0.05) followed by the primer content (p<0.1) whilst the effects due to either the content of the deoxynucleotide (dNTP) or DNA remained dormant (p>0.1). Comparison of the proposed method with other stochastic approaches is also discussed. Our technique is expected to have extensive applications in genetics and biotechnology where there is a demand for cheap, expedient, and robust information.

The combined QF-PCR and cytogenetic approach in prenatal diagnosis

In this study, the importance of quantitative fluorescence polymerase chain reaction (QF-PCR) aneuploidy diagnosis test which provides earlier and easier results were discussed. The cell cultures and DNA isolations were performed on 100 amniotic fluids. DNA isolations were made from peripheral blood samples of mothers who had blood-stained amniotic fluid samples. The reasons of references of these pregnant women to our division were increased maternal age, positive double/triple screening test and fetal anomaly history. QF-PCR applied to 19 short tandem repeat markers in the chromosomes 13, 18, 21 and genes X and Y chromosomes. All electropherogram peaks were evaluated on ABI3130. Thirty two (32%) samples have high maternal age, seven (7%) have fetal anomaly and the others have double/triple screening test positivity. Ninety-nine (99%) of the 100 amniotic fluid samples were resulted, but one (1%) of them could not examined because of the culture failure. The maternal contamination rates were determined as 3%. Of 100 samples, 2 had trisomy 21 (2%), 1 had trisomy 13 (1%), 1 had structural abnormalities (1%) and the others (97%) have not any aneuploidy. The results of QF-PCR were in compatible with the results of cell culture and chromosome analysis. Although QF-PCR is an easier and an earlier test, it has a limitation of not to able to scan full genome. It is also sensitive for maternal contamination, so it should be tested together with maternal blood samples. QF-PCR aneuploidy test is the fastest diagnostic test for prenatal diagnosis and so it provides less stressful period for pregnant women.

Chromosomal Mosaicism in Human Feto-Placental Development: Implications for Prenatal Diagnosis

Chromosomal mosaicism is one of the primary interpretative issues in prenatal diagnosis. In this review, the mechanisms underlying feto-placental chromosomal mosaicism are presented. Based on the substantial retrospective diagnostic experience with chorionic villi samples (CVS) of a prenatal diagnosis laboratory the following items are discussed: (i) The frequency of the different types of mosaicism (confined placental, CPM, and true fetal mosaicisms, TFM); (ii) The risk of fetal confirmation after the detection of a mosaic in CVS stratified by chromosome abnormality and placental tissue involvement; (iii) The frequency of uniparental disomy for imprinted chromosomes associated with CPM; (iv) The incidence of false-positive and false-negative results in CVS samples analyzed by only (semi-)direct preparation or long term culture; and (v) The implications of the presence of a feto-placental mosaicism for microarray analysis of CVS and non-invasive prenatal screening (NIPS).

Pregnancy Loss Following Amniocentesis or CVS Sampling-Time for a Reassessment of Risk

Risk of procedure-related pregnancy loss is currently widely quoted in the UK as 1% for amniocentesis and 1.5% for chorionic villus sampling. Published data suggest that these risk figures are out of date and inaccurate, and that new guidelines are required for pre-test counseling. It is our opinion that accurate and evidence-based information concerning miscarriage risk is vital when counseling women, as exaggeration of this risk may deter women from testing, or cause unjustified remorse if a miscarriage ensues. It is also essential that health-care economists are aware of the up-to-date evidence on “procedure-related risk” when applying risk-benefit analysis to assess new technology for non-invasive screening.

Chromosome aberrations identified by cytogenetic analysis of the first two clones of cultured amniotic fluid cells compared with QF-PCR results

We report on our experience of studying amniotic fluid cells by cytogenetic analysis (CA) of the first 2 clones. We investigated the incidence and types of chromosome aberrations detected by CA of 196 amniocenteses performed on pregnant women at high risk. Of these cases, 178 were analysed by QF-PCR (risk group A). The results were compared with the data obtained by CA of 1,263 amniocenteses carried out in patients with other indications. QF-PCR was used to investigate 1,030 of these cases (risk group B). The combined average turnaround time for a CA result of the first 2 clones in both risk groups was within 9 ± 2 days. The final CA results (≥6 clones) were obtained within 12 ± 4 days. In risk group A, CA was not possible in 2 cases due to cell culture failure. The foetal karyotype was abnormal in 13.8% of the cases by CA of ≥6 clones and in 13.5% of the cases by QF-PCR. Together, CA of ≥6 clones and QF-PCR detected chromosome aberrations in 14.8% of the cases. With the exception of 2 cases of in vitro culture failure and 1 case with low gonosomal mosaicism, CA of the first 2 clones detected all cases with chromosome aberrations. Five cases with clinically significant chromosome aberrations were not detected by QF-PCR. In risk group B, the foetal karyotype was found to be abnormal in 2.2% of the cases by CA of ≥6 clones and in 1.0% of the cases by QF-PCR. Together, CA of ≥6 clones and QF-PCR revealed chromosome aberrations in 2.2% of the cases. With the exception of 1 case with low gonosomal mosaicism, CA of the first 2 clones detected all other cases with chromosome aberrations. The majority of these cases were inherited chromosome aberrations. Eighteen cases with chromosome aberrations were not detected by QF-PCR. Based on our results, CA of ≥6 clones, together with QF-PCR as a first test, should be performed in all prenatal cases with abnormal ultrasound findings. In pregnancies with other indications, CA of the first 2 clones alone is sufficient to identify all clinically significant (and inherited) chromosome aberrations.

Whole-genome array CGH evaluation for replacing prenatal karyotyping in Hong Kong

Objective

To evaluate the effectiveness of whole-genome array comparative genomic hybridization (aCGH) in prenatal diagnosis in Hong Kong.

Methods

Array CGH was performed on 220 samples recruited prospectively as the first-tier test study. In addition 150 prenatal samples with abnormal fetal ultrasound findings found to have normal karyotypes were analyzed as a ‘further-test’ study using NimbleGen CGX-135K oligonucleotide arrays.

Results

Array CGH findings were concordant with conventional cytogenetic results with the exception of one case of triploidy. It was found in the first-tier test study that aCGH detected 20% (44/220) clinically significant copy number variants (CNV), of which 21 were common aneuploidies and 23 had other chromosomal imbalances. There were 3.2% (7/220) samples with CNVs detected by aCGH but not by conventional cytogenetics. In the ‘further-test’ study, the additional diagnostic yield of detecting chromosome imbalance was 6% (9/150). The overall detection for CNVs of unclear clinical significance was 2.7% (10/370) with 0.9% found to be de novo. Eleven loci of common CNVs were found in the local population.

Conclusion

Whole-genome aCGH offered a higher resolution diagnostic capacity than conventional karyotyping for prenatal diagnosis either as a first-tier test or as a ‘further-test’ for pregnancies with fetal ultrasound anomalies. We propose replacing conventional cytogenetics with aCGH for all pregnancies undergoing invasive diagnostic procedures after excluding common aneuploidies and triploidies by quantitative fluorescent PCR. Conventional cytogenetics can be reserved for visualization of clinically significant CNVs.

Chromosomal Microarrays in Prenatal Diagnosis: Time for a Change of Policy?

Microarrays have replaced conventional karyotyping as a first-tier test for unbalanced chromosome anomalies in postnatal cytogenetics mainly due to their unprecedented resolution facilitating the detection of submicroscopic copy number changes at a rate of 10-20% depending on indication for testing. A number of studies have addressed the performance of microarrays for chromosome analyses in high risk pregnancies due to abnormal ultrasound findings and reported an excess detection rate between 5% and 10%. In low risk pregnancies, clear pathogenic copy number changes at the submicroscopic level were encountered in 1% or less. Variants of unclear clinical significance, unsolicited findings, and copy number changes with variable phenotypic consequences are the main issues of concern in the prenatal setting posing difficult management questions. The benefit of microarray testing may be limited in pregnancies with only moderately increased risks (advanced maternal age, positive first trimester test). It is suggested to not change the current policy of microarray application in prenatal diagnosis until more data on the clinical significance of copy number changes are available.

Bacterial artificial chromosomes (BACs)-on-Beads™ as a diagnostic platform for the rapid aneuploidy screening of products of conception

The aim of the present study was to evaluate the use of KaryoLite™ bacterial artificial chromosomes (BACs)‑on‑Beads™ (BoBs) technology for the rapid screening of products of conception (POC). Validation and prospective studies were carried out on 85 and 95 patient samples, respectively. Validation studies had previously been analyzed using routine culture and G-banded karyotyping. BoBs resulted in an abnormality detection frequency of 27%, with a failure rate of <3%. The time required for processing was significantly lower compared with that of tissue culture. In conclusion, BoBs technology decreased the failure rate, while increasing the analytical sensitivity compared with G-banded karyotype analysis alone. Additionally, significant cost savings may be achieved with regard to the time of processing and analysis of specimens.

Simple, rapid and inexpensive quantitative fluorescent PCR method for detection of microdeletion and microduplication syndromes

Because of economic limitations, the cost-effective diagnosis of patients affected with rare microdeletion or microduplication syndromes is a challenge in developing countries. Here we report a sensitive, rapid, and affordable detection method that we have called Microdeletion/Microduplication Quantitative Fluorescent PCR (MQF-PCR). Our procedure is based on the finding of genomic regions with high homology to segments of the critical microdeletion/microduplication region. PCR amplification of both using the same primer pair, establishes competitive kinetics and relative quantification of amplicons, as happens in microsatellite-based Quantitative Fluorescence PCR. We used patients with two common microdeletion syndromes, the Williams-Beuren syndrome (7q11.23 microdeletion) and the 22q11.2 microdeletion syndromes and discovered that MQF-PCR could detect both with 100% sensitivity and 100% specificity. Additionally, we demonstrated that the same principle could be reliably used for detection of microduplication syndromes, by using patients with the Lubs (MECP2 duplication) syndrome and the 17q11.2 microduplication involving the NF1 gene. We propose that MQF-PCR is a useful procedure for laboratory confirmation of the clinical diagnosis of microdeletion/microduplication syndromes, ideally suited for use in developing countries, but having general applicability as well.

The detection of mosaicism by prenatal BoBs™

OBJECTIVE

The objective of the study was to evaluate the ability of a new prenatal diagnostic platform - prenatal BACs-on-Beads™ (BoBs™) in detecting mosaicism by comparison to quantitative fluorescence-polymerase chain reaction (QF-PCR).

METHODS

A validation study of prenatal BoBs™ was firstly performed using 18 artificially constructing mosaic samples involving various aneuploidies and microdeletion conditions. Additionally, we compared the accuracy between prenatal BoBs™ and QF-PCR for 18 archived clinical mosaic cases and nine chromosomally abnormal cell lines with reference to conventional karyotype results.

RESULTS

In the validation study, BoBs™ allowed the detection of mosaicism at a level of 20-40%. Among the clinical mosaic cases, 14/18 cases were within the detection of BoBs™, 8/14 (57.1%) could be identified by BoBs™ and 6/9 (66.7%) by QF-PCR, but 6/14 (42.9%) were missed by both tests. Three cases (16.7%) were detected by prenatal BoBs™ but missed by QF-PCR, whereas QF-PCR detected one case that was missed by BoBs™. The overall sensitivity of BoBs™ in detecting mosaicism is 44.4% (8/18), which is slightly higher than that of QF-PCR (33.3%; 6/18).

CONCLUSION

Prenatal BoBs™ has a sensitivity of 57.1% in the detection clinical mosaic cases. According to the validation test, mosaicism of 20% or greater is detectable by the BoBs™ assay.